Bruker BioSpin

User Manual
TopSpin 3.0
Version 3.0.0

NMR Spectroscopy

think forward
 Copyright (C) by Bruker BiosSpin GmbH
All rights reserved. No part of this publication may be reproduced, stored in
a retrieval system, or transmitted, in any form, or by any means without
prior consent of the publisher. Product names used are trademarks or
registered trademarks of their respective holders.

(C); Bruker BioSpin GmbH

printed in Federal Republic
of Germany 25-03-2010
Part No./Variant: H9469SA3/10
Document No: SM/User3.0.0
Document Part No: /03
Contents
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
1.1 About the User Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
1.2 Safety Regulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
1.3 User Manual Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Font Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
File/directory Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
User Action Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
1.4 TOPSPIN Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
Functionality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
Available Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
1.5 TOPSPIN license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
1.6 TopSpin program versions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Chapter 2 Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.1 Startup TOPSPIN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
2.2 Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
2.3 How to Display Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
How to Locate nmr data in any arbitrary directory . . . . . . . . . . . .22
How to Open Data from the Menu . . . . . . . . . . . . . . . . . . . . . . . .23
How to Open Data from the Browser . . . . . . . . . . . . . . . . . . . . . .23
How to Define Alias Names for Data . . . . . . . . . . . . . . . . . . . . . .24
How to Open Data in Archive Data Directories . . . . . . . . . . . . . .24
How to Open Data in Other Ways . . . . . . . . . . . . . . . . . . . . . . . .24
2.4 How to Expand a Spectral Region. . . . . . . . . . . . . . . . . . . . . . . . .24
2.5 How to Display Peaks, Integrals, ... together with the Spectrum. .25
2.6 How to Display Projections/1D Spectra with 2D Spectra . . . . . . .25
2.7 How to Superimpose Spectra in Multiple Display . . . . . . . . . . . . .26
2.8 How to Print or Export the Contents of a Data Window . . . . . . . .26
How to Print Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26
How to Copy a Data Window to Clipboard . . . . . . . . . . . . . . . . . .26
How to Store (Export) a Data Window as Graphics File . . . . . . .27
2.9 How to Process Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
2.10 How to Archive Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29
2.11 How to Import NMR Data Stored in Special Formats . . . . . . . . . .30
2.12 How to Fit Peaks and Deconvolve Overlapping Peaks . . . . . . . . .30
2.13 How to Compute Fids by Simulating Experiments . . . . . . . . . . . .31
2.14 How to Add Your Own Functionalities . . . . . . . . . . . . . . . . . . . . . .31
 How to Create Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
How to Create AU (automation) Programs . . . . . . . . . . . . . . . . . .31
How to Create Python Programs .INDEX . . . . . . . . . . . . . . . . . . . . . . . .32
2.15 How to Automate Data Acquisition . . . . . . . . . . . . . . . . . . . . . . . .32
Chapter 3 The TOPSPIN InterfaceDONE
. . . . . . . . . . INDEX
. . . . . . . . . . . . . . . . . . . . . . 34
3.1 New Flow User Interface with TopSpin 3.0 . . . . . . . . . . . . . . . . . .34
3.2 The Topspin Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
How to Use Multiple Data Windows . . . . . . . . . . . . . . . . . . . . . . .37
How to Use the Menu bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
How to Use the Upper Toolbar (1D data) . . . . . . . . . . . . . . . . . . .38
How to Use the Lower Toolbar (1D data) . . . . . . . . . . . . . . . . . . .39
3.3 Command Line Usage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
How to Put the Focus in the Command Line . . . . . . . . . . . . . . . .41
How to Retrieve Previously Entered Commands . . . . . . . . . . . . .42
How to Change Previously Entered Commands . . . . . . . . . . . . .42
How to Enter a Series of Commands . . . . . . . . . . . . . . . . . . . . . .42
3.4 Command Line History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
3.5 Starting TOPSPIN commands from a Command Prompt. . . . . . . . .43
3.6 Function Keys and Control Keys . . . . . . . . . . . . . . . . . . . . . . . . . .45
3.7 Help in Topspin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50
How to Open Online Help documents . . . . . . . . . . . . . . . . . . . . .51
How to Get Tooltips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51
How to Get Help on Individual Commands . . . . . . . . . . . . . . . . .52
How to Use the Command Index . . . . . . . . . . . . . . . . . . . . . . . . .52
3.8 User Defined Functions Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . .53
3.9 How to Open Multiple TOPSPIN Interfaces . . . . . . . . . . . . . . . . . . .53
Chapter 4 Trouble Shooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4.1 General Tips and Tricks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .56
4.2 History, Log Files, Spooler Reports, Stack Trace . . . . . . . . . . . . .56
4.3 How to Show or Kill TOPSPIN processes . . . . . . . . . . . . . . . . . . . .60
4.4 What to do if TOPSPIN hangs . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61
4.5 How to Restart User Interface during Acquisition . . . . . . . . . . . . .62
Chapter 5 Dataset Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
5.1 The Topspin Browser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .64
How to Open the Browser in a separate window . . . . . . . . . . . . .68
How to Put the Focus in the Browser . . . . . . . . . . . . . . . . . . . . . .68
How to Select Folders in the Browser . . . . . . . . . . . . . . . . . . . . .69
How to Expand/Collapse a Folder in the Browser . . . . . . . . . . . .69
How to Show/Hide Pulse program and Title in the browser . . . . .69
How to Show Dataset Dates in the Browser . . . . . . . . . . . . . . . .70
How to change the default Top Level Data Directory . . . . . . . . . .71
 How to Add, Remove or Interpret Alias Names . . . . . . . . . . . . . .71
5.2 Creating Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .72
How to Create a New Dataset . . . . . . . . . . . . . . . . . . . . . . . . . . .72
INDEX
5.3 Opening Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
How to Open Data
INDEX DONEWindows Cascaded . . . . . . . . . . . . . . . . . . . .74
How to Open Data from the Browser . . . . . . . . . . . . . . . . . . . . . .75
How to Automatically Select the first expno/procno of a dataset .76
How to Open Data from the Topspin menu . . . . . . . . . . . . . . . . .77
How to Open Data from the Explorer, Konqueror or Nautilus . . .79
How to Open Data from the Command Line . . . . . . . . . . . . . . . .80
How to Open Special Format Data . . . . . . . . . . . . . . . . . . . . . . . .82
How to Open a ZIP or JCAMP-DX file from the Windows Explorer .
83
5.4 Saving/Copying Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .84
How to Save or Copy Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .84
How to Save an Entire Dataset . . . . . . . . . . . . . . . . . . . . . . . . . .85
How to Save Processed Data . . . . . . . . . . . . . . . . . . . . . . . . . . .85
How to Save Acquisition Data . . . . . . . . . . . . . . . . . . . . . . . . . . .85
How to Save Processed Data as Pseudo Raw Data . . . . . . . . . .85
5.5 Deleting Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86
How to Delete a Specific Dataset . . . . . . . . . . . . . . . . . . . . . . . . .86
How to Delete Types of Datasets . . . . . . . . . . . . . . . . . . . . . . . . .86
5.6 Renaming Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86
How to Rename a Specific Dataset . . . . . . . . . . . . . . . . . . . . . . .86
5.7 Searching/Finding Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .89
How to Find Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .89
How to Display one of the Found Datasets . . . . . . . . . . . . . . . . .90
5.8 Handling Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .92
How to List/Open the Current Dataset Files . . . . . . . . . . . . . . . . .92
How to List/Open the current Dataset Files in the Windows Explorer
93
Chapter 6 Parameter Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
6.1 Processing Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .96
How to Set a Processing Parameter from the Command Line . . .96
How to Set Processing Parameters from the Parameter Editor . .97
How to Undo the Last Processing Parameter Change . . . . . . . . .99
How to Display Processing Status Parameters . . . . . . . . . . . . . .99
How to Switch to Maxent parameters . . . . . . . . . . . . . . . . . . . . . .99
How to Change Processed Data Dimensionality . . . . . . . . . . . . .99
6.2 Acquisition Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .100
How to Set Acquisition Parameters . . . . . . . . . . . . . . . . . . . . . .100
 How to Set an Acquisition Parameter from the Command Line .100
How to Set Acquisition Parameters from the Parameter Editor .101
How to Undo the Last Acquisition INDEX
Parameter Change . . . . . . . .103
How to Set Pulse Program Parameters . . . . . . . . . . . . . . . . . . .103
How to Display Acquisition
DONE StatusINDEX Parameters . . . . . . . . . . . . .103
How to Get Probehead/Solvent dependent Parameters . . . . . .103
How to Change Acquisition Data Dimensionality . . . . . . . . . . . .104
How to Set Lock Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . .104
How to Set Routing Parameters . . . . . . . . . . . . . . . . . . . . . . . . .104
Chapter 7 Data Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
7.1 Interactive Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .106
How to Process Data with Single Commands . . . . . . . . . . . . . .106
How to Process data with Composite Commands . . . . . . . . . . .107
7.2 Semi-automatic Processing. . . . . . . . . . . . . . . . . . . . . . . . . . . . .107
How to Use the 1D Processing Dialog . . . . . . . . . . . . . . . . . . . .107
How to Use the Processing Guide in Automatic mode . . . . . . . .108
How to Use the Processing Guide in Interactive mode . . . . . . .110
7.3 Processing Data with AU programs . . . . . . . . . . . . . . . . . . . . . . 110
7.4 Serial Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Chapter 8 Printing/Exporting Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
8.1 Printing/plotting Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
How to Print/Plot from the Menu . . . . . . . . . . . . . . . . . . . . . . . .116
How to Plot Data from the Processing guide . . . . . . . . . . . . . . .118
How to Plot Data with the Plot Editor . . . . . . . . . . . . . . . . . . . . .119
How to Print the Integral list . . . . . . . . . . . . . . . . . . . . . . . . . . . .119
How to Print the Peak list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .119
8.2 Exporting Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .120
How to Copy data to Other Applications . . . . . . . . . . . . . . . . . .120
How to Store (Export) a Data Window as Graphics File . . . . . .121
How to export projections of peak lists . . . . . . . . . . . . . . . . . . . .121
Chapter 9 1D Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
9.1 The 1D Data Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .124
9.2 Displaying one Dataset in Multiple windows . . . . . . . . . . . . . . . .125
How to Reopen a Dataset in a Second/Third etc. Window . . . .125
How to Rescale or Shift one Dataset in Multiple windows . . . . .126
9.3 Changing the Display of a 1D Spectrum or FID . . . . . . . . . . . . .127
How to Change the Vertical Scaling of the FID or Spectrum . . .127
How to Smoothly Change the Vertical Scaling of the FID/Spectrum
127
How to Change the Horizontal Scaling of the FID or Spectrum .128
How to Shift a Spectral Region to the Left or to the Right . . . . .129
 How to Shift the Spectrum Up or Down . . . . . . . . . . . . . . . . . . .129
9.4 Using the Tab bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .130
How to Display the Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . .130
INDEX
How to Set Processing Parameters . . . . . . . . . . . . . . . . . . . . . .131
How to Set Acquisition
INDEX DONEParameters . . . . . . . . . . . . . . . . . . . . . .132
How to Edit the Title . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .133
How to Edit the Pulse Program . . . . . . . . . . . . . . . . . . . . . . . . .134
How to Display the Peak list . . . . . . . . . . . . . . . . . . . . . . . . . . . .134
How to Display the Integral list . . . . . . . . . . . . . . . . . . . . . . . . . .143
How to view Sample Information . . . . . . . . . . . . . . . . . . . . . . . .151
How to Open the Jmol Molecule Structure Viewer . . . . . . . . . . .152
How to Display the FID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .154
9.5 1D Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .154
How to Toggle between Hertz and ppm Axis Units . . . . . . . . . .154
How to Switch on/off the Spectrum Overview display . . . . . . . .154
How to Switch Y-axis Display . . . . . . . . . . . . . . . . . . . . . . . . . . .155
9.6 Show Display Properties/Regions/Files . . . . . . . . . . . . . . . . . . .155
How to Superimpose the Cursor Information . . . . . . . . . . . . . . .157
How to Superimpose the Title on the Spectrum . . . . . . . . . . . . .158
How to Superimpose the main Status Parameters on the Spectrum
158
How to Superimpose the Integral Trails/Labels on the Spectrum . .
158
How to Superimpose Peak Labels on the Spectrum . . . . . . . . .158
How to Show Peak Annotations on the Spectrum . . . . . . . . . . .159
How to Show Individual Data Points of the Spectrum . . . . . . . .159
How to Superimpose the Electronic Signature on the Spectrum 159
How to Display the Main Dataset Properties . . . . . . . . . . . . . . .159
How to Display a List of Files of a Dataset . . . . . . . . . . . . . . . . .160
9.7 Saving Display Region . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .163
9.8 Synchronize Visible Region of all Data Windows . . . . . . . . . . . .164
Chapter 10 2D Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
10.1 The 2D Data Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .166
10.2 Changing the Display of a 2D spectrum . . . . . . . . . . . . . . . . . . .167
How to Change the Intensity Scaling (contour levels) . . . . . . . .167
How to Smoothly Change the Vertical Scaling (contour levels) .168
How to Display a Contour Levels Bar in the Data Window . . . .168
How to Switch on/off Square 2D layout . . . . . . . . . . . . . . . . . . .169
How to Zoom a 2D spectrum in/out . . . . . . . . . . . . . . . . . . . . . .170
How to Shift a Spectral Region in the F2 direction (left/right) . . .171
How to Shift a Spectral Region in the F1 direction (up/down) . .171
 10.3 Show Display Properties/Regions/Files . . . . . . . . . . . . . . . . . . .171
10.4 Using the Tab bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .174
How to Set Processing Parameters . . . . . . . . . . . . . . . . . . . . . .174
INDEX
How to Set Acquisition Parameters . . . . . . . . . . . . . . . . . . . . . .174
How to Display theDONE
Peak list . . . . INDEX. . . . . . . . . . . . . . . . . . . . . . . .175
How to Display the Integral list . . . . . . . . . . . . . . . . . . . . . . . . . .176
How to Display the FID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .178
10.5 2D Display Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .178
How to Switch between Hertz and ppm Axis Units in F2 and F1 . . .
178
How to Switch on/off the Spectrum Overview display . . . . . . . .178
How to Switch on/off the Projection display . . . . . . . . . . . . . . . .179
How to Switch on/off the Grid display . . . . . . . . . . . . . . . . . . . . .181
How to Display a 2D Spectrum in Contour Mode . . . . . . . . . . . .182
How to Set the 2D Contour Levels . . . . . . . . . . . . . . . . . . . . . . .183
How to Store interactively set Contour Levels . . . . . . . . . . . . . .184
How to Display a 2D spectrum in Pseudo Color Mode . . . . . . .185
How to Display a 2D Spectrum in Oblique Mode . . . . . . . . . . . .185
How to Rotate a 2D Spectrum in Oblique Mode . . . . . . . . . . . .187
How to Switch between Displaying Positive and Negative levels . .
187
Chapter 11 nD Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
11.1 Display Planes of 3D Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . .188
How to Switch to 2D Plane Display . . . . . . . . . . . . . . . . . . . . . .189
How to Display various Plane Orientations . . . . . . . . . . . . . . . .189
How to Display various Plane Positions (numbers) . . . . . . . . . .190
11.2 3D Cube Display Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .191
How to Display the 3D Cube . . . . . . . . . . . . . . . . . . . . . . . . . . .191
How to Rotate the 3D Cube . . . . . . . . . . . . . . . . . . . . . . . . . . . .191
How to Scale Up/Down the 3D Cube . . . . . . . . . . . . . . . . . . . . .192
How to Reset the Cube Size and Orientation . . . . . . . . . . . . . . .192
How to Switch Depth Cueing on/off . . . . . . . . . . . . . . . . . . . . . .192
How to Display a Cube Front or Side view . . . . . . . . . . . . . . . . .192
11.3 nD parameter display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .192
11.4 nD Fid Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .194
11.5 nD Peak and Integral Display . . . . . . . . . . . . . . . . . . . . . . . . . . .195
Chapter 12 1D Interactive Manipulation . . . . . . . . . . . . . . . . . . . . . . . . . . 198
12.1 1D Interactive Window multiplication. . . . . . . . . . . . . . . . . . . . . .198
How to Switch to Window Multiplication Mode . . . . . . . . . . . . . .198
12.2 1D Interactive Phase Correction . . . . . . . . . . . . . . . . . . . . . . . . .200
How to Switch to Phase Correction Mode . . . . . . . . . . . . . . . . .200
 How to Perform a Typical 1D Interactive Phase Correction . . . .201
How to Set the Phase Pivot Point . . . . . . . . . . . . . . . . . . . . . . .201
How to Perform Default Zero Order Phase Correction . . . . . . . .202
INDEX
How to Perform Interactive Zero Order Phase Correction . . . . .202
How to Perform Interactive
INDEX DONE First Order Phase Correction . . . . .202
How to Perform 90, -90 or 180° Zero Order Phase Correction .202
How to Reset the Phase to the Original Values . . . . . . . . . . . . .202
How to Change the Mouse Sensitivity . . . . . . . . . . . . . . . . . . . .203
How to Return from Phase Correction Mode with/without Save 203
12.3 1D Interactive Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .203
How to Switch to Integration Mode . . . . . . . . . . . . . . . . . . . . . . .204
How to Define Integral Regions . . . . . . . . . . . . . . . . . . . . . . . . .205
How to Select/Deselect Integral Regions . . . . . . . . . . . . . . . . . .206
How to Read Integral Regions from Disk . . . . . . . . . . . . . . . . . .207
How to Perform Interactive Bias and Slope Correction . . . . . . .208
How to Set the Limit for Bias Determination . . . . . . . . . . . . . . . .209
How to Change the Mouse Sensitivity . . . . . . . . . . . . . . . . . . . .209
How to Calibrate/Normalize Integrals . . . . . . . . . . . . . . . . . . . . .209
How to Scale Integrals with respect to Different Spectra . . . . . .210
How to Delete Integral Regions from the Display . . . . . . . . . . . .210
How to Scale Selected Integrals . . . . . . . . . . . . . . . . . . . . . . . .211
How to Move the Integral Trails Up/Down . . . . . . . . . . . . . . . . .212
How to Cut Integral Regions . . . . . . . . . . . . . . . . . . . . . . . . . . .212
How to Save Integral Regions . . . . . . . . . . . . . . . . . . . . . . . . . .213
How to Undo the Last Region Operation . . . . . . . . . . . . . . . . . .213
How to Return from the Integration Mode with/without Save . . .213
How to deconvolve overlapping peaks from integration mode . .214
12.4 1D Interactive Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .217
How to Switch to Calibration Mode . . . . . . . . . . . . . . . . . . . . . .217
How to Calibrate a Spectrum Interactively . . . . . . . . . . . . . . . . .217
12.5 1D Multiple Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .218
How to Switch to Multiple Display Mode and Read Multiple Spectra
218
How to work with multiple display command .md . . . . 221
How to Select/Deselect Datasets . . . . . . . . . . . . . . . . . . . . . . . .221
How to Remove a Dataset from Multiple Display . . . . . . . . . . . .222
How to Display the Sum or Difference Spectra . . . . . . . . . . . . .222
How to Save the Sum or Difference Spectra . . . . . . . . . . . . . . .222
How to Display the Next/Previous Name/Expno . . . . . . . . . . . .223
How to Toggle between Superimposed and Stacked Display . .224
How to Shift and Scale Individual Spectra . . . . . . . . . . . . . . . . .224
 How to move the selected spectrum one place up/down . . . . . .225
How to Switch on/off the Display of Datapaths and Scaling Factors
226 INDEX
How to Return from Multiple Display mode . . . . . . . . . . . . . . . .226
How to Set the Colors
DONE of the 1st, 2INDEX
nd
, .. Dataset . . . . . . . . . . . .226
12.6 1D Interactive Baseline Correction . . . . . . . . . . . . . . . . . . . . . . .226
How to Switch to Baseline Correction Mode . . . . . . . . . . . . . . .226
How to Perform Polynomial Baseline Correction . . . . . . . . . . . .227
How to Perform Sine Baseline Correction . . . . . . . . . . . . . . . . .228
How to Perform Exponential Baseline Correction . . . . . . . . . . .228
How to Preview the Baseline Corrected Spectrum . . . . . . . . . .228
How to Reset the Baseline Correction Line . . . . . . . . . . . . . . . .229
How to Change the Mouse Sensitivity . . . . . . . . . . . . . . . . . . . .229
How to Save the Baseline Correction and/or Return . . . . . . . . .229
How to Perform Cubic Spline Baseline correction . . . . . . . . . . .230
How to Delete Spline Baseline Points from the screen . . . . . . .231
How to Return from Cubic Spline Baseline mode with/without Save
231
12.7 1D Interactive Peak Picking . . . . . . . . . . . . . . . . . . . . . . . . . . . .232
How to Switch to Peak Picking Mode . . . . . . . . . . . . . . . . . . . . .232
How to Define New Peak Picking Ranges . . . . . . . . . . . . . . . . .233
How to Change Peak Picking Ranges . . . . . . . . . . . . . . . . . . . .233
How to Pick Peaks in Peak Picking Ranges only . . . . . . . . . . . .233
How to Delete all Peak Picking Ranges . . . . . . . . . . . . . . . . . . .234
How to Define Peaks Manually . . . . . . . . . . . . . . . . . . . . . . . . .234
How to Pick Peaks Semi-Automatically . . . . . . . . . . . . . . . . . . .234
How to Delete Peaks from the Peak List . . . . . . . . . . . . . . . . . .235
How to Return from Peak Picking Mode with/without Save . . . .236
How to save Peaklists and Regions in 1D interactive mode . . .236
Chapter 13 2D Interactive Manipulation . . . . . . . . . . . . . . . . . . . . . . . . . . 238
13.1 2D Interactive Phase Correction . . . . . . . . . . . . . . . . . . . . . . . . .238
How to Switch to 2D Interactive Phase Correction . . . . . . . . . . .238
How to Perform a Typical 2D Interactive Phase Correction . . . .239
How to Scale or Shift Individual Rows/Columns . . . . . . . . . . . .242
How to Perform Smooth Phase Correction . . . . . . . . . . . . . . . .243
How to Perform 90, -90 or 180° Zero Order Phase Correction .244
How to Reset the Phase to the Original Values . . . . . . . . . . . . .244
How to Change the Mouse Sensitivity . . . . . . . . . . . . . . . . . . . .244
How to Show the Next/Previous Row or Column . . . . . . . . . . . .244
How to Arrange Rows or Columns . . . . . . . . . . . . . . . . . . . . . . .245
How to Return from Multi-1D Phase to 2D Phase Display . . . . .245
 How to Return from 2D Phase Mode . . . . . . . . . . . . . . . . . . . . .245
13.2 2D Interactive Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .245
How to Move an Integral region . . . . . . . . . . . . . . . . . . . . . . . . .250
INDEX
How to Copy an Integral region . . . . . . . . . . . . . . . . . . . . . . . . .250
How to Delete allDONE
INDEX Integral Regions . . . . . . . . . . . . . . . . . . . . . . .250
How to Read/Import Integral Regions . . . . . . . . . . . . . . . . . . . .250
How to Save/Export Integral Regions . . . . . . . . . . . . . . . . . . . .251
How to Return from 2D Integration mode . . . . . . . . . . . . . . . . .251
13.3 2D Multiple Display and Row/Column Handling . . . . . . . . . . . . .251
How Switch to Multiple Display mode and Read Multiple Spectra . .
251
How to Align Multiple 2D Spectra . . . . . . . . . . . . . . . . . . . . . . . .254
How to Display the Next/Previous Name/Expno . . . . . . . . . . . .254
How to Scan Rows/Columns . . . . . . . . . . . . . . . . . . . . . . . . . . .255
How to Grab a Row/Column . . . . . . . . . . . . . . . . . . . . . . . . . . . .255
How to Show the Next/Previous Row or Column . . . . . . . . . . . .256
How to Move the Selected Dataset Up/Down in the Dataset List . .
257
How to Extract a Row/Column . . . . . . . . . . . . . . . . . . . . . . . . . .257
How to Copy Contour Levels from First to Other Spectra . . . . .258
How to Switch on/off 2D contour display . . . . . . . . . . . . . . . . . .258
How to Position the Baseline of the Row/Column . . . . . . . . . . .258
13.4 2D Interactive Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .259
How to Switch to 2D Calibration mode . . . . . . . . . . . . . . . . . . . .259
How to Perform 2D Calibration . . . . . . . . . . . . . . . . . . . . . . . . . .260
How to Measure a 2D Chemical Shift Distance . . . . . . . . . . . . .260
Chapter 14 Data Window Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
14.1 Data Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .262
How to Move a Data Window . . . . . . . . . . . . . . . . . . . . . . . . . . .263
How to Resize a Data Window . . . . . . . . . . . . . . . . . . . . . . . . . .263
How to Select (activate) a Data Window . . . . . . . . . . . . . . . . . .264
How to Open a New empty Data Window . . . . . . . . . . . . . . . . .265
How to Arrange Data Windows . . . . . . . . . . . . . . . . . . . . . . . . .265
How to Iconify (minimize) a Data Window . . . . . . . . . . . . . . . . .267
How to De-iconify a Data Window . . . . . . . . . . . . . . . . . . . . . . .268
How to Maximize a Data Window . . . . . . . . . . . . . . . . . . . . . . . .268
How to Restore the Size and Position of a Data Window . . . . .268
How to Close a Data Window . . . . . . . . . . . . . . . . . . . . . . . . . . .268
How to Iconify all Data Windows . . . . . . . . . . . . . . . . . . . . . . . .269
How to Maximize all Data Windows . . . . . . . . . . . . . . . . . . . . . .269
How to Activate the Next Data Window . . . . . . . . . . . . . . . . . . .269
 14.2 Window Layouts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .269
How to Save the Current Window Layout . . . . . . . . . . . . . . . . .269
How to Read a Window Layout . .INDEX . . . . . . . . . . . . . . . . . . . . . . .269
How to Swap Data Windows . . . . . . . . . . . . . . . . . . . . . . . . . . .270
How to Toggle Window
DONE Decoration . . . . . . . . . . . . . . . . . . . . . .270
INDEX
Chapter 15 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272
15.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .272
15.2 Chemical Shift Distance Measurement . . . . . . . . . . . . . . . . . . .273
How to Measure a Chemical Shift Distance . . . . . . . . . . . . . . . .273
15.3 1D Signal to Noise Calculation . . . . . . . . . . . . . . . . . . . . . . . . . .273
How to Perform Interactive S/N Calculation . . . . . . . . . . . . . . . .273
How to Delete the Signal Region or Noise Region . . . . . . . . . . .275
How to Edit the Limits of the Signal Region or Noise Region . .275
How to Change the Width of the Signal Region or Noise Region . .
275
15.4 Deconvolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .276
15.5 Relaxation Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .280
Chapter 16 Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288
16.1 Acquisition Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .288
16.2 Acquisition Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .290
16.3 Data window Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .292
16.4 Acquisition Status Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .294
16.5 Command Queuing and Scheduling . . . . . . . . . . . . . . . . . . . . . .297
16.6 Tuning and Matching the Probehead . . . . . . . . . . . . . . . . . . . . .298
16.7 Locking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .299
16.8 BSMS Control Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .301
16.9 Interactive Parameter Adjustment (GS) . . . . . . . . . . . . . . . . . . .303
16.10 Running an Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .305
16.11 Shape tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .309
Easy definition of Shape pulses . . . . . . . . . . . . . . . . . . . . . . . . .311
Chapter 17 Configuration/Automation . . . . . . . . . . . . . . . . . . . . . . . . . . . 316
17.1 NMR Superuser and NMR Administration password . . . . . . . . .316
How to Change the NMR Administration Password . . . . . . . . . .317
17.2 Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .317
How to Perform a Default Configuration on a Datastation . . . . .318
How to Perform a Customized Configuration on a Datastation .318
17.3 Parameter set conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .319
17.4 Automation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .319
How to Install AU Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . .319
How to Open the AU Program Dialog Box . . . . . . . . . . . . . . . . .319
How to Switch to the List of User defined AU Programs . . . . . .321
 How to Switch to the List of Bruker defined AU Programs . . . . .321
How to Define the AU Programs Source Directory . . . . . . . . . .321
How to Create an AU Program . . . . . . . . . . . . . . . . . . . . . . . . . .321
INDEX
How to Edit an Existing AU Program . . . . . . . . . . . . . . . . . . . . .322
How to Execute an
INDEX AU Program . . . . . . . . . . . . . . . . . . . . . . . .322
DONE
How to Delete an AU Program . . . . . . . . . . . . . . . . . . . . . . . . . .322
How to Show Comments (short descriptions) in the AU Program List
322
Chapter 18 Regulatory Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324
18.1 Audit Trails . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .324
18.2 Electronic Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .329
18.3 Password Controlled Login Identification . . . . . . . . . . . . . . . . . .332
Chapter 19 Remote Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338
19.1 Remote control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .338
19.2 How to Establish a Remote Connection from your PC . . . . . . . .338
19.3 How to Make a Remote Connection without a Local License . . .344
19.4 Security of Remote Connections. . . . . . . . . . . . . . . . . . . . . . . . .345
19.5 How to Access ICON-NMR from a Remote Web Browser . . . . . . .345
19.6 How to limit IP-Addresses for Remote Control . . . . . . . . . . . . . .346
Chapter 20 User Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348
20.1 User Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .348
How to Open the Last Used Dataset on Startup . . . . . . . . . . . .351
How to Define the Startup Actions . . . . . . . . . . . . . . . . . . . . . . .351
How to Define Auto-Termination after Idle Time . . . . . . . . . . . .351
How to Define Auto-Locking after Idle Time . . . . . . . . . . . . . . . .352
How to Change the Preferred Editor . . . . . . . . . . . . . . . . . . . . .353
How to Configure the Tab Bar . . . . . . . . . . . . . . . . . . . . . . . . . .354
How to Configure the Right-click Menu Function . . . . . . . . . . . .354
How to Change Colors of Data Objects on the Screen . . . . . . .355
How to Change Colors of Data Objects on the Printer . . . . . . . .355
How to Change Colors of the Lock Display . . . . . . . . . . . . . . . .356
How to Create a New Data Window Color Scheme . . . . . . . . . .356
How to Read a Different Data Window Color Scheme . . . . . . . .357
How to Change Peak and Integral table Colour/Spacings . . . . .357
How to Create Thick Lines on the Screen . . . . . . . . . . . . . . . . .359
How to Create Thick Lines on the Printer . . . . . . . . . . . . . . . . . .359
How to Change All Fonts of the Topspin Interface . . . . . . . . . . .359
How to Change the Font of the TOPSPIN menu . . . . . . . . . . . . . .360
How to Change the Font of the Tab bar . . . . . . . . . . . . . . . . . . .361
How to Change the Font of Dialog Boxes . . . . . . . . . . . . . . . . .362
How to Change the Font of the Browser . . . . . . . . . . . . . . . . . .362
 How to Change the Font of the Command Line . . . . . . . . . . . . .363
How to Change the Font of the Status Line . . . . . . . . . . . . . . . .363
How to Auto-Archive existing expnos INDEX . . . . . . . . . . . . . . . . . . . . .363
20.2 Command Line Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . .364
How to Resize the DONE
Command LineINDEX . . . . . . . . . . . . . . . . . . . . . . .364
How to Set the Minimum and Maximum Command Line Size . .365
20.3 Disabling/Enabling Toolbar Buttons, Menus and Commands . . .365
How to Hide the Upper and Lower Toolbars . . . . . . . . . . . . . . .365
How to Hide the Menubar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .366
How to Disable/Remove Toolbar Buttons . . . . . . . . . . . . . . . . .366
How to Disable/Remove Menus or Commands . . . . . . . . . . . . .367
How to (Re)enable a disabled Command/Menu . . . . . . . . . . . .369
How to (Re)enable All Commands/Menus . . . . . . . . . . . . . . . . .369
20.4 Resizing/Shifting Toolbar Icons . . . . . . . . . . . . . . . . . . . . . . . . . .369
How to Change the Toolbar Icon Size . . . . . . . . . . . . . . . . . . . .369
How to Shift Toolbar Icons to the Right . . . . . . . . . . . . . . . . . . .369
20.5 Defining Source Directory for Programs/Lists etc. . . . . . . . . . . .370
Chapter 21 User Extensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372
21.1 User Notebook . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .372
21.2 Macros. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .373
21.3 AU Programs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .373
21.4 Python Programs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .374
21.5 Button Panels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .375
21.6 Adding User Defined Buttons to the Toolbars . . . . . . . . . . . . . . .378
21.7 Adding User Defined Menus to the Menubar . . . . . . . . . . . . . . .381
21.8 Adding User Defined Guides. . . . . . . . . . . . . . . . . . . . . . . . . . . .383
 Chapter 1
Introduction

1.1 About the User Manual

1. About this document

The User Manual describes the main aspects of Brukers integrated soft-
ware package TopSpin. This manual enables all users who work with
Bruker software to get an overview of the various functionalities of Top-
Spin. The main aspects outlined in here describe the possibilities and
functionaries of the TopSpin interface and elucidate working processes
for data acquisition and processing.
2. Target audience

The Bruker User Manual for TopSpin 2.1 and newer supports all Bruker
users who already work with Bruker software products or who newly
enter the software dimension of TopSpin. The main aspect of this Man-
ual is to enable new TopSpin users and experienced TopSpin users to
work with this software package.
3. How to get the User Manual
 Introduction TOPSPIN 2.1

The User Manual is available as a hard copy just like an electronically

copy on the TopSpin DVD in the menu-section Help, where all other
Bruker Manuals are provided, too. For detailed information about all
Bruker software manuals please refer to chapter 1.4. The latest version
of the User Manual is also provided on the Bruker Web Server:

http://www.bruker-biospin.com/documentation_general.html
4. How to read the User Manual

The User Manual describes especially the TopSpin interface with all its
functionalities to acquire, process and interpret spectrometer data. To
find information more readily you can read selected chapters, depend-
ing on your requirements, or read the User Manual in succession for
general information.

1.2 Safety Regulations

In order to work safely in laboratries with NMR-spectrometers all users

have to follow the safety regulations for magnetic, electrical, cryogenic and
chemical safety. For detailed information please refer to the safety instruc-
tions in the Beginners Guide Manual provided on the TopSpin DVD.

1.3 User Manual Conventions

The User Manual utilizes different script types in order to make selected
text more transparent and explicable to users. Please note that this docu-
ment contains the following conventions:

Font Conventions
abs - commands to be entered on the command line are in Courier bold
italic
ProcPars - menus, buttons, icons to be clicked are in Arial bold
fid - filenames are in Courier
name - any name which is not a filename is in Arial italic

15
 Introduction TOPSPIN 2.1

File/directory Conventions
<tshome> - the TOPSPIN installation (home) directory
INDEX
User Action Conventions
INDEX DONE
+ a single user action
1. the first action of a sequence
2. the second action of a sequence
3. etc.
a) the first action of a sub-sequence
b) the second action of a sub-sequence
c) etc.

1.4 TOPSPIN Overview

Functionality
TOPSPIN is an integrated software package for:
• Displaying NMR spectra
• Printing and plotting spectra
• Exporting displays and plots in various graphics and metafile formats
• Importing NMR data from files of various formats
• Archiving spectra in various formats such as JCAMP-DX and ZIP
• E-mailing data
• Processing 1D-6D fids and spectra: window multiplication, various
transforms (Fourier, Hilbert, DOSY), phase correction, baseline cor-
rection, integration, peak picking, linear prediction, smoothing, add-
ing spectra etc.
• Displaying multiple superimposed spectra (1D and 2D).
• Simulating 1D and multi-dimensional fids, given a pulse program and
a spin system (“virtual spectrometer nmr-sim”)
• Calculating T1/T2 relaxation times

16
 Introduction TOPSPIN 2.1

• Fitting peaks with Lorentzian and Gaussian line shape models,

deconvolve overlapping peaks
• Multiplet analysis
• Automatic 1D, 2D and 3D peak picking
• Automatic 1D, 2D and 3D integration
• Line shape analysis of solids spectra
• Data acquisition with Bruker Avance type spectrometers
• Supporting automated and walk-up spectrometers (ICON-NMR)
• Remote spectrometer control including web-enabled ICON-NMR
• Adding user defined functionalities to TOPSPIN (AU programs, Macros
and Python programs)

Available Documentation
In TOPSPIN 2.1 and newer the Help => Manuals submenu, contains list of
available manuals for the following items:
General
Beginners Guides
Acquisition - Users Guides
Acquisition - Application Manuals
Acquisition & Processing Reference
Automation and Plotting
Analysis and Simulation
Programming Manuals
Technical Manuals
Installation Guides
Good Laboratory Practice
Each document is listed with a short description of its contents.

17
 Introduction TOPSPIN 2.1

1.5 TOPSPIN license

INDEX
TOPSPIN requires a license for startup. A license can be ordered online
from:
INDEX DONE
www.bruker-biospin.de/NMR/nmrsoftw/licenses/index.html
If your PC controls a spectrometer, TOPSPIN will start up without a license.
Furthermore, you can use TOPSPIN for developer purposes with restricted
functionality. In this case you have to start it from a Windows Command
prompt or Linux shell as follows;
topspin -developer

1.6 TopSpin program versions

The TopSpin DVD (2.1 and newer) contains the following program ver-
sions:
• TOPSPIN
• TOPSPIN Plot Editor
• ICON-NMR
• NMR-SIM
• NMR-GUIDE
• AUTOLINK
The following programs are distributed as part of the TopSpin DVD, but
they must be licensed separately:
• AMIX
• AUREMOL
• PERCH NMR TOOLS (only for Windows operating system)

18
 Chapter 2
Getting Started

2.1 Startup TOPSPIN

Under Windows
+ Click the TOPSPIN icon on the desktop
or
+ Start TOPSPIN from a Command Prompt as follows:
1. Click Start => Run, enter cmd and click OK
2. In the Command Prompt:
a) Enter cd <tshome>
b) Enter topspin
where <tshome> is the directory where TOPSPIN is installed.

Under Linux
1. Open a Linux Shell or Terminal Window
2. In the Shell/Terminal:
a) Enter cd <tshome>
b) Enter ./topspin
 Getting Started

where <tshome> is the directory where TOPSPIN is installed.

Startup TOPSPIN specifying dataset INDEX

Topspin can be started with a dataset option:
DONE INDEX
1. Open a Windows Command Prompt or Linux Shell
2. Enter topspin -j TOP_DATA:<dataset path>
The specified dataset is automatically displayed after startup.
Examples:
topspin -j TOP_DATA:c:\bio\data\guest\nmr\exam1d_1H\1\pdata\1
topspin -j TOP_DATA:c:\bio\data\guest\nmr\exam1d_1H\1\pda-
ta\1\1r
topspin -j TOP_DATA:c:\jcamp.dx
topspin -j TOP_DATA:c:\data-archive.zip

2.2 Configuration

After the installation of TOPSPIN, it must be configured once. TOPSPIN may

be used in two different ways:

on a computer which controls a spectrometer

The command cf must be executed once, to configure the spectrometer
hardware. Just type this command and follow the instructions on the
screen. At the end of the dialog, further configuration commands, like
expinstall, are offered and can be started from there.

on a computer which is used as datastation

The only configuration command to be executed is expinstall. This
allows you to install pulse programs, AU programs, lists etc. Just type this
command and follow the instructions on the screen, selecting Installa-
tion for Datastation (default).
Note that the commands cf and expinstall can be started from the
command line or from the Options or Spectrometer menu. However, the
latter menu is only available after cf has been performed once, choosing

21
Getting Started

Installation for spectrometer.

After the configuration has finished, TOPSPIN is ready to be used. The con-
figuration onlyINDEX
needs to be repeated when you have installed a new version
of TOPSPIN or ifINDEX
your spectrometer
DONE hardware has changed.
More details on configuration can be found in chapter 17.2 and the descrip-
tions of cf and expinstall in the Acquisition Reference Manual.

2.3 How to Display Spectra

In this chapter, opening data in standard Bruker format is described. Open-

ing other data formats is described in chapter 5.
Please note that a standard Bruker dataset is a directory tree rather than a
single file:
<dir>\data\<user>\nmr\<dataset name>\<expno>\pdata\<procno>
e.g.
c:\bruker\topspin\data\guest\nmr\exam1d_13C\1\pdata\1

How to Locate nmr data in any arbitrary directory

With TopSpin 2.5 Preview and newer, nmr data can be located in any arbi-
trary directory.
As described in paragraph 2.3 the standard Bruker format can still be used.
The new storage format can be located in the following way:
<dir>/<name>/<expnos>/pdata/<procnos>
e.g.
c:\mydir\sucrose\10\pdata\1
Please note the following facts about the usage of the old and new storage
format:
• The old format is still valid because it is a special case of the new
storage format.
• The old and new style data storage must not be mixed, this would
confuse TopSpin data browser.

22
 Getting Started

• The brwoser command scroll to active dataset will not work

for old style data storage.
INDEX
• The Bruker example datasets (if installed at all) can be found with
TopSpin 2.5 and newer in
DONE INDEX
<TOPSPIN INSTALLATION DIR>/examdata.
This directory is automatically shown in the browser if enabled in the
User Preferences (command set).

How to Open Data from the Menu

Open the File menu and click Open... A dialog box appears. Select the
first option, the Browser type File Chooser and click OK. A file browser
appears. Navigate to your data directory and expand it to the level of
names, expnos, or procnos (double-click a directory to expand it). Select
the desired item and click Display.
The selected dataset replaces the contents of the currently selected (ac-
tive) window. If no data window was displayed, a new one will be created.
Alternatively, you can first create a new window by clicking Window =>
New Window [Alt+w n) and then open a dataset from the file browser in
that window.
The file browser can also be opened by entering reb on the command
line.

How to Open Data from the Browser

TOPSPIN has data browser which, by default, displays the top level data di-
rectory (<dir>) with Bruker example data. You can add your own data di-
rectories, local or remote, as follows:
1. Move the cursor into the browser area
2. Right-click and choose Add New Data Dir... in the popup menu
3. Enter the desired data directory (<dir>) and click OK
Your data directory will now appear in the browser
In order to display data from the Browser, proceed as follows:
1. Expand your top level directory (<dir>) in the browser to the level
of the data name, expno or procno

23
Getting Started

2. Select the desired item and drag it into the data area

How to Define Alias Names for Data

INDEX
1. Open the dataset for which you want to define an alias name
INDEX DONE
2. Click the Alias tab at the top of the data browser.
3. Right-click in the browser and choose
Define alias for data in selected window
Alternatively, you can enter the command dalias on the command line.

How to Open Data in Archive Data Directories

Topspin 2.0 and newer allows opening datasets that are stored in the fol-
lowing directory structures:
<mydata>/<name>/<expno>/pdata/<procno>
You can do that with the TOPSPIN command reb or from the Operating
System File Browser with Copy & Paste or Drag & Drop. Actually, the
data are copied to the data directory:
<tshome>/data/<user>/nmr/<name>/<expno>/pdata/<procno>
where <tshome> is the TOPSPIN installation directory and <user> is the cur-
rent (internal) TOPSPIN user.

How to Open Data in Other Ways

TOPSPIN provides various other ways of displaying data. You can, for ex-
ample, use command line commands like re, rew, rep and dir. Details
on these features can be found in chapter 5.3 and in the Processing Ref-
erence Manual.

2.4 How to Expand a Spectral Region

To expand a certain spectral region:

+ Click-hold the left mouse button on one side of the region, drag the
cursor to the other side and release the mouse.
If you want to cancel the expansion while dragging the mouse, just move
the mouse out of the data area and release it.
24
 Getting Started

An alternative way of expanding a region is clicking the button repeat-

edly and then shifting the spectrum to the proper position.
INDEX
2.5 How to Display Peaks,DONE
Integrals,INDEX
... together with the
Spectrum

When a spectrum is displayed, you can superimpose its title, parameters,

integrals, and peaks as follows:
1. Move the cursor into the data window that contains the spectrum
2. Right-click and choose Display Properties... in the popup menu
3. Check the desired items and click OK
Please note that the selected items are only shown if they are available.
For example, peaks and integrals are only shown if peak picking and inte-
gration have been performed, respectively (see also chapter 12). The
number of displayed digits for the integral and peak labels can be set in
the User Preferences (click Options => Preferences => Spectrum).

2.6 How to Display Projections/1D Spectra with 2D

Spectra

To display projections or 1D spectra in tandem with a 2D spectrum:

1. Open a 2D spectrum
2. If no projections are shown, click the button in the upper toolbar
or enter .pr on the command line.
3. Move the cursor into the F1 or F2 projection area.
4. Right-click and choose one of the options. With External Projec-
tion... an existing 1D spectrum can be read. This can be a regular 1D
spectrum or a 2D projection that was stored as a 1D spectrum. With
Internal Projection the positive projection can be calculated and dis-
played.
An alternate way to calculate projections is the following:
+ Click Processing => Display Projections...[projd]

25
Getting Started

or
+ Right-click on a 1D dataset in the browser and choose:
INDEX
Display As 2D Projection
INDEX DONE
2.7 How to Superimpose Spectra in Multiple Display

TOPSPIN allows you to compare multiple spectra in Multiple Display mode.

To enter this mode, click the button in the upper toolbar or enter on the
command line. When you open a dataset now, for example drag one from
the browser, it will be superimposed on the current spectrum rather than
replacing it. Several multiple display functions are available now in the data
window toolbar. Most importantly, you can scale and shift each spectrum
individually. This allows exact alignment of corresponding peaks of different
spectra.

2.8 How to Print or Export the Contents of a Data Window

How to Print Data

A TOPSPIN data window may contain various objects like an fid, a spec-
trum, expansions of a spectrum, superimposed spectra, spectrum compo-
nents such as parameters, peaks, integrals, cross sections etc. Whatever
the content of the data window is, it can be printed as follows: type Ctrl+p
or click File => Print..., select Print active window in the appearing dialog
box and click OK.
The other options in this dialog box enable you to use or create plot lay-
outs. Details on this can be found in the Plot Editor manual to be found un-
der Help => Manuals => Plotting.
The colors of the printed data can be chosen in the User Preferences dia-
log box. Just enter the command set or click Options => Preferences...
and click Printer in the left part of the dialog box.

How to Copy a Data Window to Clipboard

Under MS Windows, you can easily copy the data window contents to oth-
er applications. To do that, type copy or click Edit => Copy. This will copy

26
 Getting Started

the data window contents to the clipboard. After that you can paste the
clipboard contents to any Windows application.
INDEX
How to Store (Export) a Data Window as Graphics File
DONE INDEX
The clipboard and metafile formats are resizable vector formats. In addi-
tion to this, TOPSPIN allows you to save the contents of a data window in a
graphics file of selectable type, e.g. .png, .jpg, .jpeg, .bmp, .emf and
.wmf. To do that, click File => Export.... The resolution of such a screen
dump equals the resolution of your screen.Note that when you import a
graphics file into another program and resize it you loose information.
Therefore we recommend to resample rather than resize graphics.

2.9 How to Process Data

Since this manual is not a general NMR text book, we assume here that
you are familiar with terms like window multiplication, Fourier Transform,
phase correction, etc.
Any Fid or a spectrum displayed in a TOPSPIN window can be processed by:
• typing a command on the command line, e.g. ft
• invoking a command from the Processing or Analysis menu, e.g.
Processing => Fourier Transform...
• entering an interactive mode by clicking a tool button, e.g.
• entering a user defined command (usually an AU or a Python pro-
gram, see Help => Manuals [Programming Manuals].
Processing and analysis commands require certain parameters to be set
correctly. Most commands in the Processing or Analysis menu, like wm
and ftf open a dialog box showing the available options and required
parameters for that command. Other commands such as em, ft, ... start
processing immediately. Before you use them, you must set their parame-
ters from the parameter editor. To do that, enter edp or click the ProcPars
Tab of the data window.
If you are a new or occasional user we recommend you to process your
data with the TOPSPIN Processing Guide. This will guide you through the
typical sequence of processing steps. To start the Processing Guide, click
Processing => Data => Processing Guide. In Automatic mode, the

27
Getting Started

Processing Guide will simply execute each processing command when you
click the corresponding button. This requires the processing parameters to
be set correctly. In interactive mode (Automatic mode unchecked), the
INDEX
Processing Guide will, at each step, open a dialog box offering you the
INDEX
available options and requiredDONE
parameters. For example, the phase correc-
tion button offers various automatic algorithms as well as an option to enter
interactive phasing mode.
A simple way to process 1D data is the following:
1. Click Processing => Process / Plot Current data
2. In the appearing dialog (see Fig. 2.1):
a) Enable the desired processing/plotting steps
b) Set the parameter LB for Exponential multiplication
c) Select the desired LAYOUT for plotting.
d) Click OK

28
 Getting Started

INDEX
DONE INDEX

Figure 2.1

2.10 How to Archive Data

TOPSPIN 2.1 provides the following methods for data archiving:

• Automatic archiving of raw data after the acquisition as defined in the
User preferences (click Options => Preferences => Acquisition =>
Configure ...)
• Copying a dataset to a desired destination directory which could for
instance be located on a server. Type wrpa, click File => Save... or
type Ctrl+s.
• Saving a dataset in a ZIP file. A standard Bruker dataset is a directory
tree which contains several files. “Zipping” a dataset stores the entire
data directory tree into a single file with the extension .bnmr.zip.
To zip a dataset, type tozip, click File => Save... or type Ctrl+s.
To unpack and display a zipped dataset, enter fromzip. Note that
29
Getting Started

.bnmr.zip files are fully compatible with the well known PC zip for-
mat and can be unpacked with any common unzip utility. “Zipping”
can be applied
INDEXto 1D, 2D, 3D and 4D data.
• Saving a dataset in JCAMP-DX format. This format is a IUPAC stand-
INDEX DONE
ard, and is available for 1D and 2D datasets. Data and parameters
are stored in readable text (ASCII) format. To store data in JCAMP,
type tojdx, click File => Save... or type Ctrl+s. To convert and dis-
play a JCAMP-DX file, type fromjdx.
• E-mailing data to a desired destination. Type smail or click File =>
Send To.... The mailing format is either zip or JCAMP-DX, both of
which allow for data compression in order to keep the transferred
data size as small as possible.

2.11 How to Import NMR Data Stored in Special Formats

TOPSPIN allows you to convert various data formats to standard Bruker for-
mat for display and processing. Click File => Open... and select Open
NMR data stored in special formats. Then follow the instructions on the
screen.

2.12 How to Fit Peaks and Deconvolve Overlapping Peaks

Deconvolution is a useful tool to interprete complex spectra in which the

peaks are not definite and clear.
Peaks of a 1D and 2D NMR spectrum can be approximated by a Lorentz-
ian, Gaussian, or a mixture of these line shapes. Overlapping peaks may
be deconvolved into a sum of such line shapes.
TOPSPIN shows the deconvolution result, i.e. peak positions, line widths and
integrals on the screen and stores it in the file dconpeaks.txt. Further-
more, it switches to multiple display mode to show the original spectrum
and the sum of the computed line shapes, superimposed.
To start deconvolution, expand the spectrum on the display to show the
peak or peak group of interest. Then type dcon or click Analysis --> Line
Shape Fitting --> Deconvolution....

30
 Getting Started

2.13 How to Compute Fids by Simulating Experiments

TOPSPIN includes a “virtual spectrometer” thatINDEX

computes fids of any dimen-
sion. A “real” spectrometer excites a sample with high frequency pulses
DONE INDEX
defined by a pulse program and measures the resulting fid. The virtual
spectrometer performs this task mathematically by solving the quantum
mechanical Liouville equation. The “sample” must be entered in form of a
spin system description. For the computation, the same pulse program and
acquisition parameters are taken as for the real experiment. The result is a
time domain signal which can be processed with TOPSPIN in the same way
a measured fid is processed. Techniques such a selective excitation, gradi-
ent enhanced spectroscopy, and the handling of mixtures are supported.
To start the virtual spectrometer:
+ Enter nmrsim on the command line or click Analysis --> Simulate
Fid....

2.14 How to Add Your Own Functionalities

The TOPSPIN functionality can be extended with various user defined com-
mands, programs etc.

How to Create Macros

Writing a macro is the simplest way to create a user defined command.
Just enter the command edmac, create a file, and enter a sequence of reg-
ular TOPSPIN commands and/or Python commands. Save the file under a
name of your preference. You have created a new TOPSPIN command. Just
enter its name on the command line to execute it. edmac shows a list of
all available macros and allows you to execute one.

How to Create AU (automation) Programs

Writing an AU program is another way of creating a new TOPSPIN com-
mand. AU programs are more complex and more powerful then macros.
They are C-language programs, which may contain C-statements, regular
TOPSPIN commands, and various predefined AU macros and functions. AU
programs can perform various tasks such as dataset handling, parameter
handling, acquisition, processing, analysis, and printing. Note that AU pro-

31
 grams do not support graphics related tasks.
TOPSPIN is delivered with a large set of Bruker AU programs for data
processing and acquisition. Just enter edau to see them listed in a dialog
box. The easiest way to create a new AU program is to select a Bruker AU
program, save it under a new name and modify it to your needs. The cho-
sen name is now available as a new TOPSPIN command. Alternatively, you
can open a new file from the AU dialog box and write your AU program
from scratch.
For details on Bruker AU programs and writing your own AU programs,
click Help => Manuals => [Programming Manuals] AU Programming.

How to Create Python Programs

Writing a Python program is yet another way of creating a new TOPSPIN
command. Python is a new generation scripting and object oriented pro-
gramming language. Python programs are even more powerful than AU
programs. They are easy to use and allow you to execute TOPSPIN com-
mands, handle NMR data and parameters, generate graphics, and inter-
act with the TOPSPIN user interface via dialogs, windows etc. To create a
Python program, enter the command edpy, select a file and insert your
Python statements. Graphics and interface features programmed in Py-
thon look and work the same as regular TOPSPIN features.
For details on Python programming, click Help => Manuals => [Program-
ming Manuals] Python Programming. The examples mentioned there,
like pycmd1, are delivered with TOPSPIN. Just enter their names on the
command line to execute them.
The Python dialog window is also available from the TOPSPIN menu:
+ Click File => Open...and select Open other file => Python pro-
gram.

2.15 How to Automate Data Acquisition

TOPSPIN provides special user interfaces for automation, walk-up, bio-

molecular experiments, etc. To open these interfaces:
+ Type iconnmr or click Spectrometer => ICONNMR.
 Getting Started

INDEX
DONE INDEX

33
The TOPSPIN Interface

Chapter 3
INDEX

The TINDEX
OPSPIN Interface
DONE

3.1 New Flow User Interface with TopSpin 3.0

Beginning with TopSpin 3.0 a new flow user interface is introduced to allevi-
ate all user processes.
Per default the known TopSpin user interface is activated, but the new flow
user interface can be enabled in the User Preferences.
The new workflow-based interface, with its applicable arrangement of all

34
 The TOPSPIN Interface

working processes, allows the user to control intuitional the workflows.

INDEX
DONE INDEX

Figure 3.1
The Flow menu opens a horizontal feature list which stays open with one
click and all functionality concerning this process are available and can be
started with one click.
Furthermore a mouse contact of the functionality opens a balloon help and
one click leads to the continuative menu.
The yellow data button in the upper left corner replaces the File menu.
Accesorily all buttons appear in a new design and can be detached from
the default position.

3.2 The Topspin Window

The TOPSPIN window consists of a data area, a data browser, toolbars and
a menubar. Note that the browser can be inactive [hit Ctrl+d] or displayed

35
The TOPSPIN Interface

as a separate window.
Fig. 3.2 shows the Topspin window with two data windows in the data area
INDEX
and the browser as an integral part.
INDEX DONE minimize maximize
title bar button button
menu
bar
upper close
toolbar button
lower
toolbar

data
area

browser

command line status bar 1D data window 2D data window

Figure 3.2
Note that the menus and toolbars depend on the data dimensionality. The
descriptions below holds for 1D data. For 2D and 3D data, the menus and
toolbars are similar and will be discussed in the chapters 10, 11 and 13,
respectively.

36
 The TOPSPIN Interface

How to Use Multiple Data Windows

TOPSPIN allows you to use multiple data windows. Data windows can be
INDEX
opened from the browser or from the Window menu. They can contain
the same of different datasets. Data windows can be arranged from the
DONE INDEX
Window menu. One of them is the active (current) data window. The ac-
tive data window:
• is the only data window receiving commands from the command
line
• can be selected by clicking inside the window or hitting F6 repeat-
edly.
• has a highlighted title bar
• has the mouse focus
A cursor line (1D) or crosshair (2D) is displayed in all data windows at the
same position. Moving the mouse affects the cursor in all data windows.

How to Use the Menu bar

The menu bar contains the following menus:
• File: performing data/file handling tasks
• Edit: copy & paste data and finding data
• View: display properties, browser on/off, notebook, command his-
tory
• Spectrometer: data acquisition and acquisition related tasks
• Processing: data processing
• Analysis: data analysis
• Options: setting various options, preferences and configurations
• Window: data window handling/arrangement
• Help: access various information, indices, manuals etc.
Experienced users will usually work with keyboard commands rather than
menu commands. Note that the main keyboard commands are displayed
in square brackets [] behind the corresponding menu entries. Further-
more, right-clicking any menu entry will show the corresponding com-
mand, unless right-clicking is defined otherwise.1

37
The TOPSPIN Interface

How to Use the Upper Toolbar (1D data)

The upper toolbar contains buttons for data handling, switching to interac-
INDEXsettings, and starting acquisition.
tive modes, display
INDEX DONE
Buttons for data handling:

The functions of the individual buttons are:

Create a new dataset[Ctrl+n, new]

Open a dataset [Ctrl+o, open]

Save the current dataset [Ctrl+s, sav]

Email the current dataset[smail]

Print the current dataset [Ctrl+p, print]

Copy the data path of the active data window to the clipboard
[copy]

Paste the data path on the clipboard to the active data window
[paste]

Switch to the last 2D dataset [.2d]

Switch to the last 3D dataset [.3d]

For more information on dataset handling, please refer to chapter 5.3.

Buttons for interactive functions

1. Right-click an entry part of the menubar and choose Define Right-click Action.

38
 The TOPSPIN Interface

The functions of the individual buttons are:

Enter phase correction mode
INDEX
Enter calibration mode
DONE INDEX
Enter baseline correction mode

Enter peak picking mode

Enter integration mode

Enter multiple display mode

Enter distance measurement mode

For more information on interactive functions, refer to chapter 12 and 14.

Buttons for display options

The functions of the individual buttons are:

Toggle between Hz and ppm axis units

Switch the y-axis display between abs/rel/off

Switch the overview spectrum on/off

Toggle grid between fixed/axis/off

How to Use the Lower Toolbar (1D data)

The lower toolbar contains buttons for display functions.
Buttons for vertical scaling (intensity)

Increase the intensity by a factor of 2 [*2]

39
The TOPSPIN Interface

Decrease the intensity by a factor of 2 [/2]

Increase
INDEX the intensity by a factor of 8 [*8]

INDEXthe intensity
Decrease DONE by a factor of 8 [/8]

Change the intensity smoothly

Reset the intensity (baseline positions remains unchanged)

[.vr]

Note that vertical scaling can also be changed with the mouse wheel.
Buttons for horizontal scaling (zooming):

Reset zooming (horizontal scaling) to full spectrum [.hr]

Display the entire spectrum (baseline position and intensity scal-

ing are adjusted if necessary) [.all]
Zoom in to the center (spectrum) or left edge (FID) of the dis-
played region, increasing the horizontal scaling. [.zi]
Zoom in/out smoothly

Zoom out from the center (spectrum) or left edge (FID) of the dis-
played region, decreasing horizontal scaling) [.zo]
Exact zoom via dialog box[.zx]

Toggle interactive zoom mode. When switched off, interactive

zooming only selects a horizontal region; baseline position and
intensity scaling remain the same. When switched on, interactive
zooming draws a box selecting the corresponding area.
Undo last zoom [.zl]

Retain horizontal and vertical scaling when modifying dataset or

changing to different dataset. Global button for all data windows

40
 The TOPSPIN Interface

[.keep]
Buttons for horizontal shifting
INDEX
DONE INDEX
Shift to the left, half of the displayed region [.sl]

Smoothly shift to the left or to the right

Shift to the right, half of the displayed region [.sr]

Shift to the extreme left edge of the spectrum [.sl0]

Shift to the extreme right edge of the spectrum [.sr0]

Buttons for vertical shifting

Shift the spectrum baseline to the middle of the data field [.su]

Smoothly shift the spectrum baseline up or down.

Shift the spectrum baseline to the bottom of the data field [.sd]

For more information on display options, please refer to chapter 9.5 (1D
data) and 10.5 (2D data).

3.3 Command Line Usage

How to Put the Focus in the Command Line

In order to enter a command on the command line, the focus must be
there. Note that, for example, selecting a dataset from the browser, puts
the focus in the browser. To put the focus on the command line:
+ Hit the Esc key
or

41
The TOPSPIN Interface

+ Click inside the command line

How to Retrieve
INDEXPreviously Entered Commands
All commands that have been entered on the command line since TOPSPIN
INDEX DONE
was started are stored and can be retrieved. To do that:
+ Hit the Up-Arrow) key on the keyboard
By hitting this key repeatedly, you can go back as far as you want in re-
trieving previously entered commands. After that you can go forward to
more recently entered commands as follows:
+ Hit the Down-Arrow) key on the keyboard

How to Change Previously Entered Commands

1. Hit the Left-Arrow) or Right-Arrow) key to move the cur-
sor
2. Add characters or hit the Backspace key to remove characters
3. Mark characters and use Backspace or Delete to delete them,
Ctrl+c to copy them, or Ctrl+v to paste them.
In combination with the arrow-up/down keys, you can edit previously en-
tered commands.

How to Enter a Series of Commands

If you want to execute a series of commands on a dataset, you can enter
the commands on the command line separated by semicolons, e.g.:
em;ft;apk
If you intend to use the series regularly, you can store it in a macro as fol-
lows:
+ right-click in the command line and choose Save as macro.

3.4 Command Line History

TOPSPIN allows you to easily view and reuse all commands, which were
previously entered on the command line. To open a command history con-
trol window; click View => Command Line History, or right-click in the

42
 The TOPSPIN Interface

command line and choose Command Line History, or enter the com-
mand cmdhist (see Fig. 3.3).
INDEX
DONE INDEX

Figure 3.3
It shows all commands that have been entered on the command line since
TOPSPIN was started. You can select one or more commands and apply one
of the following functions:
Execute
Execute the selected command(s).
Append
Append the (first) selected command to the command line. The ap-
pended command can be edited and executed. Useful for com-
mands with many arguments such as re.
Save as...
The selected command(s) are stored as a macro. You will be
prompted for the macro name. To edit this macro, enter edmac
<macro-name>. To execute it, just enter its name on the command
line.

3.5 Starting TOPSPIN commands from a Command Prompt

TOPSPIN commands can be executed outside of the TOPSPIN interface, from

a Windows Command Prompt or Linux Shell.

43
The TOPSPIN Interface

Under Windows
1. Open a Windows Command Prompt
2. Enter a TINDEX
OPSPIN command in the following format:

INDEX DONE
<tshome>\prog\bin\sendgui <topspincommand>
where <tshome> is the TOPSPIN installation directory.
Examples:
C:\ts2.1\prog\bin\sendgui ft
executes a 1D Fourier transform.
C:\ts2.1\prog\bin\sendgui re exam1d_1H 1 1 C:/bio joe
reads the dataset C:/bio/joe/nmr/exam1d_1H/1/pdata/1.

Under Linux
1. Open a Linux Shell
2. Enter a TOPSPIN command in the following format:
<tshome>\prog\bin\scripts\sendgui <topspincommand>
where <tshome> is the TOPSPIN installation directory.
or
sendgui <topspincommand>
if the TOPSPIN home directory is in the users search path.
Examples:
C:\ts2.1\prog\bin\scripts\sendgui ft
executes a 1D Fourier transform.
sendgui re exam1d_1H 1 1 C:/bio joe
reads the dataset C:/bio/joe/nmr/exam1d_1H/1/pdata/1.
Note that commands are executed on the currently active TOPSPINdata win-
dow.

44
 The TOPSPIN Interface

3.6 Function Keys and Control Keys

For several TOPSPIN commands or tasks, youINDEX

can use a control-key or func-
tion-key short cut.
DONE INDEX
Focus anywhere in TOPSPIN
Esc Put the focus in the command line
Shift+Esc Display menu bar and toolbars (if hidden)
F2 Put the focus in the browser
F1 Search for string in command help or NMR
Guide [help]
F6 Select the next window in the data area
Alt+F4 Terminate TOPSPIN [exit]
Ctrl+d Switch the browser on/off
Ctrl+o Open data [open]
Ctrl+f Find data [find]
Ctrl+n New data [new]
Ctrl+p Print current data [print]
Ctrl+s Save current data [sav]
Ctrl+w Close active window [close]
Ctrl+c Copy a text that you selected/highlighted in an
error box, dialog box, pulse program, title etc.,
to the clipboard
Ctrl+v Paste text from the clipboard into any editable
field.

Focus in the Command Line

Ctrl+Backspace Kill current input
Ctrl+Delete Kill current input
UpArrow Select previous command (if available).
DownArrow Select next command (if available).

45
The TOPSPIN Interface

Focus in the "striped" tables (e. b. edsolv, ednuc, peaks,

ints, cortab etc.
INDEX
Ctrl + C copy the currently selectedtable rows to the
INDEX system’s
DONEclipboard as a CSV-formatted table.
Home The table package assumes that data will
always be represented by complete rows
rather than individual cells. This makes a re-
binding of [Home] necessary, to enforce the
behaviour of jumping to the first row.
End The table package assumes that data will
always be represented by complete rows
rather than individual cells. This makes a re-
binding of [End] necessary, to enforce the
behaviour of jumping to the last row.
Shift + Home The table package assumes that data will
always be represented by complete rows
rather than individual cells. This makes a re-
binding of [Shift + Home] necessary, to enforce
the behaviour of selecting all rows starting from
the current anchor to the first row.
Shift + End The table package assumes that data will
always be represented by complete rows
rather than individual cells. This makes a re-
binding of [Shift + End] necessary, to enforce
the behaviour of selecting all rows starting form
the current anchor to the last row.
Ctrl + Numpad + Auto-resizes all colums such that the data fits
optimally.
Ctrl + Shift + X Opens the export dialog.
Ctrl + Shift + I Opens the import dialog.
Ctrl + Shift + P opens the table properties dialog.
Ctrl + Shift + V Opens the print preview.

46
 The TOPSPIN Interface

Focus in the peak table

Delete Deletes the current selection of peaks.
Enter Zooms the spectrum INDEX
pane in the current MDI
window
DONE such that INDEX
all selected obejcts are visi-
ble.
Ctrl + E Starts the annotation editor of the currently
anchored peak.
Ctrl + Shift + R Opens the "rotate peaks" dialog.
Ctrl + Shift + S Opens the "shift peaks" dialog.
Ctrl + Shift + D Opens a window displaying detailed informa-
tion of the current selection of peaks.
Ctrl + Shift + A Opens the "annotate by reference" dialog.

Focus in the Browser

UpArrow Select previous dataset
DownArrow Select next dataset
Enter dir/user/name/expno selected: expand node or
collapse node, depending on the current state
Enter procno selected: display this dataset
Ctrl+Enter name/expno selected: display this dataset
Enter multiple procnos selected: show in multiple dis-
play
Delete one or more name/expno/procno nodes
selected: delete these datasets

47
The TOPSPIN Interface

Focus anywhere in TOPSPIN

Scaling Data
INDEX
Alt+PageUp Scale up the data by a factor of 2 [*2]
INDEX
Alt+PageDown Scale
DONE down the data by a factor 2 [/2]
Ctrl+Alt+PageUp Scale up by a factor of 2, in all data windows
Ctrl+Alt+PageDown Scale down by a factor of 2, in all data windows
Alt+Enter Perform a vertical reset
Ctrl+Alt+Enter Perform a vertical reset in all data windows
Zooming data
Alt+Plus Zoom in [.zi]
Alt+Minus Zoom out [.zo]
Ctrl+Alt+Plus Zoom in, in all data windows
Ctrl+Alt+Minus Zoom out, in all data windows
Shifting Data
Alt+UpArrow Shift spectrum up [.su]
Alt+DownArrow Shift spectrum down [.sd]
Alt+LeftArrow Shift spectrum to the left [.sl]
Alt+RightArrow Shift spectrum to the right [.sr]
Ctrl+Alt+UpArrow Shift spectrum up, in all data windows
Ctrl+Alt+DownArrow Shift spectrum down, in all data windows
Ctrl+Alt+LeftArrow Shift spectrum to the left, in all data windows
Ctrl+Alt+RightArrow Shift spectrum to the right, in all data windows

48
 The TOPSPIN Interface

Focus in a Table (e.g. peaks, integrals, nuclei, solvents)

delete Delete the selected entries
home INDEX
Select the first entry
end Select the last entry
DONE INDEX
Shift+Home Select the current and first entry and all in
between
Shift+End Select the current and last entry and all in
between
DownArrow Select next entry
UpArrow Select previous entry
Ctrl+a Select all entries
Ctrl+c Copy the selected entries to the clipboard
Ctrl+z Undo last action
Ctrl+y Redo last undo action

49
 Focus in a Plot Editor
F1 Open the Plot Editor Manual
F5 Refresh
Ctrl+F6 Display next layout
ctrl+Shift+F6 Display previous layout
Ctrl+tab Display next layout
delete Delete the selected objects
Ctrl+a Select all objects
Ctrl+i Open TOPSPIN Interface
Ctrl+c Copy the selected object from the Clipboard
Ctrl+l Lower the selected object
Ctrl+s Save the current layout
Ctrl+m Unselect all objects
Ctrl+n Open a new layout
Ctrl+o Open an existing layout
Ctrl+p Print the current layout
Ctrl+q Close the Plot Editor window (Linux only)
Ctrl+r Raise the selected object
Ctrl+t Reset X and Y scaling of all marked objects
Ctrl+v Paste the object from the Clipboard
Ctrl+w Open the attributes dialog window.
Ctrl+x Cut the selected object and place it on the Clip-
board
Ctrl+z Undo the last action
Note that the function of function keys can be changed as described in
chapter 3.8.

3.7 Help in Topspin

TOPSPIN offers help in various ways like online manuals, command help
and tooltips.
How to get a Panorama Tour
For a quick overview over TOPSPIN Interface, Acquisition, Processing,
Analysis and Documentation:
 The TOPSPIN Interface

+ Click Help => Panorama Tour

INDEX
How to Open Online Help documents
DONE INDEX
The online help manuals can be opened from the Help => Manuals sub-
menu. For example, to open the manual that you are reading now:
+ Click Help => Manuals => [General] User Manual
To open the Avance Beginners Guide:
+ Click Help => Manuals => [Beginners Guides] <language>
To open the Processing Reference guide:
+ Click Help => Manuals => [Acquisition & Processing Referenc-
es] Proc. Commands and Parameters
Note that most manuals are stored in the directory:
<tshome>/prog/docu/english/xwinproc/pdf
The most recent versions can be downloaded from:
www.bruker-biospin.de

How to Get Tooltips

If you hold the cursor over a button of the toolbar, a tooltip will pop up. This
is a short explanation of the buttons function. For example, if you hold the
cursor over the interactive phase correction button, you will see the follow-
ing:

The corresponding command line command, in this case .ph, is indicated

between square brackets.
Note that the tooltip also appears in the status bar at the bottom of the TOP-
SPIN window.

51
The TOPSPIN Interface

How to Get Help on Individual Commands

To get help on an individual command, for example ft:
INDEX
+ Enter ft?
or
INDEX DONE

+ Enter help ft
In both cases, the HTML page with a description of the command will be
opened.
Note that some commands open a dialog box with a Help button. Clicking
this button will show the same description as using the help command.
For example, entering re and clicking the Help button in the appearing di-
alog box

opens the same HTML file as entering help re or re?.

How to Use the Command Index

To open the TOPSPIN command index:
+ Enter cmdindex
or

52
 The TOPSPIN Interface

+ Click Help => Command Index

From there you can search for and click any command and jump to the
corresponding help page. INDEX
DONE INDEX
3.8 User Defined Functions Keys

The default assignment of functions keys is described in chapter 3.6 and in

the document:
+ Click Help => Manuals => [General] Control & Function Keys
You may assign your own commands to functions keys. Here is an exam-
ple of how to do that:
1. Open the file cmdtab_user.prop, located in the subdirectory
userdefined of the user properties directory (to locate this directory,
enter hist and look for the entry "User properties directory="). The
file cmdtab_user.prop is initially empty and can be filled with your
own command definitions.
2. Insert e.g. the following lines into the file:
_f3=$em
_f3ctrl=$ft
_f3alt=$pk
_f5=$halt
_f5ctrl=$reb
_f5alt=$popt
3. Restart TOPSPIN
Now, when you hit the F3 key, the command em will be executed. In the
same way, Ctrl+F3, Alt+F3, F5, Ctrl+F5 and Alt+F5 will execute
the commands ft, pk, halt, reb and popt, respectively. You can as-
sign any command, macro, AU program or Python program to any func-
tion keys. Only the keys Alt+F4, F6, Ctrl+F6, and Alt+F6 are
currently fixed. Their function cannot be changed.

3.9 How to Open Multiple TOPSPIN Interfaces

TOPSPIN allows you to open multiple User Interfaces. This is, for example,

53
The TOPSPIN Interface

useful to run an acquisition in one interface and process data in another. To

open an addition interface, enter the command newtop on the command
line or click Window
INDEX=> New Topspin. To open yet another interface, enter
newtop in the first or in the second interface. The display in each interface
INDEX
is completely independent DONE
from the others. As such, you can display differ-
ent datasets or different aspects of the same dataset, e.g. raw/processed,
regions, scalings etc. When the dataset is (re)processed in one interface,
its display is automatically updated in all TOPSPIN interfaces.
The command exit closes the current Topspin interface. Interfaces that
were opened from this interface remain open. Entering exit in the last
open TOPSPIN interface, finishes the entire TOPSPIN session. The position
and geometry of each TOPSPIN interface is saved and restored after restart.

54
 The TOPSPIN Interface

INDEX
DONE INDEX

55
Trouble Shooting

Chapter 4
INDEX

Trouble Shooting
INDEX DONE

4.1 General Tips and Tricks

On a spectrometer, make sure the commands cf and expinstall have

been executed once after installing TOPSPIN. cf must be executed again if
your hardware configuration has changed. Sometimes, executing cf is
useful in case of acquisition problems.
On a datastation, a default configuration is automatically done during the
installation. No configuration commands are required. Only if you want to
use AU programs, you must run expinstall once.

4.2 History, Log Files, Spooler Reports, Stack Trace

If you have a problem with TOPSPIN and want to contact Bruker, it is useful
to have as much information as possible available. If TOPSPIN is still run-
ning, you can view log files with the commands hist and ptrace. If TOP-
SPIN hangs, you can create a stack trace by hitting Ctrl+\ (Linux) or
Ctrl+Break (Windows) in the TOPSPIN startup window.

56
4.2.1 TOPSPIN command-log
By default, the history (protocol) feature is switched on.This means all TOP-
SPIN commands will be protocolled and can be examined by entering hist
on the command line.
If, for some reason, history is switched off, you can switch it on as follows:
1. Click Options => Preferences, click Miscellaneous
2. Check the entry "Record commands in protocol file"
3. Click OK.

4.2.2 TOPSPIN spooler report

TOPSPIN reports all queued, delayed and cron jobs in the so called spooler
report file. The spooler report stores all jobs since TOPSPIN installation and
can become very large. Therefore it should be cleaned from time to time.
To do that:
1. Enter the command spooler
2. Click Tools => Show spooler report
3. Mark the entries to be deleted
4. Right-click in the dialog and choose Delete.
5. Close the Spooler report.
Note that the spooler report can also be opened from Spooler field (if ena-
bled) in the Acquisition Status Bar by right-clicking the word Spooler and
choosing Show spooler report.

4.2.3 TOPSPIN command, dataserver and network log

A full protocol including not only TOPSPIN commands but also dataserver
and network traffic is show by the command ptrace. This opens the fol-
lowing dialog window:

Figure 4.1
Here TOPSPIN log messages from various log files are displayed time
sorted.
Messages from different log files are shown in different colours. The color
assignment and location of the files is shown in the lower part of the dialog
window.
ptrace supports the following functions:
 Trouble Shooting

Search keywords
To search the displayed log files for a certain keyword, just enter it in the
INDEX
text bar at the top of the window and hit Enter.

Anchor specific entries DONE INDEX

To anchor an entry:
double-click in the first column of the entry
The entry is marked with an X. Now you can use the < > buttons at the
upper right of the window to go to the previous or next entry, respectively.

Add log files

By default, the procol.txt, history and dataserver log files are
shown.To include additional log files to the ptrace list:
click File => Add, specify the file and click Open.
Note that most log files are stored in the directory:
<tshome>/prog/curdir/<user>

Save the log messages

To save log messages in a text file;
click File => Save and specify the output text file

4.2.4 Create a Stack Trace

If TOPSPIN hangs it can be useful to sent Bruker a stack trace about a possi-
ble cause. You can create a stack trace as follows.
1. Move the cursor into the TOPSPIN startup window.
2. Under Windows: hit Ctrl+Break (=Ctrl+Pause)
Under Linux: hit Ctrl+\ (Control backslash)
3. Copy the appearing text into a text file.

4.2.5 Store complete log with => savelogs’

A complete set of TOPSPIN log files can be made automatically with the
command savelogs if the user assertively confirms.

59
Trouble Shooting

For saving logfiles with the command savelogs do the following:

Under Windows:
INDEX
• Click the Bruker Utilities<topspin version> icon on your desktop. An
Explorer will be opened.
INDEX DONE
• Double-click Miscellaneous
• Execute the script savelogs
Under Linux:
• Open a shell.
• Type savelogs
All <tshome>/prog/curdir/<user>/* files will be saved with savelogs.
The stored files can be found under following pathname:
• Under Windows XP:
<userhome>\AppData\Local Settings\Temp\
TopSpinSupportFiles_<Support-Token><operating-system-
user><year><month><day><hour><minute>.tar.gz
• Windows Vista:
<userhome>\AppData\Local\Temp\
TopSpinSupportFiles_<Support-Token><operating-system-
user><year><month><day><hour><minute>.tar.gz
• Linux:
/tmp/TopSpinSupportFiles_<Support-Token>_<operating-system-
user><year><month><day><hour><minute>.tar.gz
For detailed information about saving all possible log files and about the
upload to the Bruker FTP-server please refer to the Processing Reference
Command Manual.

4.3 How to Show or Kill TOPSPIN processes

To show the currently running TOPSPIN processes, enter the command

show or kill on the command line. A list of processes will appear show-
ing the process command, dataset etc.

60
 Trouble Shooting

INDEX
DONE INDEX

Figure 4.2
Fig. 4.2 shows a list with one process (command xfb). To kill a process,
select it in the list and click the button Kill...
The command show all or kill all work like show and kill, except
that they also show TOPSPIN system processes. Note that killing such proc-
esses may kill TOPSPIN.

4.4 What to do if TOPSPIN hangs

If, for some reason, TOPSPIN hangs, please do the following.

Under Linux:
1. Open a Shell
2. Enter <tshome>/prog/bin/script/killtopspin
where <tshome> is the TOPSPIN installation directory.
Under Windows:
1. Click Start => Programs => Bruker TOPSPIN => TOPSPIN 2.1 =>
Bruker Utilities 2.1 => Miscellaneous
2. In the appearing window:
Click killtopspin.
Normally, this kill all TOPSPIN processes including cpr, cprserver, dataserver
and java.

61
Trouble Shooting

4.5 How to Restart User Interface during Acquisition

INDEX
If Topspin hangs up during a data acquisition, you can restart the user inter-
face without disturbing the acquisition. To do that:
INDEX DONE
1. Open the file:
<tshome>/prog/curdir/<user>/history
where <tshome> is the TOPSPIN home directory and <user> is the user
who started TOPSPIN. Look for the term ’Java Virtual Machine’ and
check its PID.
2. Open the Task Manager (Windows) or System Monitor (Linux)
3. Stop the Java(w).exe process with the PID found in the history file.
4. Open a Windows Command Prompt or Linux Shell
5. Go to the TOPSPIN Installation directory
6. Enter topspin -client

62
 Trouble Shooting

INDEX
DONE INDEX

63
Dataset Handling

Chapter 5
INDEX

Dataset
INDEX
Handling
DONE

5.1 The Topspin Browser

TOPSPIN offers a data browser from which you can browse, select, and
open data.
The browser dialog offers the following tabs (see Fig. 5.1):
• Browser - data browser showing the data directory hierarchy
• Last50 - list of the 50 last open datasets
• Groups - list of user defined groups of datasets
• Alias - list of user defined alias name
The browser appears at the left of the TOPSPIN window and can be
shown/hidden with Ctrl+d or by clicking the arrow buttons at the upper
right of the browser.

The Browser tab

The browser shows data directory trees and allows you to expand/collapse
their elements. Figure 5.1 shows the browser with three top level data
directories and one dataset fully expanded.

64
 Dataset Handling
:

INDEX
DONE INDEX

Figure 5.1
The dimensionality of the data is indicated with different colors:
• black for 1D data
• blue for 2D data
• magenta for 3D data
Furthermore, the browser shows:
• the pulse program with the dataset EXPNO (e.g. 1 - hxcoqf in Fig. 5.1)
• the title with the dataset PROCNO (e.g. CH-CO Cyclosporin in Fig.
5.1)
Note that the displayed pulse program is the:
• status pulse program if an acquisition has been done (raw data exist)
• setup pulse program if no acquisition has been done (raw data do not
exist)
The display of title and pulse program can be switched of (see Fig. 5.2).

65
Dataset Handling

=> Display in current data window.

INDEX => Display in new data window.
=> Display 1D data as projection of active 2D data.
INDEX DONE
=> Scroll to PROCNO of active data window.
=> Fully expand selected node.
=> Switch pulsprogram/title display on/off.
=> Show acq. date (expno) or last mod. date (name)
=> Sort data by last modified date
=> Copy dataset entry to clipboard
=> Show dataset properties.
=> Delete selected entry (name,expno or procno)
=> Rename dataset name, expno or procno.
=> Show files in selected entry (expno or procno)
=> Add new top level data directory.
=> Remove selected top level data directory
Figure 5.2

The Last50 tab

Clicking the Last50 tab displays the list of the last 50 displayed datasets.
Each dataset that you open, is automatically added to the current list. Fig.
5.3 shows a Last50 list with four datasets. As in the browser, different
colors are used to indicate the data dimensionality.

Figure 5.3
+ Hit the Enter key to display the highlighted dataset in the current
window
+ Double-click a dataset to display it in the current window.
66
 Dataset Handling

=> Remove the selected dataset from the list.

=> Open a dialog to select a Last50 list.
INDEX
=> Open a dialog for saving the current Last50 list.
DONE INDEX
Figure 5.4
Each line displays one dataset showing its name, expno, procno, top level
directory and user.

The Groups tab

Clicking the Groups tab displays the list of user defined dataset groups.
Here you can create, modify and display groups of datasets. Defining a
group is useful is you work on projects where each project involves multiple
datasets. It allows you to easily organizes your projects and access all data
belonging to a certain project.

=> Display selected dataset(s) in active window

=> Display selected dataset(s) in new window.
=> Display all datasets in group in new windows.
=> Add selected data window to selected group.
=> Add all open data windows to selected group.
=> Update window bounds and dislay regions.
=> Remove selected datasets from group.
=> Collapse all groups.
=> Show/hide dimension, pulse program, title.
=> Add a new (empty) dataset group to the list.
=> Close all data windows of selected group.
=> Process selected dataset with serial processing.
=> Show file properties of selected dataset.
=> Show file list of selected dataset.
=> Copy pathnames of selected data to clipboard.
Figure 5.5
Note that a group not only defines the datasets involved, but also their data
window positions and dimensions and the displayed region of each spec-
trum.
67
Dataset Handling

The entry Update window bounds & displays regions

The Alias tabINDEX

Clicking the Alias tab displays the list of user defined alias names for data-
INDEX
sets. Just right-click DONE
any entry to define, remove or interpret alias names.

Figure 5.6
.

=> define alias for data in selected window.

=> Show selected data name, expno etc.
=> Show all data names, expnos etc.
=> Remove selected aliases from list.
=> Show available alias commands.
Figure 5.7

How to Open the Browser in a separate window

The browser can be opened in a separate window as follows:
+ Click Options => Preferences [set], click Window settings and
check Display dataset browser in a separate window.
You must restart TOPSPIN for the change to take effect.

How to Put the Focus in the Browser

+ Hit the F2 key
or
+ Click inside the browser

68
 Dataset Handling

How to Select Folders in the Browser

To select a particular folder:
INDEX
+ Left-click the folder button
or
DONE INDEX

+ Hit the arrow-up/down keyswhile the focus is in the browser

To select multiple folders:
+ Hold the Ctrl key and left-click multiple folders to select them
or
+ Hold the Shift key and left-click two folders to select these two and
all in between.

How to Expand/Collapse a Folder in the Browser

To expand a collapsed folder:
+ Click the + button to the left of the folder button
or Double-click the folder button
or Hit the Right-Arrow key while the folder is highlighted
To fully expand a collapsed folder:
+ Right-click the DIR, NAME or EXPNO node and choose Fully Ex-
pand Selection
To collapse an expanded folder:
+ Click the - button to the left of the folder button
or Double-click the folder button
or Hit the Left-Arrow key while the folder is highlighted

How to Show/Hide Pulse program and Title in the browser

+ Right-click the data name folder button and choose

69
Dataset Handling

Show PULPROG /Title from the popup menu (see Fig. 5.8)

INDEX
INDEX DONE

Figure 5.8

How to Show Dataset Dates in the Browser

+ Right-click the data name folder button and choose Show Date
The last modified date is shown to the right of the dataset NAME, where-
as the acquisition date is shown to the right of the dataset EXPNO (see
Fig. 5.9).

70
 Dataset Handling

INDEX
DONE INDEX

Figure 5.9

How to change the default Top Level Data Directory

By default, the browser shows the TOPSPIN installation directory with the
Bruker example datasets. To suppress this feature click Options =>
Preferences [set], click Administration and uncheck Show TOPSPIN
data examples directory in data browser.

How to Add, Remove or Interpret Alias Names

To add an alias name:
1. Click the Alias tab in the browser.
2. Right-click in the Alias table to open the popup menu (see Fig.
5.7). Click Define alias names for data in selected window.
3. Enter an alias name in the appearing dialog box and click OK.
Note that alias names must begin with a letter.
To remove an alias name:
1. Right-click the alias name
2. Click Remove selected aliases... from the popup menu (see Fig.
5.7)
Furthermore, the popup menu offers entries to display the dataset, list its
properties and print the full dataset specification.

71
Dataset Handling

5.2 Creating Data

INDEX
How to Create a New Dataset
INDEX
1. Click File => New [newDONE
, Ctrl+n]
or
Click the button in the upper toolbar.
2. Specify the dataset name, expno, procno, dir, and user in the appear-
ing dialog box. If one or more datasets are open, the fields are initial-
ized with the current dataset (see Fig. 5.10).
3. Click the down-arrow of the Solvent box and choose a solvent from
the list, or type a solvent name.
4. Click the down-arrow of the Experiment box and choose a parame-
ter set from the list, or type a parameter set name.
5. Type the dataset title in the TITLE box.
6. Click OK.

72
 Dataset Handling

INDEX
DONE INDEX

Figure 5.10
A dataset will be created and initialized with the parameters of the chosen
experiment. No fid or spectrum are available yet. They can be created by
data acquisition and data processing, respectively.

5.3 Opening Data

TOPSPIN allows you to open data in several ways, from the browser, the
menu, the Windows Explorer or the command line. Furthermore, data can
be opened:
• in an existing data window replacing the current dataset.
• in a data window which is in multiple display mode, being superim-
posed on the current spectra.
• in a new data window which becomes the active window.

73
Dataset Handling

Note that if a dataset is already displayed in one window and it is opened in

a second existing window, it still replaces the dataset in the latter one. As a
result, the same dataset will be displayed in two windows (see also com-
INDEX
mand reopen).
INDEX DONE
How to Open Data Windows Cascaded
By default, a new data window appears maximized, filling the entire data
field and covering possibly existing windows. You can, however, configure
TOPSPIN to open new windows cascaded. This is convenient if you want to
open several data windows and then select one.
To open new windows cascaded:
1. Click Options => Preferences [set]
2. Click Window Settings in the left part of the dialog box.
The right part of the dialog box shows the window settings (see Fig.
5.11).

Figure 5.11
3. Check Open new internal windows ’cascaded’ rather than ’max’.
4. Optionally you can configure the cascaded windows by clicking the
respective Change button. This will open the dialog box shown in
Fig. 5.12.

74
 Dataset Handling

INDEX
DONE INDEX

Figure 5.12
5. Here you can specify the data window sizes and offsets as fractions
of the maximum window sizes.
6. Click OK to close the dialog box.

How to Open Data from the Browser

In the browser:
+ Left-click-hold a data name, expno or procno and drag it into the
data area. The data will be displayed in a new data window.
or Left-click-hold a data name, expno or procno and drag it into an
open data window. The data will replace the currently displayed da-
ta.
or Left-click-hold a data name, expno or procno and drag it into an
empty data window created with Alt+w n.
or Left-click-hold a data name, expno or procno and drag it into a mul-
tiple display data window. The data will be superimposed on the cur-
rently displayed data.
or Right-click a data name, expno or procno and choose Display from
the popup menu; the data will be displayed in the current data win-

75
Dataset Handling

dow.
or Right-click a data name, expno or procno and choose Display in
INDEXfrom the popup menu; the dataset will be displayed in
new window
a new INDEX
data window. DONE
or Hold the Ctrl key and left-click several datasets to select them or
hold the Shift key and left-click two datasets to select these two
and all in between. Then right-click one of the selected datasets and
choose Display from the popup menu. A new window will be
opened showing the selected datasets in multiple display mode.
However, if the current window was already in multiple display
mode, the selected spectra will be superimposed on the currently
displayed spectra.

How to Automatically Select the first expno/procno of a dataset

If you open a dataset from the Browser by clicking a data name, there
might be more that one expno and/or procno available. By default, TOP-
SPIN then opens a dialog box from which you can select the desired exp-
no/procno combination (see Fig. 5.13). Clicking Open will open the
selected dataset, whereas clicking Print will print the displayed dataset
list.
You can, however configure TOPSPIN to automatically open the first avail-
able expno/procno combination. To do that:
1. Click Options => Preferences [set].
2. Click Miscellaneous in the left part of the dialog box.
3. Uncheck the item Display EXPNO/PROCNO list when opening
data.
4. Click OK to close the dialog box.

76
 Dataset Handling

INDEX
DONE INDEX

Figure 5.13
Note that the command rel also opens the dialog shown in Fig. 5.13,
showing the available EXPNO’s under the current dataset. Similarly, repl
shows the available PROCNO’s under the current dataset EXPNO.

How to Open Data from the Topspin menu

1. To open a dataset:
+ Click the button in the upper toolbar.
or
+ Click File => Open [open, Ctrl+o] (see Fig. 5.14).

77
Dataset Handling

INDEX
INDEX DONE

Figure 5.14
2. In the appearing dialog box (see Fig. 5.15)
:

Figure 5.15
a) Select the option Open NMR data stored in standard Bruker
format.
b) Select the browser type RE Dialog.

78
 Dataset Handling

c) Click OK.
3. In the appearing dialog box (see Fig. 5.16).
: INDEX
DONE INDEX

Figure 5.16
a) Specify the dataset name, expno etc.
b) Click OK.
Note that the dataset specification consists of the five variable parts of the
data directory tree, in this case:
C:\bio\data\guest\nmr\exam1d_1H\1\pdata\1
The text boxes are initialized with the dataset in the current data window.

How to Open Data from the Explorer, Konqueror or Nautilus

You can open a dataset from the Windows Explorer as follows:
1. Open the Windows Explorer. You can do that in two different ways:
+ from the Windows Start button. Navigate to the data name, exp-
no or procno.
or

79
Dataset Handling

+ by entering the command expl in TOPSPIN. The Explorer shows

the contents of the current dataset procno directory. Navigate to
the desired
INDEXdata name, expno or procno. expl can also be used
with the argument top to open the TOPSPIN installation directory,
homeINDEX
to open user DONE
home directory or with an absolute pathname
to open that directory.
The command expl spect opens the Explorer in
<tshome>/conf/instr/ current instrument>
The command expl prop opens the Explorer in the user’s prop-
erties directory
User-HOME/topspin<name_of_PC>/prop
By entering expl <illegal argument> all available options
are shown.
2. Now you can open a dataset with:
+ drag & drop: click-hold a dataset name or any of its sub-folders or
files and drag it into the TOPSPIN data area or data window.
or
+ copy & paste: right-click a dataset and choose copy from the pop-
up menu. In TOPSPIN, click Edit => Paste [paste] (see Fig. 5.17).

Figure 5.17
Likewise, a dataset can be opened from the Windows window or Internet
Browser.

How to Open Data from the Command Line

To open a dataset from the command line:
1. Enter re
2. Specify a dataset in the appearing dialog box (see Fig. 5.16).

80
 Dataset Handling

3. Click OK
To open a new procno of the current dataset:
INDEX
1. Enter rep
DONE dialog
2. Specify a procno in the appearing INDEX
box.
3. Click OK
To open a dataset in a new window:
1. Enter rew
2. Specify a dataset in the appearing dialog box.
3. Click OK
To open a new procno of the current dataset in a new window:
1. Enter repw
2. Specify a procno in the appearing dialog box.
3. Click OK
To open a data browser and read a dataset from there:
1. Enter reb
2. Select a dataset from the appearing dialog box.
3. Click Display
Note that re, rep and reb:
• Replace the data in the currently selected data window.
• Open the data in a new window when they are used after typing
Alt+w n
• Add the data in the currently selected window if this is in multiple dis-
play mode.
whereas rew and repw:
• Always open the dataset in a new window.
Topspin 2.0 and newer allows opening datasets stored in the following di-
rectories structures:
<mydata>/<dataname>/<expno>/pdata/<procno>
To do that

81
Dataset Handling

+ Enter reb on the command line, browse to the desired dataset and
click the Display button
or INDEX
INDEX
+ Open the DONE File Browser, browse to the desired da-
Operating System
taset and open it in Topspin with Copy & Paste or Drag & Drop.
Note that this will create a copy of the dataset in the standard Topspin da-
tapath:
<tshome>/data/<user>/nmr/<dataname>/<expno>/pdata/<procno>
where <user> is the current internal Topspin user. This copy can be proc-
essed, deleted or overwritten, even if the original dataset is write protect-
ed. The original data set is left unchanged.

How to Open Special Format Data

Apart from the standard Bruker data format, TOPSPIN is able to read and
display various other formats. To do this:
+ Click File => Open [open, Ctrl+o]
select the option Open NMR data stored in special formats, select the
desired file type (see Fig. 5.18) and click OK.
A dialog will appear which depends on the chosen file type. Just follow the
instructions on the screen.
The following file types are supported:
• JCAMP-DX - Bruker TOPSPIN1 data stored in JCAMP-DX format
• Zipped TOPSPIN - Bruker TOPSPIN data stored in ZIP format
• WINNMR - Bruker WINNMR data
• A3000 - Bruker Aspect 3000 data
• VNMR - data acquired on a Varian spectrometer
• JNMR - data acquired on a Jeol spectrometer
• Felix - 1D data, FID or spectrum, which are stored in FELIX format.

1. Note that the TOPSPIN data format is identical to the XWIN-NMR data format.

82
 Dataset Handling

Note that in all cases, the data are stored in a single data file which is un-
packed/converted to standard Bruker format, i.e. to a data directory tree.
INDEX
DONE INDEX

Figure 5.18

How to Open a ZIP or JCAMP-DX file from the Windows

Explorer
Data stored in ZIP or JCAMP-DX format can also be opened directly from
the Windows Explorer. You can do that in one of the tree following ways:
Drag & drop
+ Click-hold a file with the extension .dx or .zip and drag it into the
TOPSPIN data area or data window.
Copy & paste
1. Right-click a file with the extension .dx or .zip and choose copy
from the popup menu.
2. In TOPSPIN, click Edit => Paste [paste]
Associate JCAMP-DX files with a script
1. Create a file with the extension .cmd (e.g. jcamp.cmd) with a text
editor.
2. Enter the following line:
<tshome>\prog\bin\sendgui.cmd fromjdx %1

83
Dataset Handling

and store the file.

3. Open the Explorer and find the JCAMP-DX file.
INDEX
4. Right-click the filename and choose Open with => Choose pro-
gramINDEX
=> Browse DONE
5. Find and select the script and click OK.
Now, every file with the extension .dx will automatically be opened in
TOPSPIN when double clicked.

5.4 Saving/Copying Data

How to Save or Copy Data

You can save the current dataset as follows:
1. Click File => Save [Ctrl+s].
This will open a dialog box (see Fig. 5.19).

Figure 5.19
2. Select an option and, if applicable, a file type.
3. Click OK to execute the option.
The options correspond to the following command line commands:
• wrpa - copies the current data to a new data name or expno
84
 Dataset Handling

• toccpn - convert experiment information to ccpn format1

• tozip - convert a dataset of any dimension to ZIP format
INDEX
• tojdx - convert a 1D or 2D dataset to JCAMP-DX format
• totxt - convert a 1D or DONE INDEX
2D dataset text format
• wpar - write parameter set
• convdta - save digitally filtered data as analog filtered data
• wrp, wra, genfid, wmisc - write various files

How to Save an Entire Dataset

1. Click File => Save [Ctrl+s].
2. Select the option Copy dataset to a new destination [wrpa] and
click OK
3. Specify the dataset variables and click OK

How to Save Processed Data

1. Click File => Save [Ctrl+s].
2. Select the option Save other file
3. Select File type Processed data as new procno [wrp] and click OK
4. Enter a processing number (procno) and click OK

How to Save Acquisition Data

1. Click File => Save [Ctrl+s].
2. Select the option Save other file
3. Select File type Acqu. data as new expno [wra] and click OK
4. Enter a experiment number (expno) and click OK

How to Save Processed Data as Pseudo Raw Data

1. Click File => Save [Ctrl+s]
2. Select the option Save other file

1. For detailed information about the ccpn format please refer to www.ccpn.ac.uk

85
Dataset Handling

3. Select File type 1r/1i as fid [genfid] or 2rr/2ii as ser [genser]

4. Click OK
INDEX
5. Enter a destination expno.
INDEX
(optionally, DONE
you can specify further data path specifications)
6. Click OK

5.5 Deleting Data

How to Delete a Specific Dataset

+ Right-click the data name, expno or procno in the browser, then click
Delete...
A confirmation dialog will appear. Just click OK, if you are sure you want
to delete. Note that TOPSPIN does not allow you to delete the last available
dataset, e.g. the last procno under an expno, the last expno under a
name or the last name under a user.

How to Delete Types of Datasets

To delete certain types of data like 1D raw data, 2D processed data etc.:
+ Click File => Delete...
or
+ Enter delete on the command line.
The dialog window shown in Fig. 5.20 will appear. Here you can select the
data type and selection criteria.

5.6 Renaming Data

How to Rename a Specific Dataset

1. Right-click the data name, expno or procno in the browser, then click
Rename...
2. In the appearing dialog:
Enter the new name, expno or procno

86
 Dataset Handling

3. Click OK
:

INDEX
DONE INDEX

Figure 5.20
1. Select a data type option
For each option, the corresponding command appears in the title of
the dialog box. These commands can also be used to delete data from
the command line.
2. Specify the Required parameters

87
Dataset Handling

Note that you can use the wildcards:

• Asterix (*) for any character and any number of characters.
INDEX
• Question mark (?) for any single character.
3. Click OKINDEX DONE
A dialog box will appear showing the matching datasets. For example, if
you select the option An entire dataset ...:
1. Select dataset entries for deletion (selected entries are highlighted).
To select multiple entries: click them holding the Shift or Ctrl key.
2. Click OK to delete the entire data directory.
If you select the option Acquisition data or Processed data, you can
choose between deleting the data files only and deleting the entire expno
or procno directory, respectively (see Fig. 5.21).

Figure 5.21

88
5.7 Searching/Finding Data

How to Find Data

You can find TOPSPIN data according to various criteria. To start searching,
do the following:
1. Click Edit => Find data [Ctrl+f | find]
to open the Find data window (see Fig. 5.22).

Figure 5.22
 2. Enter the search items in the upper part of the dialog. Note that:
• There will be searched for items containing the specified string
• Exact matching is performed for dataset variables, NAME,
EXPNO, PROCNO and USER, if the checkboxes at the right are
enabled.
• The search is restricted to data created between the specified
dates. Note that this refers to the acquisition date.
• The Reset mask button allows you to reset the default criteria.
3. Select the Data directories to be searched in the lower part of the
dialog. If no directories are selected, all will be searched.
4. Click OK
to start the search. A list of data that fulfil the defined criteria will
appear (see Fig. 5.23).

Figure 5.23
Note that on exiting TOPSPIN, the search criteria will be rest to default.

How to Display one of the Found Datasets

In the search result window (see Fig. 5.23):
1. Click one or more datasets to select them.
 Dataset Handling

2. Click Display
to display the selected dataset(s) in the current data window. If multi-
ple datasets are selected they are displayed
INDEX in a new data window in
multiple display mode.
DONE INDEX
The search result window offers a right-click context menu with various op-
tions (see Fig. 5.24).

Figure 5.24
Display
Display the selected dataset(s) in the current data window. If multiple da-
tasets are selected they are displayed in the same data window in multi-
ple display mode. Equivalent to clicking the Display button or pressing
Enter.
Display In New Window
Display the selected dataset(s) in a new window. If multiple datasets are
selected they are displayed in the one new data window in multiple dis-
play mode.
Display As 2D Projection
Display the selected dataset as a projection of the current 2D dataset. A
dialog will appear allowing you to choose F1-projection, F2-projection or
both. If multiple datasets are selected, only the first one is considered. If
the current dataset is not a 2D dataset, nothing happens.
Sort This Column

91
Dataset Handling

Sort the selected column in ascending order.

Sort + Reverse
INDEX
Sort the selected column in descending order.
INDEX DONE
Save Selection in file...
Save the list of selected datasets in a text file. First opens a file dialog
where you can select or specify a filename. The saved dataset list can,
for example, be used for serial processing (command serial, see also
Process Selected Datasets below).
Add selection to dataset group...
Selected datasets can be defined as dataset group.
File properties
Show main dataset parameters like Dimension, Pulse program, Acquisi-
tion Date, Nuclei, Spectrometer frequency and Solvent.
Files
Show the files in the processed data directory of the selected dataset.
Process Selected Datasets
Perform serial processing on the selected datasets. Opens a dialog
where you can change or edit the dataset list and specify the command,
macro or Python program to be executed (starts the command serial).
The Close button allows you to close the search result dialog.

5.8 Handling Data Files

How to List/Open the Current Dataset Files

A Bruker dataset is represented by a directory tree which contains files in
the expno and procno subdirectories. These files contain the actual data,
parameters, lists etc.
+ Right-click inside the data window and choose Files from the popup

92
 Dataset Handling

menu.

INDEX
DONE INDEX

If the spectrum is displayed, the files in the procno subdirectory are

shown. If the Fid is displayed, the files in the expno subdirectory
are shown.
+ Select a file and click Open to view its contents.
Note that this only makes sense for ascii files.

How to List/Open the current Dataset Files in the Windows

Explorer
To list the current dataset files in the Windows Explorer:
1. Click File => Run...
2. Select Open file explorer [expl] in the appearing dialog box (see
Fig. 5.25)
3. Click OK
Alternatively, you can enter the command expl on the command line.The
Windows Explorer will be opened showing the processed data files (the
files in the procno directory) of the current dataset. Under Linux a Web
browser like KDE Konqueror or Gnome Mozilla will be opened.
To open a file:
+ Double-click the file or right-click the folder icon and choose Open

93
Dataset Handling

INDEX
INDEX DONE

Figure 5.25
If TOPSPIN data area contains no datasets, the expl command opens the
Explorer showing the users home directory. When entered on the com-
mand line, expl can also be used with the argument top to open the TOP-
SPIN installation directory, home to open user home directory or with an
absolute pathname to open that directory.

94
 Dataset Handling

INDEX
DONE INDEX

95
Parameter Handling

Chapter 6
INDEX

Parameter
INDEX
Handling
DONE

6.1 Processing Parameters

Processing parameters can be set/changed in three different ways:

• from the parameter editor: click the ProcPars tab or enter edp
• from the command line: e.g. enter si
• from a command dialog box: e.g. wm

How to Set a Processing Parameter from the Command Line

Enter the parameter name on the command line. For example to set the
size:
1. Enter si

96
 Parameter Handling

for 1D data, the following dialog box will appear:

INDEX
DONE INDEX

for 2D data, the following dialog box will appear:

2. Specify the desired value(s), e.g. 32768 or 32k

3. Click OK

How to Set Processing Parameters from the Parameter Editor

To open the processing parameter editor:
+ Click the ProcPars tab in the Tab bar of the data window.
or
+ Enter edp on the command line.

97
Parameter Handling

INDEX
INDEX DONE

Figure 6.1
At the left of the parameter editor window you will see a list of parameter
sections.
The processing parameter editor supports the following functions:

+ Collapse/expand a parameter section by clicking the button.

Note that the section Window function in Fig. 6.1 is collapsed.

+ Collapse/expand all parameter sections by clicking the large

button of the data window toolbar.
+ Enter (part of) a parameter name in the search field and click .
+ Click a parameter section, e.g. Phase at the left of the dialog box. The
section becomes highlighted and the corresponding parameters will
appear in the right part of the dialog box.
+ Click in a parameter field, e.g. PHC0, to set the parameter value.

+ Click the button to the right of parameters like AUNMP to

open a list of the corresponding programs/lists.
98
 + Right-click the button to the right of parameters like AUN-
MP to open the current program/list with an editor.
+ Hit the Tab key to jump to the next parameter field.
+ Hit Shift+Tab to jump to the previous parameter field.
+ Use the scroll bar at the right of the dialog box to move to parame-
ters further up or down in the dialog box.

How to Undo the Last Processing Parameter Change

+ Click the following button:
Undo last parameter change.

How to Display Processing Status Parameters

+ Click the following button:
Show processing status parameters.
Note that the command dpp opens the parameter editor and automatically
shows the status parameters.

How to Switch to Maxent parameters

+ Click the following button:
Switch to Maxent parameters.

How to Change Processed Data Dimensionality

+ Click the following button:
Change data dimensionality.
This changes the number of parameter columns and value of the process-
ing parameter PPARMOD. TOPSPIN 2.1 and newer support data dimen-
sionalities up to 8D.
The parameter editor does not allow you to modify status parameters.
Processing status parameters reflect the status of the processed data and
are used for further processing, display or plotting. Changing them can
make the dataset inconsistent. In rare cases, however, it can be useful to
 change a status parameter and TOPSPIN allows you to do that from the
command line. If, for instance, you want to change the F1 status parameter
MC2 of a 2D dataset, you have to enter:
s mc2
Note that the command s is used for 1D, 2D and 3D dataset. TOPSPIN auto-
matically recognizes the dimensionality of the data and displays the param-
eter in all relevant dimensions. Note that, for example, the parameter MC2
only exists in F1.

6.2 Acquisition Parameters

How to Set Acquisition Parameters

Acquisition parameters can be set/changed as follows:
• from the parameter editor: click the AcquPars tab or enter eda
• from the command line: e.g. enter td
• from the interactive parameter adjustment window (enter gs)

How to Set an Acquisition Parameter from the Command Line

Enter the parameter name on the command line. For example to set the
time domain size:
1. Enter td
for 1D data, the following dialog box will appear:
 Parameter Handling

for 2D data, the following dialog box will appear:

INDEX
DONE INDEX

2. Specify the desired value(s), e.g. 65536 or 64k

3. Click OK

How to Set Acquisition Parameters from the Parameter Editor

To open the acquisition parameter editor:
+ Click the AcquPars tab in the Tab bar of the data window.
or
+ Enter eda on the command line.
Fig. 6.2 shows an example of the acquisition parameter editor with the Ex-
periment parameters displayed.

101
Parameter Handling

INDEX
INDEX DONE

Figure 6.2
The processing parameter editor supports the following functions:

+ Collapse/expand a parameter section by clicking the button.

Note that the section Width in Fig. 6.2 is collapsed.

+ Collapse/expand all parameter sections by clicking the large

button of the data window toolbar.

+ Enter (part of) a parameter name in the search field and click .
+ Click a parameter section, e.g. Experiment at the left of the dialog
box. The section becomes highlighted and the corresponding pa-
rameters will appear in the right part of the dialog box.
+ Click in a parameter field, e.g. TD, to set the parameter value.

+ Click the button to the right of parameters like PULPROG

to open a list of the corresponding programs/lists.

102
 Parameter Handling

+ Right-click the button to the right of parameters like PUL-

PROG to open the current program/list
INDEX with an editor.
+ Hit the Tab key to jump to the next parameter field.
DONE INDEX
+ Hit Shift+Tab to jump to the previous parameter field.
+ Use the scroll bar at the right of the dialog box to move to parame-
ters further up or down in the dialog box.

How to Undo the Last Acquisition Parameter Change

+ Click the following button:
Undo last acquisition parameter change.

How to Set Pulse Program Parameters

+ Click the following button:
Show pulse program parameters [ased]
The button will change to . To make this the default setting:
Click Options => Preferences, click Miscellaneous, check the entry
"Show ased parameter selection with eda" and click OK.

How to Display Acquisition Status Parameters

+ Click the following button:
Show acquisition status parameters.
Note that the command dpa opens the acquisition parameter editor and
automatically shows the status parameters.

How to Get Probehead/Solvent dependent Parameters

+ Click the following button:
Set probehead/solvent dependant parameters [getprosol].
Probehead and solvent dependant parameters can be set up with the
command edprosol.

103
Parameter Handling

How to Change Acquisition Data Dimensionality

+ Click the following button:
INDEX
Change data dimensionality.
INDEX DONE
This changes the number of parameter columns and value of the acquisi-
tion parameter PARMODE.

How to Set Lock Parameters

Enter the command edlock and set the lock parameters in the appearing
dialog box. For a detailed description of edlock, please refer to the Ac-
quisition Reference manual or enter edlock? on the command line.

How to Set Routing Parameters

Enter the command edasp and set the routing parameters in the appear-
ing dialog box. For a detailed description of edasp, please refer to the Ac-
quisition Reference manual or enter edasp? on the command line.

104
 Parameter Handling

INDEX
DONE INDEX

105
Data Processing

Chapter 7
INDEX

Data Processing
INDEX DONE

7.1 Interactive Processing

Interactive processing allows full control over the processing sequence.

However, it requires detailed knowledge about the required parameters
(see chapter 6.1) and commands. Therefore, it is only suitable for the
advanced user. New or intermediate users are recommended to use the
Processing Guide for semi-automatic processing (see chapter 7.2).

How to Process Data with Single Commands

Data can be processed by entering single commands on the command
line. A typical 1D processing sequence would be:
em : exponential window multiplication
ft : Fourier transform
apk : automatic phase correction
sref : automatic calibration (referencing)
abs : automatic baseline correction
This allows you full control over each individual processing step.

106
 Data Processing

How to Process data with Composite Commands

Data can also be processed with so called composite commands. These
INDEX The following compos-
are combinations of single processing commands.
ite commands are available. DONE INDEX
• ef : Exponential multiplication + Fourier transform
• efp : Exponential multiplication + Fourier transform + phase correc-
tion
• fmc : Fourier transform + magnitude calculation
• fp : Fourier transform +phase correction
• gf : Gaussian multiplication + Fourier transform
• gfp : Gaussian multiplication + Fourier transform + phase correc-
tion
They can be entered on the command line or clicked from the menu. For
the latter option:
+ Click Processing => More transforms => Shortcuts
Just like single commands, composite commands can be used in Macros,
AU programs and Python programs.

7.2 Semi-automatic Processing

How to Use the 1D Processing Dialog

1D data processing often involves the same sequence of steps, which can
easily be performed as follows:
1. Click Processing => Process / Plot Current data
2. In the appearing dialog (see Fig. 2.1):
a) Enable the desired processing/plotting steps
b) Set the parameter LB for exponential multiplication
c) Select the desired LAYOUT for plotting.
d) Click OK

107
Data Processing

INDEX
INDEX DONE

Figure 7.1

How to Use the Processing Guide in Automatic mode

The Processing Guide in automatic mode guides you through the entire
processing sequence of data selection, processing, printing and archiving
with minimum user interaction.
1. Click Processing => Data => Processing Guide
The Processing Guide window will appear as an integral part of the
current data window (see Fig. 7.2).

108
 Data Processing

INDEX
DONE INDEX

Figure 7.2
2. In the Processing Guide window:
a) Check Automatic mode
b) Click Open data set and click OK to open a dataset manually, e.g.
from the browser or click Browse to open the File Chooser.

109
 c) Click Window function => Fourier Transform => etc.
Each processing step will be executed without user interaction.

How to Use the Processing Guide in Interactive mode

The Processing Guide in interactive mode guides you through the entire
processing sequence of data selection, processing, printing and archiving
requiring some user interaction.
1. Click Processing => Data => Processing Guide
The Processing Guide window will appear as an integral part of the
current data window.
2. In the Processing Guide window:
a) Uncheck Automatic mode
b) Click Open data set and click OK to open a dataset manually, e.g.
from the browser or click Browse to open the File Chooser.
c) Click Window function => Fourier Transform => etc.
For each step a dialog box will appear where you can enter options, pa-
rameters etc. For details on these items, please refer to the corresponding
commands in the Processing Reference Guide.

7.3 Processing Data with AU programs

Data processing can be performed by using AU programs. An AU program

is actually a C-program which contains TOPSPIN commands (macros)
and/or C-language statements. Various standard AU programs are deliv-
ered with TOPSPIN. A typical 1D processing AU program is proc_1d. A
simplified version of this AU program is:
EF
APK
SREF
ABS
AUTOPLOT
QUIT
It executes the commands ef, apk, sref, abs and autoplot. To run this
 Data Processing

AU program, just enter proc_1d on the command line 1. You can create
your own AU programs with the command edau. Note that an AU program
must end with QUIT or QUITMSG("your message"),INDEXand that all statements
must be specified in capital letters. For more information on AU programs,
DONEmanual:INDEX
please refer to the AU programming
+ Click Help => Manuals => [Programming Manuals] AU Program-
ming
As an alternative to AU programs, you can also write Python programs,
which allow you to use TOPSPIN commands, User Interface functions and
Graphic functions. For more information:
+ Click Help => Manuals => [Programming Manuals] Python Pro-
gramming

7.4 Serial Processing

TOPSPIN allows you to process a series of datasets using serial scripts. The
dataset list and command(s) to be used can be easily setup from the TOP-
SPIN interface as follows. Enter the command serial on the command
line. This will open the dialog window shown in Fig. 7.3.

Figure 7.3

1. Before you can use any Bruker AU program, expinstall must have been exe-
cuted once.

111
Data Processing

The same dialog window will be shown by using the menu bar Processing
Serial Processing.
INDEX
The dialog offers you the following options:
Browse forINDEX
list DONE
This buttons opens an Explorer in which you can locate an existing
datset list.
Find Datasets
You can for Datasets in all data directories marked in the appearing
dialog window list (see Abbildung 7.4).

Figure 7.4
Edit List
This button will open a texteditor in which you can edit the current or

112
 Data Processing

a new dataset list.

Next
INDEX
After having defined the full datasetpath and clicking next the follow-
ing dialog will appear: DONE INDEX

Figure 7.5
Continue with command definition, for example for Macros or Python
programs. You can even Browse for Macros or Python programs. The

113
Data Processing

following dialog will appear, dependent from your selection:

INDEX
INDEX DONE

Figure 7.6
After having chosen a Python program or a Macro, push the button ex-
ecute for finishing serial processing command. In Figure

114
 Data Processing

Abbildung 7.7 you can see the look of the actual dialog.

INDEX
DONE INDEX

Figure 7.7
After executing the serial processing, TopSpin 2.1 and newer displays
following feedback-dialog:

Figure 7.8
Cancel
Leave this dialog.

115
 Chapter 8
Printing/Exporting Data

8.1 Printing/plotting Data

How to Print/Plot from the Menu

The current data window can be printed as follows:
1. From the TOPSPIN menu:
+ Click the button in the upper toolbar
or Click File => Print
or Enter print or Ctrl+p
All these actions are equivalent; they open the Print dialog box (see
Fig. 8.1).
 Printing/Exporting Data

INDEX
DONE INDEX

Figure 8.1
2. In the Print dialog box:
a) Select Print active window [prnt]
b) Click OK
Before printing starts, the operating system print dialog box will ap-
pear. Here you can, for example, select the printer name and the print-
er properties.
The Print dialog box (see Fig. 8.1) contains two further options:
• Print with layout - start Plot Editor [plot]
If you select this option and click OK, the Plot Editor will be started.
This option is equivalent to entering plot on the TOPSPIN command
line.
• Print with layout - plot directly [autoplot]
Selecting this option activates the Plot Editor layout list box. Select

117
Printing/Exporting Data

the desired layout and click OK to print. Standard layouts are deliv-
ered with TOPSPIN. They use the Windows default printer. User
defined layouts
INDEXuse the printer defined in the Plot Editor. On a 1D
dataset, only 1D layouts are listed, on a 2D dataset only 2D layouts
are listedINDEX
etc. DONE
For the last two options, the following Required Parameters are available:
Use plot limits
• from screen/ CY
The plot limits and maximum intensity are used as they are on the
screen (processing parameter F1P, F2P and CY, respectively).
• from Plot Editor Reset Actions
The plot limits and maximum intensity are set according to the Plot
Editor Reset Actions (right-click inside the Plot Editor data field
and choose Automation to set the Reset Actions).
• as saved in Plot Editor
The plot limits and maximum intensity are set in the specified lay-
out
Fill dataset list
• from your default portfolio
The portfolio contains the current TOPSPIN dataset plus the data
from the default Plot Editor portfolio.
• from port folio saved in dataset
The portfolio contains the current TOPSPIN dataset plus the data
from the portfolio stored in this dataset.
Override Plotter saved in Plot Editor
If enabled, the plotter defined in the Plot Editor layout will be overrid-
den by de plotter defined by the processing parameter CURPLOT.

How to Plot Data from the Processing guide

Printing/plotting data can be done from the Processing guide by clicking
the Plot/Print button. If Automatic mode is checked, the active data win-
dow will be printed as it appears in the screen. If Automatic mode is un-
checked, you will get the dialog box as displayed in Fig. 8.1.

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 Printing/Exporting Data

How to Plot Data with the Plot Editor

The Plot Editor can be started from the Print dialog or from the command
line (command plot). The Plot Editor allows INDEX
you to create layouts and
plot data. The complete functionality is described in the online manual,
DONE INDEX
which can be opened as follows:
+ Click Help => Manuals => [Automation and Plotting] Plotting

How to Print the Integral list

1. Click the Integrals tab of the data window (see Fig. 8.2).
2. Enter print or Ctrl+p to print it.

Figure 8.2

How to Print the Peak list

1. Click the Peaks tab of the data window (see Fig. 8.3).
2. Enter print or Ctrl+p

119
Printing/Exporting Data

INDEX
INDEX DONE

Figure 8.3

8.2 Exporting Data

How to Copy data to Other Applications

Under MS Windows, you can easily copy the data window contents to oth-
er applications. To do that:
+ Click Edit => Copy [copy].
This will copy the data window contents to:
• the clipboard. After that you can paste the clipboard contents to
any Windows application.
On Windows systems the command Edit => Copy [copy] saves bmp-for-
mat, whereas the command copy wmf stores the old wmf-format.
On Linux systems the command copy stores png-files into a temporary
file. The pathname of this file is copied to clipboard.
Please note:
Some programs, when importing spectra from the clipboard or metafile, do
not display the contained information correctly. Particularly when you re-
size the imported graphics, sections of the text, the spectrum, or the axis
sometimes have disappeared. Usually this is only a display problem.
When you print the respective page, the representation is correct.
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 Printing/Exporting Data

How to Store (Export) a Data Window as Graphics File

The clipboard and metafile formats are resizable vector formats. In addi-
INDEX of a data window in a
tion to this, TOPSPIN allows you to save the contents
graphics file of selectable type. Supported formats are .png, .jpg, .jpeg,
DONE INDEX
.bmp, .emf, .wmf and .pdf. To do that:
1. Click File => Export.... [exportfile].
2. Navigate to the storage folder.
3. Enter the destination filename and extension.
4. Click Export
The resolution of such a screen dump equals the resolution of your
screen.When you import a graphics file into an other program, you may
loose information when resizing the graphics.
Note that exporting a data window to PDF-format is only supported in
TOPSPIN 2.1 and newer.

How to export projections of peak lists

Certain situations may require that the user wants to store a projection of
a peak list (e. g. in order to evaluate an assignment in a 3D by verifying
the annotated projected 2D-HSQC peak list on the respective 2D spec-
trum). Therefore it is useful and timesaving to use the option "export pro-
jections of peak lists".
In order to create such a peak list projection, the following steps must be
executed:
1. Switch to the peaks tab of the data set from which the peak list pro-
jection should be used

121
Printing/Exporting Data

2. Choose Export... from the peak table context menu (right-click)

INDEX
INDEX DONE

Figure 8.4
3. Select the Project Peaks flag in the options panel of the appearing
export dialogue.
Please note that the active flag Project Peak envokes the export of
the entire projections peak list. If seperate peaks should be exported,
they must be selected in the peak table and the flag Export selected
data must be set.

Figure 8.5

122
 Printing/Exporting Data

In the dialogue box the file format can be changed acoording to the
the required application.
INDEX
4. Define the desired options in the upcoming projections dialogue win-
dow (i. e. target dimension and axis mapping).
DONE INDEX

Figure 8.6
The exported peak list is now of the specified dimension, where the
axis are projected according to the specified axis mapping.

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1D Display

Chapter 9
INDEX

1D Display
INDEX DONE

9.1 The 1D Data Window

The 1D data window consists of a data field, a title bar, a Tab bar and but-
tons. Fig. 9.1 shows a data window with a 1D spectrum.

124
 1D Display

maximize
data button
field
INDEX minimize close
title bar button button
Tab bar
DONE INDEX

Figure 9.1

9.2 Displaying one Dataset in Multiple windows

TOPSPIN allows you to display one dataset in multiple data windows. This is,
for example, convenient to view various regions or various objects (spec-
trum, fid, parameters etc.) of the same dataset.

How to Reopen a Dataset in a Second/Third etc. Window

1. Select (activate) the desired dataset.
2. Click File => Reopen [reopen].
Multiple data windows with the same dataset are indicated with a number
in square brackets, e.g. [1], in the title bar (see Fig. 9.2).

125
1D Display

INDEX
INDEX DONE

Figure 9.2

How to Rescale or Shift one Dataset in Multiple windows

Display buttons like and only work on the active data window. The
same counts for the keys Alt+PageUP and Alt+PageDown. However,
when used with the control key, they work on all windows, for example:

+ Hit Ctrl+ , Ctrl+Alt+PageUp or Ctrl+Alt+PageDown

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 1D Display

9.3 Changing the Display of a 1D Spectrum or FID

INDEX vertically and horizon-
TOPSPIN offers buttons to scale or shift the spectrum
tally.
DONE INDEX
How to Change the Vertical Scaling of the FID or Spectrum
+ Hit one of the following the keys:
• Alt+PageUp: Increase the intensity by a factor of 2.
• Alt+PageDown: Decrease the intensity by a factor of 2.
• Alt+Enter: Reset the intensity.
or
+ Click one of the following buttons:
Increase the intensity by a factor of 2 [*2].

Increase the intensity by a factor of 8 [*8].

Decrease the intensity by a factor of 2 [/2].

Decrease the intensity by a factor of 8 [/8].

Reset the intensity [.vr].

Alternatively, you can enter the corresponding commands as specified be-

tween square brackets [].
To manipulate all data windows, press the Ctrl key while clicking one of
the above buttons.

How to Smoothly Change the Vertical Scaling of the FID/Spec-

trum
+ Click-hold the button and move the mouse
or
+ Turn the mouse wheel while the cursor is in the data window.

127
1D Display

How to Change the Horizontal Scaling of the FID or Spectrum

+ Click-hold the button and move the mouse:
INDEX
Zoom in/out smoothly.
or
INDEX DONE

+ Click one of the following buttons:

Zoom in to the center (spectrum) or left edge (FID) of the dis-
played region, increasing the horizontal scaling. [.zi]
Zoom out from the center (spectrum) or left edge (FID) of the dis-
played region, decreasing horizontal scaling) [.zo]
Perform an exact zoom via a dialog box [.zx].
a) Enter the coordinates of the desired region in the dialog box:

b) Click OK
Undo last zoom [.zl].

Reset horizontal scaling to show the full spectrum [.hr].

Display the entire spectrum (baseline position and intensity scal-

ing are adjusted if necessary) [.all]
Toggle interactive zoom mode. When switched off, interactive
zooming only selects a horizontal region; baseline position and
intensity scaling remain the same. When switched on, interactive
zooming draws a box selecting the corresponding area.
Retain horizontal and vertical scaling when modifying dataset or

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 1D Display

changing to different dataset [.keep]. Effects all data windows.

Alternatively, you can enter the corresponding commands as specified be-
tween square brackets []. INDEX
DONE INDEX
How to Shift a Spectral Region to the Left or to the Right
+ Click-hold the following button and move the mouse:

Smoothly shift to left or right.

or
+ Click one of the following buttons:
Shift to the left, half of the displayed region [.sl].

Shift to the right, half of the displayed region [.sr].

Shift to the extreme left edge of the spectrum [.sl0].

Shift to the extreme right edge of the spectrum [.sr0].

Alternatively, you can enter the corresponding commands as specified be-

tween square brackets [].

How to Shift the Spectrum Up or Down

To shift the FID or spectrum display up or down:
+ Click-hold the button and move the mouse:

Smoothly shift the spectrum baseline up/down.

or
+ Click one of the following buttons:
Shift the spectrum baseline to the middle of the data field [.su].

Shift the spectrum baseline to the bottom of the data field [.sd].

Alternatively, you can enter the corresponding commands as specified be-

tween square brackets [].
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1D Display

9.4 Using the Tab bar

INDEX
Tabs of the data window can be activated by clicking them or by entering
the corresponding commands, as specified between square brackets, on
INDEX DONE
the command line. Note that command line commands always work on the
currently selected (active) data window.
The Tab bar can be configured from the User Preference box (command set).

How to Display the Spectrum

+ Click the Spectrum tab [spec]

This displays the processed data. If these do not exist, the text ‘No proc-
essed data available’ appears.

130
 1D Display

How to Set Processing Parameters

+ Click the ProcPars tab [edp]
INDEX
DONE INDEX

This opens the processing parameter editor (see also chapter 6.1). The
following extra buttons are available:
Undo last value change. Can be used to undo multiple changes.
Switch to Maxent parameters.
Status parameter display. The button turns green when activated
[dpp].
Change processed dataset dimensionality (parameter PPARMOD).
Collapse/expand all parameter sections.
Search for specified parameter.
Changed parameters are automatically saved.

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1D Display

How to Set Acquisition Parameters

+ Click the AcquPars tab [eda]
INDEX
INDEX DONE

This opens the acquisition parameter editor (see also chapter 6.1)). The
following extra buttons are available:
Undo last value change. Can be used to undo multiple changes.
Show pulse program parameters [ased].
Status parameter display. The button turns green when activated
[dpa].
Set probehead/solvent dependant parameters [getprosol].
Set nuclei and routing [edasp]
Change raw dataset dimensionality (parameter PARMODE).
Collapse/expand all parameter sections.
Search for specified parameter.
Changed parameters are automatically saved.
Note that the ... and E button to the right of the PULPROG parameter allow

132
 1D Display

you to show the pulse program list or edit the current pulse program, re-
spectively.
INDEX
How to Edit the Title
Click the Title tab [edti]
DONE INDEX

This allows you to edit the title that appears in the data window and on the
plot.
Save the title file under its current name.
Save the title file under a new name.
Reload the title file. Undo modifications since the last save.
Open the title file with the external editor (defined in User Prefer-
ences).

133
1D Display

How to Edit the Pulse Program

+ Click the PulsProg tab]
INDEX
INDEX DONE

This allows you to edit the current pulse program. The following extra but-
tons are available here:
Toggle status pulse program.
Start the graphical pulse program display [edcpul].
Show the pulse program in an external editor [nmrsim].
Search for more info in the knowledge base

How to Display the Peak list

Click the Peaks tab

134
 1D Display

INDEX
DONE INDEX

Figure 9.3
This displays the peak list. By default, the peak list shows the following en-
tries:
Peak: the peak number
v(F1) [ppm]: the chemical shift
Intensity [abs]: the absolute peak intensity
Intensity [rel]: the relative peak intensity
Half width [ppm]: the peak width at half-height

Display the spectral region around a peak

+ Right-click the desired peak
this will open the popup menu shown in Fig. 9.4.

135
1D Display

INDEX
INDEX DONE

Figure 9.4
Here you can choose from the following options:
+ Show spectrum => In correlated window
to open a new data window showing the full correlated spectrum
+ Expand spectrum => In current window
to change the current data window to spectrum display, showing the
region around the selected peak
+ Expand spectrum => In correlated window
to open a new data window showing the region around the selected
peak
+ Edit Annotation
Edit the annotation of the current peak.
+ Define as reference => Complete table
Define the entire peak table as a reference for annotation.
+ Define as reference => Selection
Define the selected peaks as a reference for annotation.

136
 1D Display

+ Annotate by reference...
Create annotations according to the peaklist of the reference data-
set. You will be prompted for the allowed variation in chemical shift.
INDEX
+ Shift peaks... DONE INDEX
Shift all peaks. You will be prompted for the number of ppm to be
shifted.
+ Show detailed information
Show peak information, dataset information and peak picking pa-
rameters.
Export entries of the peak list
Entries of the peak list can easily be exported to Excel or any other pro-
gram as follows:
1. For multiple peaks:
Select the desired entries while pressing the Ctrl or Shift key
2. Right-click a peak entry to open the popup menu (see Fig. 9.4).
3. Click Export... to export the selected peaks.
4. This opens a dialog box where you can specify the filename and
file type. For the latter you can choose from:
• Auremol peaklist (.ml)
• Comma Separated Values (.cvs)
• Mixed Shape deconvolution peak list (peaklist)
• TOPSPIN peak list (.xml)
• XEASY peak list (.peaks)
• XWIN-NMR peak list (.txt)
Important: Check the box in the lower-left corner to export the se-
lected peaks only or uncheck it to export the entire list. Then click
Export.

Delete/remove peaks from the peak list

To delete one peak:
+ Right-click the peak and choose Delete from the popup menu

137
1D Display

To delete multiple peaks:

1. Select the peaks while pressing the Ctrl or Shift key
INDEX
2. Right-click one of the peaks and choose Delete from the popup
menuINDEX DONE
To remove possible duplicate peaks:
+ Right-click any entry and choose Remove => Duplicate peaks
To remove possible peaks outside of the spectrum:
+ Right-click any entry and choose Remove => Peaks positioned
outside of the spectrum
To remove solvent peaks:
+ Right-click any entry and choose Remove => Solvent Peaks

Copy the peak List

Instead of exporting entries of the peak list, they can also be copied to
the Clipboard and pasted to another application like Excel. To do that:
1. For multiple peaks:
Select the desired entries while pressing the Ctrl or Shift key
2. Right-click a peak entry to open the popup menu (see Fig. 9.4).
3. Click Copy... to copy the selected peaks to the Clipboard.

Print the peak List

To print the peaklist:
+ Right-click a peak entry and choose Print...
or
+ Enter print on the command line
or
+ Press Ctrl-p
All actions will print the entire peaklist.
To preview a print:

138
 1D Display

+ Right-click a peak entry and choose Print preview...

Import a peak List INDEX

A peak list from a different dataset or program can be imported as fol-
lows: DONE INDEX
1. Right-click an entry to open the popup menu (see Fig. 9.4).
2. Click Import...
3. In the appearing dialog box, navigate to the directory where the list
resides and select the peak list, choosing from:
• Auremol peaklist (.ml)
• MULABEL peak list (labels)
• TOPSPIN peak list (.xml)
• XEASY peak list (.peaks)
• XWIN-NMR peak list (.txt)
As such you can import a peak list from a different dataset or program
or a previously exported list from the current dataset. Note that peak
picking commands store the peak list in the processed data directory
under the name peak.xml (TOPSPIN 2.1 or newer) or peak.txt
(XWIN-NMR and TOPSPIN 2.0 or older).

Shortcuts
Double-click a peak: zoom into spectrum, i.e. show region around that
peak.
Enter key: zoom into spectrum, i.e. show region around selected
peak(s).
Delete key: delete the selected peak(s) from the peak list.
Ctrl+c: copy selected peaks to the Clipboard.
Ctrl+a: select all peaks.
Home: select the first peak.
End: select the last peak.
Shift+Home: select current and first peak and all in between.

139
1D Display

Shift+End: select current and last peak and all in between.

Note that these keys only work when the cursor focus is in the data win-
dow. INDEX
INDEX DONE
Table properties:
Various properties of the peak table can be configured. To do that:
1. Right-click an entry to open the popup menu (see Fig. 9.4).
2. Click Table properties...
3. In the appearing dialog box, with 3 tabs:
• Column
Allows you to select the columns to be displayed, set the col-
umn width and the number of fraction digits. Furthermore, you
can switch on/off scientific notation of values for each column
individually.
• Colours
Allows you to set various colours of the table.
• Spacings
Allows you to set various spacings of the table

140
 1D Display

INDEX
DONE INDEX

Figure 9.5

When you move the cursor over the peak list, the active peak will, by de-
fault, be highlighted in blue (see peak 3 in Fig. 9.6). If the correlated spec-
trum is also displayed, a vertical line moves along, showing
corresponding position in the spectrum (see Fig. 9.6)

141
1D Display

INDEX
INDEX DONE

Figure 9.6
As soon as you click a peak, it is selected and, by default, displayed in
red (see peak 1 in Fig. 9.6). Note that this peak remains selected, i.e. is
used by Enter and Delete, until a different peak is selected.
To extend the peak list, for example with Regions, Type and Index en-
tries, right-click any part of the header bar.
To sort the peaks according to peak number, ppm value or intensity, click
the header of the respective entry.
Peaks are only available if peak picking has been done (command pp).
The peak list can be printed with print [Ctrl+p]. List items can be se-
lected with the mouse, copied with Ctrl+c and pasted to other applica-
tions, e.g. a text editor.

142
 1D Display

How to Display the Integral list

+ Click the Integrals tab [li, lipp, lippf]
INDEX
DONE INDEX

Figure 9.7
This displays the integral list (upper part of Fig. 9.7). By default, this
shows the following items:
Object: the integral number
Integral [abs]: the absolute integral value
Integral [rel]: the relative integral value
Peaks: the number of peaks within the integral range
Range (F1) from: the left edge of the integral range

143
1D Display

Range (F1) to: the right edge of the integral range

Please note the difference between the following items:
INDEX
• selected integral: the entry that has been clicked last (Integral 3 in
Fig. 9.7).
INDEXIf you right-click
DONEan entry, it is selected and you can exe-
cute one of the commands from the popup menu (see Fig. 9.8)
The keys Enter and Delete work on the selected entry.
• active integral: the entry on which the cursor resides (Integral 1 in
Fig. 9.7). The active integral is also marked in the correlated spec-
trum by a black vertical line (see lower part of Fig. 9.7 and descrip-
tion below). When you move the cursor over the integral list, the
vertical line in the correlated spectrum moves along with it and
vice versa.
Note that the colours of the selected and active integral can be set in
the table properties (see below).
Display the spectral region around an integral
To display the spectral region around a particular integral:
+ Right-click the desired integral

144
 1D Display

This will open the popup menu shown in Fig. 9.8.

INDEX
DONE INDEX

Figure 9.8
Here you can choose from the following options:
+ Show spectrum => In correlated spectrum
to open a new data window showing the full correlated spectrum
+ Expand spectrum => In current window
to change the current data window to spectrum display, showing
the region around the selected integral
+ Expand spectrum => In correlated window
to open a new data window showing the region around the select-
ed integral (lower part of Fig. 9.7)
Note that clicking the marked entry in the right-click popup menu is
equivalent to pressing the Enter key.
Export/Import Entries of the Integral List
Entries of the integral list can easily be exported to Excel or any other
program as follows:
1. For multiple integrals:

145
1D Display

Select the desired entries while pressing the Ctrl or Shift key
2. Right-click an entry to open the popup menu (see Fig. 9.8)
INDEX
3. Click one of the following menu items:
INDEX
• Copy DONE
Copy the selected integral(s) entry to the Clipboard. Equivalent
to clicking Edit => Copy or hitting Ctrl+c. Copied integrals
can easily be pasted in any other application such as Excel.
• Export...
Export selected integrals. Check the box in the lower-left corner
to export the selected integrals only or uncheck it to export the
entire list. Then click Export.
Calibrate Integrals to Compare Spectra
Integrals from the current and other spectra can be calibrated with re-
spect to a reference integral. To do that:
1. Right-click the reference integral and choose Define as reference
from the popup menu. This will determine the calibration constant.
2. Right-click any integral and choose Calibrate by reference
This will divide all integrals by the calibration constant, setting the
reference integral to 1.0.
Now you can read any other spectrum, and calibrate its integrals with
respect to the reference integral defined above. To do that:
1. Read the spectrum
2. Enter int to define the integral ranges (if this has not been done
yet)
3. Click the Integrals tab
4. Right-click any integral in the list and choose Calibrate by refer-
ence from the popup menu.
Note that the calibration constant is lost when TOPSPIN is restarted.
Display the integral list with peaks
The integral list in Fig. 9.7 shows only integrals. However, if peak pick-
ing has been done, the integral list also shows the peaks within each
integral range (see Fig. 9.9).

146
 1D Display

INDEX
DONE INDEX

Figure 9.9
Note that the integral entries can be collapsed, (hiding the peaks) or ex-
panded (showing the peaks). As soon as one or more integrals entries
are expanded, two extra columns appear showing:
v(F1) [ppm]: the chemical shift of the peak
Intensity: the peak intensity
Depending on whether or not integrals are expanded, the right-click
popup menu contains the following extra items:
• Expand
Expand the current integral showing all peaks within it.

147
1D Display

• Expand all
Expand all integrals showing all peaks within them.
INDEX
• Collapse all
Collapse all integrals hiding all peaks within them.
INDEX DONE
In addition to the integral entry, an individual peak within an integral can
be activated (by placing the cursor on it) or selected (by clicking it). In
Fig. 9.9, peak 7 is selected and the correlated spectrum is displayed.
Peak 5 is active which is also shown by the vertical line in the correlated
spectrum.
Delete an Integral from the Integral List
To delete one integral:
+ Right-click the integral and choose Delete from the popup menu
To delete multiple integrals:
1. Select the integrals while pressing the Ctrl or Shift key
2. Right-click one of the integrals and choose Delete from the popup
menu
Note that these keys only work when the cursor focus is in the data win-
dow.

Table properties:
Various properties of the integral table can be configured. To do that:
1. Right-click an entry to open the popup menu (see Fig. 9.10).
2. Click Table properties...
3. In the appearing dialog box, with 3 tabs:
4. Column
Allows you to select the columns to be displayed, set the column
• width and the number of fraction digits. Furthermore, you can
switch on/off scientific notation of values for each individual col-
umn.
• Colours
Allows you to set various colours of the table.

148
 1D Display

• Spacings
Allows you to set various spacings of the table
5. INDEX
DONE INDEX

Figure 9.10
Shortcuts
Enter key: zoom into spectrum, i.e. show region around selected in-
tegral(s))
Delete key: delete the selected integral(s) from the integral list

149
1D Display

Ctrl+c: copy selected integrals to the Clipboard.

Ctrl+a: select all integrals.
INDEX
Home: select the first integral
INDEX DONE
End: select the last integral
Shift+Home: select current and first integral and all in between
Shift+End: select current and last integral and all in between
Double-clicking an integral will show the peaks within the integral re-
gion if they exist. It they do not exist, it will zoom into spectrum show-
ing the integral region.
Note that these keys only work when the cursor focus is in the data win-
dow.

150
 1D Display

How to view Sample Information

+ Click the Sample tab [edsam]
INDEX
DONE INDEX

Figure 9.11
This table can be used to fill out any sample information you want to store
with the dataset. The table can easily be modified or extended with the fol-
lowing functions:
To select an item: double-click it!
Save the sample information table with the dataset.
Save the sample information table as default.
Reload the original table discarding any changes
Add a new item to the table. You will be prompted for an identifi-
cation name and the desired number of lines
Remove the selected item from the table
Move the selected item one place up in the table
151
1D Display

Move the selected item one place down in the table

How to OpenINDEX
the Jmol Molecule Structure Viewer
+ Click the Structure tab [jmol]:
INDEX DONE

Figure 9.12
opens the Jmol molecule structure viewer. TOPSPIN 2.1 contains Jmol ver-
sion 10. This has the following features:
• The viewer displays the structure file that resides in the expno of the
current dataset. If this does not exist, the structure file defined by the
acquisition parameter CHEMSTR is displayed. CHEMSTR can
define a full pathname or a filename. In the latter case, the file is
searched for in the directory defined in the User Preferences. To set
this directory, click Options => Preferences, select Directory path
names, enter a directory and click OK. If no structure file is found,
you can open one by clicking File => Open in the Molecule Viewer
• The following structure file types are supported: .xyz, .mol, .pdb,
.cml, .out, .mmlgp, .res, .cif, .gpr, .hin, .nwo.

152
 1D Display

• Secondary structure elements of proteins (backbone, cartoons, rib-

bons, ...) can be displayed in selectable sizes and colors.
• Mouse button effects: INDEX
Rotate a molecule aroundDONE
the x- and y-axis
INDEXby pressing the left mouse
button, and moving the mouse left/right or up/down, respectively.
Rotate a molecule around the z-axis by pressing the middle mouse
button and moving the mouse left/right.
Zoom in or out a molecule by pressing the middle mouse button, and
moving the mouse up or down.
• RASmol command scripts are supported. To send a RASmol com-
mand to the currently displayed molecule enter:
+jmol <RASmol command>
Here are some example:
+jmol zoom 400
+jmol ribbon 200
+jmol color ribbon yellow
You may create TOPSPIN macros containing RASmol commands. Just
enter edmac on the TOPSPIN command line and insert the RASmol
commands in the appearing editor. Here is an example:
jmol load /mystructures/alphahelix.pdb # load a structure
jmol backbone 0.7 # display its backbone with 0.7 Angstrom size
jmol color backbone yellow # change backbone color
jmol background green # change background color
jmol zoom 200 # zoom structure
The available RASmol commands are described in the Jmol Help
menu.
• Multiple molecules (or multiple aspects of one molecule) can be dis-
played simultaneously. To do that just open multiple data sets or open
the same dataset in multiple data windows and click on the Structure
Tab in each window.

153
1D Display

How to Display the FID

+ Click the Fid tab [fid]
INDEX
INDEX DONE

displays the raw data. If these do not exist, the text ’No raw data available’
appears. The following additional buttons appear at the right of the lower
toolbar:
Show FID in shuffled mode
Show FID in unshuffled mode
If you open a new dataset, the Spectrum tab is activated, no matter which
tab was selected before. If you enter any interactive mode, for example
phase correction mode, the Tab bar is replaced by a toolbar for that mode.

9.5 1D Display Options

How to Toggle between Hertz and ppm Axis Units

Click the following toggle button in the upper toolbar:
Toggle between Hz and ppm axis units [.hz]

How to Switch on/off the Spectrum Overview display

The spectrum overview shows the entire spectrum at the top of the data
window. It is useful when only a certain region of the spectrum is dis-

154
 1D Display

played. In the overview, the displayed region is marked as a green area.

To switch on the spectrum overview, click the following toggle button in the
upper toolbar: INDEX
Switch the spectrumDONE INDEX
overview display on/off [.ov]

To shift the displayed region, simply click-hold the green area in the over-
view spectrum and move the mouse (see Fig. 9.13).

How to Switch Y-axis Display

Click the following toggle button in the upper toolbar:

Switch the y-axis display between abs/rel/off [.y]

Fig. 9.13 shows a data window with the spectrum overview on, ppm axis
units, and absolute y-axis display.

Figure 9.13

9.6 Show Display Properties/Regions/Files

If you right-click inside the data window, the following popup menu will

155
1D Display

appear:

INDEX
INDEX DONE

Figure 9.14
If you choose Display Properties..., a dialog box (see Fig. 9.14) will
appear.

156
 Figure 9.14
Here you can check or uncheck the spectrum components that you want to
be displayed in the data window.
Note that the Display Properties... dialog box can also be opened from
the View menu.

How to Superimpose the Cursor Information

To superimpose the cursor information on the spectrum:
 1. Right-click in the data window and choose Display Properties
[.dopt]
2. Check Cursor information in the appearing dialog box and click OK

How to Superimpose the Title on the Spectrum

1. Right-click in the data window and choose Display Properties...
[.dopt]
2. Check Title in the appearing dialog box and click OK

How to Superimpose the main Status Parameters on the Spec-

trum 1
1. Right-click in the data window and choose Display Properties...
[.dopt]
2. Check Status parameters in the appearing dialog box and click OK

How to Superimpose the Integral Trails/Labels on the Spectrum

1. Right-click in the data window and choose Display Properties...
[.dopt]
2. Check Integrals and, if desired, Integral labels in the appearing dia-
log box
3. Click OK
If no integrals appear, the integral regions have not been determined yet.
This can be done with the int command.

How to Superimpose Peak Labels on the Spectrum

1. Right-click in the data window and choose Display Properties...
[.dopt]
2. Check Peak labels in the appearing dialog box and click OK
If no peak labels appear, peak picking has not been done yet. This can be
done with the pp command.

1. These are the status parameters that also appear on the plot.
 1D Display

How to Show Peak Annotations on the Spectrum

1. Right-click in the data window and choose Display Properties...
[.dopt] INDEX
2. Check Peak labels and Peak
DONE Annotations
INDEX in the appearing dialog
box and click OK
Peak annotations appear, on peaks for which annotations have been de-
fined, instead of regular peak labels showing chemical shift values. If no
peak labels or annotations appear, peak picking has not been done yet.
This can be done with the pp command.

How to Show Individual Data Points of the Spectrum

1. Right-click in the data window and choose Display Properties...
[.dopt]
2. Check Show data points in the appearing dialog box and click OK
3. Expand the spectral region where you want to see individual points.

How to Superimpose the Electronic Signature on the Spectrum

1. Right-click in the data window and choose Display Properties...
[.dopt]
2. Check Electronic Signature in the appearing dialog box and click
OK
The electronic signature, entered with esign, will appear below the title.

How to Display the Main Dataset Properties

+ Right-click inside the data window and choose File Properties
An information box as displayed in Fig. 9.15 will appear.

159
1D Display

INDEX
INDEX DONE

Figure 9.15
Note that this is status information which cannot be changed.

How to Display a List of Files of a Dataset

+ Right-click inside the data window choose Files
Fig. 9.16 shows the file list when the Fid tab is active, i.e. when the raw
data are displayed. It is the contents of the expno directory.

160
 1D Display

INDEX
DONE INDEX

Figure 9.16
Fig. 9.17 shows the file list that appears when the Spectrum tab is active,
i.e. when the processed data are displayed. It is the contents of the procno
directory.

161
1D Display

INDEX
INDEX DONE

Figure 9.17
The contents of any file in the list can be displayed as follows:
1. Select a filename (it will be highlighted)
2. Click Open
Note that this only makes sense for ascii files, e.g. acqu*, proc* or files
with the extension .txt.
Dataset files can also be displayed/opened with the command expl. This
opens the Windows Explorer, or under Linux, the Konqueror or Mozilla,
showing the contents of the procno directory.

162
 1D Display

9.7 Saving Display Region

INDEX
The currently displayed spectral region can be stored as follows:
+ Right-click in the data window
DONEand choose Save Display Region To...
INDEX
This will open the dialog box shown in Fig. 9.18.

Figure 9.18
Here the following options are available:

• Parameters F1/2 [dpl]

to save the displayed region for restoring the display later. The region
is stored in the parameters F1P and F2P.
To restore the saved region, right-click in the data window and choose:
Restore Display Region from Params F1/2
• Parameters ABSF1/2
to save the displayed region for baseline correction (command absf)
or phase correction (command apkf). The region is stored in the
processing parameters ABSF1 and ABSF2.
• Parameters STSR/STSI
to save the displayed region for Strip FT (commands like ft and trf).

163
1D Display

The region is stored in the processing parameters STSR and STSI.

• Parameters NOISF1/2
INDEX
to save the displayed region as the signal region for Signal to Noise
calculation (command sino).
INDEX DONE The region is stored in the processing
parameters SIGF1 and SIGF2.
• Parameters SIGF1/2
to save the displayed region as the noise region for Signal to Noise
calculation (command sino). The region is stored in the processing
parameters NOISF1 and NOISF2.
• A text file for use with other programs
to save the displayed region in a text file. This file can be viewed with
any editor or used by external programs.

9.8 Synchronize Visible Region of all Data Windows

The visible region of all data windows can be synchronized as follows.

+ Zoom in or out one dataset while holding the Ctrl key
or
+ Zoom in or out one dataset and then enter the .sync command

164
 1D Display

INDEX
DONE INDEX

165
2D Display

Chapter 10
INDEX

2D Display
INDEX DONE

10.1 The 2D Data Window

The 2D data window consists of a data field, a title bar, a Tab bar and but-
tons.
Fig. 10.1 shows a data window with a 2D spectrum.

166
 2D Display
.

data title bar minimize maximize close

field Tab bar button button button
INDEX
DONE INDEX

Figure 10.1

10.2 Changing the Display of a 2D spectrum

TOPSPIN offers various buttons to scale or shift a 2D spectrum both verti-

cally and horizontally.

How to Change the Intensity Scaling (contour levels)

+ Click the button:

Change the intensity scaling (contour levels) [edlev]

or
+ Hit one of the keys:
• Alt+PageUp: Increase the intensity by a factor of 2.
• Alt+PageDown: Decrease the intensity by a factor of 2.
• Alt+Enter: Reset the intensity.
or

167
2D Display

+ Click one of the following buttons:

Increase the intensity (decrease the levels) by 2 [*2].
INDEX
Increase
INDEX the intensity
DONE (decrease the levels) by 8 [*8].

Decrease the intensity (increase the levels) by 2 [/2].

Decrease the intensity (increase the levels) by 8 [/8].

Reset the intensity to the last saved intensity (contour levels)

[.vr].

Alternatively, you can enter the corresponding commands as specified be-

tween square brackets [].
To manipulate all data windows, press the Ctrl key while clicking one of
the above buttons.

How to Smoothly Change the Vertical Scaling (contour levels)

To change levels, multiplying all levels with the same factor:
+ Click-hold the button and move the mouse.
or
+ Turn the mouse wheel while the cursor is in the data window.
To change the level distance (increment), leaving the base level the same:
+ Click-hold the button and move the mouse.

How to Display a Contour Levels Bar in the Data Window

1. Right-click in the data window and choose Display Properties...
[.dopt]
2. Check Contour Levels Bar in the appearing dialog box and click OK
(see Fig. 10.2).

168
 2D Display

INDEX
DONE INDEX

Figure 10.2

How to Switch on/off Square 2D layout

Right-click inside the data field and click Square Layout On/Off

Figure 10.3
The F2 scaling will be adjusted to reach a square display.

169
2D Display

How to Zoom a 2D spectrum in/out

+ Click one of the following buttons:
INDEX
Zoom in to the center (spectrum) or left edge (FID) of the dis-
INDEX
played DONE the horizontal scaling. [.zi]
region, increasing
Zoom out from the center (spectrum) or left edge (FID) of the dis-
played region, decreasing horizontal scaling) [.zo]
Perform an exact zoom via a dialog box [.zx].

Figure 10.4
a) Enter the coordinates of the desired region in the dialog box.
b) Click OK
Undo last zoom [.zl].

Show full spectral width in F2 [.f2r].

Show full spectral width in F1 [.f1r].

Show full spectrum [.all].

Retain horizontal and vertical scaling when modifying dataset or

changing to different dataset. Effects all data windows [.keep].
Alternatively, you can enter the corresponding commands as specified be-
tween square brackets [].

170
 2D Display

How to Shift a Spectral Region in the F2 direction (left/right)

+ Click one of the following buttons:
INDEX
Shift to the left, half of the displayed region [.sl].
DONE INDEX
Shift to the right, half of the displayed region [.sr].

or
+ Click-hold the button and move the mouse:

Smoothly shift in any direction.

Alternatively, you can enter the corresponding commands as specified be-

tween square brackets [].

How to Shift a Spectral Region in the F1 direction (up/down)

+ Click one of the following buttons:
Shift the spectrum up, half of the displayed region [.su].
Shift the spectrum down, half of the displayed region [.sd].

or
+ Click-hold the button and move the mouse:
Smoothly shift up/down and left/right.

Alternatively, you can enter the corresponding commands as specified be-

tween square brackets [].

10.3 Show Display Properties/Regions/Files

If you right-click inside the data window, the popup menu shown in Fig.

171
2D Display

10.5 will appear.

INDEX
INDEX DONE

Figure 10.5
Here you can select various display properties, region setting and file prop-
erties. If you choose Display Properties..., a dialog box (see Fig. 10.6) will
appear.

172
 2D Display

INDEX
DONE INDEX

Figure 10.6
Here you can set various display options including parameters, integrals,
peaks, contours, projections and electronic signature. The number of dis-
played digits for the integral and peak labels can be set in the User Pref-
erences (click Options => Preferences => Spectrum).

173
2D Display

10.4 Using the Tab bar

INDEXis a tabbed pane. This means its contents depends on
The 2D data window
the currently active tab in the Tab bar. The individual tabs are basically the
INDEX DONE
same as for 1D display (see chapter 9.4). There are, however, some differ-
ences, which are discussed below.

How to Set Processing Parameters

+ Click the ProcPars tab [edp]
The 2D processing parameter editor contains a column for each of the
two dimensions F2 and F1 (see Fig. 10.7). Note that not all parameters
exist in both dimensions.

Figure 10.7

How to Set Acquisition Parameters

+ Click the AcquPars tab [eda]
The 2D acquisition parameter editor contains a column for each of the
two dimensions F2 and F1 (see Fig. 10.8). Note that not all parameters
174
 2D Display

exist in both dimensions.

INDEX
DONE INDEX

Figure 10.8

How to Display the Peak list

+ Click the Peaks tab

Figure 10.9
This displays list of peaks if these have been calculated (command pp).

175
2D Display

The list is basically the same as for 1D spectra. The only difference is that
there are two columns for the two directions:
INDEX
v(F2) [ppm]: the chemical shift in the F2 direction
INDEX
v(F1) [ppm]: DONE
the chemical shift in the F1 direction
To specify or edit an annotation, click inside the Annotation field and enter
a character string. The peak annotations are shown in the correlated
spectrum (see Fig. 10.10)

Figure 10.10

How to Display the Integral list

+ Click the Integrals tab

176
 2D Display

INDEX
DONE INDEX

Figure 10.11
This displays the list of integrals if these have been calculated (command
int). The list is basically the same as for 1D spectra. The only difference
is that, when peaks are shown, there are two columns for the chemical
shift:
v(F2) [ppm]: the chemical shift in the F2 direction
v(F1) [ppm]: the chemical shift in the F1 direction
Furthermore, a stored or exported 2D integral list can be imported as
follows:
1. Right-click an entry to open the popup menu
2. Click Import...
3. In the appearing dialog box, navigate to the directory where the list
resides and select the integral list.
As such you can import an integral list from a different dataset or a pre-
viously exported list from the current dataset. Note that integration
commands store the integral list in the processed data directory under
the name integrals.txt. Exported integrals are stored in the files
<name>.txt and <name>.reg, where <name> is the name specified
by the user.

177
2D Display

How to Display the FID

+ Click the Fid tab [fid]
INDEX
2D raw data consist of a series of FIDs which are displayed in a row. In-
INDEX
dividual FIDs DONE
can be displayed by zooming in. To do that, click re-
peatedly. Now you can shift and zoom in/out the data to display different
FIDs (see Fig. 10.12)
.

Figure 10.12

10.5 2D Display Options

How to Switch between Hertz and ppm Axis Units in F2 and F1

+ Click the following multi-state button in the upper toolbar:
Switch between Hz and ppm axis units in F2 and F1 [.hz]

How to Switch on/off the Spectrum Overview display

+ Click the following toggle button in the upper toolbar:
Switch the spectrum overview display on/off [.ov]

With the spectrum overview on, the data window will, for example, look like

178
 2D Display

this:

INDEX
DONE INDEX

How to Switch on/off the Projection display

+ Click the following toggle button in the upper toolbar:

Switch the projection display on/off [.pr]

With the projections displayed, a 2D dataset looks like this:

179
In this example, the F1 projection is selected as indicated by the filled blue
square whereas the F2 projection is not selected. A selected projection
can be rescaled using the toolbar rescale buttons of function keys. If you
right-click inside the projection area of the data window, the following pop-
up menu appears:

Clicking External Projection opens the a dialog box where you can spec-
ify or search for a 1D dataset and display this as a projection of the current
2D dataset.
Clicking Internal Projection calculates and displays the positive projec-
tion and displays it along with the 2D spectrum.
Clicking Baseline at Bottom or Baseline at Center allows you to put the
projection baseline at the respective positions.
Alternative ways to calculate/display projections are:
+ Right-click on a 1D dataset in the browser and choose:
Display As 2D Projection
or
+ Click Processing => Calculate projections [proj]
This will open the dialog box shown in Fig. 10.13.
 2D Display

INDEX
DONE INDEX

Figure 10.13
From here, you can calculate positive, negative, sum and disco pro-
jections and either show them with the 2D spectrum or display them
in separate data window as a 1D data. For more details on the corre-
sponding commands (as shown in the header of the dialog box),
please refer to the Processing Reference Manual.

How to Switch on/off the Grid display

+ Click the following multi-state button in the upper toolbar:
Switch between ’no grid’, ’axis aligned grid’ and ’fixed grid’ [.gr]

Fig. 10.14 shows an example of axis aligned grid display.

181
2D Display

INDEX
INDEX DONE

Figure 10.14 Axis aligned grid display

How to Display a 2D Spectrum in Contour Mode

+ Click the following button in the upper toolbar:
Switch to contour display mode [.co]

In contour mode, a spectral region looks like this:

182
 2D Display

How to Set the 2D Contour Levels

+ Click the following button in the lower toolbar
INDEX
Edit contour levels [edlev, .lv]
DONE INDEX
This will open the following dialog box shown in Fig. 10.15. Contour levels
can be entered manually or they can be calculated.
Manual setup
This allows you to create an arbitrary sequence of levels
1. Enter the level values in the fields 1, 2, ... at the top of the dialog
box.
2. Click Apply to update the display or OK to store the levels, update
the display and close the dialog box.
Calculation
This allows you to easily create a geometric or equidistant sequence of
levels.
1. Click one of the following items:
• Multiply with increment
to create a geometric sequence of levels.
• Add increment
to create a equidistant sequence of levels.
2. Enter the desired Base level, Level increment and Number of lev-
els.
3. Click Fill to display and activate the sequence.
4. Click Apply to update the display or OK to store the levels, update
the display and close the dialog box.
The Contour level sign allows you to select positive levels, negative levels
or both.

183
2D Display

INDEX
INDEX DONE

Figure 10.15

How to Store interactively set Contour Levels

To store contour levels that were set interactively, for example by clicking

184
 2D Display

or pressing Alt+PageUp:
+ Click the following button in the lower toolbar:
INDEX
Store contour levels [.ls]
DONE INDEX
The levels are stored in the file:
/<dir>/data/<user>/nmr/<name>/<expno>/pdata/<procno>/clevels

How to Display a 2D spectrum in Pseudo Color Mode

+ Click the following button in the upper toolbar:
Switch to image color display mode [.im]

In pseudo color mode, a spectral region looks like this:

Note that in pseudo color mode, the contours are superimposed, in black,
when you zoom in on a small region of the spectrum.

How to Display a 2D Spectrum in Oblique Mode

+ Click the following button in the upper toolbar
Switch to oblique display mode [.st]

In oblique mode, a spectral region looks like in Fig. 10.16.

185
2D Display

INDEX
INDEX DONE

Figure 10.16
In this mode you can manipulate the display in various ways. Just right-
click inside the data window and choose one of the options from the ap-
pearing popup menu (see Fig. 10.17)

186
 2D Display
:

INDEX
DONE INDEX

Figure 10.17

How to Rotate a 2D Spectrum in Oblique Mode

Click-hold one of the following buttons and move the mouse up/down:
Rotate around x-axis.
Rotate around y-axis.

How to Switch between Displaying Positive and Negative levels

Click the following multi-state button in the lower toolbar:
Switch between positive, negative and both contours [.lt].

187
nD Display

Chapter 11
INDEX

nD Display
INDEX DONE

11.1 Display Planes of 3D Data

3D data can be displayed as 2D planes or as a 3D cube. By default, the

first F3-F1 plane is displayed (see Fig. 11.1) The plane orientation and
number is shown. The cube in the lower left corner graphically indicates
which plane is displayed. The full 2D display functionality is available (see
chapter 10).

188
 Figure 11.1

How to Switch to 2D Plane Display

If the 3D cube is displayed you can switch to 2D plane display by clicking
one of the following buttons:
Switch to 2D contour display.
Switch to 2D image display.
Switch to 2D oblique display.

How to Display various Plane Orientations

Click one of the following buttons:
Show F1-F2 planes.
nD Display

Show F2-F3 planes.

Show F3-F1 planes.

INDEX
INDEX DONE
How to Display various Plane Positions (numbers)
Click one of the following buttons:
Show the next plane.

Show the previous plane.

Scan planes smoothly.

Enter the exact plane number. This will open the dialog shown in
Fig. 11.2. Here, you can specify the desired plane number as
well as switch to a different plane orientation.

Figure 11.2

190
 nD Display

11.2 3D Cube Display Mode

INDEX
How to Display the 3D Cube
Click the following button: DONE INDEX
Show 3d cube (see Fig. 11.3).

Figure 11.3

How to Rotate the 3D Cube

Click-hold one the following buttons and move the mouse up/down:
Rotate cube around x-axis.
Rotate cube around y-axis.
Rotate cube around z-axis.

191
nD Display

How to Scale Up/Down the 3D Cube

1. Right-click inside the data window.
2. Choose INDEX
Larger or Smaller from the popup menu (see Fig. 11.4).
INDEX DONE
How to Reset the Cube Size and Orientation
Click the following button:
Reset to default size and orientation.

How to Switch Depth Cueing on/off

1. Right-click inside the data window
2. Choose Depth Cueing On/off (see Fig. 11.4)
Depth cueing makes data points which are closer to the viewer appear
brighter and those that are further away appear dimmer. This increases
the depth effect of the 3D image.

Figure 11.4

How to Display a Cube Front or Side view

Click one the following buttons:
Show F1-F2 plane.
Show F2-F3 plane.
Show F3-F1 plane.

11.3 nD parameter display

TOPSPIN 2.1 and newer support parameter display of up to 8D data. To

show processing parameters:
+ click the ProcPars tab of the data window

192
 nD Display

or
+ enter edp on the command line
INDEX
Parameters of each direction are shown in a separate column. Fig. 11.5
DONE INDEX

Figure 11.5

shows the processing parameter display of a 3D dataset.

To show acquisition parameters:
+ click the AcquPars tab of the data window
or
+ enter eda on the command line

193
nD Display

Parameters of each direction are shown in a separate column. Fig. 11.5

INDEX
INDEX DONE

Figure 11.6

shows the acquisition parameter display of a 3D dataset.

11.4 nD Fid Display

nD raw data can be displayed as a series of 1D FIDs. To do that:

+ click the FID tab of the data window
or
+ enter fid on the command line

194
 nD Display

11.5 nD Peak and Integral Display

INDEX
TOPSPIN 2.1 and newer support peak and integral display of up to 8D data.
To show the nD peak list: DONE INDEX
+ click the Peaks tab of the data window
or
+ enter peaks on the command line
Fig. 11.7 shows the peak list of a 3D dataset.

Figure 11.7

The chemical shift in each of the three dimensions is shown in a separate

column.

195
nD Display

To show the nD integral list:

INDEX
+ click the Integrals tab of the data window
INDEX DONE
or
+ enter ints on the command line
Fig. 11.7 shows the integral list of a 3D dataset.

Figure 11.8

The chemical shift in each of the three dimensions is shown in a separate

column.
Peaks and integrals only appear if they have been calculated (commands
pp and int, respectively).

196
 nD Display

INDEX
DONE INDEX

197
 Chapter 12
1D Interactive Manipulation

The upper toolbar of the 1D menu offers various buttons for interactive
manipulation. If you click such a button, the active data window will switch
to the corresponding mode. An interactive manipulation mode is data win-
dow specific, i.e. it only applies to the active window.

12.1 1D Interactive Window multiplication

TOPSPIN 2.0 and newer supports 1D interactive window multiplication.

12.1.1 1D Interactive Window Multiplication Procedure

How to Switch to Window Multiplication Mode

+ Click the Processing => Window Multiplication [wm], enable Manual
window adjustment in the appearing dialog and click OK.
or
+ Enter .winf on the command line.
The Tab bar of the active data window will be replaced by a toolbar (see
Fig. 12.2) and the data window itself will be divided into three parts:
• a parameter part at the left
 1D Interactive Manipulation

• a spectrum part at the upper right

• a FID part at the lower right.
INDEX
DONE INDEX

Figure 12.1
Show both spectrum and FID.

Show FID only.

Show spectrum only.

Switch cursor information on/off (toggle)

Save windows settings to source 2D dataset1 and return.

1. 2D data from which current 1D dataset was extracted, e.g. with rser.

199
1D Interactive Manipulation

Save window settings and return

Return
INDEXwithout save.

INDEX
You can perform DONE
interactive window manipulation as follows:
1. Select the window function (parameter WDW)
2. Set the corresponding parameter(s), e.g.
• LB for exponential
• LB and GB for Gaussian
• SSB for sine bell and squared sine
The displayed spectrum and/or FID will be automatically adjusted
as you change the window function and parameters.
3. Click to store the window settings and return.
Now you can perform further processing steps like Fourier transform,
phase correction etc.

12.2 1D Interactive Phase Correction

Manually acquired spectra can be phase corrected automatically, with com-

mands like apk or apks or, interactively, in phase correction mode.

12.2.1 1D Interactive Phase Correction Procedure

How to Switch to Phase Correction Mode

Click the indicated button in the upper toolbar:

or enter .ph on the command line.

The Tab bar of the active data window will be replaced by a toolbar (see
Fig. 12.2)

200
 1D Interactive Manipulation

INDEX
DONE INDEX

Figure 12.2 Data window in phase correction mode

The yellow button indicates that you are in phase correction mode.
Some buttons will turn green when they are clicked. As long as a
button is green, it is active.

How to Perform a Typical 1D Interactive Phase Correction

For a typical 1D phase correction, take the following steps:
1. Click-hold the button and move the mouse until the until the refer-
ence peak is exactly in absorption mode.
2. Click-hold the button and move the mouse until the entire spec-
trum is exactly in absorption mode.
3. Click the button to save and execute the phase correction and
return.

12.2.2 1D Interactive Phase Correction Details

How to Set the Phase Pivot Point

By default, the phase pivot point is set to the biggest magnitude intensity
of the displayed region of the spectrum. To change the pivot point:
1. Right-click on the desired pivot point position
2. Choose Set pivot point from the popup menu (see Fig. 12.2)

201
1D Interactive Manipulation

How to Perform Default Zero Order Phase Correction

1. Right-click in the data window
2. Choose INDEX
Calculate ph0 in the popup menu (see Fig. 12.2)
INDEX
The spectrum DONE
will automatically be corrected according to the calculated
value.

How to Perform Interactive Zero Order Phase Correction

1. Click-hold the following button (button turns green):
Zero order phase correction (parameter PHC0).
2. Move the mouse until the reference peak is exactly in absorption
mode.
3. Release the mouse (button turns grey).

How to Perform Interactive First Order Phase Correction

1. Click-hold the following button (button turns green):
First order phase correction (parameter PHC1).
2. Move the mouse until the entire spectrum is exactly in absorption
mode.
3. Release the mouse (button turns grey).

How to Perform 90, -90 or 180° Zero Order Phase Correction

+ Click one of the following buttons:
Perform 90 zero order phase correction [.ph90].

Perform -90° zero order phase correction [.phm90].

Perform 180° zero order phase correction [.ph180].

How to Reset the Phase to the Original Values

+ Click the following button:

Reset zero and first order phase values [.phr].

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 1D Interactive Manipulation

How to Change the Mouse Sensitivity

+ Click one of the following buttons:
INDEX
Increase (double) the mouse sensitivity [.inc].
DONE INDEX
Decrease (halve) the mouse sensitivity [.dec].

Reset the mouse sensitivity.

How to Return from Phase Correction Mode with/without Save

To return while saving the phase correction to the current dataset:
+ Click the following button:

Save, execute and return [.sret].

This will perform the following tasks:

• Execute phase correction (command pk).
• Save the current phase correction values.
• Leave the phase correction mode.
To return without save:
+ Click the following button:
Return, discarding any changes [.ret].

To return while saving the phase correction to the source 2D dataset:

+ Click the following button:
Save to 2D [.s2d].

This is only applicable on rows or columns extracted from 2D data.

The phase values will be saved to the 2D dataset from which the cur-
rent 1D dataset was extracted.

12.3 1D Interactive Integration

Integration of 1D data can be done automatically, with the commands abs

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and li or, interactively, as described in this paragraph.

How to Switch to Integration Mode

INDEX
+ Click the indicated button in the upper toolbar:
INDEX DONE

or enter .int on the command line.

The Tab bar of the active data window will be replaced by a toolbar (see
Fig. 12.3). The first button (define integrals) is automatically activated (is
green).

Figure 12.3 Data window in integration mode

The yellow button indicates that the data window is in integration
mode.
Some buttons will turn green when they are clicked. As long as a
button is green, it is active.
If integral regions have already been determined, for example with abs or
with a previous interactive integration, these regions are displayed in the

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data window, along with the integral values. You can remove them,
change them or add to them, as described below.
INDEX
How to Define Integral Regions
DONE
To define integral regions interactively:
INDEX
1. Click the following button (button turns green):
Define integral region interactively.
Note that the define integrals button is automatically activated on en-
tering the integrals mode.
2. Put the red cursor line at one edge of a peak or multiplet.
3. Left-click-hold and drag the cursor line to the other edge of the peak
or multiplet.
4. Do step 2 and 3 for all regions to be defined.
5. Click the green button to leave the "define region" mode (button turns
grey).
To define integral regions via a dialog box:
1. Click the following button:
Define region via dialog.
2. In the appearing dialog box:

Enter the exact values for the region limits.

3. Click OK to define the selected region.

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1D Interactive Manipulation

How to Select/Deselect Integral Regions

To select/deselect all displayed integral regions:
INDEX
+ Click the button: button
INDEX DONE
To select a single integral region:
1. Right-click in the integral region.
2. Choose Select/Deselect from the popup menu.
To select the next integral region:

+ Click the button

To select the previous integral region:

+ Click the: button.

To select multiple integral regions:

1. Click the button: button to select all integrals
2. Deselect the integral that are not to be selected.
Selected integral regions are indicated by a color filled integral label. In the
Fig. 12.4, the five left most regions are selected, the region around 6 ppm
is currently being deselected.

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 1D Interactive Manipulation

INDEX
DONE INDEX

Figure 12.4
Note that:
• If no integral is selected, the next and previous integral button select
the first or last integral respectively.
• the select all integrals button remains green while all or multiple inte-
grals are selected.

How to Read Integral Regions from Disk

You can read integrals regions from disk which have been stored by auto-
matic integration (command abs) or by a previous interactive integration.
To read integrals:
1. Click the following button:
Read integral regions.

The following popup menu will appear:

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INDEX
INDEX DONE

Figure 12.5
2. From the popup menu, choose one of the following entries:
• Read ’ intrng’
to read the last saved integral regions and apply the saved slope
and bias correction values.
• Read ’intrng’ no slope & bias corr.
to read the last saved integral regions but do not apply the saved
slope and bias correction values.
• Read ’intrng’ use last slope & bias
to read the last saved integral regions applying the last slope and
bias correction values.
• Read ’intrng’ from Relaxation Experiment
to read the last stored integral regions of the T1/T2 relaxation
experiment.
• Edit ’intrng’
to edit the file (intrng) that contains the integral regions and
slope and bias correction values. Changes in this file are automat-
ically shown on the screen, when the file is saved.

How to Perform Interactive Bias and Slope Correction

To perform interactive bias correction:
1. Select the integral(s) that you want to correct (right-click in the
region).
If no integral is selected, bias correction will work on all integrals.
2. Click-hold the following button (it turns green) and move the mouse,
Integral bias correction.

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until the integral bias is correct.

3. Release the mouse (button turns grey).
INDEX
To perform interactive slope correction:
1. Select the integral(s) thatDONE INDEX(right-click in the
you want to correct
region).
If no integral is selected, slope correction will work on all integrals.
2. Click-hold the following button (it turns green) and move the mouse,
Integral slope correction.
until the integral slope is correct.
3. Release the mouse (button turns grey).

How to Set the Limit for Bias Determination

+ Click the following button:
Limit for bias determination.

How to Change the Mouse Sensitivity

+ Click one of the following buttons:
Increase (double) the mouse sensitivity [.inc].

Decrease (halve) the mouse sensitivity [.dec].

Reset the mouse sensitivity.

How to Calibrate/Normalize Integrals

Calibrating integrals means setting the value of a reference integral and
adjusting all other integrals accordingly. To do that:
1. Right-click in the reference integral region.
2. Choose Calibrate from the popup menu (see Fig. 12.6).
3. Enter the desired value for the reference integral and click OK
Normalizing integrals means setting the sum of all integrals and adjusting
individual integral values accordingly. To do that:

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1D Interactive Manipulation

1. Right-click in the reference integral region.

2. Choose Normalize from the popup menu (see Fig. 12.6).
INDEX
3. Enter the desired sum of all integrals and click OK
INDEX DONE

Figure 12.6
Calibrating and normalizing only effects the current dataset. To scale inte-
grals with respect to a reference dataset, choose lastscal from the
right/click popup menu (see below).

How to Scale Integrals with respect to Different Spectra

Integrals can be scaled with respect to the last spectrum that was integrat-
ed interactively. To do that:
1. Right-click in the reference integral region.
2. Choose Use Lastscal for Calibration from the popup menu (see Fig.
12.6).
As such, you can compare integrals of different spectra. Note that this only
make sense for spectra which have been acquired under the same exper-
imental conditions. The scaling factor is stored in the file:
<tshome>/prog/curdir/<user>/intscale

How to Delete Integral Regions from the Display

To delete the selected integral regions from the display:
+ Click the following button:
Delete selected integral regions from the display.
To delete a single integral region from the display:
1. Right-click in the integral region.

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2. Choose Delete from the popup menu (see Fig. 12.6)

To delete all integral regions from the display:
INDEX
+ Click the following buttons:
DONE INDEX
Select all integral regions.
Delete selected integral regions from the display.
Note that regions are only deleted from the screen. Regions which are
saved on disk (in the intrng file) are not affected.

How to Scale Selected Integrals

Integral scaling only manipulates selected integrals. However, if no inte-
grals are selected, it works on all integrals.
+ Click one of the following buttons:
Scale up selected integrals by a factor of 2.

Scale down selected integrals by a factor of 2.

Scale selected integrals up/down smoothly.

To scale up/down integrals by a factor entered via a dialog:

1. Click the following button:
Scale integrals via a dialog.
2. Enter a scaling factor, e.g. 2.5. in the appearing dialog.

3. Click OK to apply this factor.

To scale all selected integrals to the same height:

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1D Interactive Manipulation

+ Click the following button:

Scale/unscale all integrals to the same height.
INDEX
The individual
INDEX scaling factor
DONE for each region is displayed above the in-
tegral. Clicking this button again rescales all integrals to their original
height.

How to Move the Integral Trails Up/Down

To move the integrals (selected and unselected) up or down:
+ Click one of the following buttons:
The left edge of the selected integral is put just above the base-
line. If no integral is selected, the lowest integral is used.
The right edge of the selected integral is put at 3/4 of the window
height. If no integral is selected, the highest integral is used.
Shift all integral trails up/down smoothly.

How to Cut Integral Regions

1. Click the following button (button turns green):
Cut integral region.
2. Move the red cursor line into an integral region to the position where
it must be cut and click the left mouse button.
3. Do step 2 for each integral region that must be cut.
4. Click the (green) button to leave the cut integral mode (button turns
grey).
In case of overlapping integrals, you must select the integral to be cut be-
fore you actually cut it. Note that if one or more integrals are selected, cut-
ting only works on selected integrals.
With TopSpin 2.2 1D Interactive Integration command cut integral can be
called directly from right-click context menu. Right mouse click on the in-
tegral opens a popup menu in which cut current integral must be selected.

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 1D Interactive Manipulation

How to Save Integral Regions

1. Click the following button:
INDEX
Save integral regions.
DONE
The following popup menu will appear:INDEX
es

Figure 12.7
2. Choose one of the following entries:
• Save regions to ’intrng’
Save the currently displayed integral regions including the slope
and bias correction values.
• Save Regions to ’reg’
Save the integral regions to the file reg.
• Export Regions To Relaxation Module and .sret
Used on relaxation data only. Exports the integral regions for
T1/T2 relaxation analysis and exits from integration mode.
• Save & show list
Save the currently displayed integral regions including the slope
and bias correction values and show the integrals on the screen.

How to Undo the Last Region Operation

+ Click the following button:
Undo the last region operation.

How to Return from the Integration Mode with/without Save

To return and save the integrals to the current dataset:
+ Click the following button:
Save integrals and return [.sret].

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1D Interactive Manipulation

As such, you will:

• save the integral regions and corresponding slope and bias
INDEX to the file intrng.
corrections
• save the integral DONE
INDEX regions, slope and bias corrections and inte-
gral values to the file integrals.txt. This file is displayed
when you click the Integrals Tab.
• leave the integration mode.
To return without save:
+ Click the following button:
Return, discarding any changes [.ret].

How to deconvolve overlapping peaks from integration mode

Deconvolution, the line shape tool to interprete complex 1D and 2D spec-
tra with overlapping peaks can be started directly from within integration
mode. As described in the Analysis chapter deconvolution calculates the-
oretical signals with different methods, i. e. Gaussian, Lorentzian or a mix-
ture of these line shapes. The values are stored in the file dconpeaks.txt
and displayed graphically. For further information please look up the Anal-
ysis chapter and the Processing Reference Manual (commands gdcon,
ldcon, mdcon, ppp, dconpl and dcon).
From within the integration mode, after the integration of the respective
peak or peak groups, deconvolution can be started by right clicking on the

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peak. The following window will appear:

INDEX
DONE INDEX

Figure 12.8
Choosing Deconvolution offers the following options:
• Deconvolve and display regions
• Change Peak Picking Parameters for Deconvolution
• Edit Peak List & Deconvolve
• Show Deconvolution Fit (graphical display)
With the latter function it is possible to display results after deconvolution
graphically:

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1D Interactive Manipulation

INDEX
INDEX DONE

Figure 12.9
The integral values of each of the deconvolved signals are available in the
integrals tab within the originally defined integral (column ’Intensity [abs]’):

Figure 12.10

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 1D Interactive Manipulation

12.4 1D Interactive Calibration

INDEX
A 1D spectrum can be calibrated (referenced), automatically, with the com-
mand sref or, interactively, as described below.
DONE INDEX
How to Switch to Calibration Mode
+ Click the indicated button in the upper toolbar

or enter .cal on the command line. The Tab bar of the active data window
will be replaced by a toolbar.

Figure 12.11 Data window in calibration mode

The yellow button indicates that the data window is in calibration
mode.

How to Calibrate a Spectrum Interactively

In calibration mode:

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1D Interactive Manipulation

1. Position the red cursor line at the reference peak.

2. Left-click at that position.
INDEX
The following dialog box will appear:
INDEX DONE

Note that the units (Hz or ppm) correspond to the axis units of the dis-
play.
3. Enter the frequency you want to assign to the reference peak.
4. Click OK
The spectrum will be calibrated and re-displayed. TOPSPIN will automati-
cally leave calibration mode.

12.5 1D Multiple Display

The multiple display mode allows you to display multiple superimposed

spectra.The spectra will be ppm aligned or Hz aligned, according to the
selected axis unit. Each spectrum can be individually shifted and scaled
allowing exact alignment of corresponding peaks in different spectra. The
number of superimposed spectra is unlimited.
Although multiple display is normally used for spectra with matching nuclei,
it allows you to superimpose spectra with non-matching nuclei. You will get
a warning that the nuclei do not match. Just just click OK to continue.

How to Switch to Multiple Display Mode and Read Multiple

Spectra
One way to superimpose data in multiple display is to read one dataset,
switch to multiple display mode and add other datasets:
1. Read a 1D dataset.

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 1D Interactive Manipulation

2. Click the button in the upper toolbar or type .md on the com-
mand line.
The data window will switch to multipleINDEX
display mode.
3. Add a dataset as follows:DONE INDEX
+ Left-click-hold the dataset in the browser and drag it into the data
window.
or
+ Right-click the dataset in the browser and choose Display from the
popup menu.
or
+ Enter re and specify the additional dataset in the appearing dialog
box.
Another way to superimpose data in multiple display is to read multiple
datasets simultaneously:
1. In the browser:
+ Hold down the Ctrl key and click multiple datasets to select them.
or
+ Hold down the Shift key and click two datasets to select these
two and all datasets in between.
2. Right-click any of the selected data:
+ Choose Display from the popup menu.
This will show the data in the active data window if that is in multi-
ple display mode or, otherwise, show the data in a new window.
or
+ Choose Display in new window from the popup menu.
This will show the data in a new window.
In multiple display mode, the Tab bar of the active data window is re-
placed by a toolbar. Fig. 12.12 shows three comparable 1D spectra and
the sum of all three.

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1D Interactive Manipulation

INDEX
INDEX DONE

Figure 12.12 Data window in multiple display mode

The yellow button indicates that the data window is in multiple
display mode.
Some buttons will turn green when they are clicked. As long as a
button is green, it is active.
Furthermore, the browser is split in two parts as shown in Fig. 12.13.

Figure 12.13

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 1D Interactive Manipulation

The additional lower part shows:

• which datasets are displayed in the active data window.
INDEX
• which datasets are selected (these are highlighted).
DONE INDEX
How to work with multiple display command .md
The following arguments of .md for controlling data sets from command
line, AU-programs or Python programs are available:
1. Specified data set names can be shown in the display by command
.md:
Enter command and full pathname for a specified dataset in the Top-
Spin command line:
md <PathToDataset1>\<expno1>\pdata\<procno> <PathToDataset2>
\<expno2>\pdata\<procno>
2. The command .md no_load ignores the datasets stored in the last
multiple display session and enters the multiple display
3. The command .md write writes only the assoc file containing the
data set list for multiple display. Please note that the multiple display
module is not started with this command.
Enter command and full pathname of specified dataset in the TopSpin
command line:
.md write <PathToDataset1>\<expno1>\pdata\
<procno> <PathToDataset2>\<expno2>\pdata\<procno>

Multiple display mode is supported for 1D and 2D spectra. For spectra

with a dimension > 2 the selected slice (subplane) is shown.

How to Select/Deselect Datasets

To select a dataset:
+ Click in the corresponding area in the data window.
or Click the small square at the upper right of the spectrum.
or Click the corresponding entry in the lower part of the browser.
In the lower part of the browser, you can:
+ Click one dataset to select it.
or Hold down the Ctrl key and click multiple datasets to select them.

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1D Interactive Manipulation

or Hold down the Shift key and click two datasets to select these two
and all datasets in between.
INDEX
When you select a dataset, the corresponding small square is filled (see
Fig. 12.12) and its entry in the
INDEX lower part of the browser is highlighted (see
DONE
Fig. 12.13).
Note that:
• no spectrum selected = all spectra selected
• scale/shift buttons of the data window toolbar only work on
selected spectra
To deselect a dataset:
+ Select a different dataset.
To deselect all datasets:
+ Click the following button:
Deselect all datasets.

How to Remove a Dataset from Multiple Display

1. Select the dataset(s) you want to remove.
2. Click the following button:
Remove selected data from the screen.
Note that the data on disk are not affected. Furthermore, the first spectrum
cannot be removed from the screen.

How to Display the Sum or Difference Spectra

+ Click one of the following button (button turns green):
Show the difference between the first and the sum of the other
datasets.

Show the sum of all datasets in the multiple display window.

How to Save the Sum or Difference Spectra

1. Click the following button:

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 1D Interactive Manipulation

Save the displayed sum or difference spectrum.

2. In the appearing dialog box, specify the destination procno.
INDEX
How to Display the Next/Previous Name/Expno
DONE INDEX
To compare a series of spectra you can interactively increment or decre-
ment the dataset name or expno. A dataset name is incremented accord-
ing to the ICON-NMR naming convention of increasing extensions, e.g.
name.001, name.002 etc.
+ Click one of the following button (button turns green):
Show the previous name/expno/procno of the last dataset

Show the previous name/expno/procno of the last dataset

Set the increment options. Clicking this button will open the fol-
lowing dialog:

Figure 12.14
Here you can choose to increment the procno, expno or name, set the
expno increment and switch individual scaling on/off.

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1D Interactive Manipulation

How to Toggle between Superimposed and Stacked Display

+ Click the following button:
INDEX
Toggle between superimposed and stacked display.
INDEX DONE
How to Shift and Scale Individual Spectra
To compare the intensity and chemical shift of corresponding peaks, you
can shift and scale individual spectra. To do this:
1. Display the spectra in multiple display mode as described above.
2. Expand the spectra to display the desired region or peak.
3. Select one of the spectra (e.g. by clicking it in the lower part of the
browser).
4. Click-hold the button and move the mouse to align the intensi-
ties.
5. Click-hold the button and move the mouse to align the peak posi-
tions.

The alignment can be facilitated by showing the difference spectrum (

button) and minimize that. Note that you can also scale the selected spec-
tra up/down with the buttons and . The button allows you to
move the selected spectra vertically. Clicking the button resets individ-
ual scaling and shifting.
The performed scaling and shifting are displayed in the data window (see
Fig. 12.15 and 12.16).

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 1D Interactive Manipulation

INDEX
DONE INDEX

Figure 12.15

Figure 12.16

How to move the selected spectrum one place up/down

+ Click the following button:
Move the selected spectrum one place up in the list.
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1D Interactive Manipulation

+ Click the following button:

Move the selected spectrum one place down in the list.
INDEX
Note that the first spectrum and calculated spectra (sum of difference)
INDEXup/down.
cannot be moved DONE

How to Switch on/off the Display of Datapaths and Scaling Fac-

tors
+ Click the following button:
Switch on/off display of datapaths and scaling factors.

How to Return from Multiple Display mode

+ Click the following button:
Return from multiple display mode [.ret].

How to Set the Colors of the 1st, 2nd, .. Dataset

The colors of the different datasets in the multiple display mode can be set
in the User preferences dialog box. To set, for example, the color of the sec-
ond spectrum:
+ Click Options => Preferences and click the Change button for the item
Color of 2nd 1D spectrum.
TOPSPIN 2.0 and newer allows you to set 8 different colors for different
spectra in multiple display.

12.6 1D Interactive Baseline Correction

Baseline correction can be performed with commands like abs or absd or,
interactively, as described below.

How to Switch to Baseline Correction Mode

+ Click the indicated button in the upper toolbar:

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 1D Interactive Manipulation

INDEX
DONE INDEX
or enter .basl on the command line.
The Tab bar of the active data window will be replaced by a toolbar (see
Fig. 12.17).

Figure 12.17 Data window in baseline correction mode

The yellow button indicates that the data window is in baseline
correction mode.
Some buttons will turn green when they are clicked. As long as a
button is green, it is active.

How to Perform Polynomial Baseline Correction

1. Click the following button (button turns green):
Perform polynomial baseline correction.
In the data window, a red horizontal line will appear as well as the
equation that describes the polynomial function:

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1D Interactive Manipulation

2. Click-hold button A and move the mouse until the red line coincides
with the first point of the spectrum.
INDEX
3. Repeat step 2 with the buttons B, C, D and E until the red line coin-
cides with the entire baseline of the spectrum.
INDEX DONE
How to Perform Sine Baseline Correction
1. Click the following button (button turns green):
Perform sine baseline correction.
A red horizontal line will appear as well as the equation describing the
sine function:

2. Click-hold button A and move the mouse until the red line coincides
with the first point of the spectrum.
3. Repeat step 2 with the buttons B, C and D until the red line coincides
with the entire baseline of the spectrum.

How to Perform Exponential Baseline Correction

1. Click the following button (button turns green):
Perform exponential baseline correction.
A red horizontal line will appear as well as the equation describing the
exponential function:

2. Click-hold button A and move the mouse until the red line coincides
with the first point of the spectrum.
3. Repeat step 2 with the buttons B and C until the red line coincides
with the entire baseline of the spectrum.

How to Preview the Baseline Corrected Spectrum

Before actually performing the baseline correction, you can preview the
result by displaying the difference between the uncorrected spectrum and
the red correction line.

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 1D Interactive Manipulation

To do that:
1. Click the following button (button turns green):
INDEX
Preview corrected spectrum (show difference).
The corrected spectrum DONE INDEX
will be displayed in red.
2. If the baseline is correct, click the button to save the correction. If
further correction is needed, click the button to show the original
spectrum and the red correction line.

How to Reset the Baseline Correction Line

1. Click the following button:
Reset the red correction line to zero.
If the difference spectrum is displayed (the button is active), click-
ing the reset button will restore the original spectrum.

How to Change the Mouse Sensitivity

+ Click one of the following buttons:
Increase (double) the Mouse Sensitivity [.inc].

Decrease (halve) the Mouse Sensitivity [.dec].

Reset the Mouse Sensitivity.

How to Save the Baseline Correction and/or Return

To return while saving the baseline correction:
+ Click the following button:
Save baseline correction and Return [.sret]
This will perform the following tasks:
• Execute the baseline correction [bcm].
• Save the baseline correction values A, B, C, D and E.
• Leave the baseline correction mode.
To return while discarding any changes:

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1D Interactive Manipulation

Click the following button:

Return, Discarding any changes [.ret].
INDEX
How to Perform Cubic Spline
INDEX DONEBaseline correction
+ Click the following button:
Define points for cubic spline baseline correction.
The toolbar of the data window will change as shown in Fig. 12.18.

Figure 12.18 Data window in spline baseline correction mode

The cursor line in the data window turns red. If a list of baseline points al-
ready exists, you are prompted to overwrite or append to these points. If
you choose Append, the labels of the existing points are displayed on the
screen. If you choose Overwrite, no labels are displayed. Nevertheless,
the existing points are only overwritten when you define and save new
points.
To define new baseline points:
1. Move the cursor line to a baseline point and left-click at that posi-
tion.
2. Do this for at least five baseline points.
Fig. 12.18 shows a spectrum with five defined baseline points. Note that
here the points have been chosen at the right part of the spectrum for dis-
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 1D Interactive Manipulation

play reasons only.

Note that the actual baseline correction is only performed when you click
the button in the spline baselineandINDEX
interactive baseline mode.
DONE INDEX
How to Delete Spline Baseline Points from the screen
To delete one baseline point:
1. Right-click the baseline point position in the data window.
2. Choose Delete Current from the popup menu (see Fig. 12.19).

Figure 12.19
To delete all baseline points:
1. Right-click any position in the data window.
2. Choose Delete All from the popup menu (see Fig. 12.19).

How to Return from Cubic Spline Baseline mode with/without

Save
To return while saving the baseline points:
+ Click the following button:
Save baseline points and Return [.retsab].
To return while discarding any changes:
+ Click the following button:
Return, Discarding any changes [.ret].
Alternatively, you can right-click in the data window and choose Save &
Quit or Quit, respectively.
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1D Interactive Manipulation

12.7 1D Interactive Peak Picking

Peak picking canINDEX

be performed, automatically, with the commands pps or,
interactively, in the peak picking mode.
INDEX DONE
How to Switch to Peak Picking Mode
+ Click the indicated button in the upper toolbar:

or enter .pp on the command line.

The Tab bar of the active data window will be replaced by a toolbar (see
Fig. 12.20).

Figure 12.20 Data window in peak picking mode

The yellow button indicates that you are in peak picking mode.
Some buttons will turn green when they are clicked. As long as a
button is green, it is active.

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 1D Interactive Manipulation

Note that the button is automatically activated, i.e. you are in Define
peak picking range mode
INDEX
How to Define New Peak Picking Ranges
DONEcorner INDEX
1. Put the cursor at the upper-left of a peak picking range.
2. Left-click-hold and drag the mouse to the lower-right corner of the
range.
The peak picking range will be marked green. The minimum and max-
imum intensity are set and the peaks in the range are picked and dis-
played.
3. Repeat step 1 and 2 for each peak picking range to be defined.
4. Click the green button to leave the "Define peak picking range"
mode.
Note that the parameters MI and MAXI are set to the lowest minimum and
the highest maximum intensity, respectively, of all ranges.

How to Change Peak Picking Ranges

1. Click the following button (button turns green):
Change peak picking ranges.
2. Put the cursor on one of the edges of the peak picking range.
The cursor turns into a double-headed arrow.
3. Left-click-hold and drag the peak range edge to its new position.
4. Optionally: repeat step 2 and 3 for the other edge and for other peak
ranges.
5. Click the green button to leave the "Change peak picking range"
mode.

How to Pick Peaks in Peak Picking Ranges only

Peaks in a peak range are automatically picked when the range is de-
fined.If peaks have been deleted from a rang, they can be picked again as
follows:
1. Right-click in the data field.
2. Choose Pick Peaks On Ranges from the popup menu.

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1D Interactive Manipulation

Alternatively, you can enter ppl on the command line. This command can
be entered in Interactive peak picking mode or in the normal display mode.
INDEX
How to Delete all Peak Picking Ranges
INDEX DONE
+ Click the button in the data window toolbar.

or
+ Right-click in the data field and click Delete All Regions in the popup
menu.

How to Define Peaks Manually

1. Click the following button (button turns green):
Define peaks manually.
A red vertical line will appear in the data window.
2. Put the red cursor line at the desired peak and click the left mouse
button.
The peak label will appear at the top of the data window.
3. Repeat step 2 for each peak to be defined.
4. Click the green button to leave the "Define peaks" mode.

How to Pick Peaks Semi-Automatically

1. Click the following button (button turns green):
Define peaks semi-automatically.
2. Move the cursor into the data window.
3. Put the cursor line near the desired peak.
4. Left-click to pick forward
or
Right-click to pick backward (see Fig. 12.21).
A red cursor line will appear at the nearest peak whose intensity is be-
tween MI and MAXI.
5. Right-click to add the selected peak to the peak list (see Fig. 12.21).

234
 Figure 12.21
The peak label will appear at the top of the data window.
6. Click the green button to leave the "define peaks semi-automatically"
mode.

How to Delete Peaks from the Peak List

To delete a specific peak:
1. Right-click on a defined peak.
2. Choose Delete peak under cursor from the popup menu (see Fig.
12.22).
99

Figure 12.22
To delete all peaks:

+ Click the button in the data window toolbar.

or
+ Right-click in the data field and click Delete All Peaks in the popup
menu.
How to Return from Peak Picking Mode with/without Save
To return while saving the peak list and peak ranges:
+ Click the following button:

Save the Peak Region and Peak List and Return [.sret].

This will:
• Save the peak list to the file peak.xml and the peak ranges to
the file peakrng.
• Leave the peak picking mode.
To return while discarding any changes:
+ Click the following button:

Return, discarding any changes [.ret].

How to save Peaklists and Regions in 1D interactive mode

In 1D interactive Peak Picking the Save as ... button opens a
window in which three options of saving can be chosen:
a) Save Peaklists and Regions
b) Save Peaklist for Deconvolution
(Peaklist will be saved in a format which is needed for deconvolution)
c) Save Peak list and start Deconvolution
(The Peaklist is saved and the Deconvolution will be started, after
that returning to Peak Picking)
 1D Interactive Manipulation

INDEX
DONE INDEX

237
2D Interactive Manipulation

Chapter 13
INDEX

2D Interactive
INDEX DONE
Manipulation

The upper toolbar of the 2D menu offers various buttons for interactive
manipulation. If you click such a button, the active data window will switch
to the corresponding mode. An interactive manipulation mode is data win-
dow specific, i.e. it only applies to the active window.

13.1 2D Interactive Phase Correction

2D spectra can be phase corrected interactively in both the F2 and F1

direction by selecting certain rows and/or columns and phase correct them.

13.1.1 2D Interactive Phase Correction Procedure

How to Switch to 2D Interactive Phase Correction

Click the corresponding button in the upper toolbar as indicated below:

or enter .ph on the command line.

The Tab bar of the active data window will be replaced by a toolbar. Fig.

238
 2D Interactive Manipulation

13.1 shows an example of an unphased 2D inverse spectrum.

INDEX
DONE INDEX

Figure 13.1 Data window in phase correction mode

The yellow button indicates that you are in phase correction
mode.

Toggle the contour display on/off.

Switch to phase row mode to display rows of selected peaks.

Switch to phase columns mode to display columns of selected

peaks.

Save the phase values to the 3D data from which this 2D was ex-
tracted.

Return.

How to Perform a Typical 2D Interactive Phase Correction

In this example we will perform F1 phase correction (columns) only. Take
the following steps:
1. Select two or more peaks in different parts of the spectrum. To do

239
2D Interactive Manipulation

that:
a) Zoom in on a peak by drawing a box around it. To do that, click-
INDEX
hold the left mouse button and move the mouse (see Fig. 13.2).
b) Right-click
INDEX at the peak position and choose Add from the popup
DONE
menu.

Figure 13.2
c) Click the button to display the full spectrum.
d) Zoom in on the next peak and add in the same way as the first
one.
e) Zoom in on the next peak etc.
Fig. 13.3 shows an example of three selected peaks.

240
 2D Interactive Manipulation

INDEX
DONE INDEX

Figure 13.3
2. Click the button to phase correct the columns (F1).
A new data window called Phase 2D will appear showing the columns
of the selected peaks (see Fig. 13.4).

Figure 13.4

241
2D Interactive Manipulation

Note that the toolbar and the right-click popup menu offer the full 1D
phase correction functions.
INDEX
By default, all columns are selected as indicated by the filled blue
squares INDEX
. The red vertical
DONE line indicates the default pivot point in the
upper column.
3. A typical way to perform phase correction is:
• Click-hold the button for zero order correction and move the
mouse until the reference peak of the first column is exactly in absorp-
tion mode.
• Click-hold the button for first order correction and move the
mouse until the reference peak in other column is exactly in absorption
mode.
• Click the button to execute, save and return (see Fig. 13.5).

Figure 13.5

13.1.2 2D Interactive Phase Correction Details

How to Scale or Shift Individual Rows/Columns

To select one row or column:

242
 2D Interactive Manipulation

+ Click in the corresponding part of the data window.

The selected row/column will be marked with a filled blue square where-
as unselected rows/columns will be markedINDEX
with an unfilled blue
square . Selecting a singleDONE
row /column INDEX
allows you to shift and scale it
separately from the other rows/columns as shown in Fig. 13.6.

Figure 13.6
To select all rows or columns,
+ Click the following button:
Select all rows or columns.

How to Perform Smooth Phase Correction

To perform zero order phase correction:
1. Click-hold the following button (it turns green) and move the mouse:
Zero order phase correction.
until the reference peak of the first row/column is exactly in absorption
mode.
2. Release the mouse (button turns grey).
The parameter PHC0 will be set accordingly.
243
2D Interactive Manipulation

To perform first order phase correction:

1. Click-hold the following button (it turns green) and move the mouse:
INDEX
First order phase correction.
until theINDEX
reference peakDONE
of the second and further rows/columns is ex-
actly in absorption mode.
2. Release the mouse (button turns grey).
The parameter PHC1 will be set accordingly.

How to Perform 90, -90 or 180° Zero Order Phase Correction

Click one of the following buttons:
90° zero order phase correction.

-90° zero order phase correction.

180° zero order phase correction.

How to Reset the Phase to the Original Values

Click the following button:
Reset zero and first order phase.

How to Change the Mouse Sensitivity

Click one of the following buttons:
Increase (double) the mouse sensitivity [.inc].

Decrease (halve) the mouse sensitivity [.dec].

Reset the mouse sensitivity to 2.0.

How to Show the Next/Previous Row or Column

To show the next row/column, click the following button:
Show next row/column.
Note that only the selected row/column is increased. If all rows/columns

244
 2D Interactive Manipulation

are selected, only the first one is increased.

To show the previous row/column, click the following button:
INDEX
Show previous row/column.
DONE INDEX
Note that only the selected row/column is decreased. If all rows/columns
are selected, only the first one is decreased.

How to Arrange Rows or Columns

Click one of the following buttons:
Arrange rows/columns horizontally.

Arrange rows/columns vertically (see Fig. 13.6).

Arrange rows/columns vertically in a split window.

How to Return from Multi-1D Phase to 2D Phase Display

Click the following button:
to save, execute and return.
This will perform the following tasks:
• Execute phase correction.
• Save the current phase correction values.
• Leave the multi-1D phase mode.
Click the following button:
to return to the 2D phase display without save.

How to Return from 2D Phase Mode

Click the following button:
Return.

13.2 2D Interactive Integration

TOPSPIN 2.1 and newer supports interactive 2D integration.

245
2D Interactive Manipulation

13.2.1 How to Switch to 2D Interactive Integration

Click the corresponding button in the upper toolbar as indicated below
INDEX
INDEX DONE

or enter .int on the command line.

The Tab bar of the active data window will be replaced by a toolbar. Fig.
13.7 shows an example of a 2D inverse spectrum.

Figure 13.7 Data window in interactive integration mode

The yellow button indicates that you are in integration mode.

"Define integral region" mode (active when green)

Move integral region (green when active).

Copy a region.

Delete all integral regions.

246
 2D Interactive Manipulation

Read/import integral regions.

Save/Export integral regions. INDEX

DONE
Integrate current regions/define INDEX
reference.

Save integral regions and return.

Return without save.

13.2.2 2D Interactive Integration Procedure

When you switch to 2D integration mode, the "Define integral region" mode
is active by default. This means you can immediately start defining the inte-
gral regions. To do that:
1. Click and hold the left mouse button at any corner of a region to be
defined, move the mouse to draw a box around that region and
release the mouse.
2. Choose one of the following options from the appearing popup menu:
Integrate: a : to add up all intensities in the region
Integrate: + : to add up all positive intensities in the region
Integrate: - : to add up all negative intensities in the region
Integrate: a + - : to add up all intensities in the region and store sepa-
rate entries for all, positive and negative intensities.
Integrate: a + : to add up all intensities in the region and store separate
entries for all and positive intensities.
Integrate: a - : to add up all intensities in the region and store separate
entries for all and negative intensities
Integrate: + - : to add up all intensities in the region and store separate
entries for positive and negative intensities.
The integral regions will be displayed along with their storage num-

247
2D Interactive Manipulation

bers and modes (see Fig. 13.8).

INDEX
INDEX DONE

Figure 13.8
3. Click the button and choose Integrate current regions from the pull-
down menu to integrate the defined regions.
4. Click the button again and choose List integral values from the
pulldown menu to show the list of integrals.
Table 13.1 shows the list of integrals based on the regions defined in Fig.
13.8.

248
 2D Interactive Manipulation

# SI_F row1 row2 row1 row2 Abs. Int. Inte-

1 ppm ppm INDEX gral
SI_F col1 col2 col1 ppm
DONEcol2 ppm
INDEX
2
1 1024 666 689 50.1458 46.4313 9.2529e+00 882.42 a
3 2 8
1024 510 522 6.04420 5.89291
2 1024 597 632 61.2893 55.7175 1.1135e+00 1062 +
4 9 9
1024 520 533 5.91452 5.74162
3 1024 652 692 52.4673 45.9670 - - -
9 1 3.7699e+00 35.953
7
1024 566 579 5.31659 5.15089
4 1024 683 721 47.3599 41.3238 1.0072e+00 960.57 a
5 8 9
1024 589 605 5.02122 4.81230
5 1024 683 721 47.3599 41.3238 1.064e+009 1014.7 +
5 8
1024 589 605 5.02122 4.81230
6 1024 683 721 47.3599 41.3238 - - -
5 8 5.6725e+00 54.097
7
1024 589 605 5.02122 4.81230
7 1024 502 543 76.6116 70.11130 1.2637e+00 1205.2 a
8 9
1024 637 649 4.38726 4.23598
8 1024 502 543 76.6116 70.11130 1.2911e+00 1231.3 +
8 9
1024 637 649 4.38726 4.23598
Table 13.1

249
2D Interactive Manipulation

Alternatively, you can define a reference integral and integrate the defined
regions of the same or of a different dataset, relative to this integral. For
this purpose theINDEXbutton offers the following menu items:
• Integrate current regions rel. to reference
INDEX DONE
You will be prompted for the reference integral number and value.
• List integral values
The output list will now show an additional column with the normal-
ized integral values.
• Define current dataset as reference
You will be prompted for the reference integral number and value.
• Integrate and use ref. dataset for calibration
The integral value defined on the reference dataset is used for cali-
bration.

How to Move an Integral region

1. Click the button (it turns green).
2. Move the mouse into the region to be moved.
3. Left-click-hold and move the mouse to move the region.
4. Release the mouse at the desired position.

How to Copy an Integral region

1. Click the button (it turns green)
2. Move the mouse into the region to be copied
3. Left-click-hold and move the mouse to the desired position
4. Release the mouse to copy the region.

How to Delete all Integral Regions

1. Click the button .
2. Click OK to confirm deletion.

How to Read/Import Integral Regions

1. Click the button .
2. Click Read intrng to read the last stored integral ranges

250
 2D Interactive Manipulation

or
Click Import Integration Regions to import an exported integral region
file (see below) INDEX
DONE INDEX
How to Save/Export Integral Regions
1. Click the button
2. Click Save Regions to intrng to save the regions to the current dataset
PROCNO (file int2drng)
or
Click Export Integration Regions to export the integration region file for
general usage; i.e. usage with other datasets.

How to Return from 2D Integration mode

Click the following button:
to save the current integral regions and return.
Click the following button:
to return to the 2D integration mode without save.

13.3 2D Multiple Display and Row/Column Handling

2D multiple display shows a 2D spectrum with an arbitrary number of 1D

and/or 2D spectra superimposed.
Spectra are ppm aligned or Hz aligned, according to the selected axis unit.
A superimposed 1D spectrum is automatically displayed in the direction of
the matching nucleus (for a hetero-nuclear 2D) or in the F2 direction (for a
homo-nuclear 2D).
Although multiple display is normally used for spectra with matching nuclei,
it allows you to superimposed spectra with non-matching nuclei. You will
get a warning that the nuclei do not match. Just just click OK to continue.

How Switch to Multiple Display mode and Read Multiple Spectra

Switching to multiple display and reading multiple spectra can be done in

251
2D Interactive Manipulation

two different ways:

• Read a 2D dataset and click to switch to multiple display
mode.INDEX
Then add 1D and/or 2D spectra, e.g. from the browser or
with re.
INDEX DONE
or
• Select multiple spectra in the browser, right-click one of them and
click Display.
For a more detailed description of reading multiple data in multiple dis-
play mode, see chapter 12.5.
In multiple display mode, the Tab bar of the active data window is re-
placed by a toolbar (see Fig. 13.9).

Figure 13.9 Multiple display with two 2D spectra superimposed

252
 2D Interactive Manipulation

INDEX
DONE INDEX

Figure 13.10 Multiple display with a 1D spectrum superimposed on a 2D spectrum

The yellow button indicates that the data window is in multiple
display mode.
Some buttons will turn green when they are clicked. As long as a
button is green, it is active.
The browser in multiple display is split in two parts (see Fig. 13.11).The ad-
ditional lower part shows:
• which datasets are displayed in the active data window
• which datasets are selected (they are highlighted)

Figure 13.11

253
2D Interactive Manipulation

How to Align Multiple 2D Spectra

2D spectra in multiple display can be individually shifted. To do that:
INDEX
1. Select one of the spectra in the lower part of the browser.
INDEX
2. Click-hold the DONE
button and move the mouse.
Fig. 13.12 shows a region of two comparable 1H/13C inverse 2D data-
sets which are shifted relative to each other.
Clicking the button resets individual scaling and shifting.

Figure 13.12

How to Display the Next/Previous Name/Expno

To compare a series of spectra you can interactively increment or decre-
ment the dataset name or expno. A dataset name is incremented accord-
ing to the ICON-NMR naming convention of increasing extensions, e.g.
name.001, name.002 etc.
+ Click one of the following button (button turns green):
Show the previous name/expno/procno of the last dataset

254
 2D Interactive Manipulation

Show the previous name/expno/procno of the last dataset

Set the increment options. Clicking this button will open the fol-
INDEX
lowing dialog where you can choose to increment the procno, ex-
DONE
pno or name, set the INDEX
expno increment and switch individual
scaling on/off.

How to Scan Rows/Columns

Click the following button (it turns green) and move the mouse in the data
field:
to scan rows in the 2D spectrum.
Click the following button (it turns green) and move the mouse in the data
field:
to scan columns in the 2D spectrum.
Click the following button (it turns green) and move the mouse in the data
field:
to scan rows and columns in the 2D spectrum.
To scale up the displayed row/column:
+ Click the left mouse button or turn the mouse wheel up.
To scale down the displayed row/column:
+ Click the middle mouse button or turn the mouse wheel down.

How to Grab a Row/Column

You can grab a row or column, i.e. keep it displayed in the data window
as follows:
1. Scan rows or columns as described above and hold at the desired
position.
2. Right-click in the data window.
3. Choose Grab Row/Column from the popup menu (see Fig. 13.13).
Note that a grabbed row/column appears in the lower apart of the brows-
er. It can be selected there and individually scaled or shifted.

255
2D Interactive Manipulation

INDEX
INDEX DONE

Figure 13.13

Figure 13.14
Fig. 13.14 shows row 619 with the 1D baseline at the center of the data
window.

How to Show the Next/Previous Row or Column

To show the next row/column, click the following button:
Show next row/column.
To show the previous row/column, click the following button:
Show previous row/column.

256
 2D Interactive Manipulation

Alternatively, you can turn the mouse wheel, while pressing the Shift key
to show the next/previous rows/columns.
INDEX
How to Move the Selected Dataset Up/Down in the Dataset List
DONE INDEX
To move the selected dataset up, click the following button:
Move the selected dataset up.
To move the selected dataset down, click the following button:
Move the selected dataset down.

How to Extract a Row/Column

1. Scan rows or columns as described above and hold at the desired
position.
2. Right-click in the data window and choose Extract Row/Column from
the popup menu (see Fig. 13.13).
3. Specify the row/column number and output procno in the dialog box.
Note that the ROW/COLUMN field is initialized with the grabbed
row/column or, if no grabbing was done, with the current row/column.
4. Click OK
The extracted row or column is stored as a 1D dataset under the specified
PROCNO and displayed in a new data window. In the upper left part of
this, the row number and source 2D dataset is specified (see Fig. 13.15).

257
2D Interactive Manipulation

INDEX
INDEX DONE

Figure 13.15

How to Copy Contour Levels from First to Other Spectra

Click the following button:
Copy contour levels from the first to the other spectra.
Note that the contour levels are only changed on screen, not on disk.

How to Switch on/off 2D contour display

Click the following button:
Switch on/off 2D contour display.

How to Position the Baseline of the Row/Column

To put the baseline at the center of the data window:
1. Right-click in the data window.
2. Choose in Baseline At Center from the popup menu (see Fig. 13.13).
To put the baseline at the bottom of the data window:

258
 2D Interactive Manipulation

1. Right-click in the data window.

2. Choose in Baseline At Bottom from the popup menu (see Fig. 13.13).
INDEX
This works both in the scan submode or on a grabbed row/column.
DONE INDEX
13.4 2D Interactive Calibration

A 2D spectrum can be calibrated, automatically with the command sref

or, interactively as described below.

How to Switch to 2D Calibration mode

+ Click the corresponding button in the upper toolbar:.

or enter .cal on the command line. The Tab bar of the active data window
will be replaced by a toolbar (see Fig. 13.16).

Figure 13.16 Data window in calibration mode

The yellow button indicates that the data window is in calibration
mode.

259
How to Perform 2D Calibration
In calibration mode:
1. Left-click in the data window at the reference peak.
The following dialog box will appear:

Note that the units for F2 and F1 (Hz or ppm) correspond to the axis
units of the display.
2. Enter the F2 and F1 frequency you want to assign to the reference
peak.
3. Click OK.
The spectrum will be calibrated and re-displayed. 2D Chemical Shift Dis-
tance Measurement

How to Measure a 2D Chemical Shift Distance

1. Click the following button (button turns green):
Chemical shift distance measurement.
2. Click-hold the left mouse button at one peak position and drag the
mouse to another peak position.
The distance in ppm, will be displayed.

3. Right-click in the data window to quit distance mode (button turns

grey).
 2D Interactive Manipulation
4.

INDEX
DONE INDEX

Figure 13.17 Data window in distance measurement mode

261
Data Window Handling

Chapter 14
INDEX

Data Window
INDEX DONE
Handling

14.1 Data Windows

The TOPSPIN window has a data area that may contain multiple data win-
dows. The size of the data area depends on the overall size of the TOPSPIN
window and on presence of the Browser and/or Processing Guide. Fig.
14.1 shows the TOPSPIN window with the Browser and three data windows.

262
 Data Window Handling

INDEX
DONE INDEX

Figure 14.1
Note that the three data windows show different data objects: 1D process-
ing parameters, a 1D spectrum and a 2D spectrum.

How to Move a Data Window

+ Click-hold the title bar and move the mouse.

How to Resize a Data Window

1. Move the cursor to the window edge until it becomes a double-
headed arrow.
2. Left-click-hold that position and move the mouse.
Depending on the position of the double-headed arrow, you can change
the window height, width or both (see Fig. 14.2)

263
Data Window Handling
.

INDEX
INDEX DONE

Figure 14.2

How to Select (activate) a Data Window

The active data window is the window of which the title bar is highlighted.
The TOPSPIN menu, tool bars and command line commands correspond to
and act on that window. Only one data window is active at a time.
To activate a different data window:
+ Click in the desired data window or click its title bar.
or
+ Click one of the colored radio buttons above the data area. The
pressed radio button (the green one in the example below) corre-
sponds to the current dataset.

If you hold the cursor over one of the buttons without clicking it and
wait a few seconds, the corresponding dataset specification will be
shown.
or

264
 Data Window Handling

+ Click Window => x dataname expno procno dir user

where x is the number of the desired window and dataname, expno,
INDEX
procno, dir and user refer to the dataset displayed in that window.
or DONE INDEX
+ Hit the F6 key to activate the next window. Repeat that until the de-
sired window is the active window.

How to Open a New empty Data Window

+ Click Window => New window [Alt+w-n]
The new data window will become the active window and will, by default,
cover the entire data area, hiding possible existing data windows. To open
a dataset in the new window, drag a dataset from the browser or from the
Windows Explorer into the new window or click File => Open (see also
chapter 5.3).

How to Arrange Data Windows

If the data area contains multiple data windows, you can arrange them in
various ways. All the arrange commands arrange the windows left to right
and/or top to bottom in the order in which the windows have been active.
The currently active data window will therefore be positioned at the top
and/or left of the data area.
To arrange the data windows as a grid:
+ Click Window => Arrange as a Grid
Depending on the number of windows, they will be arranged vertically
and/or horizontally (see Fig. 14.3).

265
Data Window Handling

INDEX
INDEX DONE

Figure 14.3
To arrange data windows in stack (see Fig. 14.4):
+ Click Window => Arrange in Stack

Figure 14.4

266
 Data Window Handling

To arrange data windows side by side (see Fig. 14.5):

+ Click Window => Arrange Side-by-Side
INDEX
DONE INDEX

Figure 14.5
To cascade data windows (see Fig. 14.6):
+ Click Window => Cascade

Figure 14.6
Note that you can instruct TOPSPIN to open new data windows cascaded
rather than maximized as well configure cascaded windows (command
set => Window settings, see also chapter 5.3)

How to Iconify (minimize) a Data Window

+ Click the button in the windows title bar

267
Data Window Handling

or
+ Click Window => Iconify all to iconify all windows.
INDEX
How to De-iconify
INDEXa DataDONE
Window
+ Click the button or double-click the title bar.

How to Maximize a Data Window

+ Click the button or double-click the title bar.
The window will cover the entire data area. Note that a maximized window
cannot be moved of resized but can be restored (in size and position),
iconified or closed.

How to Restore the Size and Position of a Data Window

+ Click the button or double-click the title bar.
Note that this is only possible if the title bar contains the button. This
is only the case after the window has been maximized or iconified.

How to Close a Data Window

To close the active data window:
+ Click File => Close [Crtl-w]
or
+ Click the button in the windows title bar.
To close any data window:
+ Click the button in the data windows title bar
or
+ Click the title bar and then click File => Close [Crtl-w].
To close all data windows:
+ Click File => Closeall [closeall]

268
 How to Iconify all Data Windows
+ Click Window => Iconify all

How to Maximize all Data Windows

+ Click Window => Maximize all
The active window will be displayed on top, all other windows are hidden.

How to Activate the Next Data Window

+ Click Window => Next window [F6].
The windows title bar will become highlighted.

14.2 Window Layouts

A data window layout defines the position, geometry and window type of
one or more TOPSPIN windows. The following windows types are available:
• data windows
• lock display window
• acquisition display window
• BSMS display window
• temperature unit window

How to Save the Current Window Layout

1. Click Window => Save layout
2. In the appearing dialog box:
Specify the layout File name (extension .prop) and click Save Layout

How to Read a Window Layout

1. Click Window => Read layout
2. In the appearing dialog box:
Specify or click the layout File name and click Read Layout
Windows are arranged according to the following rules:
 • Each currently displayed window type gets the position and geom-
etry to the corresponding definition in the layout.
• If a window type is displayed but not defined in the layout, it keeps
its current position and geometry.
• If a window type is defined in the layout but not displayed, the lay-
out definition is ignored.
• Multiple data windows are, arbitrarily, assigned to the available
data window definitions.

How to Swap Data Windows

Within a certain layout, you can easily swap two TOPSPIN windows with the
command swin. If the data area contains exactly two windows, swin sim-
ple swaps their position and geometry. If it contains more than two data
windows, swin opens a list from which you can select any window to be
swapped with the currently selected (active) window. Swapping windows
can also be executed from the Window menu.

How to Toggle Window Decoration

By clicking Window => Window Layout => Toggle Window Decoration easy
toggling of window decoration is available. Especially users who work with
many different windows will get more space on their monitor by using this
function that hides - respectively shows - the title of the current window
and reduces the used font.
 Data Window Handling

INDEX
DONE INDEX

271
Analysis

Chapter 15
INDEX

Analysis
INDEX DONE

15.1 Introduction

TOPSPIN offers various data analysis methods including chemical shift

measurement, signal to noise calculation and T1/T2 relaxation analysis as
described in this chapter. Furthermore, it offers the following structure anal-
ysis tools:
• Multiplet Analysis
This allows you to easily define multiplets and deduce chemical
shifts, coupling constants, multiplicities and connections.
• Daisy (TOPSPIN 2.0 and newer)
This allows you to simulate spectra based on chemical shifts and
coupling constants.
• Solids Line Shape Analysis
This allows you to simulate and fit calculated spectra to various
experimental 1D solid NMR spectra.
• Jmol
A 3D Structure Viewer for displaying chemical structures.

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 Analysis

• 2D molecule structure editor

A program for drawing chemical structures, offering a large number
of drawing tools. INDEX
• DNMR (Dynamic NMR) Lineshape Analysis
DONE INDEX
A program to simulate temperature dependent NMR spectra, interac-
tively set up and iteratively refine the model parameters to get the
best fit of the measured and simulated 1D NMR spectra.
Structure analysis tools can be started from the Analysis menu. They are all
described in the following manuals:
+ Click Help => Manuals => [Analysis and Simulation] Structure
Analysis Tools
except for Daisy, which is described in the separate manual:
+ Click Help => Manuals => [Analysis and Simulation] Daisy

15.2 Chemical Shift Distance Measurement

How to Measure a Chemical Shift Distance

1. Click the following button (button turns green):
Chemical shift distance measurement.
2. Left-click-hold at one peak position and drag the mouse to another
peak position.
The distance in ppm, will be displayed.
3. Right-click in the data window or move the cursor out of the data win-
dow to leave distance measurement mode (button turns grey).

15.3 1D Signal to Noise Calculation

How to Perform Interactive S/N Calculation

1. Click Analysis => Signal/Noise Calculation [.sino].
The current signal region (parameters SIGF1-SIGF2) and noise re-
gion (parameters NOISF1-NOISF2) are displayed.

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Analysis

INDEX
INDEX DONE

Figure 15.1 Data window in S/N measurement mode

2. Move the mouse into the data window.
3. Left-click-hold and drag the mouse from one edge of the signal region
to the other edge.
A horizontal double-headed arrow will indicate the signal region.
4. Left-click-hold and drag the mouse from one edge of the noise region
to the other edge.
A horizontal double-headed arrow will indicate the noise region.
5. Right-click any position in the data window. The popup menu as
shown in Fig. 15.2 will appear.

Figure 15.2

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 Analysis

Choose Start S/N calculation

The other entries allow you to redefine or clear the regions. After the
INDEX
noise calculation has finished, the result will appear on the screen.
DONE INDEX
How to Delete the Signal Region or Noise Region
To delete the current signal region:
1. Right-click in the data window.
2. Choose Clear SIGREG from the popup menu (see Fig. 15.2).
To delete the current noise region:
1. Right-click in the data window.
2. Choose Clear NOISEREG from the popup menu (see Fig. 15.2).

How to Edit the Limits of the Signal Region or Noise Region

1. Right-click in the data window.
2. Choose Edit regions... from the popup menu (see Fig. 15.2).
3. Enter new limit values in the appearing dialog box.

4. Click OK
The S/N value is automatically recalculated and displayed.

How to Change the Width of the Signal Region or Noise Region

1. Right-click in the data window.
2. Choose Change region width... from the popup menu (see Fig. 15.2).

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Analysis

3. Enter new width values in the appearing dialog box.

INDEX
INDEX DONE

4. Click OK
Note that as you change the width, the right limit is modified correspond-
ingly. The left limit is kept. The S/N value is automatically recalculated and
displayed.

15.4 Deconvolution

The Analysis menu of TopSpin offers the possibility of deconvolution. This

line shape tool is especially useful to interprete complex spectra in which
peaks can not be defined clearly. Deconvolution calculates theoretical sig-
nals with different methods, for example Gaussian, Lorentzian or a mixture
of these line shapes. As a result information of peak position, line width and
integrals of deconvolved signals are available. Furthermore it is possible to
display them graphically. With this auxiliary tool peaks of 1D and 2D NMR
spectrum can be interpreted more easily. Overlapping peaks may be
deconvolved into a sum of such line shapes.
To start deconvolution, expand the spectrum on the display to show the
peak or peak group of interest. Deconvolution can be activated from the
command line by typing dcon or from TopSpin toolbar by clicking Analysis
--> Line Shape Fitting --> Lorentz / Gauss Deconvolution. The following

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 Analysis

dialog box will appear:

INDEX
DONE INDEX

Figure 15.3
After clicking OK different adjustments can be made.

Figure 15.4
For further information about all deconvolution options and the parameters
to be set, please look up the Processing Reference Manual (commands
gdcon, ldcon, mdcon, ppp, dconpl and dcon).
TopSin shows the deconvolution result, i.e. peak positions, line widths and
integrals on the screen and stores it in the file dconpeaks.txt within the

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Analysis

respective procno of the dataset (look up Fig. 15.5).

INDEX
INDEX DONE

Figure 15.5
After closing the editor window which shows the deconvolution result, Top-
Spin switches automatically to multiple display mode to show the original

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 Analysis

spectrum and the sum of the comuputed line shapes superimposed

INDEX
DONE INDEX

Figure 15.6
With the option Display the Lorentz/Gauss curves of the last Deconvolution
of the Deconvolution window (Fig. 15.4) it is possible to display the results
of the deconvolution also graphically:

Figure 15.7

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Analysis

Please note that the results of deconvolution are approximated achieve-

ments to interprete complex spectra. These amounts are acoording to real-
ity if the signalINDEX
is an ideal Gauss- or Lorentzian shape and if the complete
region of the signals is deconvolved.
INDEX DONE
15.5 Relaxation Analysis

Typically, relaxation data consist of a series of 1D FIDs measured with var-

ying delays and stored as pseudo 2D data. To analyze these data, Topspin
offers an easy to use T1/T2 Relaxation Guide. Relaxation curves of various
experiment types with up to six components can be fitted.
To start the Relaxation Guide:
+ Click Analysis => T1/T2 Relaxation [t1guide].
This will open the dialog box as shown in Fig. 15.8.

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 Analysis

INDEX
DONE INDEX

Figure 15.8
Just click the successive icons and follow the instructions on the screen.
Note that holding the cursor over an icon shows the command line com-
mand that is executed when the icon is clicked. If you prefer to execute
these commands from the command line, just click the Close button to
close the Relaxation Guide.

Extract Slice
Prompts you for the FID or spectrum to be extracted for peak determina-
tion (see Fig. 15.9). Click FID to extract an FID or Spectrum to extract a
spectrum. Note that the latter only works if the pseudo 2D data have been
processed. If you click FID, the extracted FID is automatically processed.

281
 We recommend to enter the FID or spectrum number which was meas-

Figure 15.9
ured with the longest delay. It can be found in the vdlist file in the EXPNO
data directory. Then you can choose between:
• Manual Integration. This will switch to Interactive integration mode
The highest peak in each region will be used for relaxation analy-
sis.
• Manual Peak Picking. The selected peaks will be used for relaxa-
tion analysis.

Figure 15.10
Peaks/Ranges
Switches to interactive integration or peak picking mode as chosen
 Analysis

above. Here you can define the ranges or peaks to be included in the re-
laxation analysis. Then use button to export regions/peaks to Relax-
ation Module and quit the interactive mode.
INDEX
Relaxation Window DONE INDEX
Switches the 1D data window to relaxation analysis mode (see Fig.
15.11)
ES

Figure 15.11
and performs a default fitting. By default, this is one-component, T1-in-
tensity fitting (Function type uxnmrt1) for peak 1. If the dataset was al-
ready fitted, the previous type of fitting is performed. The fitting curve is
displayed in the data section and a Brief Report is shown in the parameter
section. If this default fitting is appropriate, you can view, interpret and
print the results as described below. If not, you can perform the desired
fitting as described below.
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Analysis

Perform Fitting and Calculate the Relaxation Time

Depending on the experiment, you can perform the appropriate fitting as
follows: INDEX
1. SelectINDEX
a Fitting type:DONE
Intensity or Area. Either every point reflects
the intensity of the biggest peak in the defined integral range or
the integral itself. Both of them can be used but, depending on the
experiment, one of them usually give a better fitting curve.
2. Click the button to open the parameter dialog box. Select a
Function Type and set the required parameters (see below).
3. Click OK.
4. Perform fitting and calculate the relaxation time:
Fit the relaxation curve for the current peak.

Fit the relaxation curve for all peaks.

Fit data according to the ASCII file t1ascii.

View and interpret the results as described below.

Function Types and Parameters
The TOPSPIN relaxation routine offers functions for various relaxation ex-
periments with up to 6 components:
uxnmrt1 for one-component T1 experiments. Set the parameter List
file name to the list type used during the acquisition. Set Pick data points
to PD or PD0 (see below). The T1 fitting function is defined by the
function:

t
I  t  = I  0  + P  exp  ------
 T1

where I is Intensity or Area according to the Fitting Type. The best fit
is calculated by varying I(0), P and T1 in an iterative process accord-
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 Analysis

ing to the Levenberg-Marquardt algorithm. Clicking and exe-

cutes the commands ct1 (current peak) and dat1 (all peaks),
respectively. INDEX
uxnmrt2 for one-component DONET2 experiments.
INDEXSet the parameter List
file name to the list type used during the acquisition. Set Pick data points
to PD or PD0 (see below). A T2 fitting function is defined by the func-
tion:

t
I  t  = P  exp  ------
 T2

where I is Intensity or Area according to the Fitting Type. The best fit
is calculated by varying P and T2 in an iterative process according to
the Levenberg-Marquardt algorithm. Clicking and executes
the commands ct2 (current peak) and dat2 (all peaks), respectively.
invrec, satrec, cpt1rho, expdec, gaussdec, lorgauss linear, var-
bigdel, varlitdel, vargrad, vardamp: these functions can be used for
various experiments with up to 6 components, except for cpt1rho and
lorgauss which allow only 4 and 3 components, respectively. They all
use the simplex algorithm and require some parameters to be set:
• Enter the Number of components
• Click the Setup button to set the Iteration Control parameters. For
each component, the initial guess (G) and step rate (S) can be
set. The initial guess for I[0] must be selected such that the
sum of all components does not exceed 1. If there is only one
component, I[0] is usually set to 1.The step rate is usually set to
about one tenth of the initial guess. If the step rate of a variable
is set to zero, then this variable is not changed during the itera-
tions. Note that the initial guesses can also be set with the
toolbar button. Clicking and executes the commands
simfit (current peak) and simfit all (all peaks), respec-
tively.

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Analysis

The Fitting Function to pick data points can be:

• pd - pick data points for relaxation analysis (Drift value
INDEX
interpreted)
• pd0 - pick data DONE
INDEX points for relaxation analysis at constant
peak positions (drift value ignored)
• pft2 - pick data points for T2 calculation of 1D raw data.

View the Fitting Results

When the fitting procedure has finished, the fitting curve is displayed in
the data section and a Brief Report appears in the parameter section (see
Fig. 15.11). The latter consists of:
• the calculated relaxation value
• the fitted parameters
• the standard deviation SD
For further examination of the result, click one of the following buttons:
Show the fitting result of the previous peak/area.

Show the fitting result of the next peak/area.

Switch x-axis to linear scaling.

Switch x-axis to logarithmic scaling.

Switch x-axis to square root scaling.

Switch y-axis to logarithmic scaling. Note that this only works for
curves with positive intensities/areas only.
Import integrals from dataset ~TEMP.

Export integrals to dataset ~TEMP

Toggle button to hide/show information in the curve field, includ-

ing algorithm, peak number and relaxation value.
Show an extended report, including the fitted intensity or area

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 Analysis

distribution. This consists of the same information as the brief report

plus a table with the intensity or area distribution. Example:
INDEX
Dataset : C:/bio/data/guest/nmr/t1test/1/pdata/1
INTENSITY fit : DONE INDEX
I[t]=I[0]+P*exp(-t/T1)
12 points for Peak 1, Cursor Point = 7.221 ppm
Results Comp. 1

I[0] = 1.215e+000
P = -2.211e+000
T1 = 19.449s
SD = 3.685e-003
tau ppm integral intensity
30.000s 7.221 2.5811e+009 1.9737e+008
10.000s 7.221 -3.2898e+008 -2.9056e+007
8.000s 7.221 -7.8525e+008 -6.4616e+007
5.000s 7.221 -1.6289e+009 -1.3101e+008
...
Print, Export of Copy the Fitting Results
To print the fitting curve:
+ Click File => Print
To export the fitting curve as a graphics file:
+ Click File => Export
To copy the fitting curve to the Windows Clipboard:
+ Click Edit => Copy

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Acquisition

Chapter 16
INDEX

Acquisition
INDEX DONE

This chapter describes TOPSPIN acquisition as far as the interface is con-

cerned. Individual acquisition command are described in the Acquisition
Reference manual.

16.1 Acquisition Guide

If you are a new or occasional user, we recommend you to acquire your

data with the TOPSPIN Acquisition Flowchart. This will guide you through the
typical sequence of acquisition steps. To start the Acquisition Guide, click
Spectrometer => Acquisition Flowchart.

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 Acquisition

INDEX
DONE INDEX

Figure 16.1
In Automatic mode, the Acquisition Flowchart will simply execute each com-
mand when you click the respective button. This requires the acquisition
parameters to be set correctly. In interactive mode (Automatic mode
unchecked), the Acquisition Flowchart will, at each step, open a dialog box

289
Acquisition

offering you the available options and required parameters. Note that the
last button To processing will open the processing equivalent of the Acquisi-
tion Flowchart,INDEX
the Processing Guide.

INDEX DONE
16.2 Acquisition Toolbar

Acquisition can be prepared, started and controlled from Spectrometer

menu. Clicking this menu opens the pulldown menu shown in Fig. 16.2 :

Figure 16.2
Here you find several cathegories of acquisition related commands. Each
entry give access to a submenu with various commands. Fig. 16.3, for
example, shows the Setup submenu.

290
 Acquisition

INDEX
DONE INDEX

Figure 16.3
For most entries, the command line command, for example expinstall,
is specified in square brackets. Furthermore, Topspin can be configured
such that right-clicking any menu entry will display the corresponding com-
mand line command. To do that right-click in an empty part of the menubar
and choose Define Right-click Action.
For convenience, common acquisition commands can also be started from
the TOPSPIN toolbar. The right part of the upper toolbar shows the following
buttons:

Start the acquisition. Acquires NS scans in the current dataset, over-

writing
possibly existing data. Equivalent to the command zg.
Halt the acquisition. This stops the acquisition after the current scan
has finished. All data acquired so far are saved. Equivalent to the
command halt.
Stop the acquisition. This stops the acquisition immediately. Data
acquired after the last disk write (if any) are lost. Equivalent to the
command stop.
Open the online FID display window. Shows the currently acquired

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Acquisition

FID. Only works during acquisition. Equivalent to the command acqu.

Open the Lock display window. Shows the lock signal. Equivalent to
INDEX
the command lockdisp.
Open theINDEX DONE
BSMS contrrol suite.
Calculate the experiment time. Shows the total experiment time and
file size of the raw data. Equivalent to the command expt.
Set SFO1, O1, O2 and O3 interactively. Puts a red cursor line in the
data window. A left-click at the desired frequency opens a dialog box
where you can set O1, O2 and/or O3.
Set the sweep width to the current region and the spectrometer fre-
quency to the center of the current region. Update the parameters SW
and SFO1, respectively.
Setup a frequency list interactively.

16.3 Data window Toolbar

TOPSPIN 2.0 and newer support dataset specific acquisition display (Figure
16.5). It is activated by clicking the Acqu tab of the data window toolbar.
Alternatively to open the Acqu tab you can right click in the staturs bar
under the TopSpin command line (Figure 16.4):

Figure 16.4

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 Acquisition

INDEX
DONE INDEX

Figure 16.5
From here, you can start various acquisition commands like:
Start acquisition [zg]

Halt the acquisition [halt]

Stop the acquisition [stop].

Probe matching and tuning [wobb].

Interactive Parameter Adjustment [gs].

Data specific acquisition display allows you to open multiple acquisition

display windows, one for each dataset.
Note that the Acqu tab is automatically activated when the acquisition is
started from the TOPSPIN menu, toolbar or command line.

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Acquisition

16.4 Acquisition Status Bar

INDEX
The acquisition can be followed and controlled from the acquisition status
bar. Before you use the acquisition status bar, it must be configured from
INDEX DONE
the User Preferences window. To do that:
1. Click Options => Preferences [set].
2. Click Acquisition status bar in the left part of the User preferences box.
This will show the status bar items (see Fig. 16.6).

Figure 16.6
3. Check the desired entries.
To switch the acquisition status bar on:
+ Click Spectrometer --> Acquisition Status Bar On/Off
or
+ Right-click in the status line at the bottom of the TOPSPIN window and
choose the popup menu Acquisition Status Bar On/Off
With the entries selected above, the right part of the status bar will look like

294
 Acquisition

this.

INDEX
DONE INDEX

Acquisition display (left side) see above.

Acquisition display (right side) see below.

The acquisition status bar not only displays information, it also allows you
to perform various actions, e.g.:
• Double-click the Time field to view detailed time and date information.
• Double-click the Lock field to open the lock display.
• Left-click the Spooler /queued /delayed /cron field to open the spooler
main window.
• Double-click on sample field to open BSMS control suite.
• Double-click on VTU opens the edte window
• Right-click the Fid Flash field to switch on/off FID flashing or to stop
the acquisition.
• For more information about peak power check (POWCHK) please
look up the Acquisition Reference Guide, Chapter 3 - Spectrometer
configuration commands. Within the command explanation of cf you
will find the functionality of POWCHK.

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Acquisition

• Right-click the Acquisition information field to open the following

popup menu:
INDEX
INDEX DONE

from this menu, you can start various acquisition commands.

• Right-click the VTU field to open the following popup menu:

Clicking Options will open the following dialog box:

Figure 16.7

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 Acquisition

• Right click the Lock field to opent the following popup menu:

INDEX
DONE INDEX

Figure 16.8
• Right click the Spooler field to open the following popup menu:

Figure 16.9
•

16.5 Command Queuing and Scheduling

TOPSPIN 2.0 and newer support command queuing (spooling) and schedul-
ing. Acquisition commands like zg, go, rga and atma are automatically
queued, if this feature is on (default off). This allows you, for example, to
enter multiple zg commands on different datasets. Automatic queuing can
be switched on as follows:
1. Click Options => Preferences
2. In the User Preferences dialog:
+ Enable Auto-Spooling under Administration Items
Processing commands can be queued with the command qu. For exam-
ple, the command sequence zg ; qu xfb on a 2D dataset, will start an

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Acquisition

acquisition and, when this has finished, process the data.

Acquisition and processing commands can be scheduled with the com-
INDEX
mand at. Enter help qu or help at, for more details on the respective
commands. INDEX DONE
Queued commands can be viewed in the Spooling field of the acquisition
status bar. Note that the spooling field must be activated in the User Pref-
erences window (command set).

16.6 Tuning and Matching the Probehead

Tuning and matching of conventional probeheads, (non ATM), is performed

with the wobble procedure. To start this:
1. Enter wobb on the command line.
The data window toolbar switches to the Acqu tab and the wobble win-
dow is opened (see Fig. 16.10).

Figure 16.10
The buttons of the wobble toolbar have the following functions:

298
 Acquisition

Change the number of wobble steps [wbst].

Change the wobble sweep width [wbsw].

INDEX
DONE
Change the wobble frequency.INDEX

Switch to the next channel/nucleus (if available).

Stop the wobble procedure.

2. Turn the tuning and matching knobs on the probehead until the wob-
ble curve is exactly in the middle and its minimum reaches the zero
line.
Automatic tuning and matching of ATM probeheads can be performed with
the command atma.

16.7 Locking

The lock display can be opened by clicking the button in the toolbar or
entering lockdisp on the command line. The lock display window will
appear (see Fig. 16.11).

299
Acquisition
:

INDEX
INDEX DONE

Figure 16.11
Here, you can view the lock signal, either during the lock-in procedure or,
as shown above, after lock-in has been successful. At the top of the lock
window the following buttons are available:
Open the user preferences window [set].
Toggle lock monitor mode.
Lock the magnetic field [lock].
Toggle lock display mode between single and dual color. Colors
can be set in the User preferences (command set).
Switch grid mode between both, vertical, horizontal and off.
Make the lock display external.
Put focus into TOPSPIN window.
Close the lock display window.
Note that an external lock display window is independent from the TOPSPIN
window. You can for example, minimize TOPSPIN while keeping the lock dis-
play open.
The lock display can also be opened by double-clicking the lock field in the

300
 Acquisition

acquisition status bar (see par. 16.4)

The lock process can be started by entering lock on the command line.
This command is described in the AcquisitionINDEX
Reference manual.
DONE INDEX
16.8 BSMS Control Panel

The BSMS control panel allows shimming, locking, sample handling and
helium level measurement. To open this panel:
+ Enter bsmsdisp on the command line
The BSMS Control Suite window will appear (see Fig. 16.12)

301
Acquisition

INDEX
INDEX DONE

Figure 16.12
The individual functions BSMS control panel are described in detail in the
Acquisition Reference manual.

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 Acquisition

16.9 Interactive Parameter Adjustment (GS)

INDEX
Several parameters can be adjusted interactively, while observing the
acquired FID. To start this:
DONE INDEX
+ Enter gs on the command line.
A split window will appear showing:
• the FID display (see Fig. 16.13)
• the GS parameter adjustment dialog (see Fig. 16.14)

Figure 16.13
The buttons of the FID display are the same as for the acquisition com-
mand zg (see paragraph Fig. 16.10).
The GS parameter adjustment dialog offers tabs at the top of the window to
select power, frequency, delay etc. The selected parameter is shown in the
middle of the window. The slider at the right of the window allows you to
change the selected parameter. The current value can be viewed and mod-
ified in the field below the slider. The sensitivity of the slider can be set in

303
Acquisition

INDEX
INDEX DONE

Figure 16.14
the field Sensitivity above the slider. The effect of the change can be viewed
in the FID display, the right part of the window. This can be manipulated
with the FID display buttons as described in chapter 16.10.

At the bottom of the window you find the following buttons:

• Save : Save the value of the current parameter.
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 Acquisition

• Save all : Save the values of all changed parameters.

• Restore : Restore the value of the current parameter.
INDEX
• Restore all : Restore the value of all changed parameters.
• Stop : Stop the acquisitionDONE
and quit the INDEX
GS window.

16.10 Running an Acquisition

A typical acquisition is performed as follows:

1. Create a new dataset.
a) Click File => New [new, Ctrl+n].

Figure 16.15
b) Specify the datapath variables name, expno, procno, dir and user,
select the desired Solvent and Experiment, enter the Title and click
OK.

305
Acquisition

The dataset will appear in the data field with no raw and no processed
data available.
2. Click theINDEX
AcquPars tab to display the acquisition parameters.
INDEX DONE

Figure 16.16
a) Optionally: click to show the pulse program parameters only.
b) Click the button to read the prosol parameters
or
Set the relevant parameters manually.
As an alternative to step 2, you can set the acquisition parameters in-
teractively in the GS window (see par. 16.9).
3. To start the acquisition:
• Click in the upper toolbar or enter zg on the command line.
The data window toolbar will automatically switch to the Acqu tab and
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 Acquisition

the FID display window will appear:

INDEX
DONE INDEX

Figure 16.17
The buttons in the toolbar have the following functions:
Show FID in shuffled mode.

Show FID in unshuffled mode, horizontally arranged.

Show FID in unshuffled mode, vertically arranged.

Show FID in unshuffled mode, interleaved.

Switch between FID and spectrum.

Stop the acquisition [stop].

Halt the acquisition [halt].

Clicking the button to switch to real time FT, turns the button

307
 green and opens two extra buttons:

Switch between FID and spectrum.

Real time FT settings.

Toggle calculation of peak with at 50%, 5.5% and 1.1% height

(Shown as status parameters).

Clicking the button opens the following dialog window:

The acquisition information will appear in the acquisition status bar at

the bottom of the TOPSPIN window, for example:

4. When the acquisition has finished:

+ Enter efp to process the FID.
The processed spectrum will be displayed in the data window that was
opened upon creating the dataset (see Fig. 16.18).
 Acquisition
:

INDEX
DONE INDEX

Figure 16.18
From here, the processed data can be analysed, printed and/or ar-
chived.

16.11 Shape tool

The Shape tool interface allows you to create/manipulate RF shapes and

waveformat.
To start the Shape Tool interface:
+ Click Spectrometer => Shape Tool
or enter stdisp on the command line.
The Shape Tool window will appear (see Fig. 16.19.). This consists of a
toolbar, a command line and a split pane with a data section at the right and
a parameter section at the left.
If Shape Tool is opened with a dataset the current dataset will be displayed
(see Fig. 16.20).

309
Acquisition

INDEX
INDEX DONE

Figure 16.19
By default, a 1000 point Gauss shape is displayed with Truncation level
1.0.
The TOPSPIN menu is changed showing the additional Shapes and Manipu-
late menus and the adjusted File, Analysis and Options menus.

Note that all functions of the interactive Shape Tool can also be performed
non-interactively with the TOPSPIN command st. This command must
entered with the appropriate arguments on the command line while the
associated dataset is displayed and selected.
A full description of the interactive and non-interactive Shapetool can be
found under:
+ Click Help => Manuals => [Acquisition Application Manuals] Sha-
petool

310
 Acquisition

Easy definition of Shape pulses

The usage of shaped pulses for the selective excitation is a nontrivial task
INDEX
that couples together all parameters such as the power level, pulse length
and the excited region.
DONE INDEX
TopSpin 2.1 and newer offers easy setup of selective experiments.
For usage Shape tool is typically started by the command stdisp on a fin-
ished 1D preparation experiment.
1. Define the excitation regions (also see Fig. 16.10)
a) creates a new region on the display.
The region is put in the middle of the currently visible area. By using
the mouse position and width can be changed.
b) deletes defined regions.
This command removes all regions. Single region can be removed
using the region pop up menu.

311
Acquisition

INDEX
INDEX DONE

Figure 16.20
2. Edit the excitation parameters
a) opens a region editor.
The region extent, the excitation type and the waveform assigned to

312
 Acquisition

the region can be edited. Selection "Use same shape for all regions"
button assigns the same rotation type and waveform to all regions.
INDEX
DONE INDEX

Figure 16.21
The setting of available waveforms depends on the selected rotation
type. The following itemization explains the rotation types:
• Excitation
Used for selective excitation, the magnetization rotates from Iz
to horizontal plane
• Inversion
Inverts the magnetization vector in the vertical plane (Iz to -Iz)
• Refocusing
Inverts the magnetization in the transversal plane (Iy to -Iy)
3. Calculate the pulse and display the excitation profile (see Fig. 16.22)
• The resulting waveform is generated and the excitation pro-
file is calculated.

313
Acquisition

INDEX
INDEX DONE

Figure 16.22
4. Store the results
• Pressing the save button writes the waveform on the disk an
saves the necessary parameters (pulse length, power level) to the
target data set. Used parameters are set in Options => Define Param-
eter Table. The target dataset may differ from the current data (e.g.
the spectrum on which Shape Tool started).
All regions and corresponding parameters (rotation type, waveform name)
are stored on the disk in the directory where the acquisition parameters
reside.
Following simple text format is used by the file "Region File":

314
 Acquisition

#Topspin excitation region list

#Mon Apr 30 08:59:43 CEST 2007 INDEX
#Used format:
# Left (ppm) Rigth (ppm) RotationType
DONE Waveform
INDEXRotationAngle
#Field RotationAngle is not mandatory
5.4886 5.2586 0 EBurp2 93.6
2.4758 2.1678 0 EBurp2 93.6

This region definition is stored automatically after each change. The defini-
tion is also read automatically when starting Shape Tool.
For further information about Shape Tool and its functionalities please refer
to the Shapetool Manual.

315
 Chapter 17
Configuration/Automation

17.1 NMR Superuser and NMR Administration password

During TOPSPIN installation, you are prompted to define:

• the username for the so called NMR Superuser. Under Windows this
must be the name of an existing user. Under Linux it can also be a
non-existing user, which is then automatically created by the installa-
tion program. After the installation, the NMR Superuser is the owner
of all TOPSPIN program files. Logging in as this user allows you to
remove these files, change file permissions etc. The name of the
NMRSUPERUSER will be stored in the file:
<tshome>/conf/nmrsuperuser
• the NMR Administration password to be used for TOPSPIN configura-
tion commands. This password can be freely chosen and is not con-
nected to any user. It is asked for by TOPSPIN commands like cf,
expinstall etc. The encrypted NMR Administration password is
stored in the file:
<tshome>/conf/nmradminpassword
Note that the NMR Superuser login password and the NMR Administra-
tion password have different purposes and are totally independent.
 Configuration/Automation

Changing one of them does not affect the other.

How to Change the NMR Administration Password

INDEX
The NMR Administration password can be changed as follows
DONE INDEX
Under Windows
1. Login as NMR Superuser or Administrator.
2. Open a Command Prompt.
3. Enter:
<x>\perl\bin\perl <x>\prog\bin\installnmr <x> <NMRSUPERUS-
ER>
where <x> in the TOPSPIN installation directory.
4. Enter the old password and new password as requested.

Under Linux
1. Login as NMR Superuser or root.
2. Open a Shell.
3. Enter:
<x>/prog/bin/installnmr <x> <NMRSUPERUSER>
where <x> in the TOPSPIN installation directory.
4. Enter the old password and new password as requested.
If you don’t know the old NMR Administration password, you can still define
a new one. In that case, you have to delete the file:
<x>\conf\nmradminpassword
before you run the installnmr script.

17.2 Configuration

The main configuration steps are performed by the commands cf and

expinstall. They can be started from the:
• Command line
• Options => Spectrometer tools menu
317
Configuration/Automation

• Spectrometer => Setup menu

However, the Spectrometer menu is only available after cf has been per-
INDEX Installation for spectrometer.
formed once, choosing
INDEX DONE
How to Perform a Default Configuration on a Datastation
A default configuration can be used on a datastation. It is automatically
performed (no cf required) during the installation of TOPSPIN on a new
computer, a new disk or in a new TOPSPIN installation directory. The default
configuration name is Bruker_default_av500 and corresponds to a Avance
500 MHz spectrometer.
For manual or interactive data processing, the automatic default configu-
ration is sufficient. If, however, you want to use AU programs, you must
execute expinstall once, selecting Installation for Datastation (Default).

How to Perform a Customized Configuration on a Datastation

If you want to configure your datastation according to a spectrometer other
than default, you must first copy the configuration directory:
<tshome>/conf/instr/<instrum>
from that spectrometer to the datastation. Here:
<tshome> is TOPSPIN home, the directory where TOPSPIN is installed.
Note that this can be different on the spectrometer than on the dat-
astation.
<instrum> is the configuration name.
After copying the configuration directory, you have to perform expin-
stall as follows:
• Click Spectrometer => Setup => Experiment installation or enter
expinstall on the command line
Follow the instructions on the screen. In successive dialog boxes
check/select the options below and click Next to continue:
• Installation for Datastation (Customize)
• High Resolution Systems
• The configuration name as it was copied from your spectrometer

318
 Configuration/Automation

• The items you want to install

• Select the desired printer and paper format for the parameter sets
INDEX
• The spectrometer frequency, acquisition mode and pre-scan-delay
DONE
In the last dialog box, click Finish. INDEX
The installation of the selected items, will
start now. Wait until this process has finished.
For more details on expinstall, please refer to the description of this
command in the Acquisition Reference manual.

17.3 Parameter set conversion

The command paracon changes the basic frequency in parameter sets.

This allows you to use parameter sets which were created on a spectrome-
ter with a different frequency. It opens dialog box shown in Fig. 17.1
Here you can setup a list of available parameter sets. You can select
Bruker and/or User defined parameter sets and use a match string. The
matching parameter sets appear in the right part of the dialog box. To start
the conversion, select one or more parameter sets and click OK.

17.4 Automation

How to Install AU Programs

To install AU programs, you have to run the command expinstall (see
chapter 17.2).

How to Open the AU Program Dialog Box

To get a list of all AU programs, enter edau or:
1. Click File => Run...
2. Click Execute an AU program in the appearing dialog box.
3. Click OK
A dialog box showing either the Bruker defined or User defined AU pro-
grams. Fig. 17.2 shows a dialog box with two User defined AU programs.

319
Configuration/Automation

INDEX
INDEX DONE

Figure 17.1

320
 Configuration/Automation

INDEX
DONE INDEX

Figure 17.2 List with two User defined AU programs

Note that Bruker AU programs are only shown if the command expin-
stall has been executed once, after the installation of TOPSPIN.

How to Switch to the List of User defined AU Programs

+ Click Options => Preferences => direcotries => Manage Source Directories
in the menu bar to open the AU program dialog box

How to Switch to the List of Bruker defined AU Programs

+ Click Options => Preferences => Directories => Manage Source Directo-
ries in the menu bar to open the AU program dialog box

How to Define the AU Programs Source Directory

1. Click Options => Manage Source Directories in the AU program dialog
box
2. In the field AU Programs: Add or modify AU program source directo-
ries

How to Create an AU Program

1. Click File => New in the AU program dialog box.
2. Enter the AU program name in the field New name and click OK.
3. Enter the AU program lines in the edit field of the appearing dialog
box.

321
Configuration/Automation

4. Click Compile to compile the AU program.

5. Click File => Save to store the AU program.
INDEX
6. Click File => Close to close the editor.
Alternatively,INDEX
you can enterDONE
edau <name> on the command line to create
the AU program <name>.

How to Edit an Existing AU Program

1. Double-click the AU program name in the AU program dialog box
or
Click the Edit button to edit the highlighted AU program.
2. Modify the AU program according to you wishes.
3. Click Save to store the AU program under the name shown in the title
bar.
4. You will be prompted to compile the AU program: click OK.
Alternatively, you can enter edau <name> on the command line to edit
the AU program <name>.

How to Execute an AU Program

1. Select the AU program in the AU program dialog box.
2. Click the Execute button.
Alternatively, you can enter <name> or xau <name> on the command
line to execute the AU program <name>.
If the AU program has not been compiled, compilation is automatically per-
formed before the execution starts.

How to Delete an AU Program

1. Select the AU program in the AU program dialog box.
2. Click File => Delete or click the Delete button.

How to Show Comments (short descriptions) in the AU Program

List
To switch on/off the comments in the AU program list:

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 Configuration/Automation

+ in the AU program dialog box: Click Options and select the entry
Comment.
INDEX which is also part of
A comment is a short description of the AU program
the AU program header. DONE INDEX

323
Regulatory Compliance

Chapter 18
INDEX

Regulatory
INDEX
Compliance
DONE

TopSpin complies with the FDA 21 CFR Part 11 regulations. Please read
the , accessible under Help => Manuals => [Good Laboratory Practice] 21
CFR Part 11 compliance. This chapter describes the respective functionali-
ties provided by TOPSPIN in detail.

18.1 Audit Trails

A TOPSPIN data set consists of acquisition (= raw) data and processed data.
These are stored in a directory tree with the following structure:
<dir>\data\<user>\nmr\<name>\<expno>\pdata\<procno>
The acquisition data are stored in the expno subdirectory and the proc-
essed data are stored in the procno subdirectory.

18.1.1 The raw data audit trail

Each expno sub-directory contains a text file audita.txt, the audit trail of the
raw data. This reflects the acquisition state of the raw data, and contains a
checksum for the file itself (audita.txt) and one for the raw data file (fid or
ser). The latter checksum links the audit file with the raw data. By means of
the checksums, any illegal manipulation of the audit file or the raw data file
can be detected, using the TOPSPIN commands audit or auditcheck.

324
 Regulatory Compliance

Whenever an acquisition is started, the possibly existing audit file is over-

written by a new one, belonging to the new raw data file. By default, the
user is warned when the current dataset already
INDEXcontains raw data, thus
preventing accidental overwriting (The option “Override existing fid without
DONE => Preferences
inquiry” is, by default, off (see Options INDEX => Acquisition).

18.1.2 The processed data audit trail

Each procno sub-directory contains a text file auditp.txt, the audit trail
of the processed data. It reflects the processing state of the processed data
and contains a checksum for the file itself (auditp.txt), and a checksum
for the real processed data files (1r, 2rr, 3rrr, ...). The latter checksum
links the audit file with the processed data. By means of the checksums,
any illegal manipulation of the audit file or the processed data file can be
detected, using the TOPSPIN commands audit or auditcheck. Whenever
a processing command is performed, the current audit file is updated with
this command and its associated parameters. When processing starts from
scratch (from a raw data file), the existing audit file is overwritten. As such,
the processed data can always be regenerated from raw data by applying
the commands and parameters listed in the audit trail.
If the laboratory management does not allow data files or audit trails to be
deleted, a respective saving procedure must be established. For this pur-
pose, TOPSPIN provides data copying commands, which may be called in a
user defined macro or AU program, before a new acquisition or processing
starts.

18.1.3 Viewing audit trails

Since audit trails are regular ASCII text files, they can be viewed or printed
with any text editor, outside of TOPSPIN. Within TOPSPIN, you can use the
command audit for this purpose. This opens the dialog box show in Fig.
18.1.

325
Regulatory Compliance

INDEX
INDEX DONE

Figure 18.1
The first two entries allow you to view the audit trail files. The third entry
performs an audit trail check, i.e. a data consistency check. If both raw and
processed data are consistent, you will get the message shown in Fig.
18.2.

Figure 18.2
If the data have been manipulated outside of TOPSPIN, e.g. with third party
software, the checksum will be inconsistent. Fig. 18.3 shows the message

326
 Regulatory Compliance

for inconsistent processed data.

INDEX
DONE INDEX

Figure 18.3
The fourth and fifth entry in Fig. 18.1 allow you to add a comment to the
raw or processed audit trail files, respectively.

18.1.4 Audit trail contents

The contents of an audit file is grouped in the following way:
(NUMBER, WHEN, WHO, WHERE, PROCESS, VERSION, WHAT)
These entries have the following meaning:
NUMBER
Running number of an entry, starting with 1.
WHEN
Date of the entry, e.g. <2004-03-30 10:55:36.171 +0200>, where the
last value represents the offset in hours to Universal Time (UTC).
WHO
The user logged in, at the time the entry was generated. It has one of
the two forms: <user1> or <user1/user2>. <user1> is always the
user who is logged into the operating system (Windows or Linux user),
and who started TOPSPIN. <user2> only appears, if the NMR adminis-
trator has setup an internal TOPSPIN user administration, and the op-

327
Regulatory Compliance

tion Enforce "login" for working with TOPSPIN in the User

Administration dialog is enabled (see below, command uadmin). In
this caseINDEX
<user2> is the current internal TOPSPIN user.
WHERE INDEX DONE
The network name of the current computer, e.g. <EOS2>.
PROCESS
The TOPSPIN process (module) which performed the acquisition or
processing.
VERSION
The TopSpin version which performed the acquisition or orocessing.
WHAT
The type of acquisition or data manipulation performed.
Note that if only the entries NUMBER, WHEN, WHO, WHERE, WHAT are
present, then the audit trail was created by TOPSPIN 1.3 or older.

18.1.5 Adding a comment to an audit trail

Audit trail entries are normally generated automatically by a respective
acquisition or processing command. However, a user can also add a com-
ment manually, using the audit command. This will generate a regular
entry, the comment will appear under the WHAT section and is preceded
by the tag “user comment:”.
You may also add a comment to the raw data or processed data audit trail
from an AU program, using the macros AUDITCOMMENTA(comment) or
AUDITCOMMENTP(comment), respectively. Alternatively, you can store
the comment in a file auditc.txt in the expno or procno directory, and use
the macros GDCHECK_RAW or GDCHECK

18.1.6 Auditing user-defined data manipulations

When manipulating a data file with a user-defined algorithm, e.g. by means
of an AU program or external program, the data file and the respective
audit trail become inconsistent (detectable with the command auditch-
eck), and the data set is no longer compatible with regulations. In order to

328
 solve this problem, TOPSPIN provides a function CheckSumFile, which adds
the correct data checksum to the audit trails, and a function AuditAppend
for additional text (an alternative to the comment function described
above). These functions are described in the AU manual which can be
opened by clicking Help => Manuals => [Programming Manuals] AU pro-
gramming.

18.1.7 Audit Trails in JCAMP-DX and ZIP archives

The TOPSPIN commands tojdx and tozip allow you to store a data set
into a single file in the internationally standardized ASCII-type JCAMP-DX
format or in the well-known ZIP format, respectively. Both storage formats
retain the audit trails. When unpacking such files with fromjdx or
fromzip, respectively, the original data set in standard Bruker format is
restored. The command auditcheck may be used to check whether the
data are still consistent. If, for example, JCAMP-DX or ZIP file have been
manipulated, the data might not be consistent.

18.2 Electronic Signatures

18.2.1 Signing a data set

The command esign adds an electronic signature to the raw data or to the
processed data of a data set. It opens a dialog where you can select the
data component to be signed, the signature meaning and, optionally, add a
comment. esign requires that the NMR administrator has set up a list of
users who are allowed to sign a data set, along with definitions of signature
meanings (e.g. review, approval). See below for details, command uad-
min.
 Figure 18.4

18.2.2 Structure of a signature

In TOPSPIN, an electronic signature is realized as a special entry appended
to the audit trail of the raw or processed data. It is therefore linked with the
data and protected against manipulations just like any other audit trail
entry. Signatures can be viewed with the command audit. An electronic
signature consists of the following items:
USER ID
The ID of the user logged in at the time esign was executed. This is
either the user who was logged into the operating system (Windows
or Linux user), and who started TOPSPIN, or the TOPSPIN internal user.
Which of these two modes is applied depends on how the NMR ad-
ministrator configured TOPSPIN: If the option Enforce "login" for work-
ing with TOPSPIN is disabled (see below, command uadmin), the first
mode is active, otherwise the second.
What is the difference between the modes?
• In the first case, the System User (= Windows or Linux user)
who started TOPSPIN signs the data set. Prior to signing, esign
requests this user's password, which is administrated by the
operating system (OS). No internal TOPSPIN user management
 Regulatory Compliance

plays a role. Advantage: This mode is entirely OS compliant.

Disadvantages: a) TOPSPIN termination/restart is required when
a different user wants to sign data (alternatively several
INDEX
licenses would admit simultaneous TOPSPIN sessions). b) All
TOPSPIN users mustDONE
have an OS INDEX
login.
• In the second case, any TOPSPIN internal user who is enabled
by the NMR administrator (with uadmin) may sign. Advantage:
Convenient and easy usage. Disadvantage: TOPSPIN internal
user management is required (internal users and their pass-
words).
USER NAME
The complete name of the signer as specified by the NMR administra-
tor during user administration (command uadmin).
SIGNATURE MEANING
The meaning of a signature, e.g. Review or Approval. A user may only
select meanings that were assigned to him by the NMR administrator
during user administration.
SIGNATURE COMMENT
Any text.

18.2.3 Displaying the electronic signature in the data window

The electronic signature can be displayed in the data window by setting the
corresponding display component. To do that:
1. Right-click in the data window and choose Display Properties...
[.dopt].
2. Check Electronic Signature in the appearing dialog box and click OK.
The electronic signature will appear, at the upper left corner, below the
title.

18.2.4 Plotting the electronic signature

When plotting a dataset using TOPSPIN's plot editor (commands plot and
autoplot), an electronic signature is automatically plotted (unless this
feature is disabled), if the last entry of the audit trail of the data to be plot-

331
Regulatory Compliance

ted is an electronic signature. This ensures that after signing no more data
manipulations have been performed.
INDEX
18.2.5 Multiple signatures
INDEX DONE
The command esign may be applied several times to a data set, for
instance if two persons (say an operator and an administrator) must sign in
accordance with company regulations.

18.2.6 Validity and security of signatures

TOPSPIN electronic signatures of data sets must not be confused with digital
signatures as defined in applicable law. Digital signature laws are usually
country dependent. They require the administration of passwords (more
general: electronic keys which authenticate the owner of the document) to
be performed by authorized trust centers. In contrast, TOPSPIN uses OS-
encrypted passwords or internal user passwords encrypted by TOPSPIN
itself.
For this reason, a Standard Operating Procedure (SOP) of the company or
institution that wishes to apply TOPSPIN signatures must exist defining the
role of TOPSPIN signatures.
For this reason, companies and institutions that want to apply TOPSPIN sig-
natures must have a Standard Operating Procedure (SOP), which defines
the role of these signatures.
Note that digital signatures complying with respective laws requires special
software, and the involvement of trust centers. Bruker refers to the respec-
tive commercial software for this purpose.

18.3 Password Controlled Login Identification

18.3.1 Definition of an internal user

In TOPSPIN, the NMR administrator may set up a list of internal TOPSPIN
users. An internal user need not have a user account for the operating sys-
tem and is only known to TOPSPIN. Such a user is characterized by the fol-
lowing items:

332
 Regulatory Compliance

USER ID
A short unique string of characters identifying a user (e.g. guest)
INDEX
USER NAME
DONE INDEX
A long string of characters, usually the full name of a user (e.g. Franz
J. Maier)
SIGNATURE MEANINGS
A list of items separated by comma (e.g. Approval, Review), an empty
string or the special string “-NONE-”. In the latter two cases, this user
cannot electronically sign data. In all other cases, the user is allowed to
sign. The esign dialog allows the user to select one of the items to
specify the meaning of the signature.
PASSWORD
A password for this user, required for using TOPSPIN and for applying
an electronic signature.

18.3.2 How to set up internal users

In order to define or modify the list of internal users:
+ enter the command uadmin
or
+ Click Options => Preferences => Administration items
Click the Change button to the right of the object Setup users for Top-
Spin-internal login/logoff and esign.
You will be prompted for the NMR administrator password. A dialog will
appear.

333
Regulatory Compliance

INDEX
INDEX DONE

Figure 18.5
where you can add, remove and/or modify users

18.3.3 How to change the internal user password

To change the password of the internal user:
+ enter chpwd on the command line
or
+ Click Options => Administration => Change internal user password
and enter the new password twice, as requested.

18.3.4 Login/Logoff
The uadmin command allows the administrator to make a TOPSPIN internal
user mandatory. To do that, enable Enforce "login" for working with Top-
Spin at the top of the dialog, click Save+Close and restart TOPSPIN. After the
restart, a login prompt will be displayed and TOPSPIN cannot be used with-

334
 Regulatory Compliance

out entering an internal user and his password.

To log off the internal user:
INDEX
+ Enter logoff on the command line
DONE INDEX
or
+ Click Options => Administration => Log off
and enter the user name and password as requested.
If TOPSPIN internal user is not mandatory, i.e. the entry Enforce "login" for
working with TopSpin is disabled, you are not prompted to login after TOP-
SPIN startup. You can, however, still login as internal user with the com-
mand login.

18.3.5 Locking TOPSPIN's Graphical User Interface

TOPSPIN can be locked, such that it does no longer accept user input via
mouse or keyboard. To do that:
+ enter lockgui on the command line
or
+ Click Options => Administration => Lock TopSpin user interface
A window will appear (see Fig. 18.6) indicating the locked status and offer-

335
Regulatory Compliance

ing buttons to unlock.

INDEX
INDEX DONE

Figure 18.6
Only the current user or the NMR Administrator can unlock the user inter-
face. While TOPSPIN is locked, all background activities such as data acqui-
sition and processing continue.
For safety reasons TOPSPIN can be forced to execute lockgui automati-
cally when no commands from the command line, menus or toolbar buttons
have been entered for a certain period of time (for instance because the
current user has left). In order to enable automatic locking
1. Click Options => Preferences [set]
2. Click Administration Items in the left part of the dialog box.
3. Click the Change button to the right of the object Automatic locking
of TopSpin when idle time exceeded.
4. Enter the maximum allowed idle time (in minutes) in the dialog and
click OK.

336
 Regulatory Compliance

INDEX
DONE INDEX

337
Remote Control

Chapter 19
INDEX

Remote
INDEX
Control
DONE

19.1 Remote control

TOPSPIN supports remote control. This means, for example, that you can
control your spectrometer from any PC in the laboratory network or, over
the internet, from your PC at home. Using your local TOPSPIN interface, you
have access to the remote data directories and remotely running TOPSPIN
commands. Furthermore, in TOPSPIN 1.3 and newer, ICON-NMR is web-ena-
bled which means it can be controlled from any web browser which is net-
worked to the spectrometer. Note that remote access is operating system
independent.

19.2 How to Establish a Remote Connection from your PC

In order to establish a remote connection, you have to perform a few steps,

both on the local and on the remote system. Note that the local system is
the computer you are sitting at, and the remote system is the computer you
are connecting to. Up to 5 local systems can connect to TOPSPIN on a
remote system.

338
19.2.1 Setup the remote system
The remote system must be enabled for remote access and, furthermore,
individual data directories must be exported.

Enable the system for network access

1. Log in on the remote system
2. Start TOPSPIN
3. Click Options --> Preferences [set]
4. Click Miscellaneous in the left part of the dialog box.
5. Click the Change button to the right of the object Configure remote
access.
6. Enter the Administration password as requested
7. In the appearing dialog box (see Fig. 19.1):
a) Click Remote Access Enabled
b) Click Add and enter the data directories that you want to export
for remote access, e.g.: C:\bio and click OK.
c) Click OK to close the dialog.
 Figure 19.1
8. Click OK to save and close the preferences dialog.
9. Restart TOPSPIN.
A list of exported directories is stored the file:
<tshome>/prog/server/export.conf
Now a running TOPSPIN on this system can be accessed from any com-
puter in the network.

Identify the port number

To identify the TCP/IP port number used by TOPSPIN:
 Remote Control

1. Start TOPSPIN
2. Enter hist
3. Look for the line
INDEX
DONE.... use host=<xxxx>.,
To connect to this TOPSPIN INDEX port=<yyyy>
in the upper part of the dialog window. The number at the end of
this line (<yyyy) is the desired port number, which must be used to
set up the local system (see chapter 19.2.2). By default, this is port
number 5500. Only if this port is already used by a program other
than TOPSPIN, a different port is used.

19.2.2 Setup the local system

Define the remote system

1. Log in on the local system
2. Start TOPSPIN
3. Click Options --> Preferences [set].
4. Click Miscellaneous in the left part of the dialog box.
5. Click the Change button at the entry Setup remote systems. In the
appearing dialog (see Fig. 19.2),

Figure 19.2
enter the following information:
• Server ID: an arbitrary name for the remote system
• Hostname or address: the hostname or IP address of the remote
host
• TCP/IP port number of the remote TOPSPIN as identified in chapter
19.2.1.

341
Remote Control

6. Click Add to add the remote host.

7. Click OK to save the changes and close the dialog.
INDEX
Note that you can define multiple remote systems, for example different
spectrometers in your laboratory.
INDEX DONE
Connect to the remote system
1. Click Options => Remote connection...
2. Select the desired Remote system from the appearing dialog box and
click OK.

Figure 19.3
Now you are prompted for a user and password (both case sensi-
tive) on the remote computer.

342
 Remote Control

INDEX
DONE INDEX

Figure 19.4
The TOPSPIN browser will show the exported data directory trees of the
remote system. You are now ready to acquire, process or analyse remote
data.

19.2.3 Setup the firewall

A remote system in a network can be protected by a firewall. Any firewall
between the local and remote TOPSPIN must be configured for TOPSPIN
remote access.
If the remote PC is running under Windows XP with Service Pack 2 or
higher, the Windows Firewall is, by default, installed and running. Consider
the following possibilities:
Firewall on PC with Windows XP-SP2 or higher, Topspin installed
If TOPSPIN is installed, the firewall is probably configured for TOPSPIN
remote access 1. If it is not or you are not sure, you can configure it as
follows:
1. Click Start => Programs => Bruker TOPSPIN =>

1. During TOPSPIN installation, you can choose to automatically configure the firewall
or not. PC’s delivered by Bruker Germany, always have the firewall configured for TOP-
SPIN.

343
Remote Control

TOPSPIN <version> => Bruker Utilities

2. Click Miscellaneous
INDEX
3. Double click Command Prompt
4. In theINDEX DONE
Command Prompt window, enter:
cd prog\bin\utilities\Miscellaneous\setfirewall.cmd auto

Firewall on PC with Windows XP-SP2, no Topspin installed

Configure the firewall as described in the Installation Guide for Win-
dows XP.
On all other systems, the firewall must be configured manually by the net-
work administrator. To do that view the file:
<tshome>/prog/server/corba.conf
and open the ports specified here, incremented by 50.
For more information, please refer to the installation guides for Windows
or Linux or inspect the contents of the file corba.conf.
Note that the firewall must be configured for TOPSPIN:
• spectrometer control
• remote access
TOPSPIN can be used for processing/analysis on a local datastation, even if
it is not registered on the firewall. However, you will get a few Security Alert
messages during startup.

19.3 How to Make a Remote Connection without a Local

License

TOPSPIN requires a license to operate on your local computer. However,

you can make a remote connection without a local license.
To do this, you have to start TOPSPIN as follows:
1. Open a Windows Command Prompt or Linux Shell.
2. Go to the TOPSPIN installation directory.
3. Enter topspin -client

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 Remote Control

4. TOPSPIN will start up and show an empty data field but no browser.
Before startup you will get the error message: "The program failed to
communicate with local ....". Just click OKINDEX
to continue.
5. Click Options => Remote connection...
DONE INDEX
and establish a remote connection as described in chapter 19.2.
Note that without a local license:
• TOPSPIN on the remote system must run with a licence.
• Local data cannot be accessed.

19.4 Security of Remote Connections

All data transferred during a remote control session is, by default,

encrypted. This ensures that nobody can see data or commands by
observing and recording your network traffic. TOPSPIN uses the Secure
Socket Layer (SSL) technology for encryption, which is also used for
secure web sites. SSL needs digital certificates on both sides of a connec-
tion to achieve a valid authentication. After a TOPSPIN installation, default
certificate files are provided to secured connections. There is a chance,
however small, such connections are attacked by a malicious person who
also has the same default certificate files. If, for this reason, you want to
create your own set of certificate files, you can do this by executing a script
that is installed in <tshome>/prog/server/make_new_certificates
and follow the instructions given there. To start a remote connection, the
new certificate files must be installed on BOTH machines.

19.5 How to Access ICON-NMR from a Remote Web Browser

In TOPSPIN 1.3 and newer, ICON-NMR is web-enabled. The standard Bruker

Automation Software now provides a built-in website which can be acti-
vated to allow remote access to ICON-NMR from any web browser which is
networked to the spectrometer workstation. Experiments may be can-
celled/submitted, the run may be paused or halted and spectra in PDF for-
mat are available from the browser window. No additional software apart
from ICON-NMR and Webbrowser is required and configuration is per-
formed via the standard ICON-NMR Configuration window. For security a
SSL/HTTPS connection is supported. Pocket PC Internet Explorer is also
345
Remote Control

supported for full spectrometer control via Windows Mobile 2003 (TM) or
equivalent. PDF files of spectra may also be viewed on this platform mak-
ing the mobileINDEX
pocket spectrometer a reality.
The configuration
INDEX of ICON-NMR web interface is described in the ICON-NMR
DONE
manual, accessible Help => Manuals => [Automation and Plotting] Icon-
Nmr Automation Interface. Note that ICON-NMR remote control does not
require and is fully independent of TOPSPIN remote control.

19.6 How to limit IP-Addresses for Remote Control

TopSpin offers the possibility of limiting the IP Addresses for remote con-
trol, in order to permit more security for all spectrometer control. This fea-
ture is especially useful for big companies and concerns that work with
different NMR spectrometers and many members of staff, respectively
many PCs.
Please note that the functionality of limiting IP Addresses is a feature for
technical experienced users and IT-Experts, therefore the following
description is given by an example.
By default remote connection is disabled. You have to enable remote con-
trol first. For enabling remote control and limiting the IP Addresses the fol-
lowing file has to be edited:
<tshome>/prog/server/omniorb.conf
In this file you have to search for the following section which enables every
IP-Address for remote connection:
"To enable the Remote Connection feature using SSL en-
cryption the '#' character at the beginning of the next
line should be removed:
#serverTransportRule = 0.0.0.0/0.0.0.0 ssl".
After removing the ’#’ an unlimited number of IP-Addresses may use
remote control. The IP-Address can be limited as it is shown in the follow-
ing example by editing the respective IP-Address line:
serverTransportRule = 149.236.14.0/255.255.255.0 ssl
After editing the IP Addresses belonging to your special requirements,

346
 Remote Control

every IP Address of the permitted subnet may use the feature remote con-
trol and all other addresses have no longer permission to connect remotely.
INDEX
DONE INDEX

347
User Preferences

Chapter 20
INDEX

User Preferences
INDEX DONE

20.1 User Preferences

TOPSPIN can be tailored to your preference in many respects. This ranges

from startup options to spectrum objects, menu settings, remote connec-
tions etc. Every standard user can create his/her own set of preferences.
To set user preferences:
• Click Options => Preferences [set]
A dialog box will appear with, at the left side, the categories that can be tai-

348
 User Preferences

lored (see Fig. 20.1)

INDEX
DONE INDEX

Figure 20.1
Click the cathegory of which you want to view/change certain objects. It will
become highlighted and the corresponding objects will be displayed at the
right part of the dialog box. For example, if you click Spectrum, the spectrum
objects will appear at the top of the dialog box. The rest of this paragraph
will describe some examples of setting various user preferences.

20.1.1 Define User Preferences Location for all Users

User Preferences are, by default, stored in the current users home direc-
tory:
<userhome>/.topspin-<hostname>
During the first TOPSPIN session, files with default settings are created
there. They can then be modified with the set command and used in later
sessions.
You can, however, also store user preferences at one central location,

349
User Preferences

which are then used by all users. This location can even be a remote drive
allowing you to use the same preferences on all computers in the network.
To do that: INDEX
1. Make a backup
INDEXcopy ofDONE
the file <tshome>/javaenv.cmd.
2. Open the file <tshome>/javaenv.cmd using a text editor.
3. Locate the line "set SYSTEM_PROPS=-DXWIN-
NMRHOME="%XWINNMRHOME%" -DCOMPUTERNAME=%COM-
PUTE........" near the beginning of the file.
4. Append a white space character and then:
-DPROPDIR=<dir>
to the end of this line, where <dir> is the definition of the storage
directory, consisting of one or more parts (see below)
5. Close the editor.
The definition of the storage directory for User Preferences can take three
forms:
-DPROPDIR=<mydir>
Stores the user properties in <mydir>/prop
Example: -DPROPDIR="/x y z" 1
-DPROPDIR=<mydir> USER 2
Stores the user properties in <mydir>/<login id>/prop, where <login
id> is the id under which the user is logged into the operating system
Example: -DPROPDIR="/x y z USER" 1
-DPROPDIR=CURDIR
Stores the user properties in <tshome>/prog/curdir/<login id>/prop,
where <login id> is the id under which the user logged into the operat-
ing system
Please note that the specified directory must writable for all TOPSPIN users.

1. The double quotes are only required if the directory contains white spaces
2. Specify exactly 1 space between the pathname and the string USER

350
 User Preferences

20.1.2 TOPSPIN Startup Actions

How to Open the Last Used Dataset onINDEX

Startup
1. Click Options => Preferences [set].
DONE INDEX
2. Check, under Administration items, the option :
Auto-open last used data set when restarting TopSpin

How to Define the Startup Actions

TOPSPIN allows you to define any commands to be executed automatically
after startup. To do that:
1. Click Options => Administration => Edit Startup File.
2. Enter the desired startup command(s), in the appearing editor, for
example:
re exam1d_13C 1 1 c:\\bio guest
efp
apk
abs
The above lines would cause TOPSPIN to display the dataset:
C:/bio/data/guest/nmr/exam1d_13C/1/pdata/1
and execute the command efp, apk and abs on it.
Note that you can use a single forward slash (/) or a double backslash (\\)
as path separator.
Note that in TOPSPIN 2.1 and newer, the file autostart.mac is a regular
Topspin macro. In older versions, however, the file autostart.prop
was used with a different format.

How to Define Auto-Termination after Idle Time

TOPSPIN can be configured to be terminated after a user specified idle time.
To do that:
1. Click Options => Preferences [set].
2. Click the Change button to the right of the object

351
User Preferences

Automatic termination of TOPSPIN when idle time has exceeded

enter the NMR Administration password as requested and enter
INDEXof minutes of allowed idle time.
the number
3. Click INDEX
OK to close theDONE
dialog, click OK to close the Preferences dia-
log.
4. Restart TOPSPIN to activate the change.
If the user does not execute any commands (from the command line,
menu or toolbar buttons), a dialog will appear with an OK button (to ter-
minate immediately) and/or Cancel button (to continue).
Automatic termination frees the license used by this TOPSPIN in-
stance for other users. This solves the problem of users leaving
TOPSPIN open and blocking a floating license although they do not
currently use it.

How to Define Auto-Locking after Idle Time

TOPSPIN can be configured to lock the interface after a user specified idle
time. To do that:
1. Click Options => Preferences [set].
2. Click the Change button to the right of the object
Automatic locking of TOPSPIN when idle time has exceeded
enter the NMR Administration password as requested and enter
the number of minutes of allowed idle time.
3. Click OK to close the dialog, click OK to close the Preferences dia-
log.
If the user does not execute any commands (from the command line,
menu or toobarl buttons), the TOPSPIN interface will be locked (see Fig.

352
 User Preferences

20.2).

INDEX
DONE INDEX

Figure 20.2

How to Change the Preferred Editor

You can choose your preferred editor as it is used by commands like
edau, edpul, edcpd etc. To do that:
1. Click Options => Preferences [set].
2. Click Miscellaneous in the left part of the dialog box.
3. Click the Change button to the right of the object Preferred text edi-
tor
enter the desired Editor and its path. For example for Wordpad
under Windows 2000/XP, this would look like:

353
User Preferences

4. Click Save to save the changes.

If no editor is specified here, the TOPSPIN internal editor is used. It the file
being editedINDEX
is read-only, the TOPSPIN internal viewer is used.
INDEX DONE
How to Configure the Tab Bar
The default Tab bar at the top of the data window consist of Tabs to switch
between various dataset objects like Spectrum, Parameters, Title, etc. You
can, however, configure the Tab bar to contain Tabs for interactive data
manipulation like phase correction, integration etc. These Tabs have the
same function as the corresponding buttons in the upper tool bar (see
chapter 2 and 14) but are easier to access. You can configure the Tab bar
as follows:
1. Click Options => Preferences
2. Click Spectrum in the left part of the User preferences box.
3. Click the Change button to the right of the object Tabbed pane layout.
4. Check the desired Tabs, uncheck the others.
5. Click OK
+ Note that you can change the relative positions of a Tab by selecting it
and then clicking the Up or Down button.

How to Configure the Right-click Menu Function

Right-clicking a pull-down or popup menu, can perform various actions.
This can be configured as follows:
1. Right-click an empty part of the menubar and choose Define Right-

354
 User Preferences

Click Action from the popup menu.

INDEX
DONE INDEX

Figure 20.3
2. In the appearing dialog (see Fig. 20.3), select the desired action.
3. Click OK

20.1.3 Changing Colors

How to Change Colors of Data Objects on the Screen

The color of various objects in a data window on the screen, like 1st, 2nd
and 3rd spectrum, axis, parameters etc. can be changed. To set these
colors:
1. Click Options ’ Preferences [set].
2. Click Spectrum in the left part of the User preferences box.
3. Click the Change button to the right of the object you want to change
e.g.:

4. Select the desired color in the appearing dialog box and click OK
5. Click Apply

How to Change Colors of Data Objects on the Printer

The color of data objects on the printer is independent from the color of the

355
User Preferences

corresponding object on the screen. To set print colors:

1. Click Options ’ Preferences [set].
INDEX
2. Click Printer in the left part of the User Preferences box.
3. Click theINDEX
Change buttonDONE
to the right of the object you want to change,
e.g.:

4. Select the desired color in the appearing dialog box and click OK
5. Click Apply

How to Change Colors of the Lock Display

The colors of lock display objects can be changed as follows:
1. Click Options => Preferences [set].
2. Click Lock display in the left part of the User preferences box.
3. Click the Change button to the right of the object you want to change,
e.g.:

4. Select the desired color in the appearing dialog box and click OK
5. Click Apply

How to Create a New Data Window Color Scheme

To create a new data window color scheme:
1. Click Options => Preferences [set].
2. Change any color of the objects Spectrum, Spectrum title, Spectrum cur-
sor or Spectrum parameters.
3. Click Apply
4. Click Spectrum in the left part of the User preferences box.
5. Click the button Save as... to the right of the object:
Save spectral window colors as a new color scheme
and enter a new name in the appearing dialog box.
356
 User Preferences

6. Click OK

How to Read a Different Data Window INDEX

Color Scheme
1. Click Options => Preferences [set].
DONE INDEX
2. Click Spectrum in the left part of the User preferences box.
3. Click in the list box to the right of the object:
Change spectral window color scheme
and select an element from the appearing list.
4. Click OK
TOPSPIN is delivered wit two colors schemes:
• light (default): a white background with black axes
• dark: a dark blue background with a white axes

How to Change Peak and Integral table Colour/Spacings

1. Click Options => Preferences [set].
2. Click Miscellaneous in the left part of the User preferences box.
3. Click in the list box to the right of the object:
Table colors (see Fig. 20.4)
for simple tables like peaks, solvents, nuclei tables
Tree table colors

357
User Preferences

for nested lists like the integral table.

INDEX
INDEX DONE

Figure 20.4
Set the desired colours and spacings.
4. Click OK
Note that table colours and spacings can also be changed from a table. To
do that, right-click any table entry and choose Table properties...

358
 User Preferences

20.1.4 Changing Lines

How to Create Thick Lines on the Screen

INDEX
To create thick (double width) lines for high resolution display or screen-
DONE INDEX
dumps:
1. Click Options => Preferences [set].
2. Click Spectrum in the left part of the dialog box.
3. Enable the entry Use thick lines
4. Click OK

How to Create Thick Lines on the Printer

To create thick (double width) lines for high resolution display or screen-
dumps:
1. Click Options => Preferences [set].
2. Click Printer in the left part of the dialog box.
3. Enable the entry Use thick lines
4. Click OK

20.1.5 Changing Fonts

How to Change All Fonts of the Topspin Interface

1. Click Options => Preferences [set].
2. Click Fonts/Dialogs/Icons in the left part of the dialog box.
3. Set the entry Change size fonts listed above by .... points
You can enter a positive or negative number.

359
User Preferences

Fig. 20.5 shows an example of increasing the font sizes by 4 points.

INDEX
INDEX DONE

Figure 20.5
4. Click OK to store the new value.

Figure 20.6
Fig. 20.6 shows the same part of the Preferences dialog box after the
change of fonts. Note that:
• The value of all font entries has been increased by 4.
• The font of the dialog box itself is larger.
• The change size has been reset to 0.

How to Change the Font of the TOPSPIN menu

To change the font of the TOPSPIN menu:
1. Click Options => Preferences [set].

360
 User Preferences

2. Click Fonts/Dialogs/Icons in the left part of the dialog box.

3. Click the Change button to the right of the Menu font object:
INDEX
DONE INDEX

4. Select the desired name, style and/or size in the appearing dialog box.
5. Click OK to store the new font.
6. Click Apply
The default menu font is Dialog/Plain/18 and looks like this:

After changing the font to, for instance, to Serif/Italic/18, the menu looks
like this:

A change in menu font also affects all sub-menus and popup menus.

How to Change the Font of the Tab bar

1. Click Options => Preferences [set].
2. Click Fonts/Dialogs/Icons in the left part of the dialog box.
3. Click the Change button to the right of the Spectrum TABS font object.
4. Select the desired name, style and/or size in the appearing dialog box.
5. Click OK to store the new font.
6. Click Apply
Fig. 20.7 and Fig. 20.8 shows a Tab bar with font size 10 and 14 respec-
tively.

Figure 20.7 Tab bar with font size 10

361
User Preferences

INDEX
Figure 20.8 Tab bar with font size 14
INDEX DONE
How to Change the Font of Dialog Boxes
1. Click Options => Preferences [set].
2. Click Fonts/Dialogs/Icons in the left part of the dialog box.
3. Click the Change button to the right of the Dialog window font object.
4. Select the desired name, style and/or size in the appearing dialog box.
5. Click OK to store the new font.
6. Click Apply
Fig. 20.9 shows an example of a dialog box with the font Times New Roman
Italic

Figure 20.9

How to Change the Font of the Browser

To change the font of the browser:
1. Click Options => Preferences [set].
362
 User Preferences

2. Click Fonts/Dialogs/Icons in the left part of the dialog box.

3. Click the Change button to the right of the Dialog window font object.
INDEX
4. Select the desired name, style and/or size in the appearing dialog box.
5. Click OK to store the newDONE
font. INDEX
6. Click Apply
TOPSPIN must be restarted for this change to become effective. Note that
this change will affect all dialog boxes.

How to Change the Font of the Command Line

1. Click Options => Preferences [set].
2. Click Fonts/Dialogs/Icons in the left part of the dialog box.
3. Click the Change button to the right of the Command line font object.
4. Select the desired name, style and/or size in the appearing dialog box.
5. Click OK to store the new font.
6. Click Apply

How to Change the Font of the Status Line

1. Click Options => Preferences [set].
2. Click Fonts/Dialogs/Icons in the left part of the dialog box.
3. Click the Change button to the right of the Status line font object.
4. Select the desired name, style and/or size in the appearing dialog box.
5. Click OK to store the new font.
6. Click Apply

20.1.6 Changing Acquisition settings

How to Auto-Archive existing expnos

1. Click Options => Preferences [set].
2. Click Acquisition in the left part of the dialog box.
3. Click the Change button to the right of the item Configure Accounting &
Data Archiving after ’zg’ (see Fig. 20.10).
4. In the appearing dialog (see Fig. 20.11), configure archiving as

363
 described in the dialog.
5. Click OK.

Figure 20.10

Figure 20.11

20.2 Command Line Preferences

How to Resize the Command Line

By default, the TOPSPIN command line shows one command, the com-
 User Preferences

mand that is currently entered, e.g.:

INDEX
DONE INDEX
However, you can resize the command line to show the currently entered
command plus the last and second last command, e.g.:

You can toggle between the two different command line sizes as follows:
• Click View => Resize command line
or
• Right-click in the command line and click Resize command line

How to Set the Minimum and Maximum Command Line Size

By default, the size of the command line can be toggled between 1 and 3.
You can, however, change this minimum and maximum value, respective-
ly. To do that:
1. Click Options => Preferences [set].
2. Click Fonts/Dialogs/Icons in the left part of the dialog box.
3. Specify the Minimum visible command lines (> 0).
4. Specify the Maximum visible command lines ( Minimum visible).
5. Click Apply

20.3 Disabling/Enabling Toolbar Buttons, Menus and

Commands

How to Hide the Upper and Lower Toolbars

Right-click in an empty area of one of the toolbars and choose:
Hide the toolbars

365
User Preferences

from the appearing popup menu (see Fig. 20.12).

To restore the toolbars:
INDEX
+ press the keys SHIFT+ESC
INDEX DONE

Figure 20.12

How to Hide the Menubar

Right-click in an empty area of the Menubar and choose:
Hide the menubar
from the appearing popup menu.
To restore the menubar:
+ press the keys SHIFT+ESC

How to Disable/Remove Toolbar Buttons

Buttons of the upper or lower toolbar can be disabled or removed as fol-
lows:
1. Right-click a toolbar button.
2. Choose one of the entries:
+ Make this button invisible to remove the button from the toolbar
+ Make this button inactive to disable the button (it will appear greyed)
To restore the complete toolbars, click:

366
 User Preferences

+ Reactivate all invisible or inactive buttons to restore the default tool-

bar
INDEX
How to Disable/Remove Menus or Commands
DONE INDEX
By default, all existing TOPSPIN commands can entered from the menu
and/or from the command line. You can, however, selectively disable/re-
move commands or menus. This is typically done by system administra-
tors who want to disable certain functions for standard users.
Open the Menu Configuration table as follows:
1. Click Options => Preferences [set].
2. Click Fonts/Dialogs/Icons in the left part of the dialog box.
3. Click the Change button of the entry Disable/Enable menus and com-
mands.
The table consists of the following columns:

Command Description Menu Status

You can disable/remove:

• Menus, e.g. Options
to be found in the column Menu
• Sub-menus, e.g. Options => Administration tools
to be found in the column Menu
• Menu entries, e.g. Options => Preferences
to be found in the column Description
• Commands, e.g. set
to be found in the column Command
Note that in this configuration table, each menu entry corresponds to a cer-
tain command. In the TOPSPIN menu, most commands are indicated in
square brackets behind the corresponding menu entries, e.g.:
+ Processing => Fourier transform [ftf]
Menu entries which are not used very often appear without the corre-

367
User Preferences

sponding command indicated, e.g.:

+ Options => Preferences
INDEX
However, if you want, you can look up the corresponding command, in this
case set, inINDEX DONE
the configuration table and use it.
As an example, we will describe how you can disable/remove the menu en-
try Remote connection.. in the Options menu:
1. Open the configuration table as described above.
2. Scroll to the Description Remote connection
3. Set the Status to disabled.
4. Click Apply
Clicking the TOPSPIN Options menu, will now show the following popup
menu:

The entry Remote connection.. is greyed and can no longer be used.

Go back to the Configuration table, change the Status of Remote connec-
tion... to invisible and click Apply.
Clicking the TOPSPIN Options menu, will now show following popup menu:

The entry Remote connection.. has disappeared.

Note that if you disable or remove a menu entry, the corresponding com-
mand is automatically disabled. For example, if you disable:

368
 User Preferences

+ Analysis => Deconvolution [dcon]

entering dcon on the command line will lead to an error message.
INDEX
How to (Re)enable a disabled
DONECommand/Menu
INDEX
1. Open the Menu Configuration table as described above.
2. Set the Status of a disabled or removed (invisible) entry to enabled.
3. Click OK to close the Configuration table.

How to (Re)enable All Commands/Menus

1. Open the Menu Configuration table as described above.
2. Click the Reset button to enable all menus and commands.
3. Click OK to confirm the appearing message.
4. Click the OK button to close the Configuration table.

20.4 Resizing/Shifting Toolbar Icons

How to Change the Toolbar Icon Size

1. Right-click of any part of the toolbar,
2. In the appearing popup menu (see Fig. 20.13), click:
+ Change Icon Size...

Figure 20.13
3. Enter the icon size in the appearing dialog and click OK.

How to Shift Toolbar Icons to the Right

1. Right-click of any part of the toolbar.

369
User Preferences

2. In the appearing popup menu (see Fig. 20.13), click:

+ Change Toolbar Offset...
INDEX
3. Enter the toolbar offset in the appearing dialog and click OK.
INDEX DONE
20.5 Defining Source Directory for Programs/Lists etc.

TOPSPIN 2.1 and newer allow you to define the source directories for pulse
programs, AU programs, integral ranges, various lists etc. In TOPSPIN 2.0
and older, the source directory for these items was fixed:
<tshome>/exp/stan/nmr. Now you can define a individual source directories
for each item. To do that:
1. Open the dialog of any of the items, e.g. with the command edau,
edlist or edmisc.
2. Click Options => Manage Source Directories
A dialog will appear showing a list of items with the current source di-

Figure 20.14

rectories. By default, two source directories are present, one for user
defined items and one for Bruker items. This list can be modified or
extended with your preferred source directories, e.g.:
C:\my-pulse-programs\
C:\ts21\exp\stan\nmr\lists\pp\user
C:\ts21\exp\stan\nmr\lists\pp

370
 User Preferences

You can do this for each item separately. Items will be searched for in
the order of the directories specified.
INDEX
DONE INDEX

371
User Extensions

Chapter 21
INDEX

User Extensions
INDEX DONE

TOPSPIN offers various ways to extend the standard commands, buttons,

programs etc.

21.1 User Notebook

You can create your own user specific notebook with the command:
+ View => Notebook [nbook]

Figure 21.1
This can be used to store and retrieve any personal notes, information etc.

372
 User Extensions

21.2 Macros
INDEX It can be created with
A macro contains a sequence of TOPSPIN commands.
the command edmac. A simple macro for processing and plotting the cur-
DONE INDEX
rent dataset is:
em
ft
apk
sref
autoplot
All entries in a macro file must be written in lower case letters.
In TOPSPIN 1.3 and newer, a macro may contain Python commands. Any
line in a macro that starts with:
py>
executes a Python command. An example of such a macro is:
re exam1d_13C 1 1 C:\bio guest
efp
py>NEWWIN() # open new window
re exam1d_1H 1 1 C:\bio guest
efp
py>x = INPUT_DIALOG()
py>if x == None: EXIT()
py>y = 2* int(x[0])
py>MSG("done: y=" + str(y))
Note that commands like NEWWIN(), INPUT_DIALOG(), MSG() and EXIT()
are Bruker defined whereas "x=" and "if" are original Python commands.
Once created, a macro can be executed by entering its name on the com-
mand line.

21.3 AU Programs

An AU program may contain TOPSPIN commands, AU macros and C-lan-

guage statements. It can be created with the command edau. A simple AU
program which performs the efp command on a series of dataset expno’s
is:

373
User Extensions

#include <lib/util.h>
int first, max;
INDEX
char string[80];
INDEX
first = expno; DONE
GETINT ("Enter first expno to process : ",first)
max = 10;
GETINT ("Enter number of expnos : ",max)
WPAR("tmpmefp","proc")
expno = first;
TIMES(max)
RPAR("tmpmefp","proc")
EFP
IEXPNO
END
DEXPNO
DELPAR("tmpmefp")
QUITMSG("--- multiefp finished ---")
Note that TOPSPIN commands like EFP and RPAR and AU macros like IEX-
PNO are written in upper case letters whereas C-language statements like
"max = 10;" are written in lowercase letters. Once created, an AU program
can be executed by entering its name on the command line.
For more information on writing AU programs:
+ Click Help => Manuals => [Programming Manuals] AU programming

21.4 Python Programs

A Python program may contain TOPSPIN commands, User Interface func-

tions and Graphic functions. It is created with edpy.
The Python program below reads a region of the real part of a spectrum
and the corresponding region of the imaginary part and displays both. The
simplest form of DISPLAY_DATALIST is used.
from TopCmds import *
import math
region = [80, 72] # define region in ppm

374
 User Extensions

# open testdata, don't display

testdata = ["exam1d_13C", "1", "1", "c:/Bruker/topspin", "guest"]
RE(testdata, "n") INDEX
# read real and imaginary points of the region
reals = GETPROCDATA(region[0], DONE region[1])
INDEX
imags = GETPROCDATA(region[0], region[1], data-
const.PROCDATA_IMAG)
if reals == None or imags == None: EXIT()
# set up list of data to be displayed and respective axis info list
dataList = [reals, imags]
# display the data in the list
DISPLAY_DATALIST(dataList)
For more information on writing Python program:
+ Click Help => Manuals => [Programming Manuals] Python program-
ming

21.5 Button Panels

A button panel is a window with user-defined buttons for executing TOPSPIN

commands, AU programs, Python programs or macros. It appears as an
integral part of the active data window and acts on that Bruker delivers a
few standard button panels like bnmr and bnmrsel. To create your own
button panels, you can modify one this or write one from scratch.
In this description we will create a very simple button panel with some 1D
processing commands and print/export buttons (see Fig. 21.2)

Figure 21.2

375
User Extensions

To write this button panel, take the following steps:

1. Open the Windows Explorer and navigate to the subdirectory
INDEX
userdefined
INDEX
of the users properties DONE
directory 1.
2. Create a text file with the name
cmdpanel_<name>.prop
where <name> is the name of the button panel.
3. Enter the button definitions including Panel title, Colors, Toggle buttons,
Top buttons, Panel layout, Panel buttons and Tooltips.
4. Save the file under a name cmdpanel_<xxx>.prop
where <xxx> is the actual name of your command panel.
Make sure the extension of the file is .prop and not .txt,
.prop.txt or anything else.
5. Enter bpan <xxx> on the command line to open the button panel.
Here is an example for a small button panel for 1D processing:
# Color definitions used in this file (RGB)
BLUE1=51$ 204$ 255
YELLOW1=255$ 255$ 0
GREEN1=84$ 196$ 20
# Title definition
TITLE=1D Processing Panel
TITLE_COLOR=0$ 0$ 255
# Toggle button definition
TOGGLE_BUTTON=To 2D
TOGGLE_CMD=bpan bproc2d
TOGGLE_TIP=Switch to 2D processing
# Top row button definition
TOP_BUTTONS=EM$ $FT$ $PK$ $

1. To locate this, enter hist and look for the entry "User properties directory=".

376
 User Extensions

TOP_COLORS=YELLOW1$ YELLOW1$ YELLOW1

TOP_CMDS=em$ ft$ pk
TOP_TIPS=Exponential multiplication
INDEX $\
Fourier transform$\
Phase correction DONE INDEX
# Panel button definitions
# LAYOUT format: rows columns hgap vgap
PAN_LAYOUT=1$ 3$ 8$ 8
PAN_BUTTONS=Print$ $ EXPORT$ $SEND TO$ $
PAN_COLORS=BLUE1$ BLUE1$ BLUE1
PAN_CMDS=prnt$ exportfile$ smail
PAN_TIPS=Print the spectrum<br>\
as it appears on the screen$\
Export the dataset<br>\
to png, jpg, bmp etc.$\
Send the dataset by email
If you type bpan exam, a panel with 75 buttons will appear: 5 rows and 15
columns. The corresponding panel file is called cmdpanel_exam.prop,
which resides in the directory:
<tshome>/classes/prop/English
In the same directory, you can find the files cmdpanel_bnmr.prop and
cmdpanel_bnmrsel.prop, which are used to display the bnmr and bnmr-
sel panel described above.
The texts displayed on the buttons can be graphically adjusted in various
ways, because the text may optionally be specified in html format. In the
example above, the PAN_BUTTONS property has no html tags, therefore
the texts are displayed in black using the default TOPSPIN Dialog window font
as specified in the User Preferences (command set). If you replace the
text Print by the following:
<html><font size=10><font
color=\"00BF00\">Print<br>Now</font></html>
then the new text "Print Now" is displayed in green (the color to be speci-
fied in RGB hex code), with 10 points font size. Also, "Now" is display
below "Print" due to the html <br> (= break line) tag.
Note that:

377
User Extensions

• The Close button and Tips switch are automatically created. You don’t
need to specify them.
INDEX
• The TOGGLE button is typically, but not necessarily, used to call
another button panel. In this example it calls the panel bproc2d. If
INDEX DONE
TOGGLE_BUTTON is specified without a value, i.e. the entry is
"TOGGLE_BUTTON=" instead of "TOGGLE_BUTTON=action text",
the corresponding button is not shown in the panel.
• Items must be separated with the "$" character, button items with "$
$"
• A "\" followed by "end of line" continues an item on the next line.
• Tooltips may use html tags for text formatting.
• Commands may be specified as single commands like "em" or as
composite commands like "em\nft\npk". Note that in the latter case,
the commands must be separated by "\n".
• When the bpan <name> command comes up with an error mes-
sage, carefully check the syntax of your cmdpanel file. A common
mistake is to specify the button items incorrectly. With the keyword
PAN_LAYOUT you define the number of rows and columns, and the
number of items will become rows*cols. All specifications such as
PAN_BUTTONS, PAN_COLORS, etc. must have this number of
members, otherwise you will get some kind of TOPSPIN error. Please
insert the "$" separator to make sure the item count is correct.

21.6 Adding User Defined Buttons to the Toolbars

The upper and lower toolbar at the top of the TOPSPIN window can be
extended with user defined buttons. They can be assigned to any TOPSPIN
command, macro, AU program or Python program.
To create a user defined button, take the following steps:
1. Right-click at an empty area of the toolbar.
2. In the appearing popup menu, click:

378
 User Extensions

Add User-Defined Button

INDEX
DONE INDEX

3. In the appearing dialog box (see Fig. 21.3)

a) Choose between the options text label or icon
The corresponding parameters are enabled/disabled.
b) Enter the command name, the tool tip and the label text or icon file
pathname.
c) For a text label: set its font, text color and background color.
d) For an icon label: specify the icon image filename
e) Set the separator flag to yes or no and select the data dimension(s)
for which the button must appear.
For an icon label, you must stored the icon image file in one of the following
directories:
• <user-home>/.topspin-<hostname>/prop/userdefined (only available
for this user)
• <tshome>/classes/prop (available for any user)
• any directory (the full pathname must be specified in the icon label
field)
The formats .gif, .jpg, .jpeg and .png, are supported. Standard TOP-
SPIN toolbar icons have a size of 16 * 16 pixels. If your own icons have a
different size, they are automatically rescaled and displayed at the stand-
ard size.

379
User Extensions

INDEX
INDEX DONE

Figure 21.3
In the example above, a button FT is created with a separator, which only
appears for 1D datasets, and executes the command ft.
How do I Remove a User Defined Toolbar Button
Right-click the toolbar button and click:
Remove this user-defined button...
in the appearing popup menu (see Fig. 21.4).
How do I Shift a User Defined Toolbar Button to the left/right
Right-click the toolbar button and click:
Shift left
or
Shift right

380
 User Extensions

in the appearing popup menu (see Fig. 21.4).

INDEX
DONE INDEX

Figure 21.4
The button definitions are stored in the file toolbar_user.prop which
resides in the subdirectory userdefined of the user properties directory.
To locate this directory enter the TOPSPIN command hist. A dialog box
will show the contents of the history file. Near the top of this file, you will
see an entry "User properties directory=".
For icon image buttons, the formats .gif, .jpg, .jpeg and .png, are
supported. Standard TOPSPIN toolbar icons have a size of 16 * 16 pixels. If
your own icons have a different size, they are automatically rescaled and
displayed at the standard size.

21.7 Adding User Defined Menus to the Menubar

The menubar at the top of the TOPSPIN window can be extended with user
defined menus. They can be assigned to any TOPSPIN command, macro,
AU program or Python program. They are specific for the dimensionality of
the active dataset.
To create a user defined menu, take the following steps:
1. Open a dataset of the desired dimensionality.

381
User Extensions

2. Right-click at an empty area of the menubar.

3. In the appearing popup menu, click:
INDEX
User_defined Menus
INDEX DONE

4. In the appearing dialog box (see Fig. 21.5).

a) Click Add Menu and specify the Menu Name in the appearing dia-
log.
b) Click Add Menu Item and specify the Menu Item (menu entry)
name and the corresponding Command in the appearing dialog.
c) Click Apply.

Figure 21.5
The new menu will appear in the menubar.
Furthermore the dialog box in Fig. 21.5 contains the following buttons:
• Remove : Remove menu names and/or menu items

382
 User Extensions

• Apply+Close : Apply any changes and close the dialog box

• Up/Down : Move up/down the menu name list
INDEX
• Cancel : Close the dialog box discarding any changes.
User defined menu definitions DONE INDEX
are stored in the file
umbar_menubar1d.prop, umbar_menubar2d.prop or
umbar_menubar3d.prop depending on the data dimensionality. These
files resides in the subdirectory userdefined of the user properties direc-
tory. To locate this directory enter the TOPSPIN command hist.

21.8 Adding User Defined Guides

TOPSPIN offers several guides like the Acquisition Guide (command

aqguide), the Processing Guide (command prguide) and the
T1/T2 Guide (command t1guide). You can set up your own guides,
which can be adaptations of Bruker guides or new written ones. In
order to do that, you must edit the file toolbar_user.prop and
cmdtab_user.prop in the directory:
<user properties directory>/userdefined/
To identify this directory, enter the command hist in TOPSPIN.
The file toolbar_user.prop contains the guide definition. If the file does
not exist, it must be created. Here is an example of a user-modified T1/T2
guide.
MyT1T2Toolbar=\
NM=t1fid_40.gif, NM2=$Extract fid, TIP=$Do rser,
CMD=_t1_fid, END=,\
NM=t1spec_40.gif, NM2=$Transform, TIP=$Do ef+apk,
CMD=_t1_spec, END=,\
NM=t1ranges_40.gif, NM2=$Ranges, TIP=$Enter integ. mode,
CMD=_t1_ranges, END=,\
NM=t1screen_40.gif, NM2=$Relax. Window, TIP=$Enter Relax
mode, CMD=_t1_relax, END=,\
NM=-, END=,\
NM=myicon.gif, NM2=$Fit Methods, TIP=$Select fit funcs.,
CMD=_t1_func, END=,\
NM=c:/myicons/myicon1.gif, NM2=$Start, TIP=$ct1,ct2, simfit,

383
User Extensions

CMD=_t1_start, END=,\
NM=c:/myicons/myicon2.gif, NM2=$Show Report, TIP=$report,
CMD=_t1_report,
INDEXEND=,\
NM=t1print_40.gif, NM2=$Print it, TIP=$print,
CMD=_t1_export,
INDEX END=DONE
Notes to this guide definition:
• The original Bruker guides are defined in the file toolbar.prop
in the directory <tshome>/classes/prop. The corresponding
commands are defined in cmdtab_main.prop in the same
directory.
• The bold lines in the example above are user-modified lines.
• NM=t1fid_40.gif: a Bruker defined icon with a size of 40x40 pixels
• NM=myicon.gif: a user-defined icon, which must be located in the
user properties directory (Caution: not in its subdirectory userdefined)
• NM=C:/myicons/myicon1.gif: a user-defined icon located C:/myi-
cons. Using the absolute pathname allows you to store icons in an
arbitrary directory.
• NM=- : indicates the start of the second icon column
• NM2= : the text to appear underneath of the icon. The $ sign is man-
datory.
• CMD= : the command to be executed when the icon is clicked. This
can be a regular TOPSPIN command, a macro or an AU or Python pro-
gram.
• TIP= : the tooltip to be displayed when the cursor is held over the
icon. Note that the $ sign is mandatory.
Before you can start a user defined guide, you must edit the file
cmdtab_user.prop and define the corresponding command in the
file, for example:
myt1guide=EM=J, MC=N, CL=tutor.TutStarter, ME=startTuto-
rial,AR=MyT1T2Toolbar;My T1 T2 Tutorial=
Here:
• "MyT1T2Toolbar" is the toolbar identifier as it is used in the file
toolbar_user.prop.

384
 User Extensions

• "My T1 T2 Tutorial" is the title as it appears at the top of the

guide.
INDEX
If your guide is a Bruker modified guide, you can also redefine the
original Bruker command,DONE
i.e. specify INDEX
t1guide instead of
myt1guide. Note that the original Bruker guide is then no longer acces-
sible.
If you want to access a user defined guide from the TOPSPIN toolbar, you
have to create a new toolbar button. To do that, right-click in an empty
area of the toolbar and define a button in the appearing dialog.

385
 Index

.pr command 24, 170

Symbols .prop files 256
.ret command 194, 205, 214, 218, 219, 224
*2 command 35, 42, 118, 159 .retsab command 219
*8 command 35, 118, 159 .s2d command 194
.2d command 34 .sd command 37, 120, 162
.3d command 34 .sino command 260
.all command 36, 119, 161 .sl command 37, 120, 162
.basl command 215 .sl0 command 37, 120
.bmp files 25 .sr command 37, 120, 162
.bzip files 27, 76 .sr0 command 37, 120
.cal command 205, 246 .sret command 194, 204, 217, 224
.co command 173 .st command 176
.dec command 194, 200, 217, 231 .su command 37, 120, 162
.dopt command 149, 150, 159, 312 .tif files 114
.dx files 76 .txt files 153
.emf files 25 .vr command 36, 118, 159
.f1r command 161 .wmf files 25, 114
.f2r command 161 .y command 146
.gif files 360, 362 .zi command 36, 119, 161
.gr command 172 .zl command 36, 119, 161
.hr command 36, 119 .zo command 36, 119, 161
.hz command 145, 169 .zx command 36, 119, 161
.im command 176 /2 command 35, 42, 118, 159
.inc command 194, 200, 217, 231 /8 command 36, 118, 159
.int command 195, 233 ? command help 46
.jpeg files 25, 360, 362
.jpg files 25, 360, 362 Numerics
.keep command 36, 120, 161 12 23
.ls command 176 180 degree phase correction
.lt command 178 1D 193
.lv command 174 2D 231
.md command 24, 207 3D molecule viewer 259
.ov command 146, 169 -90 degree phase correction
.ph command 45, 191, 225 1D 193
.ph180 command 193 2D 231
.ph90 command 193 90 degree phase correction
.phr command 193 1D 193
.png files 25, 114, 360, 362 2D 231
.pp command 220

I-1
A AU programs 20, 29, 103, 300, 354, 359, 362
audit
abs command 99, 103, 194, 195, 198, 214
trail check 307
absd command 214 INDEX automate data acquisition 30
absorption mode 192, 193, 229, 230, 231
automatic
acqu command 275 INDEX DONE 1D baseline correction 99
acquisition
1D calibration 99, 205
commands 274, 278
1D integration 194
mode 300
1D peak picking 220
parameters 93, 94, 287
1D phase correction 99, 191
status bar 276, 289
2D calibration 246
toolbar 273, 275
compilation of an AU program 303
Acquisition Reference Manual 21, 97, 282, 283,
configuration of a datastation 299
300
selection of the first expno/procno 69
AcquPars tab 93, 123, 165, 287
tuning and matching 280
activate
automatic mode
a data window 251
of the Acquisition Guide 272
the next data window 256
of the Processing Guide 26, 101
add
automation 29, 30, 300
comment to audit file 308
autoplot command 103, 110
directory to the browser 22
autostart.mac file 332
functionalities to Topspin 29
Avance spectrometers IV, 299
peak in 2D phase correction 227
axis units 35, 145, 169, 206, 247
peak to peak list 222
add increment in 2D levels 174 B
align
intensities in multiple display 212 background of a data window 338
peak positions in multiple display 212 Backspace key 38
Alt-F11 key 118, 158 backward peak picking 222
Alt-F4 key 41, 47 baseline correction
Alt-F6 key 47 1D 99, 214
Analysis menu 25, 26, 33 mode 35, 214
apk command 99, 103, 191 bcm command 217
apks command 191 bias correction 199
arrange bio-molecular experiments 30
data windows 252 bnmr command 356
data windows horizontally 254 bnmrsel command 356
data windows vertically 253 bpan command 357
rows/columns in 2D phase correction 232 browser 31, 32, 41, 57, 68
ascii files 86, 153 font 343
ased command 96, 123 in multiple display mode 209, 240
Aspect 3000 data 75 Bruker
ATM probehead 279, 280 AU programs 30, 302
atma command 280 data format 21, 27, 28, 71, 75, 76, 85
AU macros 29, 354, 355 example datasets 22, 64
AU program reference manual 104 BSMS control panel 282

I-2
BSMS display window 256 Command Prompt 19, 298
bsmsdisp command 282 compile
AU program 302, 303
C INDEX components
calibration 99 of a spectrum 24
1D interactive 205
INDEX DONEcomposite commands 100
2D interactive 246 configuration
mode 35, 205, 246 commands 20
cf command 20, 49, 297, 298, 299 customized 299
chemical shift 212 default 299
chemical shift distance directory 299
1D 260 name 299
2D 247 of a datastation 20
CHEMSTR parameter 143 of a spectrometer 20
C-language 29, 103, 354, 355 of the acquisition status bar 276
clevels file 176 of the tab bar 335
clipboard 25, 41 of the Topspin menu 348
close password 297
active data window 255 consistency check 307
lock display window 281, 282 contour display 226
the active data window 41 of 2D spectra 173
close command 41 of 3D planes 180
cmdhist command 38 contour levels 158, 174
cmdindex command 46 control keys 40
cmdtab_user.prop file 47 convdta command 78
collapse a data directory 57, 62 convert
color scheme 337 data to JCAMP-DX 78
colors data to text 78
of data objects 336 data to ZIP 78
of the lock display 337 copy & paste data 33, 73, 76
on the printer 336 copy command 25, 34, 113
command copy data 77
definition 47 C-program 103
dialog box 89 create
help 44 an AU program 29, 104, 302, 354
index 46 an empty data window 68
line 37, 38, 345 data window color scheme 337
command line dataset 34
commands 274 macro 29, 354
focus 37, 41 new data window 21
font 344 new dataset 65, 286
history 37, 38 plot layouts 25, 112
preferences 345 Python program 30, 355
resize 346 set of user preferences 329
usage 37 user defined command 29

I-3
 user notebook 353 in S/N measurement mode 261
C-statements 29 in spline baseline correction mode 218
Ctrl key 62, 69, 81, 118, 159, 208, 209 objects 24
Ctrl-c key 38, 41, 133 INDEX popup menu 146, 162
Ctrl-d key 31, 41 printing 109
Ctrl-f key 41 INDEX DONE reopen 116
Ctrl-F3 key 47 tab bar 1D 121
Ctrl-F5 key 47 tab bar 2D 165
Ctrl-F6 key 47 toolbar 24
Ctrl-n key 34, 41, 65, 286 dataset
Ctrl-o key 34, 41, 70, 75 active 251
Ctrl-p key 25, 34, 41, 112, 133 colors 214
Ctrl-s key 27, 34, 41, 77, 78 dir 21, 305
Ctrl-v key 38, 41 directory tree 21, 72
Ctrl-w key 41 expno 21, 60, 65, 305
cube display 179 files 86, 153
cubic spline baseline correction 218 handling 29, 57
cursor information 148 last 2D 34
customized configuration 299 last 3D 34
cut integrals 203 last used 332
name 21, 60, 65, 73
D procno 21, 60, 65, 305
data procno directory 73
area 22, 31, 68, 73, 76, 249, 252, 255 properties 150
compression 28 selection in multiple display 209
dimensionality 32, 92, 97, 122, 123 specification 72, 251
directory 57, 64, 81 title 65
field 37, 115, 120, 157 top level directory 60
object colors 336 user 21, 60, 65, 305
data window 21, 31, 33, 68, 73, 76 variables 78
2D 157 datastation
3D 179 configuration 299
color scheme 337 dcon command 28, 350
contents 25, 113 dconpeaks.txt file 28
creation 68 deconvolution 28
handling 33, 249 default
in 1D peak picking mode 220 color scheme 338
in 1D phase correction 192 command line size 345
in 2D calibration mode 246 configuration 299
in 2D multiple display mode 239 find criteria 83
in 2D phase mode 226, 233 menu font 342
in baseline correction mode 215 pivot point in 1D phase correction 192
in calibration mode 206 pivot point in 2D phase 229
in integration mode 195 plane in 3D display 179
in multiple display mode 208 printer 111

I-4
 Tab bar 335 1D spectrum 121
zero order phase correction 193 1D spectrum overview 145
define 2D contours 173
INDEX
cubic spline baseline points 218 2D data 157
integral regions 196 2D FID 169
NMR ADMINISTRATOR INDEX password 297 DONE 2D grid 172
NMR SUPERUSER 297 2D integral list 167
peak ranges 221 2D peak list 166
peaks 222 2D projections 170
de-iconify 2D spectrum in contour mode 173
data window 255 2D spectrum in oblique mode 176
delete 2D spectrum in pseudo color mode 176
AU program 303 3D cube 182
data 79 3D data 179
integrals from display 201 columns in 2D phase correction 226
noise region S/N 262 contours in 2D phase 226
peaks from a peak list 223 data from the browser 22, 59
signal region S/N 262 data from the portfolio 59
spline baseline points 219 data in multiple windows 116
Delete key 38 dataset file list 151
depth cueing in 3D 183 dataset properties 150
deselect expno/procno list 69
data in multiple display 209, 210 found dataset 83
integral regions 197 full spectrum in 2D phase correction 227
dialog box font 343 integrals 23
difference spectrum JCAMP data 28
in baseline correction 217 manipulation 117
in multiple display 210 manipulations 35
dimensionality of a dataset 32, 92, 93, 97, 122 mode of the lock window 281
dir command 22 molecule structure 143
disable options 35
commands 348 options 1D 145
menus 348 peaks 23
toolbar buttons 347 planes of 3D data 179, 180
Display positive/negative 2D levels 178
button 21, 74, 84 processing status parameters 1D 122
menu item 68, 69, 208 projections 23
display rows in 2D phase correction 226
1D acquisition status parameters 123 settings 34
1D data 115 special data formats 75
1D FID 145 spectra 21
1D integral list 134 spectrum overview in 2D 169
1D peak list 125 status parameters 92, 96
1D processed data 121 sum/difference spectrum 210
1D raw data 145 superimposed 1D spectra 207

I-5
 superimposed 2D spectra 238 equidistant sequence of levels 174
y-axis 35, 146 Esc key 37
zipped data 27 execute
display properties 23 INDEX AU program 300, 303
distance measurement macro 29, 354
1D 260 INDEX DONE Python program 30
2D 247 exit command 41, 48
mode 35 expand
double-headed arrow 250, 261 a data directory 42
Down-Arrow key 38, 41, 42 data directory 21, 22, 57
dpa command 123 data directory in the browser 62
dpp command 92, 96, 122 individual spectra in multiple display 212
drag & drop data 73, 76 spectrum 28
expand a region 23
E experiment time 275
eda command 93, 94, 123, 165 expinstall command 20, 49, 274, 297, 298, 299,
edasp command 97, 123 300
edau command 30, 104, 300, 302, 354 expl command 73, 86, 87, 153
edcpul command 125 Explorer 72, 86, 153
edit expno 65, 69, 72, 78, 151
AU program 303 exponential
commands 38 baseline correction 216
contour levels 174 window multiplication 99, 100
integral ranges 199 export data 24, 114
pulse program 125 expt command 275
signal/noise regions 262 extend the Topspin functionality 353
title of a dataset 124 external projection 24
Edit menu 33 extract a row/column in 2D 244
edlev command 158, 174
edlock command 97 F
edmac command 29, 354 F1 dimension 162, 169, 225
edp command 26, 89, 90, 122, 165 F1 key III, 41
edprosol command 96 F1-F2 plane 180, 183
edpul command 125 F2 dimension 162, 169, 225
edpy command 30, 355 F2 key 41, 61
edti command 124 F2-F3 plane 181, 183
ef command 100, 103 F3 key 47
efp command 100, 289 F3-F1 plane 179, 181, 183
em command 26, 99 F5 key 47
email data 28 F6 key 41, 47, 252
empty data window 68 fid command 145, 169
enable FID display 274, 278, 284, 288
disabled commands 350 Fid tab 145, 151, 169
menus/commands 346 File Chooser 21
Enter key 42, 59 File menu 21, 33

I-6
file size of raw data 275 gs command 93, 276, 284
files of a dataset 73, 78, 86, 151, 153 GS parameter adjustment window 284
find command 41, 82
find data 33, 82 INDEX H
first order phase correction halt an acquisition 274, 275
1D 193 INDEX DONEhalt command 274, 276, 288
2D 229, 231 Hardware requirements V
fitting peaks 28 helium level 282
fmc command 100 Help
focus 37, 41, 61, 62 button 46
font menu 33, 45
of dialog windows 343 help
of the browser 343 in Topspin 44
of the command line 344 on commands 46
of the interface 340 help command 46
of the menu 341 Hertz axis units 145, 169
of the status line 344 hist command 47, 50, 357, 362, 364
of the tab bar 342 history file 362
forward peak picking 222 hostname of a remote system 323
Fourier transform 99, 100 HTML page 46
fp command 100
fromjdx command 28 I
fromzip command 27 iconify
ft command 25, 26, 99 all data windows 256
ftf command 26, 348 data window 254
function keys 40 iconnmr command 30
image display
G
of 2D data 176
Gaussian deconvolution 28 of 3D planes 180
Gaussian window multiplication 100 import data 28
genfid command 78, 79 inconsistent dataset 92
genser command 79 initial guess 268
geometric sequence of levels 174 install
geometry of a Topspin window 256, 257 AU programs 20, 300
getprosol command 96, 123 pulse programs 20
gf command 100 Topspin 297
gfp command 100 installation directory 64, 298, 299
Gnome Mozilla 86 installnmr script 298
grab rows/columns in 2D 242 int command 149
gradient enhanced spectroscopy 29 Integral
graphic functions 355 list 2D 167
graphics files 25, 114 integral
grid bias 199
display 35, 172, 281 display 23
window arrangement 252 label 197

I-7
 list 1D 134 Jmol molecule structure viewer 143
regions 195, 196, 197, 198, 203 JNMR data 75
scaling factor 203
slope 200 INDEX K
trails 149, 203 KDE konqueror 86
values 196 INDEX DONEkeyboard commands 33
Integrals tab 134, 167, 205 kill command 53
integrals.txt file 205 Konqueror 86, 153
integration
1D automatic 194, 198 L
1D interactive 194, 195, 198 Left-Arrow key 38, 42, 62
mode 35, 195, 204, 205 Levenberg-Marquardt algorithm 268
intensity li command 134, 195
alignment in multiple display 212 Liouville equation 29
decrease 1D 118, 158 lipp command 134
increase 1D 118, 158 lippf command 134
manipulation 35 list 167
reset 1D 36, 118, 158 1D integrals 134
scaling 2D 159 2D integrals 167
interactive 2D peaks 166
1D baseline correction 214 AU programs 300
1D calibration 205 baseline points 218
1D data manipulation 189 Bruker AU programs 302
1D integration 194 color schemes 338
1D peak picking 220 data files 85, 151
1D phase correction 189, 191 EXPNOS/PROCNOS 69
1D signal to noise calculation 260 found data 83
2D calibration 246 integrals 112, 204
2D data manipulation 225 macros 29
2D phase correction 225 opened datasets 59, 60, 61
data manipulation 25, 34, 335 parameter sets 65
modes 34 peaks 112, 222
parameter adjustment 93, 284 peaks 1D 125
processing 99 plot layouts 110
Processing Guide mode 103 solvents 65
interface fonts 340 user defined AU programs 302
internal projection 24 local
Internet Browser 73 Topspin interface 319
intrng file 199, 202, 204 lock
IP address of a remote system 323 parameters 97
IUPAC standard 28 signal 281
lock command 282
J
lock display
JCAMP-DX format 28, 75, 76, 78 colors 337
Jeol spectrometer 75 mode 281

I-8
 window 256, 275, 277, 281 2D 24, 238
lockdisp command 275, 281 in deconvolution 28
lock-in procedure 281 multiple display mode 69, 207
Lorentzian deconvolution 28 INDEX multiple window display 116
lower toolbar 35 multiplet 196
INDEX DONEmultiply with increment in 2D levels 174
M
macros N
in AU programs 103, 355 nbook command 353
in Topspin 29, 47, 100, 354, 359, 362 negative
magnitude calculation 100 2D levels 178
matching the probehead 279 new command 34, 41, 65, 286
MAXI parameter 222 newtop command 48
maximize next
all data windows 256 channel for wobbling 280
data window 255 command 41
maximum dataset in Browser 42
command line size 346 parameter field 92, 96
MC2 parameter 93 plane in 3D 181
menu row/column in 2D phase correction 231, 243
bar 33 window in data area 41, 252, 256
commands 33 NMR ADMINISTRATION password 297
configuration table 348, 350 NMR SUPERUSER 297
entries 33, 348 nmradminpassword file 297
font 341, 342 nmrsim command 29
settings 329 nmrsuperuser file 297
MI parameter 222 noise region 260, 261
minimize NOISF1 parameter 260
data window 254 NOISF2 parameter 260
minimum notebook 353
command line size 346 NS parameter 274
Minus key 42
mixtures 29 O
molecule structure viewer 143 O1 parameter 275
mouse sensitivity O2 parameter 275
in 1D baseline correction 217 O3 parameter 275
in 1D integration 200 objects
in 1D phase correction 194 of a dataset 24, 116, 250, 329, 335, 336,
in 2D phase correction 231 337
move oblique display
data window 250 of 2D spectra 176, 178
Mozilla 86, 153 of 3D planes 180
multiple display online help 45
1D 35, 207, 238 online manual
1D/2D 24, 69, 74 plot editor 112

I-9
 Topspin 44 list 1D 125, 222
open list 2D 166
browser/portfolio 61 picking mode 220
data 34, 41, 57, 68, 70 INDEX position 260
data from the browser 21 position alignment 212
INDEX
data from the command line 73, 76 DONE ranges 224
data from the Explorer 72 peak picking
data from the menu 21 1D automatic 220
IconNmr interfaces 30 1D interactive 220
Linux Shell 19 mode 35
new data window 252 mode 1D 220
new procno 74 ranges in 1D 221, 222
online help documents 45 peak.txt file 224
special format data 75 peakrng file 224
Topspin command index 46 Peaks tab 112, 125, 166
open command 34, 41, 70, 75 phase correction
Options menu 33 1D automatic 99, 100
overview spectrum 1D interactive 191
1D 145 2D interactive 225
2D 169 first order 1D 193
mode 34
P mode 1D 192
paper format 300 mode 2D 226
paracon command 300 pivot point in 1D 192
parameter values 1D 194
adjustment window 93, 284 zero order 1D 193
change 92, 96, 97 PHC0 parameter 91, 193, 230
display 23 PHC1 parameter 193, 231
editor 89, 90, 93, 94 pivot point
field 91, 92, 95, 96 in 1D phase correction 192
files 85 in 2D phase correction 229
handling 89 pk command 194
name 89, 93 plane display in 3D 180
search 122, 123 plot
value 91, 95 data from the menu 109
parameter set 65, 78 data from the Plot Editor 112
PARMODE parameter 123 data from the Processing Guide 111
paste command 34, 73, 76 layouts 25
peak plot command 110, 112
alignment 24, 212 Plot Editor 25, 110
display 23 Plus key 42
fitting 28 polynomial
group 28 baseline correction 215
labels 149, 150, 222 position
list 223, 224 of a Topspin window 257

I-10
position of a Topspin window 256 Processing Reference Manual 23
position the baseline of a row/column in 2D 245 procno 69, 74, 78, 86, 152
positive ProcPars tab 26, 89, 90, 122, 165
2D levels 178 INDEX projections of a 2D spectrum 23, 170
pp command 133, 149, 150 properties
PPARMOD parameter 92, 97,INDEX 122 DONE of a dataset 150
ppl command 222 of a printer 110
ppm axis units 145, 169 prosol parameters 287
pps command 220 pseudo raw data 78
preferences 33, 329 pulse program 20, 29, 62, 125
pre-scan-delay 300 display 125
preview parameters 96, 123, 287
the baseline corrected spectrum 216 PulsProg tab 125
previous Python programs 30, 355, 359, 362
commands 37
dataset in browser 42 Q
parameter field 92, 96 QUIT AU macro 104
plane in 3D 181 QUITMSG AU macro 104
row/column in 2D phase correction 231, 243
print R
1D peak list 133 re command 22, 73, 207
active window 25, 110 read
colors 337 color scheme 338
data from the menu 109 data formats 75
data from the Processing Guide 111 integrals from disk 198
integral list 112 the prosol parameters 287
metafiles 113 window layout 256
peak list 112 reb command 21, 74
the current dataset 41 re-enable disabled commands 350
print command 34, 41, 109, 112, 133 reference peak
printer colors 336 in 1D calibration 206
prnt command 110 in 1D phase correction 192, 193
probehead/solvent dependent parameters 96 in 2D calibration 247
proc_1d AU program 103 in 2D phase correction 229
process data 25, 33 referencing 99
from the command line 99 reg file 204
from the Processing Guide 100 relaxation
with AU programs 103 curve 263
with composite commands 100 remote connections 329
processing remove
parameters 89, 90 commands 348
parameters 1D 122 data from multiple display 210
parameters 2D 165 menus 348
Processing Guide 26, 101, 103 toolbar buttons 347
Processing menu 25, 26, 33 reopen a dataset 116

I-11
reopen command 67, 116 cubic spline baseline points 219
rep command 22, 74 current window layout 256
repw command 74 data 27, 34, 41, 77
rescale INDEX data in analog filtered format 78
2D projection 171 data to a JCAMP-DX file 28
data in multiple windows INDEX
117 DONE data to a ZIP file 27
reset data window to a graphics file 25, 114
1D baseline correction 217 entire dataset 77, 78
1D phase values 193 integral regions 203
3D cube size and orientation 183 macro 29
F1 zoom factor in 2D 161 parameters 122, 123
F2 and F1 zoom factor 161 peak list and peak ranges 224
intensity 1D 118 phase correction 2D 229, 232, 238
intensity in 2D 159 processed data 78
search mask 83 processed data as pseudo raw data 78
zoom factor 36, 119 pulse program 142
resize sum or difference spectrum 210
command line 346 title of a dataset 124
data window 250 scale
graphics 113 1D integrals 202
resolution of a screen dump 25, 114 1D spectrum 118
restore 2D spectrum 158
adjusted acquisition parameters (GS) 286 3D cube 183
size and position of a data window 255 individual spectra in multiple display 24,
toolbar 348 207, 212
uncorrected baseline 217 row/column in 2D phase 230
retrieve scaling factor
previously entered commands 37, 38 of integrals 203
rew command 22, 74 scan
Right-Arrow key 38, 42, 62 planes of 3D data 181
rotate 3D cube 178, 182 rows/columns in 2D 242
routing parameters 97 screen dump 25, 114
scroll bar 92, 96
S search
S/N value 262 criteria 82
Sample tab 142 data 82
sav command 34, 41 field in the parameter editor 91, 95
save result window 83
1D baseline correction 217 select
1D integrals 204 AU program 303
1D phase correction 194 color scheme 338
acquisition data 78 data 57
adjusted acquisition parameters (GS) 285 data in multiple display 208, 209
AU program 30, 302 data window 251
color scheme 337 default printer 300

I-12
 expno/procno combination 69 1D data to the extreme left 120
first expno/procno 69 1D data to the extreme right 120
folders in the browser 62 1D data to the left 120
font 342, 343, 344 INDEX 1D data to the right 120
integral regions 197, 199 1D data up 120
lock signal color 337 INDEX DONE 1D/2D data 37, 42
multiple datasets 69 2D data down 162
multiple folders 62 2D data smoothly 162
peaks in 2D phase correction 226 2D data to the left 162
plot layout 110 2D data to the right 162
printer 110 2D data up 162
remote system 323 data in multiple windows 117
row/column in 2D phase 229 individual spectra in multiple display 24,
spectra in 2D multiple display 241 207, 212
spectrum color 336 row/column in 2D phase 230
spectrum print color 337 Shift key 62, 69, 81, 208, 209
Topspin window 257 Shift-Tab key 92, 96
selective excitation 29 short description
semi-automatic of an AU program 303
peak picking 222 shortcuts for processing 100
processing 100 show command 53
sensitivity SIGF1 parameter 260
of the GS slider 284 SIGF2 parameter 260
of the mouse 194, 200, 217, 231 signal region 260, 261
serial command 104 signal to noise calculation 260
serial processing 104 Simplex algorithm 268
Server ID 323 simulating experiments 29
set sine
1D acquisition parameters 123 baseline correction 216
2D acquisition parameters 165 single commands 99
2D processing parameters 165 slider sensitivity 284
colors for multiple display 214 slope correction 199
contour levels 174 smail command 28, 34
lock parameters 97 smooth
phase pivot point 192 1D phase correction 230
processing parameters 89 1D scaling 36
processing parameters 1D 122 1D shifting 120
routing parameters 97 1D zooming 36, 119
user preferences 330 1D/2D shifting 37
set command 121, 329 2D shifting 162
SFO1 parameter 275 scaling of 1D integrals 202
Shell 19 scanning of planes in 3D 181
shift shifting of 1D integrals 203
1D data down 120 solvent 65
1D data smoothly 120 spec command 121

I-13
special format data 28 to the last 2D data 34
spectrometer to the last 3D data 34
frequency 275
spectrometer hardware 20, 21INDEX T
Spectrometer menu 33, 273 T1 calculation III
spectrum INDEX DONET1/T2 Relaxation 263
display 1D 121 t1guide command 263
objects 329, 330 T2 calculation III
overview 1D 145 Tab bar
overview 2D 169 1D 116, 121
Spectrum tab 121, 145, 152 2D 158, 165
square 2D layout 160 configuration 121, 335
square brackets 33, 45, 116, 121 font 342
sref command 99, 103, 205, 246 usage 121
stacked multiple display 211 Tab key 92, 96
Start button 72 tabbed pane 165, 335
startup actions 329 TCP/IP port 321
status line font 344 temperature unit window 256
status parameter Terminal Window 19
change 93 time domain signal 29
display 96, 149 title bar 115, 116, 157, 250, 251, 254, 255, 256,
display 1D 122, 123 303
stdisp command 292 title file 124
stop an acquisition 274 title of a dataset 23, 62, 65, 124, 149, 286, 337
stop command 274, 276, 288 Title tab 124
store toccpn command 78
2D contour levels 175 tojdx command 28, 78
structure file 143 toolbar
Structure tab 143 1D 189
sum spectrum 2D 225
in multiple display 210 configuration 347
superimpose extension 359
1D spectra 207 for acquisition 273
cursor information 148 icons 360, 362
electronic signature 150 of the data window 24, 145
integral trails/labels 149 of the FID display window 288
main status parameters 149 tips 45
peak labels 149 usage 34
spectra 24 tooltips 44, 45
title of a dataset 149 top level directory 21, 22, 57, 64
SW parameter 275 Topspin
swap data windows 257 color schemes 338
sweep width 275 data area 73, 76
swin command 257 fonts 341
switch help 44

I-14
 installation 299 WINNMR data 75
installation directory 299 wm command 26, 89
startup V, 19 wmisc command 78
tailoring 329 INDEX wobb command 276, 279
window 31 wobble
topspin command 19 INDEX DONE display 277
Topspin icon 19 frequency 280
totxt command 78 procedure 279
tozip command 27, 78 steps 280
tshome directory 19, 45, 299 sweep width 280
tuning the probehead 279 window 279
wpar command 78
U wra command 78
undo wrp command 78
last parameter change 92, 96 wrpa command 27, 77, 78
last region operation 204
unzip utility 28 X
Up-Arrow key 38, 41 xau command 303
upper toolbar x-axis rotation in 3D 178, 182
1D 34, 189 xmac command 29
2D 225
user defined Y
AU programs 300 y-axis display 35, 146
buttons 359, 362, 364 y-axis rotation in 3D 178, 182
commands 26, 29
functions keys 47 Z
plot layouts 111 z-axis rotation in 3D 182
User Interface functions 355 zero order phase correction
user preferences 329 1D 193
user properties directory 47 2D 229, 230
zg command 274, 276, 287
V
ZIP data format 27, 75
Varian spectrometer 75 zoom
vertical scaling 118, 159 1D data 36, 119
View menu 33, 148 2D data 161
virtual spectrometer 29 in 2D phase correction 227
VNMR data 75 zoom 1D/2D data 42
W Symbols
walk-up 30 ? command help 52
wbst command 280 .2d command 38
wbsw command 280 .3d command 38
wildcards 81 .all command 40, 128, 170
window layout 256 .basl command 227
Window menu 33, 257 .bmp files 27

I-15
.bzip files 29, 83 .zl command 40, 128, 170
.cal command 217, 259 .zo command 40, 128, 170
.co command 182 .zx command 40, 128, 170
.dec command 203, 209, 229, INDEX
244 *2 command 39, 48, 127, 168
.dopt command 158, 159, 168, 331 *8 command 40, 127, 168
.dx files 83 INDEX DONE/2 command 40, 48, 127, 168
.emf files 27 /8 command 40, 127, 168
.f1r command 170
.f2r command 170 Numerics
.gif files 379, 381 12 25
.gr command 181 180 degree phase correction
.hr command 40, 128 1D 202
.hz command 154, 178 2D 244
.im command 185 3D molecule viewer 272
.inc command 203, 209, 229, 244 -90 degree phase correction
.int command 204, 246 1D 202
.jpeg files 27, 379, 381 2D 244
.jpg files 27, 379, 381 90 degree phase correction
.keep command 41, 129, 170 1D 202
.ls command 185 2D 244
.lt command 187
.lv command 183 A
.md command 26, 219
.ov command 155, 178 abs command 106, 110, 203, 204, 207, 226
.ph command 51, 200, 238 absd command 226
.ph180 command 202 absorption mode 201, 202, 242, 243, 244
.ph90 command 202 acqu command 292
.phr command 202 acquisition
.png files 27, 121, 379, 381 commands 291, 296
.pp command 232 mode 319
.pr command 25, 179 parameters 100, 101, 306
.prop files 269 status bar 294, 308
.ret command 203, 214, 226, 230, 231, 236 toolbar 290, 292
.retsab command 231 Acquisition Reference Manual 22, 104, 301,
.s2d command 203 302, 319
.sd command 41, 129, 171 AcquPars tab 100, 132, 174, 306
.sino command 273 activate
.sl command 41, 129, 171 a data window 264
.sl0 command 41, 129 the next data window 269
.sr command 41, 129, 171 add
.sr0 command 41, 129 comment to audit file 327
.sret command 203, 213, 229, 236 directory to the browser 23
.st command 185 functionalities to Topspin 31
.su command 41, 129, 171 peak in 2D phase correction 240
.tif files 121 peak to peak list 234
.txt files 162 add increment in 2D levels 183
.vr command 40, 127, 168 align
.wmf files 27, 121 intensities in multiple display 224
.y command 155 peak positions in multiple display 224
.zi command 40, 128, 170 Alt-F11 key 127, 167

I-16
Alt-F4 key 45, 53 bias correction 208
Alt-F6 key 53 bio-molecular experiments 32
Analysis menu 27, 37 bnmr command 375
apk command 106, 110, 200 INDEX bnmrsel command 375
apks command 200 bpan command 376
arrange INDEX DONEbrowser 35, 36, 45, 64, 75
data windows 265 font 362
data windows horizontally 267 in multiple display mode 220, 253
data windows vertically 266 Bruker
rows/columns in 2D phase correction 245 AU programs 32, 321
ascii files 93, 162 data format 22, 29, 30, 78, 82, 83, 92
ased command 103, 132 example datasets 23, 71
Aspect 3000 data 82 BSMS control panel 301
ATM probehead 298, 299 BSMS display window 269
atma command 299 bsmsdisp command 301
AU macros 31, 373, 374
AU program reference manual 111 C
AU programs 21, 31, 110, 319, 373, 378, 381 calibration 106
audit 1D interactive 217
trail check 326 2D interactive 259
automate data acquisition 32 mode 39, 217, 259
automatic cf command 21, 56, 316, 317, 318
1D baseline correction 106 chemical shift 224
1D calibration 106, 217 chemical shift distance
1D integration 203 1D 273
1D peak picking 232 2D 260
1D phase correction 106, 200 CHEMSTR parameter 152
2D calibration 259 C-language 31, 110, 373, 374
compilation of an AU program 322 clevels file 185
configuration of a datastation 318 clipboard 26, 45
selection of the first expno/procno 76 close
tuning and matching 299 active data window 268
automatic mode lock display window 300
of the Acquisition Guide 289 the active data window 45
of the Processing Guide 27, 108 close command 45
automation 31, 32, 319 cmdhist command 43
autoplot command 110, 117 cmdindex command 52
autostart.mac file 351 cmdtab_user.prop file 53
Avance spectrometers 17, 318 collapse a data directory 64, 69
axis units 39, 154, 178, 218, 260 color scheme 356
colors
B
of data objects 355
background of a data window 357 of the lock display 356
Backspace key 42 on the printer 355
backward peak picking 234 command
baseline correction definition 53
1D 106, 226 dialog box 96
mode 39, 226 help 50
bcm command 229 index 52

I-17
 line 41, 42, 364 plot layouts 26, 119
command line Python program 32, 374
commands 291 set of user preferences 348
focus 41, 45 INDEX user defined command 31
font 363 user notebook 372
history 42 INDEX DONEC-statements 31
preferences 364 Ctrl key 69, 76, 88, 127, 168, 219, 221
resize 365 Ctrl-c key 42, 45, 142
usage 41 Ctrl-d key 35, 45
Command Prompt 20, 317 Ctrl-f key 45
compile Ctrl-F3 key 53
AU program 322 Ctrl-F5 key 53
components Ctrl-F6 key 53
of a spectrum 26 Ctrl-n key 38, 45, 72, 305
composite commands 107 Ctrl-o key 38, 45, 77, 82
configuration Ctrl-p key 26, 38, 45, 119, 142
commands 21 Ctrl-s key 29, 38, 45, 84, 85
customized 318 Ctrl-v key 42, 45
default 318 Ctrl-w key 45
directory 318 cube display 188
name 318 cubic spline baseline correction 230
of a datastation 21 cursor information 157
of a spectrometer 21 customized configuration 318
of the acquisition status bar 294 cut integrals 212
of the tab bar 354
of the Topspin menu 367 D
password 316 data
consistency check 326 area 24, 35, 36, 75, 80, 83, 262, 265, 268
contour display 239 compression 30
of 2D spectra 182 dimensionality 36, 99, 104, 131, 132
of 3D planes 189 directory 64, 71, 88
contour levels 167, 183 field 41, 124, 129, 166
control keys 45 object colors 355
convdta command 85 data window 23, 36, 37, 75, 80, 83
convert 2D 166
data to JCAMP-DX 85 3D 188
data to text 85 color scheme 356
data to ZIP 85 contents 26, 120
copy & paste data 37, 80, 83 creation 75
copy command 26, 38, 120 handling 37, 262
copy data 84 in 1D peak picking mode 232
C-program 110 in 1D phase correction 201
create in 2D calibration mode 259
an AU program 31, 111, 321, 373 in 2D multiple display mode 252
an empty data window 75 in 2D phase mode 239, 246
data window color scheme 356 in baseline correction mode 227
dataset 38 in calibration mode 217
macro 31, 373 in integration mode 204
new data window 23 in multiple display mode 220
new dataset 72, 305

I-18
 in S/N measurement mode 274 NMR ADMINISTRATOR password 316
in spline baseline correction mode 230 NMR SUPERUSER 316
objects 26 peak ranges 233
popup menu 155, 171 INDEX peaks 234
printing 116 de-iconify
reopen 125 INDEX DONE data window 268
tab bar 1D 130 delete
tab bar 2D 174 AU program 322
toolbar 26 data 86
dataset integrals from display 210
active 264 noise region S/N 275
colors 226 peaks from a peak list 235
dir 22, 324 signal region S/N 275
directory tree 22, 79 spline baseline points 231
expno 22, 67, 72, 324 Delete key 42
files 93, 162 depth cueing in 3D 192
handling 31, 64 deselect
last 2D 38 data in multiple display 221, 222
last 3D 38 integral regions 206
last used 351 dialog box font 362
name 22, 67, 72, 80 difference spectrum
procno 22, 67, 72, 324 in baseline correction 229
procno directory 80 in multiple display 222
properties 159 dimensionality of a dataset 36, 99, 100, 104,
selection in multiple display 221 131
specification 79, 264 dir command 24
title 72 disable
top level directory 67 commands 367
user 22, 67, 72, 324 menus 367
variables 85 toolbar buttons 366
datastation Display
configuration 318 button 23, 81, 91
dcon command 30, 369 menu item 75, 76, 219
dconpeaks.txt file 30 display
deconvolution 30 1D acquisition status parameters 132
default 1D data 124
color scheme 357 1D FID 154
command line size 364 1D integral list 143
configuration 318 1D peak list 134
find criteria 90 1D processed data 130
menu font 361 1D raw data 154
pivot point in 1D phase correction 201 1D spectrum 130
pivot point in 2D phase 242 1D spectrum overview 154
plane in 3D display 188 2D contours 182
printer 118 2D data 166
Tab bar 354 2D FID 178
zero order phase correction 202 2D grid 181
define 2D integral list 176
cubic spline baseline points 230 2D peak list 175
integral regions 205 2D projections 179

I-19
 2D spectrum in contour mode 182 E
2D spectrum in oblique mode 185
2D spectrum in pseudo color mode 185 eda command 100, 101, 132, 174
3D cube 191 INDEX edasp command 104, 132
3D data 188 edau command 32, 111, 319, 322, 373
INDEX
columns in 2D phase correction 239 DONEedcpul
edit
command 134
contours in 2D phase 239
data from the browser 23, 66 AU program 322
data from the portfolio 66 commands 42
data in multiple windows 125 contour levels 183
dataset file list 160 integral ranges 208
dataset properties 159 pulse program 134
expno/procno list 76 signal/noise regions 275
found dataset 90 title of a dataset 133
full spectrum in 2D phase correction 240 Edit menu 37
integrals 25 edlev command 167, 183
JCAMP data 30 edlock command 104
manipulation 126 edmac command 31, 373
manipulations 39 edp command 27, 96, 97, 131, 174
mode of the lock window 300 edprosol command 103
molecule structure 152 edpul command 134
options 39 edpy command 32, 374
options 1D 154 edti command 133
peaks 25 ef command 107, 110
planes of 3D data 188, 189 efp command 107, 308
positive/negative 2D levels 187 em command 27, 106
processing status parameters 1D 131 email data 30
projections 25 empty data window 75
rows in 2D phase correction 239 enable
settings 38 disabled commands 369
special data formats 82 menus/commands 365
spectra 22 Enter key 47, 66
spectrum overview in 2D 178 equidistant sequence of levels 183
status parameters 99, 103 Esc key 41
sum/difference spectrum 222 execute
superimposed 1D spectra 218 AU program 319, 322
superimposed 2D spectra 251 macro 31, 373
y-axis 39, 155 Python program 32
zipped data 29 exit command 45, 54
display properties 25 expand
distance measurement a data directory 47
1D 273 data directory 23, 64
2D 260 data directory in the browser 69
mode 39 individual spectra in multiple display 224
double-headed arrow 263, 274 spectrum 30
Down-Arrow key 42, 45, 47 expand a region 24
dpa command 132 experiment time 292
dpp command 99, 103, 131 expinstall command 21, 56, 291, 316, 317, 318,
drag & drop data 80, 83 319
expl command 80, 93, 94, 162

I-20
Explorer 79, 93, 162 fromzip command 29
expno 72, 76, 79, 85, 160 ft command 27, 106
exponential ftf command 27, 367
baseline correction 228 INDEX function keys 45
window multiplication 106, 107
export data 26, 121 INDEX DONEG
expt command 292 Gaussian deconvolution 30
extend the Topspin functionality 372 Gaussian window multiplication 107
external projection 25 genfid command 85, 86
extract a row/column in 2D 257 genser command 86
geometric sequence of levels 183
F
geometry of a Topspin window 269, 270
F1 dimension 171, 178, 238 getprosol command 103, 132
F1 key 16, 45 gf command 107
F1-F2 plane 189, 192 gfp command 107
F2 dimension 171, 178, 238 Gnome Mozilla 93
F2 key 45, 68 grab rows/columns in 2D 255
F2-F3 plane 190, 192 gradient enhanced spectroscopy 31
F3 key 53 graphic functions 374
F3-F1 plane 188, 190, 192 graphics files 27, 121
F5 key 53 grid
F6 key 45, 53, 265 display 39, 181, 300
fid command 154, 178 window arrangement 265
FID display 291, 295, 303, 307 gs command 100, 293, 303
Fid tab 154, 160, 178 GS parameter adjustment window 303
File Chooser 23
File menu 23, 37 H
file size of raw data 292 halt an acquisition 291, 292
files of a dataset 80, 85, 93, 160, 162 halt command 291, 293, 307
find command 45, 89 Hardware requirements 18
find data 37, 89 helium level 301
first order phase correction Help
1D 202 button 52
2D 242, 244 menu 37, 51
fitting peaks 30 help
fmc command 107 in Topspin 50
focus 41, 45, 68, 69 on commands 52
font help command 52
of dialog windows 362 Hertz axis units 154, 178
of the browser 362 hist command 53, 57, 376, 381, 383
of the command line 363 history file 381
of the interface 359 hostname of a remote system 341
of the menu 360 HTML page 52
of the status line 363
of the tab bar 361 I
forward peak picking 234
Fourier transform 106, 107 iconify
fp command 107 all data windows 269
fromjdx command 30 data window 267
iconnmr command 32

I-21
image display modes 38
of 2D data 185 parameter adjustment 100, 303
of 3D planes 189 processing 106
import data 30 INDEX Processing Guide mode 110
inconsistent dataset 99 interface fonts 359
initial guess 285 INDEX DONEinternal projection 25
install Internet Browser 80
AU programs 21, 319 intrng file 208, 211, 214
pulse programs 21 IP address of a remote system 341
Topspin 316 IUPAC standard 30
installation directory 71, 317, 318
installnmr script 317 J
int command 158 JCAMP-DX format 30, 82, 83, 85
Integral Jeol spectrometer 82
list 2D 176 Jmol molecule structure viewer 152
integral JNMR data 82
bias 208
display 25 K
label 206
list 1D 143 KDE konqueror 93
regions 204, 205, 206, 207, 212 keyboard commands 37
scaling factor 212 kill command 60
slope 209 Konqueror 93, 162
trails 158, 212 L
values 205
Integrals tab 143, 176, 214 Left-Arrow key 42, 48, 69
integrals.txt file 214 Levenberg-Marquardt algorithm 285
integration li command 143, 204
1D automatic 203, 207 Liouville equation 31
1D interactive 203, 204, 207 lipp command 143
mode 39, 204, 213, 214 lippf command 143
intensity list 176
alignment in multiple display 224 1D integrals 143
decrease 1D 127, 167 2D integrals 176
increase 1D 127, 167 2D peaks 175
manipulation 39 AU programs 319
reset 1D 40, 127, 167 baseline points 230
scaling 2D 168 Bruker AU programs 321
interactive color schemes 357
1D baseline correction 226 data files 92, 160
1D calibration 217 EXPNOS/PROCNOS 76
1D data manipulation 198 found data 90
1D integration 203 integrals 119, 213
1D peak picking 232 macros 31
1D phase correction 198, 200 opened datasets 66, 67, 68
1D signal to noise calculation 273 parameter sets 72
2D calibration 259 peaks 119, 234
2D data manipulation 238 peaks 1D 134
2D phase correction 238 plot layouts 117
data manipulation 27, 38, 354 solvents 72

I-22
 user defined AU programs 321 move
local data window 263
Topspin interface 338 Mozilla 93, 162
lock INDEX multiple display
parameters 104 1D 39, 218, 251
signal 300 INDEX DONE 1D/2D 26, 76, 81
lock command 301 2D 26, 251
lock display in deconvolution 30
colors 356 multiple display mode 76, 218
mode 300 multiple window display 125
window 269, 292, 295, 299 multiplet 205
lockdisp command 292, 299 multiply with increment in 2D levels 183
lock-in procedure 300
Lorentzian deconvolution 30 N
lower toolbar 39 nbook command 372
negative
M
2D levels 187
macros new command 38, 45, 72, 305
in AU programs 110, 374 newtop command 54
in Topspin 31, 53, 107, 373, 378, 381 next
magnitude calculation 107 channel for wobbling 299
matching the probehead 298 command 45
MAXI parameter 234 dataset in Browser 47
maximize parameter field 99, 103
all data windows 269 plane in 3D 190
data window 268 row/column in 2D phase correction 244, 256
maximum window in data area 45, 265, 269
command line size 365 NMR ADMINISTRATION password 316
MC2 parameter 100 NMR SUPERUSER 316
menu nmradminpassword file 316
bar 37 nmrsim command 31
commands 37 nmrsuperuser file 316
configuration table 367, 369 noise region 273, 274
entries 37, 367 NOISF1 parameter 273
font 360, 361 NOISF2 parameter 273
settings 348 notebook 372
MI parameter 234 NS parameter 291
minimize
data window 267 O
minimum O1 parameter 292
command line size 365 O2 parameter 292
Minus key 48 O3 parameter 292
mixtures 31 objects
molecule structure viewer 152 of a dataset 26, 125, 263, 348, 354, 355, 356
mouse sensitivity oblique display
in 1D baseline correction 229 of 2D spectra 185, 187
in 1D integration 209 of 3D planes 189
in 1D phase correction 203 online help 51
in 2D phase correction 244 online manual

I-23
 plot editor 119 position 273
Topspin 50 position alignment 224
open ranges 236
browser/portfolio 68 INDEX peak picking
data 38, 45, 64, 75, 77 1D automatic 232
data from the browser 23 INDEX DONE 1D interactive 232
data from the command line 80, 83 mode 39
data from the Explorer 79 mode 1D 232
data from the menu 23 ranges in 1D 233, 234
IconNmr interfaces 32 peak.txt file 236
Linux Shell 20 peakrng file 236
new data window 265 Peaks tab 119, 134, 175
new procno 81 phase correction
online help documents 51 1D automatic 106, 107
special format data 82 1D interactive 200
Topspin command index 52 2D interactive 238
open command 38, 45, 77, 82 first order 1D 202
Options menu 37 mode 39
overview spectrum mode 1D 201
1D 154 mode 2D 239
2D 178 pivot point in 1D 201
values 1D 203
P zero order 1D 202
paper format 319 PHC0 parameter 98, 202, 243
paracon command 319 PHC1 parameter 202, 244
parameter pivot point
adjustment window 100, 303 in 1D phase correction 201
change 99, 103, 104 in 2D phase correction 242
display 25 pk command 203
editor 96, 97, 100, 101 plane display in 3D 189
field 98, 99, 102, 103 plot
files 92 data from the menu 116
handling 96 data from the Plot Editor 119
name 96, 100 data from the Processing Guide 118
search 131, 132 layouts 26
value 98, 102 plot command 117, 119
parameter set 72, 85 Plot Editor 26, 117
PARMODE parameter 132 Plus key 48
paste command 38, 80, 83 polynomial
peak baseline correction 227
alignment 26, 224 position
display 25 of a Topspin window 270
fitting 30 position of a Topspin window 269
group 30 position the baseline of a row/column in 2D 258
labels 158, 159, 234 positive
list 235, 236 2D levels 187
list 1D 134, 234 pp command 142, 158, 159
list 2D 175 PPARMOD parameter 99, 104, 131
picking mode 232 ppl command 234
ppm axis units 154, 178

I-24
pps command 232 Python programs 32, 374, 378, 381
preferences 37, 348
pre-scan-delay 319 Q
preview INDEX QUIT AU macro 111
the baseline corrected spectrum 228 QUITMSG AU macro 111
previous INDEX DONE
commands 42 R
dataset in browser 47
parameter field 99, 103 re command 24, 80, 219
plane in 3D 190 read
row/column in 2D phase correction 244, 256 color scheme 357
print data formats 82
1D peak list 142 integrals from disk 207
active window 26, 117 the prosol parameters 306
colors 356 window layout 269
data from the menu 116 reb command 23, 81
data from the Processing Guide 118 re-enable disabled commands 369
integral list 119 reference peak
metafiles 120 in 1D calibration 218
peak list 119 in 1D phase correction 201, 202
the current dataset 45 in 2D calibration 260
print command 38, 45, 116, 119, 142 in 2D phase correction 242
printer colors 355 referencing 106
prnt command 117 reg file 213
probehead/solvent dependent parameters 103 relaxation
proc_1d AU program 110 curve 280
process data 27, 37 remote connections 348
from the command line 106 remove
from the Processing Guide 107 commands 367
with AU programs 110 data from multiple display 222
with composite commands 107 menus 367
processing toolbar buttons 366
parameters 96, 97 reopen a dataset 125
parameters 1D 131 reopen command 74, 125
parameters 2D 174 rep command 24, 81
Processing Guide 27, 108, 110 repw command 81
Processing menu 27, 37 rescale
Processing Reference Manual 24 2D projection 180
procno 76, 81, 85, 93, 161 data in multiple windows 126
ProcPars tab 27, 96, 97, 131, 174 reset
projections of a 2D spectrum 25, 179 1D baseline correction 229
properties 1D phase values 202
of a dataset 159 3D cube size and orientation 192
of a printer 117 F1 zoom factor in 2D 170
prosol parameters 306 F2 and F1 zoom factor 170
pseudo raw data 85 intensity 1D 127
pulse program 21, 31, 69, 134 intensity in 2D 168
display 134 search mask 90
parameters 103, 132, 306 zoom factor 40, 128
PulsProg tab 134 resize

I-25
 command line 365 2D spectrum 167
data window 263 3D cube 192
graphics 120 individual spectra in multiple display 26, 218,
INDEX
resolution of a screen dump 27, 121 224
restore row/column in 2D phase 243
INDEX
adjusted acquisition parameters (GS) 305 DONEscaling factor
size and position of a data window 268 of integrals 212
toolbar 367 scan
uncorrected baseline 229 planes of 3D data 190
retrieve rows/columns in 2D 255
previously entered commands 42 screen dump 27, 121
rew command 24, 81 scroll bar 99, 103
Right-Arrow key 42, 48, 69 search
rotate 3D cube 187, 191 criteria 89
routing parameters 104 data 89
field in the parameter editor 98, 102
S result window 90
S/N value 275 select
Sample tab 151 AU program 322
sav command 38, 45 color scheme 357
save data 64
1D baseline correction 229 data in multiple display 219, 221
1D integrals 213 data window 264
1D phase correction 203 default printer 319
acquisition data 85 expno/procno combination 76
adjusted acquisition parameters (GS) 304 first expno/procno 76
AU program 32 folders in the browser 69
color scheme 356 font 361, 362, 363
cubic spline baseline points 231 integral regions 206, 208
current window layout 269 lock signal color 356
data 29, 38, 45, 84 multiple datasets 76
data in analog filtered format 85 multiple folders 69
data to a JCAMP-DX file 30 peaks in 2D phase correction 239
data to a ZIP file 29 plot layout 117
data window to a graphics file 27, 121 printer 117
entire dataset 84, 85 remote system 342
integral regions 213 row/column in 2D phase 242
macro 31 spectra in 2D multiple display 254
parameters 131, 132 spectrum color 355
peak list and peak ranges 236 spectrum print color 356
phase correction 2D 242, 245, 251 Topspin window 270
processed data 85 selective excitation 31
processed data as pseudo raw data 85 semi-automatic
pulse program 151 peak picking 234
sum or difference spectrum 222 processing 107
title of a dataset 133 sensitivity
scale of the GS slider 303
1D integrals 211 of the mouse 203, 209, 229, 244
1D spectrum 127 serial command 111
serial processing 111

I-26
Server ID 341 slope correction 208
set smail command 30, 38
1D acquisition parameters 132 smooth
2D acquisition parameters INDEX
174 1D phase correction 243
2D processing parameters 174 1D scaling 40
INDEX
colors for multiple display 226 DONE 1D shifting 129
contour levels 183 1D zooming 40, 128
lock parameters 104 1D/2D shifting 41
phase pivot point 201 2D shifting 171
processing parameters 96 scaling of 1D integrals 211
processing parameters 1D 131 scanning of planes in 3D 190
routing parameters 104 shifting of 1D integrals 212
user preferences 349 solvent 72
set command 130, 348 spec command 130
SFO1 parameter 292 special format data 30
Shell 20 spectrometer
shift frequency 292
1D data down 129 spectrometer hardware 21, 22
1D data smoothly 129 Spectrometer menu 37, 290
1D data to the extreme left 129 spectrum
1D data to the extreme right 129 display 1D 130
1D data to the left 129 objects 348, 349
1D data to the right 129 overview 1D 154
1D data up 129 overview 2D 178
1D/2D data 41, 48 Spectrum tab 130, 154, 161
2D data down 171 square 2D layout 169
2D data smoothly 171 square brackets 37, 51, 125, 130
2D data to the left 171 sref command 106, 110, 217, 259
2D data to the right 171 stacked multiple display 224
2D data up 171 Start button 79
data in multiple windows 126 startup actions 348
individual spectra in multiple display 26, 218, status line font 363
224 status parameter
row/column in 2D phase 243 change 100
Shift key 69, 76, 88, 219, 222 display 103, 158
Shift-Tab key 99, 103 display 1D 131, 132
short description stdisp command 311
of an AU program 322 stop an acquisition 291
shortcuts for processing 107 stop command 291, 293, 307
show command 60 store
SIGF1 parameter 273 2D contour levels 184
SIGF2 parameter 273 structure file 152
signal region 273, 274 Structure tab 152
signal to noise calculation 273 sum spectrum
Simplex algorithm 285 in multiple display 222
simulating experiments 31 superimpose
sine 1D spectra 218
baseline correction 228 cursor information 157
single commands 106 electronic signature 159
slider sensitivity 303 integral trails/labels 158

I-27
 main status parameters 158 Topspin
peak labels 158 color schemes 357
spectra 26 data area 80, 83
title of a dataset 158 INDEX fonts 360
SW parameter 292 help 50
swap data windows 270 INDEX DONE installation 318
sweep width 292 installation directory 318
swin command 270 startup 18, 20
switch tailoring 348
to the last 2D data 38 window 35
to the last 3D data 38 topspin command 20
Topspin icon 20
T totxt command 85
T1 calculation 16 tozip command 29, 85
T1/T2 Relaxation 280 tshome directory 20, 51, 318
t1guide command 280 tuning the probehead 298
T2 calculation 16
U
Tab bar
1D 125, 130 undo
2D 167, 174 last parameter change 99, 103
configuration 130, 354 last region operation 213
font 361 unzip utility 30
usage 130 Up-Arrow key 42, 45
Tab key 99, 103 upper toolbar
tabbed pane 174, 354 1D 38, 198
TCP/IP port 340 2D 238
temperature unit window 269 user defined
Terminal Window 20 AU programs 319
time domain signal 31 buttons 378, 381, 383
title bar 124, 125, 166, 263, 264, 267, 268, 269, commands 27, 31
322 functions keys 53
title file 133 plot layouts 118
title of a dataset 25, 69, 72, 133, 158, 305, 356 User Interface functions 374
Title tab 133 user preferences 348
toccpn command 85 user properties directory 53
tojdx command 30, 85
toolbar V
1D 198 Varian spectrometer 82
2D 238 vertical scaling 127, 168
configuration 366 View menu 37, 157
extension 378 virtual spectrometer 31
for acquisition 290 VNMR data 82
icons 379, 381
of the data window 26, 154 W
of the FID display window 307
tips 51 walk-up 32
usage 38 wbst command 299
tooltips 50, 51 wbsw command 299
top level directory 23, 64, 71 wildcards 88
window layout 269

I-28
Window menu 37, 270
WINNMR data 82
wm command 27, 96
wmisc command 85 INDEX
wobb command 293, 298
wobble INDEX DONE
display 295
frequency 299
procedure 298
steps 299
sweep width 299
window 298
wpar command 85
wra command 85
wrp command 85
wrpa command 29, 84, 85
X
xau command 322
x-axis rotation in 3D 187, 191
xmac command 31
Y
y-axis display 39, 155
y-axis rotation in 3D 187, 191
Z
z-axis rotation in 3D 191
zero order phase correction
1D 202
2D 242, 243
zg command 291, 293, 306
ZIP data format 29, 82
zoom
1D data 40, 128
2D data 170
in 2D phase correction 240
zoom 1D/2D data 48

I-29
INDEX
INDEX DONE

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