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TopSpin

User Manual

Version 003

NMR

Innovation with Integrity

Copyright ? by Bruker Corporation 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 the prior consent of the publisher. Product names used are trademarks or registered trademarks of their respective holders.

This manual was written by NMR Software Department ? June 30, 2016 Bruker Corporation

Document Number: SM/User3.0.4 P/N: H9469SA3

For further technical assistance for this product, please do not hesitate to contact your nearest BRUKER dealer or contact us directly at: Bruker Corporation Am Silberstreifen 76287 Rheinstetten Germany Phone: +49 721 5161 0 E-mail: nmr-support@ Internet:

Contents

Contents

1 Introduction......................................................................................................................................... 9

1.1

About the User Manual ....................................................................................................... 9

1.2

Safety Regulations.............................................................................................................. 9

1.3

User Manual Conventions................................................................................................. 10

1.4

TopSpin Overview............................................................................................................. 11

1.5

TopSpin License ............................................................................................................... 12

1.6

TopSpin Program Versions............................................................................................... 12

2 Getting Started.................................................................................................................................. 13

2.1

Startup TopSpin ................................................................................................................ 13

2.2

Configuration..................................................................................................................... 13

2.3

How to Display Spectra..................................................................................................... 14

2.4

How to Expand a Spectral Region .................................................................................... 15

2.5

How to Display Peaks, Integrals, ... together with the Spectrum ...................................... 16

2.6

How to Display Projections/1D Spectra with 2D Spectra.................................................. 16

2.7

How to Superimpose Spectra in Multiple Display ............................................................. 16

2.8

How to Print or Export the Contents of a Data Window .................................................... 17

2.9

How to Process Data ........................................................................................................ 17

2.10

How to Archive Data ......................................................................................................... 18

2.11

How to Import NMR Data Stored in Special Formats ....................................................... 19

2.12

How to Fit Peaks and Deconvolve Overlapping Peaks..................................................... 19

2.13

How to Compute FIDS by Simulating Experiments .......................................................... 19

2.14

How to Add Your Own Functionalities .............................................................................. 19

2.15

How to Automate Data Acquisition ................................................................................... 20

3 The TopSpin Interface...................................................................................................................... 21

3.1

New Flow User Interface with TopSpin 3.0....................................................................... 21

3.2

The TopSpin Window........................................................................................................ 21

3.3

Command Line Usage ...................................................................................................... 25

3.4

Command Line History ..................................................................................................... 26

3.5

Starting TopSpin commands from a Command Prompt ................................................... 27

3.6

Function Keys and Control Keys....................................................................................... 27

3.7

Help in TopSpin ................................................................................................................ 31

3.8

User Defined Functions Keys ........................................................................................... 33

3.9

How to Open Multiple TopSpin Interfaces ........................................................................ 33

4 Troubleshooting ............................................................................................................................... 35

4.1

General Tips and Tricks.................................................................................................... 35

4.2

History, Log Files, Spooler Reports, Stack Trace ............................................................. 35

4.2.1

Topspin Command Log..................................................................................................... 35

4.2.2

Topspin Spooler Report .................................................................................................... 35

4.2.3

Topspin Command, Data Server and Network Log .......................................................... 35

4.2.4

Create a Stack Trace ........................................................................................................ 37

4.2.5

Store Complete Log with => savelogs .............................................................................. 37

4.3

How to Show or Kill TopSpin Processes........................................................................... 37

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Contents

4.4

What to do if TopSpin Hangs ............................................................................................ 38

4.5

How to Restart User Interface During Acquisition............................................................. 38

5 Dataset Handling .............................................................................................................................. 39

5.1

The Topspin Browser........................................................................................................ 39

5.2

Creating Data.................................................................................................................... 45

5.3

Opening Data.................................................................................................................... 46

5.4

Saving/Copying Data ........................................................................................................ 52

5.5

Deleting Data .................................................................................................................... 54

5.6

Renaming Data ................................................................................................................. 54

5.7

Searching/Finding Data .................................................................................................... 55

5.8

Handling Data Files........................................................................................................... 58

6 Parameter Handling.......................................................................................................................... 61

6.1

Processing Parameters..................................................................................................... 61

6.2

Acquisition Parameters ..................................................................................................... 63

7 Data Processing ............................................................................................................................... 67

7.1

Interactive Processing....................................................................................................... 67

7.2

Semi-automatic Processing .............................................................................................. 67

7.3

Processing Data with AU programs .................................................................................. 70

7.4

Serial Processing .............................................................................................................. 70

8 Printing/Exporting Data ................................................................................................................... 75

8.1

Printing/Plotting Data ........................................................................................................ 75

8.2

Exporting Data .................................................................................................................. 77

9 1D Display ......................................................................................................................................... 81

9.1

The 1D Data Window........................................................................................................ 81

9.2

Displaying one Dataset in Multiple Windows .................................................................... 81

9.3

Changing the Display of a 1D Spectrum or FID................................................................ 82

9.4

Using the Tab Bar ............................................................................................................. 84

9.4.1

2D molecule structure editor ............................................................................................. 97

9.5

1D Display Options ........................................................................................................... 99

9.6

Show Display Properties/Regions/Files .......................................................................... 100

9.7

Saving Display Region.................................................................................................... 102

9.8

Synchronize Visible Region of all Data Windows ........................................................... 103

10 2D Display ....................................................................................................................................... 105

10.1

The 2D Data Window...................................................................................................... 105

10.2

Changing the Display of a 2D Spectrum......................................................................... 105

10.3

Show Display Properties/Regions/Files .......................................................................... 108

10.4

Using the Tab Bar ........................................................................................................... 108

10.5

2D Display Options ......................................................................................................... 111

11 nD Display ....................................................................................................................................... 117

11.1

Display Planes of 3D Data .............................................................................................. 117

11.2

3D Cube Display Mode ................................................................................................... 118

11.3

nD Parameter Display..................................................................................................... 120

11.4

nD FID Display................................................................................................................ 121

11.5

nD Peak and Integral Display ......................................................................................... 121

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12 1D Interactive Manipulation........................................................................................................... 123

12.1

1D Interactive Window Multiplication .............................................................................. 123

12.1.1 1D Interactive Window Multiplication Procedure............................................................. 123

12.2

1D Interactive Phase Correction ..................................................................................... 125

12.2.1 1D Interactive Phase Correction Procedure ................................................................... 125

12.2.2 1D Interactive Phase Correction Details ......................................................................... 126

12.3

1D Interactive Integration................................................................................................ 127

12.4

1D Interactive Calibration................................................................................................ 136

12.5

1D Multiple Display ......................................................................................................... 137

12.6

1D Interactive Baseline Correction ................................................................................. 143

12.7

1D Interactive Peak Picking ............................................................................................ 147

13 2D Interactive Manipulation........................................................................................................... 151

13.1

2D Interactive Phase Correction ..................................................................................... 151

13.1.1 2D Interactive Phase Correction Procedure ................................................................... 151

13.1.2 2D Interactive Phase Correction Details ......................................................................... 153

13.2

2D Interactive Integration................................................................................................ 156

13.2.1 How to Switch to 2D Interactive Integration .................................................................... 156

13.2.2 2D Interactive Integration Procedure .............................................................................. 157

13.3

2D Multiple Display and Row/Column Handling ............................................................. 159

13.3.1 2D Calibration in Multiple Display ................................................................................... 164

13.4

2D Interactive Calibration................................................................................................ 165

14 Data Window Handling................................................................................................................... 169

14.1

Data Windows................................................................................................................. 169

14.2

Window Layouts.............................................................................................................. 173

15 Analysis........................................................................................................................................... 175

15.1

Introduction ..................................................................................................................... 175

15.2

Chemical Shift Distance Measurement........................................................................... 175

15.3

1D Signal to Noise Calculation ....................................................................................... 175

15.4

Deconvolution ................................................................................................................. 177

15.5

Relaxation Analysis......................................................................................................... 179

16 Acquisition ...................................................................................................................................... 185

16.1

Acquisition Guide ............................................................................................................ 185

16.2

Acquisition Toolbar ......................................................................................................... 185

16.3

Data Window Toolbar ..................................................................................................... 187

16.4

Acquisition Status Bar..................................................................................................... 188

16.5

Command Queuing and Scheduling ............................................................................... 189

16.6

Tuning and Matching the Probe...................................................................................... 190

16.7

Locking............................................................................................................................ 191

16.8

BSMS Control Panel ....................................................................................................... 191

16.9

Interactive Parameter Adjustment (GS) .......................................................................... 192

16.10 Running an Acquisition ................................................................................................... 193

16.11 Shape Tool...................................................................................................................... 196

17 Configuration/Automation ............................................................................................................. 201

17.1

NMR Super User and NMR Administration Password.................................................... 201

17.2

Configuration................................................................................................................... 202

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