TOPSPIN Users Guide Copyright (C) 2005 by Bruker BioSpin GmbH All rights reserved. No part of this publication may be reproduced, stored in a retrieval sys- tem, or transmitted, in any form, or by any means without the prior consent of the publisher. Part Number H9469SA1 V2/January 31st 2005 Product names used are trademarks or registered trademarks of their respective holders. INDEX DONE INDEX Bruker software support is available via phone, fax, e-mail, Internet, or ISDN. Please contact your local office, or directly: Address: Bruker BioSpin GmbH Software Department Silberstreifen D-76287 Rheinstetten Germany Phone: +49 (721) 5161 455 Fax: +49 (721) 5161 943 E-mail: [email protected] FTP: ftp.bruker.de / ftp.bruker.com WWW: www.bruker-biospin.de / www.bruker-biospin.com Chapter 1 Getting Started . 15 1.1 Document Conventions . 15 Font Conventions . 15 File/directory Conventions . 15 User Action Conventions . 15 1.2 TOPSPIN Overview . 16 Functionality . 16 Available Documentation . 17 1.3 TOPSPIN license . 17 1.4 Startup TOPSPIN . 18 1.5 Configuration . 18 1.6 How to Display Spectra . 19 How to Open Data from the Menu . 19 How to Open Data from the Browser . 20 How to Define Alias Names for Data . 20 How to Open Data in Other Ways . 20 1.7 How to Display Peaks, Integrals, ... together with the Spectrum . 20 1.8 How to Display Projections/1D Spectra with 2D Spectra . 21 1.9 How to Superimpose Spectra in Multiple Display . 21 1.10 How to Print or Export the Contents of a Data Window . 22 How to Print Data . 22 How to Copy a Data Window to Clipboard . 22 How to Store (Export) a Data Window as Graphics File . 22 1.11 How to Process Data . 22 1.12 How to Archive Data . 23 1.13 How to Import NMR Data Stored in Special Formats. 24 1.14 How to Fit Peaks and Deconvolve Overlapping Peaks . 24 1.15 How to Compute Fids by Simulating Experiments . 24 1.16 How to Add Your Own Functionalities . 25 How to Create Macros . 25 How to Create AU (automation) Programs . 25 How to Create Python Programs . 26 1.17 How to Automate Data Acquisition. 26 Chapter 2 The TOPSPIN Interface . 27 2.1 The Topspin Window. 27 How to Use Multiple Data Windows . 28 How to Use the Title bar . 29 How to Use the Menu bar . 29 How to Use the Upper Toolbar . 30 How to Use the Lower Toolbar . 31 2.2 Command Line Usage . 33 3 4 How to Put the Focus in the Command Line . 33 How to Retrieve Previously Entered Commands . 33 HowINDEX to Change Previously Entered Commands . 33 How to Enter a Series of Commands . 34 2.3 CommandINDEX Line HistoryDONE . 34 2.4 Starting TOPSPIN commands from a Command Prompt . 35 2.5 Function Keys and Control Keys. 36 2.6 Help in Topspin . 39 How to Open Online Help documents . 39 How to Get Tooltips . 39 How to Get Help on Individual Commands . 40 How to Use the Command Index . 40 2.7 User Defined Functions Keys . 41 2.8 How to Open Multiple TOPSPIN Interfaces . 41 Chapter 3 Trouble Shooting . 43 3.1 General Tips and Tricks . 43 3.2 History, Log Files, Stack Trace . 43 3.3 How to Show or Kill TOPSPIN processes . 47 3.4 What to do if TOPSPIN hangs . 47 3.5 How to Restart User Interface during Acquisition . 48 Chapter 4 Dataset Handling . 49 4.1 The Topspin Browser and Portfolio. 49 How to Open the Browser/Portfolio . 51 How to Open the Browser/Portfolio in a separate window . 51 How to Put the Focus in the Browser/Portfolio . 51 How to Select Folders in the Browser . 51 How to Expand/Collapse a Folder in the Browser . 52 How to Expand a Folder showing Pulse program and Title . 52 How to Add/Remove a Top Level Data Directory . 53 How to Open a New Portfolio . 53 How to Save the current Portfolio . 54 How to Remove Datasets from the Portfolio . 54 How to Find Data and Add them to the Portfolio . 54 How to Sort Data in the Portfolio . 54 How to Add, Remove or Interpret Alias Names . 55 4.2 Creating Data . 56 How to Create a New Dataset . 56 4.3 Opening Data . 57 How to Open Data Windows Cascaded . 58 How to Open Data from the Browser . 59 How to Open Data from the Portfolio . 60 5 How to Automatically Select the first expno/procno of a dataset . 60 How to Open Data from the Topspin menu . 61 HowINDEX to Open Data from the Explorer, Konqueror or Nautilus . 63 How to Open Data from the Command Line . 64 HowINDEX to Open SpecialDONE Format Data . 65 How to Open a ZIP or JCAMP-DX file from the Windows Explorer . 66 4.4 Saving/Copying Data . 66 How to Save or Copy Data . 66 How to Save an Entire Dataset . 67 How to Save Processed Data . 68 How to Save Acquisition Data . 68 How to Save Processed Data as Pseudo Raw Data . 68 4.5 Deleting Data . 68 How to Delete a Specific Dataset . 68 How to Delete Types of Datasets . 69 4.6 Searching/Finding Data . ..