Delta Users Guide

DELTA Users Guide, v 3.2

Delta NMR SoftwareUsers Guide

Copyright 1990-2000 by JEOL USA, INC.Eleven Dearborn Road

Peabody, MA 01960-3823All Rights Reserved


Trademarks GLTM, Indigo, Indigo MagicTM, Indigo2TM,IRIX, OpenGL, SGITM, Silicon

Graphics Octane, and Silicon Graphics are trademarks of Silicon Graphics, Inc. UNIX is a trademark registered in the United States and other countries, licensed

exclusively through X/Open Company, Ltd. X Window System is a trademark of Massachusetts Institute of Technology. Motif is a trademark of Open Software Foundation, Inc. PostScript is a trademark of Adobe Systems Incorporated All other company and product names are trademarks or registered trademarks of their

respective companies.


Table of Contents

Table of Contents................................................................................................................. iList of Figures .................................................................................................................... ixList of Tables ................................................................................................................... xiiiChapter 1. Introduction................................................................................................... 1-1

Introduction................................................................................................................ 1-1About This Guide....................................................................................................... 1-1Before You Begin ...................................................................................................... 1-1Special Symbols......................................................................................................... 1-1Font Conventions ....................................................................................................... 1-1Keystroke Conventions.............................................................................................. 1-2Color Conventions ..................................................................................................... 1-2

Chapter 2. User Interface Basics .................................................................................... 2-1Power-on .................................................................................................................... 2-1Login .......................................................................................................................... 2-1Mouse and Keyboard ................................................................................................. 2-3

Input Focus........................................................................................................... 2-3Keyboard.............................................................................................................. 2-3Structure of a Window......................................................................................... 2-3

Window Menu Buttons .............................................................................................. 2-4Iconifying or Minimizing Windows....................................................................... 2-5Maximizing Windows to Full Screen ........................................................................ 2-6Moving Windows....................................................................................................... 2-6Resizing Windows ..................................................................................................... 2-6Toolchest.................................................................................................................... 2-6Workstation System Usage ........................................................................................ 2-8Terminal Shell............................................................................................................ 2-8Logout Window ......................................................................................................... 2-9

Chapter 3. Getting Started On Delta .............................................................................. 3-1Introduction................................................................................................................ 3-1Starting DELTA......................................................................................................... 3-1The Delta Console...................................................................................................... 3-2The Delta Console Menu Bar .................................................................................... 3-3

Pull-Down Menus ................................................................................................ 3-3Accelerator Keys.................................................................................................. 3-3

Tool Bar Icons............................................................................................................ 3-3Exiting Delta .............................................................................................................. 3-6On-line Help .............................................................................................................. 3-6Preferences Tool ........................................................................................................ 3-7File Manager ............................................................................................................ 3-15File Converter .......................................................................................................... 3-17

Chapter 4. Eclipse Spectrometer Control ....................................................................... 4-1


Introduction................................................................................................................ 4-1Spectrometer to Host Workstation Communication .................................................. 4-1Spectrometer Control Tool ........................................................................................ 4-2Selecting a Spectrometer............................................................................................ 4-2

Default Spectrometer Connection........................................................................ 4-5Spectrometer Control Tools....................................................................................... 4-7 Spectrometer Control Tools...................................................................................... 4-9Sample Control Tool.................................................................................................. 4-9

Shim Tool Controls............................................................................................ 4-13Queue Management ................................................................................................. 4-21

Experiment Data ................................................................................................ 4-22Additional Experiment Information................................................................... 4-23 Deleting Queue items........................................................................................ 4-23

Experiment Tool ...................................................................................................... 4-24 Experiment Selection ........................................................................................ 4-25Local Experiment Directory .............................................................................. 4-25Global Experiment Directory............................................................................. 4-25Loading an Experiment...................................................................................... 4-26The Header Section............................................................................................ 4-26The Instrument Section ...................................................................................... 4-29The Acquisition Section..................................................................................... 4-30The Pulse Section............................................................................................... 4-31

Automation Window................................................................................................ 4-34Automation Queue ............................................................................................. 4-37

Automation Console ................................................................................................ 4-38Automation Editor ................................................................................................... 4-39

Methods for Customizing Automation .............................................................. 4-41Lock Signal Display - Sawtooth .............................................................................. 4-43View Tool ................................................................................................................ 4-44Copy......................................................................................................................... 4-46

Chapter 5. Processing 1D Data....................................................................................... 5-1Introduction................................................................................................................ 5-11D Processor .............................................................................................................. 5-2

Default Start-up Mode ......................................................................................... 5-31D Processor Start-Up Procedure .............................................................................. 5-4

The Open File Tool.............................................................................................. 5-41D Processor Window - Extended Mode................................................................... 5-6

Processing Lists ................................................................................................... 5-7Extended Mode Icon Buttons - Top Row .......................................................... 5-10Extended Mode 1D Processing Icons -- Second Row ....................................... 5-13

Menus for Extended 1D Processing......................................................................... 5-14PreTransform Functions..................................................................................... 5-14Window Functions ............................................................................................. 5-17Transform Functions.......................................................................................... 5-17

Cursor Tool .............................................................................................................. 5-19Cursor Modes........................................................................................................... 5-22


Zoom, Region, PiP -- a Sampler ........................................................................ 5-23 Menus for Extended 1D Processing........................................................................ 5-26

Post Transform Functions .................................................................................. 5-26Display Functions .............................................................................................. 5-33Integrals.............................................................................................................. 5-46Peak Deconvolution ........................................................................................... 5-51Annotation.......................................................................................................... 5-55Molecules........................................................................................................... 5-57

Data Window Manipulations: Level Tool ............................................................... 5-59Data Window Manipulations: Geometry Options Menu......................................... 5-60Data Information Display: Spreadsheet Tool .......................................................... 5-64

Loading Data into the Spread Sheet................................................................... 5-65Drag and Drop.................................................................................................... 5-65

Saving Processed Data............................................................................................. 5-66Plotting Data ............................................................................................................ 5-67Presentation Manager............................................................................................... 5-69

Presentation Manager Templates....................................................................... 5-70Presentation Manager Boxes.............................................................................. 5-72Ruler Links Tool ................................................................................................ 5-72

Presentation Manager Menus................................................................................... 5-77Presentation Manager Tool Bar ............................................................................... 5-77Simple Mode 1D Processing.................................................................................... 5-78

Simple Mode Processor Buttons........................................................................ 5-79Chapter 6. Using Data Slate ........................................................................................... 6-1

Loading Data into the Data Slate ............................................................................... 6-2Data Source Toggle Buttons ................................................................................ 6-2

Loading Multiple Data Files ...................................................................................... 6-3Horizontal and Vertical Views............................................................................. 6-3Box Data View..................................................................................................... 6-4

Selecting Active Data Sets......................................................................................... 6-5Data Slate Icons ......................................................................................................... 6-7

The File Math Tool ............................................................................................ 6-10Connected Objects ................................................................................................... 6-11

Individual Data Presentation Control................................................................. 6-12Panning, Rotating and Expanding Data ............................................................. 6-13

Peak Picking, Data Reduction and Integration ........................................................ 6-14Peak Deconvolution ........................................................................................... 6-14

Annotation................................................................................................................ 6-14Spreadsheet Tool...................................................................................................... 6-14Plotting Data ............................................................................................................ 6-14Connect Options on the View Menu........................................................................ 6-15Advanced Data Slate Operations ............................................................................. 6-15

Slicing ................................................................................................................ 6-15Expansion........................................................................................................... 6-17

Chapter 7. Processing 2D Data....................................................................................... 7-1


Introduction................................................................................................................ 7-1Loading 2D Data into the nD Processor .................................................................... 7-1Elements of 2D Processing ........................................................................................ 7-3Preparing 2D Processing Lists ................................................................................... 7-5

Selecting a Data Output destination..................................................................... 7-8Toggling between processing list view and geometry view: ............................... 7-9Selecting Preferences ........................................................................................... 7-9

Loading and Processing 1D Slices............................................................................. 7-9Phasing 2D Data ...................................................................................................... 7-10

2D Phasing Tool ................................................................................................ 7-102D Viewer Tool ....................................................................................................... 7-13

Two Dimensional Display Modes ..................................................................... 7-142D Cursor Tool functions .................................................................................. 7-17Contouring 2D Data........................................................................................... 7-17Overview Area ................................................................................................... 7-21Zooming and Panning 2D Data.......................................................................... 7-21Slice and Projection Areas ................................................................................. 7-22

2D Peak Pick and Data Reduction ........................................................................... 7-23Peak Grouping ................................................................................................... 7-25Peak Melding ..................................................................................................... 7-26Integrating 2D Data............................................................................................ 7-27Annotating 2D Spectra....................................................................................... 7-27Spreadsheet Tool................................................................................................ 7-30Plotting 2D Data ............................................................................................... 7-30

Chapter 8. Processing Relaxation Data .......................................................................... 8-1Introduction................................................................................................................ 8-1Collecting Relaxation Data ........................................................................................ 8-1Collecting T1 Data..................................................................................................... 8-3Calculating Relaxation Times.................................................................................... 8-3

Chapter 9. Processing 3D Data....................................................................................... 9-1Introduction................................................................................................................ 9-1Loading 3D Data into the nD Processor .................................................................... 9-1Elements of 3D Processing ........................................................................................ 9-2

Domains ............................................................................................................... 9-2Processing Lists ................................................................................................... 9-3Creating a Processing List ................................................................................... 9-5Building and Manipulating Processing Lists ....................................................... 9-6Editing a Processing List ..................................................................................... 9-6Loading and Processing 1D Slices....................................................................... 9-7

3D Data Slate ............................................................................................................. 9-83D Viewer.................................................................................................................. 9-8

Three-Dimensional Display Modes ................................................................... 9-10Loading 3D Data................................................................................................ 9-12

3D Slicer .................................................................................................................. 9-12Multidimensional geometry options .................................................................. 9-13


3D Slice Plotter ........................................................................................................ 9-13Cursor Tool ........................................................................................................ 9-15Rotating and Translating 3D Data ..................................................................... 9-18Slice and Projection Areas ................................................................................. 9-183D Peak Pick and Data Reduction ..................................................................... 9-18

Chapter 10. Experiment Tool and Eclipse Experiment Programming......................... 10-1Introduction.............................................................................................................. 10-1Definition ................................................................................................................. 10-1

Pulse Sequences ................................................................................................. 10-2Parameter Files................................................................................................... 10-2

Loading Experiments ............................................................................................... 10-2Spectrometer Control Tool ................................................................................ 10-2

Experiment Tool ...................................................................................................... 10-5Loading Experiments from Other Data Sets...................................................... 10-5

Syntax and Operators............................................................................................... 10-7Syntax Rules ...................................................................................................... 10-7Operators............................................................................................................ 10-8Define statement .............................................................................................. 10-13Strings .............................................................................................................. 10-13Units................................................................................................................. 10-14Align ................................................................................................................ 10-14Macro ............................................................................................................... 10-14Loop ................................................................................................................. 10-15Begin ................................................................................................................ 10-15Conditional if-then-else statements.................................................................. 10-15

Include files............................................................................................................ 10-16User Include Files ............................................................................................ 10-16Standard Include Files...................................................................................... 10-16Standard Include Files..................................................................................... 10-16

Header Section ....................................................................................................... 10-17filename............................................................................................................ 10-17sample_id ......................................................................................................... 10-18comment........................................................................................................... 10-18process.............................................................................................................. 10-18Autosample Changer slot................................................................................. 10-19Header Flags .................................................................................................... 10-19Header Parameters ........................................................................................... 10-22Adding Header Flags and Parameters Dynamically ........................................ 10-23

Instrument Section ................................................................................................. 10-23Solvent ............................................................................................................. 10-24Receiver gain (recvr_gain)............................................................................... 10-24Temperature control (temp_state and temp_set).............................................. 10-25Adding Instrument Parameters Dynamically................................................... 10-26

Acquisition Section................................................................................................ 10-26Domains ........................................................................................................... 10-27Spectral Offset ................................................................................................. 10-27


Spectral (Sweep) Widths.................................................................................. 10-28Data Points ....................................................................................................... 10-28Scans ................................................................................................................ 10-28Prescans............................................................................................................ 10-29

Pulse Section.......................................................................................................... 10-29total_time ......................................................................................................... 10-30x_pulse ............................................................................................................. 10-30 relaxation_delay.............................................................................................. 10-30j_constant ......................................................................................................... 10-30

Submitting Experiments ........................................................................................ 10-32Probe Codes and Probe Files ........................................................................... 10-32Probe Attributes ............................................................................................... 10-3390 Degree Pulses.............................................................................................. 10-33Spin Lock Pulses.............................................................................................. 10-34Temperature Limits.......................................................................................... 10-34Irr_code ............................................................................................................ 10-34Domains ........................................................................................................... 10-35Probe Tuning Values........................................................................................ 10-35

Calculations............................................................................................................ 10-36Calculation of Pulse Widths and Angles ......................................................... 10-36Calculation of Audio Filter Delays .................................................................. 10-37Total Time........................................................................................................ 10-38

Phase Tables........................................................................................................... 10-38Concatenation of Phase Sets ............................................................................ 10-39Addition of Phase Sets ..................................................................................... 10-3990 Degree Phases ............................................................................................. 10-40Sub-90 Degree Phases...................................................................................... 10-40

Multiple Buffer Acquisition................................................................................... 10-40module_config Options.......................................................................................... 10-41

Hardware Options ............................................................................................ 10-41Collection Mode..................................................................................................... 10-43Macros.................................................................................................................... 10-43Pulse Programs....................................................................................................... 10-44

Specifications................................................................................................... 10-44Begin/end Statement ........................................................................................ 10-44Time States....................................................................................................... 10-44Referencing Time Variables ............................................................................ 10-44Referencing Spectrometer Parameters............................................................. 10-44In-line Calculations.......................................................................................... 10-45End of Sequence .............................................................................................. 10-45

Gate Assignments and Options.............................................................................. 10-45RF Gates........................................................................................................... 10-46RF Phase .......................................................................................................... 10-46Attenuators....................................................................................................... 10-46Frequency Offset.............................................................................................. 10-46Noise Modulation............................................................................................. 10-46


Acquisition Macro ........................................................................................... 10-47Interactions with irr_code and module_config ................................................ 10-47

Compiling and Error Messages.............................................................................. 10-48Arrayed Parameters................................................................................................ 10-48

Interaction with multi_file Option ................................................................... 10-48Syntax .............................................................................................................. 10-49

Exceptions to Arrayed Parameters......................................................................... 10-50Setting Array Parameters ....................................................................................... 10-50Collecting T1 Data................................................................................................. 10-51

Appendix A. Standard Include Files A-1std_acquisition .......................................................................................................... A-1std_2d_acquisition .................................................................................................... A-1std_3d_acquisition .................................................................................................... A-2set_dec_instrument ................................................................................................... A-2std_domains .............................................................................................................. A-3std_domaind_master_list .......................................................................................... A-3std_header ................................................................................................................. A-4std_instrument........................................................................................................... A-5std_pulse ................................................................................................................... A-5std_solid_instrument ................................................................................................. A-6

Appendix B. Instrument Parameters B-1Appendix C. Irradiation Codes C-1Appendix D. Decoupling on a GX, GSX, or CPF Delta Upgrade Spectrometer D-1

Proton decoupling from either IRR or TRR channel ................................................ D-1High Power 1H Decoupler Sequences from either IRR or TRR channel................. D-2Bilevel 1H Decoupling ............................................................................................. D-2Low frequency (X-nucleus) decoupling from the TRR channel .............................. D-2

Appendix E. Directories and Files used by Delta E-1Delta User Account....................................................................................................E-1Delta System Directories, /usr/delta/ .........................................................................E-3/usr/delta/global/ Files................................................................................................E-3/usr/delta/global/ Directories....................................................................................E-13/usr/delta/setup/ ........................................................................................................E-14Eclipse Files for Acquisition system........................................................................E-16Delta Configuration Files.........................................................................................E-17Eclipse Spectrometer Files and Directories .............................................................E-46Machine action files.................................................................................................E-59

/eclipse/shapes/ ..................................................................................................E-63/eclipse/ Program Files.......................................................................................E-64/usr/eclipse/testprogs/.........................................................................................E-67/etc/init.d ............................................................................................................E-68

Appendix F. Description of the Automation Template File F-1SAMPLES .................................................................................................................F-1METHODS ................................................................................................................F-2


GROUPS....................................................................................................................F-3EXPERIMENTS and PRESENTATIONS ................................................................F-4

Experiments .........................................................................................................F-4Presentations ........................................................................................................F-7

Logic of Flow in the Automation Editor....................................................................F-9Appendix G. Presentation Manager and Template File Format G-1

Console commands ................................................................................................... G-1A sample template File (.pmt) ............................................................................ G-2

Appendix H. Terminal Console Program H-1Appendix I. Tool Icons I-1Appendix J. Unix and Vi Commands J-1

I. Unix Commands ......................................................................................................J-1II. VI Commands ........................................................................................................J-2

Appendix K. Installing JEOL AutoTune probes K-1Probe Tuning............................................................................................................. K-3

Appendix L. Delta V3.2 Software Installation and Configuration Instructions L-1I. System Requirements for Delta V3.2 .....................................................................L-1

Workstations: .......................................................................................................L-1SGI - IRIX: .........................................................................................................L-1Intel - Linux .........................................................................................................L-1IBM - AIX............................................................................................................L-2Sun - Solaris.........................................................................................................L-2Acquisition Systems: ...........................................................................................L-2NMR Spectrometers: ...........................................................................................L-2

II. Preparing for the Delta V3.2 Software Installation or Upgrade............................L-2III. Installing or Upgrading the Delta Software on SGI IRIX Systems ..................L-3IV. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System from anSGI Workstation ........................................................................................................L-5V. Installing or Upgrading the Delta Software on Intel Linux or Sun Solaris Systems ..L-6VI. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System fromLinux, or Solaris.........................................................................................................L-7VII. Installing or Upgrading the Delta Software on IBM AIX Systems ...................L-7VIII. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System fromAIX. ...........................................................................................................................L-8IX. USER Account Setup ..........................................................................................L-8

Appendix M. X Windows Emulation M-1SGI IRIX setup: ..................................................................................................M-1X-Server Requirements for PC or MAC:............................................................M-1PC X-Servers: .....................................................................................................M-2MAC X-Servers: .................................................................................................M-2

Index ..................................................................................................................................I-i

DELTA Users Guide, v 3.2 ix

List of Figures

Silicon Graphics Login Screen 2-1Silicon Graphics User Interface Screen (detail) 2-2Basic IRIX Window Structure 2-4Window Menu Button 2-5Minimized and Maximized Windows 2-5Moving and Resizing Windows 2-6Silicon Graphics User Toolchest 2-7Selected Menu 2-7System Usage Monitor 2-8Silicon Graphics UNIX Shell Window 2-9Silicon Graphics Logout Confirmation Window 2-9The Delta Console Window 3-2Delta Console Menu Bar 3-3Delta Console Tool Bar 3-4Confirm window 3-6Preferences Tool - Personal Page 3-7Search Tool 3-10Directory Tool 3-11Preferences Tool - Data Page 3-12Preferences Tool - Geometry Page 3-13Preferences Tool - Miscellaneous Page 3-14File Manager 3-15Data File Converter 3-17Delta Console Window 4-2Spectrometer Control Tool 4-3Spectrometer Control Tool Top Buttons 4-3Spectrometer Control Tool Info Display 4-4Spectrometer Control window after connection of the workstation and spectrometer 4-5Spectrometer Control Tool in Monitor Mode 4-6Spectrometer Control Tool Lower Buttons 4-7Sample/Shim Tool 4-9Lock Control section displays the NMR-lock level 4-13Set the axis for shimming 4-13System Shims Acknowledge Window 4-15Open Shim File window 4-16Save Shim File window 4-17Lock Level Meter (Minimum 0, Maximum 4095) 4-18Lock Control 4-18Gradient Shim and Lock Buttons 4-18Acknowledge message window 4-22Spectrometer Control with Experiment Pending 4-22Spectrometer Control with Experiment Running 4-22Experiment Information Window 4-23

x DELTA Users Guide, v 3.2

Open Experiment Tool 4-25Experiment Header Section 4-27Set Process Window 4-28Experiment Instrument Section 4-30Experiment Acquisition Section 4-31Experiment Pulse Section 4-32Pulse Viewer 4-33Automation Tool 4-34Automation Queue Window 4-37Automation Console 4-38Automation Editor 4-39Flow Chart for an Automation Editor 4-42SAWTH or swept lock signal display 4-44View Tool -- raw data 4-45View Tool - processed data 4-461D Processor 5-11D Processor with untransformed and processed data 5-2Open File Tool Window 5-4Extended Mode 1D Processor after Performing FFT and Phasing 5-61D Processing List 5-7Open Process List window 5-8Save Data File window 5-12Empty Process List 5-16Process List after Adding DC balance 5-16Process List after Adding DC Balance and Zerofilling 5-16Process list after adding Window function 5-17Process list after adding Fast Fourier Transform 5-181D Zoom mode operations 5-19Sample Key command menu 5-21Sample Zoom Operation 5-23Sample Region Operation 5-24Sample PiP Operation 5-25Spectrum before Phase Correction. 5-27Phase Correction Performed Using P0 5-28Further Phase Correction Using P1 5-28Applying the Phase Correction 5-29Interactive Baseline Correction - a) Polynomial and b) Piece wise Linear 5-31Interactive Baseline Correction Preview 5-32Interactive Baseline Correction with Show Curve Enabled 5-32Process list after converting data axis to PPM 5-34Reference Tool 5-34Reference in Processing List 5-35Copy Reference Tool 5-36Spreadsheet Tool 5-381D Processor with auto-peakpicked 1H data 5-401D Processor with adjusted peak threshold 5-41

DELTA Users Guide, v 3.2 xi

Pick Tool 5-42Peak Pick Threshold Display 5-43Peak Display (default) 5-45Peak Display with Peaks Above Option Enabled 5-46Peak Display with J Coupling Constants 5-461D processor with data peaks integrated 5-47Integral Slope Adjustment 5-49Transfer Integral Tool 5-51Data before Deconvolution 5-52Deconvolved Data 5-52Deconvolved Data with Deconvolve Sum 5-54Deconvolved Data with Deconvolve Unsel 5-54Spreadsheet after a Deconvolution 5-55Annotation Rotation & Shift Keys 5-56Data after Annotation 5-57Level Tool -- Contour View (I) and Colors View (II) 5-59Zoomed view of data showing Data points 5-61Spreadsheet Tool 5-65Save Data File Window 5-67Print Options Window 5-68Presentation Manager 5-69Ruler Links (Links) 5-73Ruler Limits 5-74Ruler Links (Y Scale) 5-75Presentation Manager (Preview) 5-76Simple Mode 1D Processor 5-78Data Slate 6-1Vertical Data Slate Views 6-3Horizontal Data Slate Views 6-4Box Data Slate View 6-4Data Overlay 6-6Print Options 6-8Resulting File Window 6-11Connection Tool after and before a Connection is Made 6-12Geometry Tool 6-13Data Slate Slicing Menu 6-16Data Slate Slicing 6-16Expand Options Menu 6-17Data Slate Expand Display 6-18Expand Size Selection 6-18Open File 7-2Empty nD Processor 7-3nD Processor Window 7-4X-Domain processing list 7-5nD Process Data Destination Buttons 7-82D Phasing Tool 7-11

xii DELTA Users Guide, v 3.2

2D Phasing Tool Region Display 7-122D Viewer - Contour Mode 7-13Mesh(a), Surface(b), Stack(c), and Image(d) Modes 7-16Level Tool 7-18Data with too few (only topmost) contours selected 7-20Data with too many contours selected (well into the noise floor) 7-20Data with a sensible distribution of contours selected 7-21Peak Pick Overlay 7-232D Peak Pick Display 7-242D Peak Multiplet with Fine Structure 7-25Peak Grouping 7-26Peak Melding 7-262D Integration. 7-272D Annotation 7-282D Spreadsheet 7-30T1 Analyze Tool 8-4Open Data for Processing Window 9-2Empty 3D Processor Window 9-33D Data Slate 9-83D Viewer Right Mouse Button Mode Selection Menus 9-93D Viewer 9-103D Viewer - Slices 9-113D Viewer - Zoomed 9-113D Slicer with Overlaid Spears 9-123D View Control 9-17Spectrometer Control Tool after Connection 10-3Open Experiment File Tool 10-4Experiment Tool 10-5Experiment Tool Header 10-17Adding Header Fields 10-23Experiment Tool Instrument Section 10-24Adding Instrument Parameters 10-26Experiment Tool Acquisition Section 10-27Experiment Tool Pulse Section 10-30Pulse Display Widget 10-31Set Array Parameters Windows 10-51


List of Tables

Window Menu Functions2-4Delta Console Tool Bar Icons3-4Shim Tool Nomenclature 4-14Data Slate Icons6-7Connect Functions6-15Relaxation Experiment8-2Experiment Tool Icons10-5Experiment Header Parameter Definitions10-10Experiment Acquisition Parameter Definitions10-12Experiment Pulse Parameter Definitions10-13Header Process Information Options10-18Header Flags10-19Temperature Parameter List10-25Scans Parameter Limits10-29Eclipse Probe Code List10-33GX, GSX and CPF Assignments 10-33IRR Codes for Probes10-34Multiple Buffer Phase Cycles10-41RF Channel settings10-41Time-shared Homonuclear Decoupling10-42Noise Modulation Gating10-42Amplifier Power Settings10-42Combination Features10-42PGX-300 Pulser Specifications10-44Irradiation Modulation Modes10-47Irradiation CodesC-1Conversion Example for TH5 ProbeC-1GX Decoupler Amplifier ControlD-1Delta NMR software package componentsL-4

DELTA Users Guide, v 3.2 1-1

CHAPTER 1: INTRODUCTION

INTRODUCTIONDELTA is a graphically-oriented NMR data processing software package running onSilicon Graphics computer workstations. DELTA uses a mouse-driven graphical userinterface with pull-down menus and icons to perform common NMR data manipulationsand to control the Eclipse NMR spectrometer.

ABOUT THIS GUIDEThis DELTA NMR Software User's Guide provides a useful overview of DELTA. Itcovers basic 1D, 2D, and nD NMR processing and data acquisition (see Chapters 5 and 7).For more information about the Eclipse NMR spectrometer, please consult Chapter 4.Other chapters and appendices provide a wealth of information. The introduction to eachchapter provides links to its important topics. For further information on specific featuresof the DELTA software, consult the Delta Users Reference and Online Help, or thePercival Reference Manual.

BEFORE YOU BEGINDELTA must be correctly installed and configured on your workstation or network. If theDELTA software does not run correctly, please consult your system manager. Refer toAppendix L, Delta V3.2 Software Installation and Configuration Instructions.

You must have an account on the workstation that runs the software. Please see yoursystem manager to set up an account for you.

SPECIAL SYMBOLSSpecial attention:This symbol marks an important explanation of an operation or a function.

Warning:This symbol indicates that the operation could seriously affect operation of thesoftware or hardware.

FONT CONVENTIONSFile names which are part of the DELTA software are shown in Courier font (forexample,.delta_configure). Courier font is also used to designate UNIXconsole input, sample file contents, and output from DELTA programsin a console window.

DELTA commands and tools are shown in bold type.

Chapter 1: Introduction

1-2 DELTA Users Guide, v 3.2

References to other manual names are shown in Times bold italics.

SGI commands and window titles are shown in Helvetica bold italics.

KEYSTROKE CONVENTIONSTwo modifier keys are commonly used as accelerator keys or as keyboard shortcuts:

The CONTROL key is abbreviated in this manual as CTRL, or represented with the^ character used in all the DELTA menus. For example, CTRL-G or ^G meanspress the CONTROL key, then press the g key.

Note that DELTA accelerator keys are never case sensitive, whereas UNIXcommands are always case sensitive.

CTRL-1 means hold down the CTRL key, and then press the number 1 key. Zero(0) is also spelled out (CTRL-zero) to avoid confusion with the letter O.

The ALTERNATE key is abbreviated ALT in this manual. ATL-g means hold downthe ALT key, then press the g key.

Note that, in SGI Windows Menus, ALT+F1 means hold down theALTERNATE key, then press the F1 key.

The ESCAPE key is abbreviated in this manual as ESC.

The SPACEBAR key is abbreviated in this manual as SPACE.

COLOR CONVENTIONSWhen a color is mentioned, it is assumed that the DELTA software is running with thedefault color scheme. If you customize the color scheme with the Configuration Editor orby editing the.delta_configure file, the colors mentioned in the manual may notmatch your screen display.

It is not advisable to change different color preferences to the same color.Doing so may cause parts of the display to be obscured by other parts whosecolor is the same. Displaying data using the same color as the backgroundcolor is definitely not advised!


CHAPTER 2: USER INTERFACE BASICS

This chapter covers only the basic operation of the Silicon Graphics user interface as itpertains to DELTA. For additional information, consult the documentation that came withyour workstation. Some window features may not be available or active in other softwareapplications.

POWER-ONConsult the Silicon Graphics documentation that came with your workstation to determinethe location of the power switches for both computer and monitor. Before proceeding,make sure that the workstation and monitor are turned on.

LOGINPlease refer to Figure 2-1.

Figure 2-1. Silicon Graphics Login Screen

To log onto the workstation: Double-click on the DELTA icon with your mouse:

A password box will appear on the screen.

DELTA-J

Chapter 2: User Interface Basics


Place the mouse in this box and type your password. If the password is correct, thiswindow will open (see Figure 2-2).

The following figures and pictures may look different on your screen if you arerunning a different version of the UNIX operating system on your workstation.

Figure 2-2. Silicon Graphics User Interface Screen (detail)

Silicon Graphics provides you with a graphical user interface (GUI) in which you initiateand input instructions using the mouse and cursor position. This contrasts with the olderstyle command line (text) user interface where all commands are entered by typing on akeyboard. The keyboard is still used for text input, but the location is selected by themouse cursor.

Another important characteristic of the Silicon Graphics user interface is that multiplewindows display on the screen simultaneously. Each window may represent a separateprogram, or a different part of a single application. Windows may perform operationssimultaneously. Windows may be iconified to recover screen space or to move awindow out of the way.

DELTA-J

delta Delta UserPassword: password input box

Mouse and Keyboard


MOUSE AND KEYBOARDAll user input is made using the keyboard and the mouse. The mouse controls a pointer orcursor on the screen. The shape of the mouse cursor will change, depending on the mode.The mouse has three buttons: left, middle, and right. The left mouse button is the mostcommonly used button for selecting objects, although all three buttons are used in DELTA.Input FocusBecause multiple windows can be displayed simultaneously on the screen, the user mustunderstand the concept of input focus. The input focus, or active window, isdetermined by the position of the mouse cursor on the screen. To enter text or otherkeyboard input, the mouse cursor must be in the desired window and at the desiredlocation in the window. As the mouse moves from one window to another, the windowborder and window title bar will change from a dark to a lighter gray color to mark theactive input focus window.

To click the mouse:Press down briefly, then release the mouse button. The mouse button to use -- left, middle,or right -- may be specified. Use the left mouse button unless this manual specifies themiddle or right mouse button. A mouse click is also called a single click.

Certain operations may be performed by a double click -- two single clicks in rapidsuccession. The second click of a double click sequence is interpreted as an OK. For thisreason, double clicks are commonly used to select files.

Do not develop a habit of excessively clicking the mouse. The response time ofthe workstation may slow during times of high CPU loading. However, theDelta software will remember all the mouse clicks and all of them will beexecuted as time allows. Unwanted functions could be performed!

To drag the mouse:Press the mouse button and hold it down while moving the mouse to a new location.Dragging the mouse is commonly used for repositioning and resizing windows on thescreen.

KeyboardUse the keyboard for all text input. The keypad may also be used for numeric input. Arrowkeys may also be used for zooming and panning the NMR data. The keyboard functionkeys (F1 through F12) are also assigned to special functions inside the Delta software.

Structure of a WindowThe basic structure of a window is shown in Figure 2-3. This figure shows the mostcommonly used parts of a window. For more detailed information, see Anatomy of aWindow in the section Getting Started shown in the Index for Desktop Help. This can beviewed by selecting Desktop Help from the Help submenu in the standard Toolchest. (Seethe Toolchest section on page 2-6.)



Figure 2-3. Basic IRIX Window Structure

WINDOW MENU BUTTONSOn the left top corner of the window is a menu button, shown in Figure 2-4. Click with themouse to display a menu of window options. The menu will remain displayed after themouse button is released. Click with the right mouse button in the Title bar to display thesame menu of window options; this menu will disappear when the mouse button isreleased. Drag the mouse to the desired option, then release, to execute the selectedfunction. The most useful functions are Raise, Lower, and Quit.

Table 2-1: Window Menu Functions

Select:

Restore Alt F5 To refresh the Delta Console window.Move Alt F7 To move the Delta Console window.Size Alt F8 To change the window size.

Minimize Alt F9 To turn the window into a postage stamp size icon.

Maximize Alt F10 To size the window to fill the terminal screen.

Raise Alt F1 To position the window in front of the other windows.

Lower Alt F3 To position the window in back of the other windows.

Close To close the window.

Path Bar

Pathname

Drop Pocket

FieldRecycleButton

Maximize ButtonWindow TitleWindow Menu Button

Scroll BarsWindow Border

Iconize Button

Iconifying or Minimizing Windows


Note: If there is a key combination next to the function, the keyboardcombination will effect the same operation. These keyboard combinations arecalled accelerator keys.

Figure 2-4. Window Menu Button

ICONIFYING OR MINIMIZING WINDOWSFigure 2-5 shows two symbols that appear on the right side of the window menu bar. Clickon the small square icon to minimize (or iconify) the window. Click again on the smalliconified window to restore it to the original size.

Figure 2-5. Minimized and Maximized Windows

mouse click

Minimize (Alt+F8) Maximize (Alt+F10)[or Restore (Alt+F5)][or Iconifying]



MAXIMIZING WINDOWS TO FULL SCREENClicking on the large square shown in Figure 2-5 causes the window to fill the entirescreen. The full screen window will cover all other windows. This button acts as a toggleswitch. Click on the large square again to restore the window to the original size.

MOVING WINDOWSThe title bar of a window displays the name of the window. If you position the mouse onthe title bar and drag the mouse while pressing the left button, you can move the window(visible as a red outline) to a new location. When the mouse button is released, thecontents of the window will be redrawn.

RESIZING WINDOWSWindows displayed on the screen may be resized by selecting the border with the mouseand dragging it to a new position (see Figure 2-6.) The border and corners of a window arecalled handles. If you put the mouse pointer on the border or corner of a window, thepointer will change. This means you have grabbed the handle, and may resize thewindow by dragging the mouse from this point.

Figure 2-6. Moving and Resizing Windows

TOOLCHESTA list of programs and utilities is displayed in the upper left corner of the screen asillustrated in Figure 2-7. This menu is called the Toolchest. If you select a category,programs within that category will appear. Drag the mouse to select the desired programor utility. The contents of the Toolchest are controlled by the.auxchestrc or.chestrc file in the user's home directory. The default Toolchest setup file is /usr/

Toolchest


lib/X11/system.chestrc. You should customize your own account by using the.auxchestrc file in the user's home directory. See Modifying the Toolchest in thesection Customizing Your Environment shown in the Index for Desktop Help. This can beviewed by selecting Desktop Help from the Help submenu in the standard Toolchest.

If the right mouse button is clicked on the screen background (any blank area of screenoutside a window), a menu is displayed as illustrated in Figure 2-8. If the workstation hasbeen configured by JEOL, the menu will allow you to open a UNIX terminal shell and tolog out; other options may also be available.

Figure 2-7. Silicon Graphics User Toolchest

Figure 2-8. Selected Menu



WORKSTATION SYSTEM USAGEEach workstation has a utility program called gr_osview. This program, a performancemonitor for the system, is shown in Figure 2-9. To start the monitor: select System Usage under the Programs option in the

Toolchest. To close the monitor window: place the mouse in the window and press the ESC key. To move this borderless window to another position on the screen: place the mouse

cursor over the gr_osview window and, while holding down the ALT key, hit theF7 key (ALT+F7). The cursor will change to a four-sided arrow. The red outline maynow be positioned anywhere on the screen. A mouse click will place the window at thenew position.

To get the Window Menu (see Figure 2-4) for a borderless window: press the ALTkey and click the right mouse button. Unlike other borderless utility windows, thegr_osview window can not be resized.

For more information on the system monitor and gr_osview, consult the SGIdocumentation or the man pages for gr_osview.

Figure 2-9. System Usage Monitor

TERMINAL SHELLA window containing a standard UNIX shell, as shown in Figure 2-10, can be created byusing the Desktop - Shell command located under the Toolchest menu. The Shell may belisted as Unix Shell, or Shell (terminal), depending on the operating system version.

Logout Window


Figure 2-10. Silicon Graphics UNIX Shell Window

LOGOUT WINDOWTo log out from the workstation: select Log Out from either the Background menu orthe Toolchest menu.

A logout will ask for a confirmation shown in Figure 2-11. Select Yes to log out. Allapplications and windows will be closed on logout.

Figure 2-11. Silicon Graphics Logout Confirmation Window


CHAPTER 3: GETTING STARTED ON DELTA

INTRODUCTIONThis section will briefly describe the fundamental operation of basic DELTA processingtools. It covers procedures for: starting Delta (page 3-1) running Delta from the Delta Console menus and icons (page 3-3) tailoring the look and feel of Delta using the Preferences Tool (page 3-7) managing files (page 3-15) converting files (page 3-17).

The DELTA software program is composed of tools. Each DELTA tool uses one or morewindows to process, analyze and/or plot NMR data. Each tool is built with widgetswhich offer you different ways of entering information or manipulating data on the screen.These widgets allow you to input parameters, select functions, execute processing, etc.

STARTING DELTAAfter you have logged onto the workstation, do the following:1. Start the application by selecting Delta under Programs in the Toolchest menu in the

upper left-hand corner of the screen. Or Double-Click on the Delta icon in the GUIwindow.

Note: If DELTA is not listed under the Toolchest, see your system manager orconsult Appendix O, Section II.If DELTA is running over a network, start-up could be delayed slightly bynetwork traffic. If the application does not start up, look under the UNIXConsole window for error messages, or use the System Usage tool tomonitor CPU performance.

Note: When running DELTA from your desktop, if autoplacement is turned onin the Miscellaneous Page of the Preferences Tool, then the DeltaConsole window will open automatically.

Note: Train yourself from the outset to give Delta clear signals. Delta respondsto each click of the mouse. For instance, use a single click of the mouse toopen a window (otherwise, Delta will read each signal and duplicate windowswill come up).

Double-click on the Delta icon

Chapter 3: Getting Started On Delta


Note: As a general rule, it is better to complete processing and analysis of thedata before employing virtual geometry features.

Note: Extremely large data files can slow down Delta.

THE DELTA CONSOLEWhen you launch DELTA -- in all cases except where a preserve location is specified inthe.delta_configure file -- a red outline of the Delta Console (Figure 3-1)appears.

To activate the window:Move the mouse to position the Delta Console window anywhere on the screen and clickto open the window. The window can be repositioned at any time.

The Delta Console window pull-down menus and icons are used to invoke all Delta tools.

To activate either menus or icons:Place the mouse cursor on your selection and click.

This section will not cover all of the Delta Console options. For a moredetailed discussion, refer to the (See Delta Users Reference: The DeltaConsole on page 6-1).

Figure 3-1. The Delta Console Window

The Delta Console Menu Bar


THE DELTA CONSOLE MENU BARAlong the top of the Delta Console window frame is a selection of topics called theMenu Bar (Figure 3-2). The Menu Bar lets you use the mouse to select functions and toolsusing the mouse.

Figure 3-2. Delta Console Menu BarNote: The User menu is for user-defined choices. It is described in AppendixE on page 41.

Pull-Down Menus

Each topic on the Menu Bar has a pull-down menu like the one illustrated above. Clickand hold the mouse on a Menu Bar topic to display its menu of choices. Consult the Helpand Delta Users Reference Guide for a description of these menus (page 6-4).

To select an item from a pulldown menu:Drag the mouse down the list (keeping the mouse button pressed down) to highlight thedesired feature. If you have chosen an incorrect menu, simply move the mouse outside themenu and release the button.

Accelerator KeysAlso displayed in the pull-down menus are accelerator key combinations. Hit a keycombination on the keyboard to invoke a tool or an option. The carat character (^) on anaccelerator key in the pull-down menu indicates the CTRL key. For example, in themenu illustrated above, ^S means hit CTRL S to access the Presentation Manager.

TOOL BAR ICONSLocated below the Delta Console Menu Bar is a set of icons representing many commonlyused functions. This area is called the Tool Bar (Figure 3-3). Each icon has a uniquepicture that represents the tool or function you may select by clicking the mouse button.Clicking on the icon changes its appearance to that of a button that has been pressed down.Many of the Icon functions duplicate the functions under the Menu Bar. Table 3-1 listsand describes the function of these icons.



Note: Selecting any icon with the right mouse button will bring up a labelidentifying it.

Figure 3-3. Delta Console Tool Bar

Table 3-1: Delta Console Tool Bar Icons

Select:

To open the NMR data into a Data Processor. Thedimensional size of the data is checked and the correctprocessor invoked. See Chapter 5 for more information onusing the Data Processor (page 5-1).

Note: to start the 1D processor, you may eitherselect this Icon or select the 1D Processoroption under the Processors menu.

To use the Data Slate to display and manipulate 1D, 2D,and 3D data. See Chapter 6 for more information on usingthe Data Slate (page 6-1).

To use a Data Viewer to view NMR data. The window issized to the dimensions of the data displayed. See Chapter7 for more information on the 2D Data Viewer (page 7-13).

To navigate the subdirectories Delta uses for different files.The File Manager also allows you to copy, edit, delete,and rename files. Open this tool to consult its online Help.

To use the Presentation Manager to customize designof a printout of NMR data and to organize the differentprocessing of one or more data sets. Open this tool toconsult its online Help.

Tool Bar Icons


To display parameters and the processing history for anydata set. Open this tool to consult its online Help.

To use a Spreadsheet to display peak, integral andassignment information in table form. Open this tool toconsult its online Help (page 57-1).

To use the Connection Tool to create connectionsbetween different data sets. Use the axial reference scale toestablish links. Any data sets, regardless of data pointdensity, sweep width and field strength, may be connected.Open this tool to consult its online Help (page 19-1).To use the Eclipse Spectrometer Connection utility toconnect to, or monitor, a spectrometer. See Chapter 4(page 4-1).

To use on-line help. Help will display a picture of the toolwith a brief description of its functionality.

To use the mouse cursor to finger text to cut from theselected data geometry into another window on the Deltaconsole.

Note: To clear an input box, double click theright mouse button.

To finger and paste text from the selected data geometry onthe Delta console to a preselected window. A Paste canalso be performed by clicking the middle mouse buttonwhen the cursor is in an input box.

Table 3-1: Delta Console Tool Bar Icons

Select:



EXITING DELTA

To exit Delta after completing measurement or NMR data processing:

1. Select Quit in the File menu.2. The Confirm window opens, asking whether you want to quit the program.

Figure 3-4. Confirm window3. Select OK.

Note: If you decide not to quit the Delta program, click on the Cancel button.

ON-LINE HELP

Located on most tools in Delta is a help icon button, which connects you, via NetscapeBrowser, to a .MIF help file offering useful guidance on that tool. The contents of this helpfile are identical to the framemaker/.pdf version of the Delta Users Reference Guide.

1. To start on-line help for the tool currently displaying on Delta: simply click on thehelp icon, or select Help in the menu bar.

2. Use the scroll bar to scroll up and down in the file.

Preferences Tool


PREFERENCES TOOL

Figure 3-5. Preferences Tool - Personal PageThe Delta Preferences Tool allows you to change the parameters that control the lookand feel of Delta. These parameters are kept in the .delta_configure file, whichresides in the users home directory and is described in Appendix E.

Note: The .delta_configure file is not meant to be edited with the texteditor, but with the Preferences Tool.Note: Most parameters take effect when they are changed, without restartingDelta. Every parameter listed in the Preferences Tool with a * next to itsname is one that does NOT take effect until Delta restarts.



To invoke the Preferences Tool:Select File, then select Preferences, from the Delta Console window menu bar. Ascreen containing personal information about the user will display. At the top of thisscreen are icons that enable you to go from one page to any other page (or if you prefer,you can use the Options menu to access one of these pages or to configure the printer.)

Use the icons to select a page in the Preferences Tool:

Select:

To return to the Personal Information Page illustratedabove from any other page.

To turn to the Directory Page, which contains a list ofavailable directories.

To select Printer and printer options such as orientation(landscape or portrait), paper size, tessellates, andparameter location.

To turn to the Data Page, which contains information andfeatures specific to the data found in geometries.

To turn to the Geometry Page, which containsinformation and features specific to the display of thegeometry.

To change the Alternate Cursor selections.

To select colors for displays, widgets, etc. You may alsoelect to display icons in black and white and changecolor mapping defaults.

Preferences Tool


Use the buttons at the bottom of any pages to save new parameters or restore apage to its original settings:Selecting:

Saves modified preferences to .delta_configure and exits.

Restores only the parameters on the current page to their originalsettings.

Restores all parameters to their original settings.

To turn to the System page.

To turn to the Miscellaneous page.

To turn to the Delta Tools page.

To turn to the Processors page.

To turn to the Automation page.

Select:



Disregards the changes and exits the Preferences Tool.

Note: Click on any title on any page with the right mouse button to get a helplabel.

To search in the preference settings and pop-up help for any keyword:

Select Search in the Options menu. A search window pops up. Type the word you want to find into the box marked Search: (geom was typed into

the Search Tool window illustrated below) Select the Go button. The Search tool then returns a list of all preferences or popup help containing the

keyword (see the example below): page, # of preference on that page, title and whenthe word appears in the online help, that line of help.

Select the reference you desire -- Colors #5, below - and click on it to go directly to it.

Figure 3-6. Search Tool

To change parameters in the Preferences Tool:

Select a field with your mouse, and: Type in a new value. Select a new value from a list that appears. Move the slider to increase/decrease a value. Toggle the ON/OFF button.

To start the directory tool:

Select . The Show Hidden Files button expands the directory tool to include filenames. You can either select a file from the File list or type in a filename. Select Apply toset the preference to the current directory. You can also drag the directory to a destinationby selecting the input box at the bottom of this tool.

Preferences Tool


Figure 3-7. Directory Tool

Sample pages from the Preferences Tool -- geometry page, data page, and misc page --follow. All pages of the Preferences Tool are discussed in detail in the online Help, SeeDelta Users Reference: Preferences Tool on page 45-1.



Figure 3-8. Preferences Tool - Data Page

Preferences Tool


Figure 3-9. Preferences Tool - Geometry Page



Figure 3-10. Preferences Tool - Miscellaneous Page

File Manager


FILE MANAGERDeltas File Manager makes it possible to edit, compile, delete, move, copy, purge,inherit, or keep a processing history of files.

Figure 3-11. File Manager

To invoke the File Manager:

Select on the Delta Console. Or, select the File Manager command from File Access in the File menu of Delta

Console.

Select a file using the list and input boxes.The Directory Input Box displays the current directory.If you want to see a different directory, you can type the name of the directory andthe path to it in the input box, and then press the enter key.Subdirectory List Box lists all the subdirectories in the current directory.

File Toggle Buttons

Version Number List Box

File Management Buttons

DirectoryInput Box

SubdirectoryList

File ListBox

Tool Bar

Hop ButtonsDirectory

BoxFile Input

File Info



Note: if the Show Hidden Files option in the Options menu is toggled on, allthe hidden directories will be listed as well.

File List Box lists all files that are in the current directory.

Version Number List Box displays all version numbers of the selected file.

Use the Tool bar icons to call up these tools with the selected file in them: (in order) Data Processor, Spectrum Phaser, Data Slate and Data Viewer:

An appropriate tool will be opened based on the dimension of the selected file.

Note: click and hold the right mouse button on the icon to reveal the name ofthe tool.

Use the buttons along the right hand side to perform File Management Tooloperations.See Delta Users Reference: File Manager on page 27-1 for a description of this tool.

File Converter


FILE CONVERTER

Figure 3-12. Data File Converter

Deltas Data File Converter lets you copy a file from one format to another. See DeltaUsers Reference: File Converter on page 26-1.

To invoke the Data File Converter:Select File Conversion in the File menu of the Delta Console.



To convert data:1. Select a file type button in the From column, then one in the To column to convert

from the first file type to the second selected.2. A blue arrow points from the source file to the output file.

Select:

To choose the directory and name of the file you want to convert. Youmay also enter the name of a Percival data file directly into the input box.

To choose the directory and filename to store converted data. You mayalso enter the name of the Percival data file directly into the output box.

To start converting the data.

To save the intermediate JEOL Generic files.

To exit the Conversion tool.

Use the Options Menu:To toggle on/off automatic extension correction and the display of progress messages.


CHAPTER 4: ECLIPSE SPECTROMETER CONTROL

INTRODUCTIONDELTA communicates with and controls the Eclipse NMR spectrometer through severalseparate windows and tools. This section provides an introduction to these tools, andexamples of basic NMR spectrometer control. This chapter discusses the following toolsand processes:

Spectrometer Control, page 4-2 Sample loading, page 4-9 Experiment and Queue management, page 4-21 Experiment, page 4-24 Experiment Automation, page 4-34 Automation Queue, page 4-37 Automation Editor, page 4-39 Sawth (Lock signal display), page 4-43, and View Tool (Real-Time monitor display), page 4-44.

Note: To close any window: use the pull-down menu in the upper left corneror press the ESC key while that tool is the input focus.

SPECTROMETER TO HOST WORKSTATION COMMUNICATIONAll communication from the workstation to the Eclipse spectrometer uses Ethernet usingthe TCP/IP Protocol. This means the user may establish and control an Eclipse NMRspectrometer thousands of miles away from the workstation. This distributed network hasmany benefits for multi-user environments. Several different users from separate workstations can connect to the spectrometer to

submit experiments or to retrieve data. Remote connection can even be established through a terminal emulator, or through X

window emulation.The Eclipse NMR spectrometer has a complete UNIX computer embedded inside it. Thatcomputer is assigned a TCP/IP node address and name. This node name is what displayswhen the Spectrometer Control Tool is started.

Chapter 4: Eclipse Spectrometer Control


SPECTROMETER CONTROL TOOL To invoke the Spectrometer Control Tool:

1. Click on this icon in the Delta Console window .

Figure 4.0-1. Delta Console Windowor select Acquisition, then Connect, from the Delta Console Menu Bar.

The Spectrometer Control Tool, from which all spectrometer functions and controlsmay be accessed, opens.

SELECTING A SPECTROMETERWhen you start the Spectrometer Control Tool, its display screen lists all availableEclipse NMR spectrometers on the network (see below). If you have a single Eclipsespectrometer, only one node name is displayed

Selecting a Spectrometer


.

Figure 4-1. Spectrometer Control Tool

Use these Spectrometer Control Tool function buttons (Figure 4-2):

Info to get information about a particular spectrometer (page 4-3), Connect to connect (page 4-4) or Monitor to monitor a spectrometer (page 4-6), Unlink (page 4-7) to terminate connection to a spectrometer, or Free (page 4-7) to ping the network for the status of the spectrometers.

Figure 4-2. Spectrometer Control Tool Top ButtonsSelect:

to display the contents of the machine.info file from the currently selectedspectrometer (Figure 4-3).



Figure 4-3. Spectrometer Control Tool Info Display

Select:

after first selecting a spectrometer, to connect to a FREE spectrometer, and to gainownership of the spectrometer and control of all its features. Depending on Ethernettraffic, it may take several seconds to establish connection. During this time, theworkstation is uploading parameters from the spectrometer.

The spectrometer name will be displayed in reverse video. If connection is successful, themessage Connect is displayed at the top of the window, as shown in Figure 4-4.

Selecting a Spectrometer


Figure 4-4. Spectrometer Control window after connection of the workstation andspectrometer

After data collection, the data is automatically uploaded to the workstation if thespectrometer connection is valid. The data is placed in a file specified by the filenamestring in the experiment header. If the connection does not exist, the data is retained on thespectrometer for a time specified in the machine.config file. The next time aconnection is made to the spectrometer, the data is automatically uploaded. If the processline in the experiment header contains a valid processing program, the program is invoked.

Note: Connection to a spectrometer is necessary prior to scheduling anyspectrometer activities.

Default Spectrometer ConnectionEach user in the.delta_configure file has a Default instrument string. This string isthe name of the spectrometer to which Delta will automatically try to connect when theConnect command is given. This string may be changed with the Preferences Tool.

Note: In locations with only one spectrometer, the system is usually set up toconnect to the spectrometer automatically after clicking on the icon.



Select:

after first selecting the spectrometer, to monitor (or observe an experiment on) aspectrometer already in use by another user. The Spectrometer Control Tool changesto look like Figure 4-5.

Note: Only one user can connect to a given spectrometer at a time. However,users from other workstations can monitor the status of the spectrometer. Auser can submit experiments while monitoring the spectrometer. However,those experiments are held in the experiment queue until the current userunlinks.

Figure 4-5. Spectrometer Control Tool in Monitor Mode

Spectrometer Control Tools


Select:

to terminate connection to the spectrometer. Unlink is used to terminate both the Connectand Monitor connections.

to ping the network for the status of all Eclipse NMR spectrometers. The node nameswill be listed in the Spectrometer Control Tool window.

Console modeIn console mode -- which acts like a spectrometer superuser -- you have exclusive right tothe spectrometer and can do any of the following: remove any job from the queue, change experiment priorities, write system shim files, etc.To connect to the spectrometer in console mode, select Tools-Mode-Console to bring up awindow into which you enter the password. When a user connects as console, theSpectrometer Control Tool displays this information in the top window, which wouldread:console: nodename not connect:nodename

SPECTROMETER CONTROL TOOLSOnce you have successfully connected to the spectrometer, you may then select fromvarious spectrometer functions and tools using the bottom row of buttons on theSpectrometer Control Tool (Figure 4-6). Most importantly, they make it possible foryou to load a sample and to run an experiment. More information on any one of thesetools can be found by first opening the tool, then consulting online Help.

Figure 4-6. Spectrometer Control Tool Lower Buttons

Select:

To load a sample, lock it, spin it, adjust its shims, etc.



Select:

to start the queue.

to stop the queue. (For a full listing of menu functions in this tool, consult page 56-5).

To select an experiment, and to modify its variousparameters (header, instrument, acquisition, and pulse).

To open the automation window that lets you automatecollection and processing of NMR experiments.

To activate the swept lock signal display.

To activate the Real Time monitor display tool.Note: Once in this View Tool, you must selectthe View Vector button to activate it.

To copy data from spectrometer to workstation while datacollection is in progress.

Select:

Spectrometer Control Tools


SPECTROMETER CONTROL TOOLSThe Spectrometer Control Tools -- Sample, Experiment, Automation,Sawtooth, View and Copy -- are described in order here.

SAMPLE CONTROL TOOL

Figure 4-7. Sample/Shim ToolSelect:

to display, in the Sample Control Tool (Figure 4-7) all the following: magnetic field strength in Tesla



cryogen level display, liquid He and N2 physical sample state (Load/Eject) sample changer slot (optional) sample spinning state and rate variable temperature state lock solvent lock control shim controls, and lock level.

To use the Options menu:Select Options - Verify on System Shim Modify To ask for verification before modification of the

system shims. Load Shims from Data File To get the shims by clicking on an open data file and load

them into the Sample Control Tool.

To set up a sample:

1. Set the sample tube (with the sample in it) in the spinner and adjust with the depthgauge. See your NMR administrator for the proper alignment procedure.

Note: When inserting a sample tube into a spinner or removing it, do not applyexcessive force to the sample tube wall. If it is difficult to smoothly insert orremove the sample tube, warm up the spinner by wrapping it up in your hand.This causes the spinner to thermally expand, ensuring easy insertion andremoval.

Warning: Never place an empty spinner into the magnet.

2. Check that the air is flowing by holding your hand over the sample-insertion port ofthe magnet.

If no air is flowing, DO NOT insert the sample tube into the insertion port of the magnet.Another sample may already have been inserted or there might be a problem with the airsystem.

3. Put the spinner containing the sample tube into the sample-insertion port of themagnet and gently release it.

The sample floats on compressed air.

To load samples:Select:

L to load a sample; E to eject a sample in order to load a new one.

Sample Contro

Documents

Delta Users Guide