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CHAPTER 0: Table of Contents

NMRanalyst Manual

User Manual

CHAPTER 1: Overview
1.1 The Automated Spectral Analysis
1.2 Identification of Best Matching Structures
1.3 Using this Manual
1.4 Typographic and Keyboard Conventions
CHAPTER 2: NMRanalyst Installation
2.1 Supported Computer Platforms
2.2 Contents of the NMRanalyst Distribution
2.3 Preparation for the Linux Installation
2.4 Installing NMRanalyst
2.5 De-installing NMRanalyst
2.6 NMRanalyst Software Support
CHAPTER 3: Tutorial I: Using NMRanalyst
3.1 findit Script for Molecular Structure Identification
3.2 Selecting Full NMRanalyst Mode
3.3 Selecting 2D INADEQUATE Spectrum Type
3.4 The 1D Analysis Workwindow
3.5 The FFT Workwindow
3.6 The nD Analysis Workwindow
3.7 The Report Workwindow
3.8 Determined Prednisone Structure
3.9 Exiting the Software
CHAPTER 4: Tutorial II: Setting Analysis Parameters
4.1 The UNIX Shell Window
4.2 1D Analysis Workwindow Settings for Prednisone
4.3 VerifyIt: Molecular Structure Verification and Shift Assignments
4.4 FFT Workwindow Settings for Prednisone
4.5 Displaying All Workwindow Input Fields
4.6 Determining Phase Functions
4.7 Prednisone Spectrum With 1D Carbon & Correlation Locations
4.8 Experimental, Simulated, and Residual Spectrum of One Correlation
4.9 The History Mechanism for Input Values
4.10 Directory Editor and the Sucrose FID Analysis
4.11 Analysis of the Sucrose VNMR Created Spectrum
CHAPTER 5: Tutorial III: Combining Analysis Results
5.1 Analysis of 1D Spectra
5.2 Analysis of Multiplicity Edited HSQC Spectrum
5.3 Analysis of Gradient HMBC Spectrum
5.4 AssembleIt: HSQC & HMBC Derived Gibberellic Acid Structure
5.5 Structure Identification Without 1D Carbon Spectrum
5.6 Structure Elucidation Without 1D Carbon Spectrum
CHAPTER 6: Tutorial IV: Advanced Structure Elucidation
6.1 1D Carbon, 1D Proton, Edited HSQC, and HMBC Analyses
6.2 Generation of a Generic 15N Resonance List
6.3 15N HMBC Spectrum Analysis
6.4 Strychnine Structures Derived From Previous Analysis Results
6.5 Using DQF-COSY
6.6 Using DQ 1,1-ADEQUATE
6.7 Adding Heteroatoms
6.8 Identifying the Molecular Structure Through Shift Prediction
CHAPTER 7: Tutorial V: Additional NMRanalyst Features
7.1 Using an HSQC FID for the findit Structure Identification
7.2 Displaying Experimental, Simulated, and Residual NMR Spectra
7.3 Surface Plot of a 2D Spectrum
7.4 Analyzing 3D Spectra
7.5 Incorporating NMRanalyst Programs in Other Software
7.6 The On-line Help System

Reference Manual

CHAPTER 8: Using the Help System
8.1 Starting the On-Line Help
8.2 Navigating Through the Help Text
8.3 Using the JavaHelp Navigation
8.4 Copyright JavaHelp
CHAPTER 9: Using the NMRanalyst Window
9.1 Starting NMRanalyst
9.2 Error Message "analyst: not found"
9.3 Error: Incorrectly Set DISPLAY Variable
9.4 NMRanalyst Cannot Find Its Installation Directory
9.5 Structure and Function of the Application Window
9.6 The Workwindow Tabs
9.7 The Speed Button Panel
9.8 The Application Window Menus
9.9 The Print Popup
9.10 Copyright Enscript Program
9.11 Copyright GNU Ghostscript Program
9.12 Copyright Java Runtime Environment
9.13 Copyright PC Cygwin UNIX Toolset
CHAPTER 10: Using the Directory Editor
10.1 NMRDIR, NMRUSER, NMRDATA, and NMRSPEC Shell Variables
CHAPTER 11: Using the Filebox Popup
11.1 Interactive Item Specification
CHAPTER 12: Using the Workwindows
12.1 The Workwindow Input Screen
12.2 The Workwindow Output Screen
12.3 The Workwindow File Locking
12.4 Summary of Workwindow File Usage
CHAPTER 13: 1D Analysis Workwindow
13.1 Input File
13.2 Output Files
13.3 Spectral Description
13.4 Analysis Parameters
13.5 General 1D Resonance Analysis
13.6 Copyright Freely Distributable LIBM
CHAPTER 14: FFT Workwindow
14.1 Input Files
14.2 Output File
14.3 Spectral Description
CHAPTER 15: nD Analysis Workwindow
15.1 Input Files
15.2 Output Files
15.3 Analysis Parameters
15.4 Select Plot Data to be Saved
15.5 Automatically Running Report After nD Analysis
CHAPTER 16: Report Workwindow
16.1 Input File
16.2 Output Files
16.3 Select Items to Be Reported
16.4 Generate NOE Build-up Curves
CHAPTER 17: AssembleIt Workwindow
17.1 Combine NMR Analysis Results
17.2 FindIt: Identify Database Structures Best Matching NMR Data
17.3 VerifyIt: Rate Specified Structure by Agreement With NMR Data
17.4 AssembleIt: Elucidate Molecular Structure From NMR Data
CHAPTER 18: Graphic Workwindow
18.1 Settings for All Plots
18.2 NMRplot Specific Settings
18.3 Multidimensional Spectrum Specific Settings
18.4 Function of the Graphic Programs
CHAPTER 19: NMRgraph: Molecular Correlation Editor
19.1 Pull-Down Menus
19.2 The Atom Property Editor
19.3 The Correlation Property Editor
19.4 Mouse Operations
19.5 Keyboard Key Operations
19.6 Copyright InChI
19.7 Copyright NIH PubChem
CHAPTER 20: NMRplot: Plotting Multidimensional Spectra
20.1 Spectral Phasing
20.2 Mouse Interactions
20.3 Pull-Down Menus
20.4 Copyright Mesa
20.5 Copyright OpenGL to PostScript Printing Library GL2PS
20.6 Copyright Visualization Toolkit (VTK)

Appendix

CHAPTER 21: Frequently Asked Questions
21.1 How are the CCBond, FRED, and NMRanalyst programs related?
21.2 Any differences between MS Windows and LINUX NMRanalyst?
21.3 How can I access Linux files from a PC running MS Windows?
21.4 Can I run NMRanalyst on an Apple Macintosh?
21.5 How to display new MS Windows applications as foreground windows?
21.6 Any UNIX editor available from the Windows UNIX Shell?
21.7 How to copy and paste text in Windows NMRanalyst?
21.8 What should I do about the Windows XP NMRanalyst security alert?
21.9 How can I get NMRanalyst printing to work?
21.10 How can I capture NMRgraph and NMRplot displays?
21.11 Why can't I switch NMRanalyst to a different spectrum type?
21.12 Why are the NMRplot colors wrong?
21.13 How to fix incorrect NMRplot or NMRgraph rendering?
21.14 How to increase the paging space on Linux?
21.15 How to specify correlations for the AssembleIt structure generation?
CHAPTER 22: Index

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