NMRView: The Found Manual

Table of Contents

Draft

I. Usage

1. Introduction

2. Installation

3. Quick User's Guide

Overview

Helpful Concepts

Clicking

Guide Nomenclature

Viewing and Plotting a 2D Spectrum

Presumptions

Start NMRView

Orient Yourself

Set Preferences

Open and Draw a Dataset

Opening and drawing datasets and spectrum windows as separate steps

Using Spectrum Windows

Familiarize yourself with the Spectrum Window

Familiarize yourself with the cursors

The Spectrum Window buttons

Plotting your spectrum

Practice zooming in and out

Orient yourself with respect to the window menus

4. Control Panel

The File Menu

The Dataset Menu

The Windows Menu

The Assign Menu

The Analysis Menu

The Molecule Menu

The Help Menu

5. Datasets

Datasets

Dataset Formats

Adding File Formats

Loading Datasets

Changing Reference Information

Dataset Parameter File

Datasets Table

Manage Datasets

6. Creating and Using Spectral Display Windows

Adding Spectral Display Windows

Using the Graphical Interface

Using Tcl Commands

Using Spectral Windows

Display Modes

The Spectrum Icon Bar

Cursors

Crosshair Correlation

Keypad Navigation

Spectral Attributes Dialog

The File Panel

The View Panel

The Graph Panel

The Plot Panel

The PeakPick Panel

The Peak Display Panel

The Peak Attributes Panel

The Analysis Panel

Spectral Display Menu

Managing Spectral Display Windows

Spectrum Synchronization

Preserving the Spectral Window State between Sessions

7. Peaks

The Peak Inspector

The Peak Table

Peak Filtering

Systematic Peak Examination

Peak Menu Commands

Measuring Peak Volumes

Identifying Peaks

Transferring assignments to peaks

Linking peak lists together

Interactive peak link viewing and adjustment

The Resonance Table

8. STAR Files for Data Storage and Archival

STAR Format

The NMRViewJ STAR Editor

Retrieving STAR Files

9. Molecular Structures

10. Strips

11. RunAbout

General Description

Required Data

Preparing the Spectra, PeakLists, and Sequence File

Checking out your Spectrum Levels

RunAbout Parameters Panel - Selecting Peaklists

Details of RunAbout's peak list patterns

Runabout -Edit Peaks Mode

Peak Registration

Automatic Peak Actions

RunAbout -Edit Clusters (HN-C)

Enter into Edit Clusters Mode

Orientation - Helm's Left:

Orientation - Helm's Right

Editing Clusters

RunAbout - Edit Links

Edit Links Overview

Orientation and sketch of actions

Automation

Semi-automated Assignment Strategy

Continuing and Finishing

Sidechain Assignments

TocsyCONNH Assignment Mode

HCCH Assignment Mode

12. CSI Display

13. Rate Analysis

14. Titration Analysis

15. Tables

16. Charts

II. Jacl Programming tcltutorial

17. Introduction

Introduction

Additional Resources

Credits

18. Simple Text Output

Simple Text Output

Example

19. Assigning values to variables

Assigning values to variables

Example

20. Evaluation & Substitutions 1: Grouping arguments with ""

Evaluation & Substitutions 1: Grouping arguments with ""

Example

21. Evaluation & Substitutions 2: Grouping arguments with {}

Evaluation & Substitutions 2: Grouping arguments

22. Evaluation & Substitutions 3: Grouping arguments with []

Evaluation & Substitutions 3: Grouping arguments with []

Example

23. Results of a command - Math 101

Results of a command - Math 101

OPERANDS

OPERATORS

MATH FUNCTIONS

TYPE CONVERSIONS

Example

24. Numeric Comparisons 101 - if

Numeric Comparisons 101 - if

Example

25. Textual Comparison - switch

Textual Comparison - switch

Example

26. Looping 101 - While loop

Looping 101 - While loop

Example

27. Looping 102 - For and incr

Looping 102 - For and incr

Example

28. Adding new commands to Tcl - proc

Adding new commands to Tcl - proc

Example

29. Variations in proc arguments and return values

Variations in proc arguments and return values

Example

30. Variable scope - global, upvar, and unset

Variable scope - global and upvar

Example

31. Tcl Data Structures 101 - The list

Tcl Data Structures 101 - The list

Examples

32. Adding & Deleting members of a list

Adding & Deleting members of a list

Example

33. More list commands - lsearch, lsort, lrange

More list commands - lsearch, lsort, lrange

Example

34. String Subcommands - length index range

String Subcommands - length index range

Example

35. String comparisons - compare match first last wordend

String comparisons - compare match first last wordend

Example

36. Modifying Strings - tolower, toupper, trim, format

Modifying Strings - tolower, toupper, trim, format

Example

37. Regular Expressions 101

Regular Expressions 101

Example

38. More Quoting Hell - Regular Expressions 102

More Quoting Hell - Regular Expressions 102

Example

39. Associative Arrays

Associative Arrays.

Example

40. More On Arrays - Iterating and use in procedures

More Array Commands - Iterating and use in procedures

Example

41. File Access 101

File Access 101

Example

42. Information about Files - file, glob

Information about Files - file, glob

Example

43. Learning the existence of commands and variables ? - info

Learning the existence of commands and variables ? - info

Example

44. State of the interpreter - info

State of the interpreter - info

Example

45. Information about procs - info

Information about procs - info

Example

46. Modularization - source

Modularization - source

Example

47. Building reusable libraries - packages and namespaces

Building reusable libraries - packages and namespaces

Using packages

Creating a package

Namespaces

Using namespace with packages

Example

Ensembles

48. Creating Commands - eval

Creating Commands - eval

Example

49. More command construction - format, list

More command construction - format, list

Example

50. Substitution without evaluation - format, subst

Substitution without evaluation - format, subst

Example

51. Changing Working Directory - cd, pwd

Changing Working Directory - cd, pwd

Example

52. Debugging & Errors - errorInfo errorCode catch error return

Debugging and Errors - errorInfo errorCode catch error return

Example

53. More Debugging - trace

More Debugging - trace

Example

54. Command line arguments and environment strings

Command line arguments and environment strings

Example

55. Timing scripts

Timing scripts

Example

56. Time and Date - clock

Time and Date - clock

Example

57. Child interpreters

Child interpreters

Example

III. Low level command reference

I. Reference Pages

bioppmscore — Scoring based on chemical shift ranges.

cluster — Multidimensional clustering of a list of data values.

export — Export graphical representation of window to file.

mmcif — Read MMCIF files.

mol — Interact with molecular structures.

nv_atom — Query and set atom-based values for current molecule.

nv_dataset — Analyze NMR datasets

nv_idpeak — Identify atoms consistent with chemical shift values.

nv_noe — Interact with lists of NOEs.

nv_peak — Analyze and manipulate spectral peak lists.

nv_pkcluster — Worth with clusters of peaks.

nv_residue — Deprecated

nv_resonance — Query and assign resonances.

nv_sread — Read molecular structures.

nv_swrite — Write molecular structures.

nv_win — Control spectral windows.

nv_xy — Non-linear regression fitting of XY data.

print — Print windows.

star — Read NMR-STAR (version 2) files.

star3 — Read and write NMR-STAR (Version 3) files.

vecmat — Math and statistics with vectors and matrices.

vnmr — Load and VNMR parameter files.