Copyright © 2010 One Moon Scientific, Inc.
| Revision History | |
|---|---|
| Revision 9 | 22 Nov 2010 |
| Draft | |
Table of Contents
- Draft
- I. Usage
- 1. Introduction
- 2. Installation
- 3. Quick User's Guide
- Overview
- Viewing and Plotting a 2D Spectrum
- Datasets
- 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. Menus
- 5. Datasets
- 6. Creating and Using Spectral Display Windows
- 7. Projects and Data
- 8. Peaks
- 9. Molecular Structures
- 10. Strips
- 11. RunAbout
- 12. Atoms and Assignments
- 13. Rate Analysis
- 14. Constraint Generation, Evaluation and Export
- 15. Titration Analysis
- 16. Tables
- 17. Charts
- 18. Appendix I Open Source Software
- II. 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.
- III. Jacl Programming tcltutorial
- 19. Introduction
- 20. Simple Text Output
- 21. Assigning values to variables
- 22. Evaluation & Substitutions 1: Grouping arguments with ""
- 23. Evaluation & Substitutions 2: Grouping arguments with {}
- 24. Evaluation & Substitutions 3: Grouping arguments with []
- 25. Results of a command - Math 101
- 26. Numeric Comparisons 101 - if
- 27. Textual Comparison - switch
- 28. Looping 101 - While loop
- 29. Looping 102 - For and incr
- 30. Adding new commands to Tcl - proc
- 31. Variations in proc arguments and return values
- 32. Variable scope - global, upvar, and unset
- 33. Tcl Data Structures 101 - The list
- 34. Adding & Deleting members of a list
- 35. More list commands - lsearch, lsort, lrange
- 36. String Subcommands - length index range
- 37. String comparisons - compare match first last wordend
- 38. Modifying Strings - tolower, toupper, trim, format
- 39. Regular Expressions 101
- 40. More Quoting Hell - Regular Expressions 102
- 41. Associative Arrays
- 42. More On Arrays - Iterating and use in procedures
- 43. File Access 101
- 44. Information about Files - file, glob
- 45. Learning the existence of commands and variables ? - info
- 46. State of the interpreter - info
- 47. Information about procs - info
- 48. Modularization - source
- 49. Building reusable libraries - packages and namespaces
- 50. Creating Commands - eval
- 51. More command construction - format, list
- 52. Substitution without evaluation - format, subst
- 53. Changing Working Directory - cd, pwd
- 54. Debugging & Errors - errorInfo errorCode catch error return
- 55. More Debugging - trace
- 56. Command line arguments and environment strings
- 57. Timing scripts
- 58. Time and Date - clock
- 59. Child interpreters
List of Figures
- 3.1. NMRView Main Toolbar
- 3.2. NMRView SwkCon Console
- 3.3. Main Toolbar Pulldowns
- 3.4. Preferences Panel
- 3.5. Paths and Filenames Preferences
- 3.6. The Open and Draw panel
- 3.7. The Open and Draw panel with a file selected.
- 3.8. The Spectrum Panel, as first drawn.
- 3.9. The Spectrum Panel, more aesthetically displayed.
- 3.10. The Windows...Add panel
- 3.11. A new, blank Spectrum Window
- 3.12. The Spectrum Attributes panel
- 3.13. Key features of the Spectrum Window
- 3.14. Cursor information displays.
- 3.15. The Spectrum Window buttons
- 3.16. The Spectrum Window's Print button's menu
- 3.17. Output from the Spectrum Window's Print..."Plot"
- 3.18. The Spectrum Window menu with sub-menus.
- 5.1. Serial and Sub-matrix Data Formats
- 6.1. Windows laid out in a 2x3 matrix
- 6.2. One Dimensional Spectrum
- 6.3. The Spectrum Attributes...File...Add panel (cut for space considerations)
- 6.4. Removing a dataset in Spectrum Attributes...File...Remove The Colors... Button The
- 6.5. The Spectrum Attributes...File Display panel
- 6.6. The Spectrum Attributes File panel Colors submenus
- 6.7. A standard color palette
- 6.8. Preset color schemes for background, axes, and cursors - but not peaks
- 6.9. Color Schemes in Spectrum Attributes for overlaid spectra (arrows indicate selected schemes)
- 6.10. The effects of different settings in Spectrum Attributes - Plot
- 6.11. The Spectrum Attibute Peak Pick pulldown menus
- 6.12. Immediate effects of picking peaks in the Peak Pick panel and spectrum display
- 6.13. Peaks on an HSQC spectrum
- 6.14. The Spectrum Attributes Peak Attributes panel, with pulldown menus
- 6.15. Application of the "Extract/Replace" button in the Spectrum Attributes...Analysis panel
- 6.16. Toolbars available in the Extracted Spectrum window
- 7.1. Structure Analysis GUI
- 7.2. Structure Analysis GUI
- 8.1. peak_keypress.png
- 9.1. Structure Analysis GUI
- 9.2. Residue RMSD Plot
- 9.3. Ramachandran Plot
- 9.4. Molecular Viewer
- 10.1. Strip Plot GUI
- 10.2. Strip Table
- 10.3. Strip Sorter
- 11.1. Peak Pick All - Results
- 11.2. Runabout Main Panel - initial
- 11.3. Peak Lists
- 11.4. Details of patterns expected for different peak lists
- 11.5. RunAbout's Edit Peaks Mode
- 11.6. RunAbout's Actions panel
- 11.7. RunAbout's Actions panel
- 11.8. RunAbout in Edit Clusters mode, Helm panel displayed
- 11.9. Edit Clusters - Helm Panel, close-up
- 11.10. Edit Clusters - Spectrum panels (Helm's Right)
- 11.11. Runabout's display of single-letter spectrum commands
- 11.12. Results of toggling peak identity using the "t" command
- 11.13. Checking the i/i-1 statuses of peaks
- 11.14. Cluster Details
- 11.15. Entering Edit Links mode
- 11.16. The Edit Links Helm display
- 11.17. Edit Links - Matching Clusters display
- 11.18. Editing Links - Cluster #0 matched up with clusters #9 and #77 to the N- and C-terminal sides, respectively
- 11.19. Editing Links - Cluster #0 matched up with clusters #20 and #77 to the N- and C-terminal sides, respectively
- 11.20. Highlights of peaks constituting links between clusters
- 11.21. Changes visible upon confirming an N-terminal link (cluster #9 to cluster #0)
- 11.22. Changes visible upon confirming a C-terminal link (cluster #0 to cluster #77)
- 11.23. RunAbout's assignment automation buttons
- 11.24. Results of automatically extending assignments
- 11.25. Overcoming hurdles - Results of extension after manual confirmation
- 11.26. Frozen sequence displayed in Runabout's Helm
- 11.27. Calling up the Atom Assignments panel
- 11.28. Results of freezing RunAbout assignments manifested in the Assign Atoms panel.
- 11.29. Final assignments, as seen in Atom Assignments panel and RunAbout’s Helm.
- 11.30. Tocsy NNH Helm Display
- 13.1. rateanalysis_fitpar.png
- 13.2. rateanalysis_equexamp.png
- 13.3. Rate Analysis Data Table and Graph
- 13.4. Rate Analysis Profile Graph
- 14.1. Distance Constraint Table
- 14.2. Distance Constraint Table Columns
- 14.3. Distance Constraint Table Filtering
- 14.4. Distance Constraint Table Filtering
- 14.5. Distance Constraint Table Filtering
- 14.6. Distance Constraint Tolerances
- 14.7. Distance Constraint Table Filtering
- 14.8. Distance Constraint Table Filtering
- 14.9. Distance Constraint Table Controls
- 14.10. Constraint Display in Molecular Viewer
- 14.11. Distance Constraint Table Controls
- 14.12. Distance Constraint Table Controls
- 14.13. Distance Constraint Table Filtering
- 15.1. titration_fitpar.png
- 16.1. Simple Table Example
- 16.2. Simple Table Example
- 16.3. Sorted Table
- 17.1. XY Chart
- 17.2. XY Chart
- 17.3. XY Chart
- 17.4. XY Chart
- 17.5. XY Chart
- 17.6. XY Chart
- 17.7. XY Chart
List of Tables
- 5.1. File Formats for Some NMR Processing Programs
- 6.1. Cursor Correlation
- 14.1.
- 18.1. Open Source Software