Table of contents for the WHAT IF manual

Clicking on the chapter name takes you to the chapter in the manual. Clicking on the [TOC] sign gets you a detailed table of contents. Clicking here brings up the WHAT IF home page.

[TOC] General notes (GENERAL)
[TOC] Input and output of coordinates (SOUP)
[TOC] General options (GENERAL)
[TOC] Making notes (NOTES)
[TOC] Logging commands or results
[TOC] The script option
[TOC] Introduction to menus (GENERAL)
[TOC] Tutorial
[TOC] Surface area calculations (ACCESS)
[TOC] Water operations (WATER)
[TOC] Quality control (QUALTY)
[TOC] Hydrogen bonds (HBONDS)
[TOC] Graphical contact analysis (ANACON)
[TOC] Building proteins (BUILD)
[TOC] Superimposing structures (SUPPOS)
[TOC] Van der Waals menu (SETVDW)
[TOC] Nmr specific options (NMR)
[TOC] Families and clusters (CLUFAM)
[TOC] Data spread sheet (TABLES)
[TOC] Sequence files (PIRPSQ)
[TOC] Torsion angle evaluation and manipulation (CHIANG)
[TOC] Drug design module (DRUG)
[TOC] Structure verification (CHECK)
[TOC] Hssp related commands (HSSP)
[TOC] Extra commands (EXTRA)
[TOC] The neural network (NEURAL)
[TOC] Introduction to X-ray related menus
[TOC] Working with maps (MAP)
[TOC] Manipulating map values (MASMAP)
[TOC] Manipulating reflection files (CHKMDF)
[TOC] Editing envelop maps (MAPEDT)
[TOC] Symmetry operations (SYMTRY)
[TOC] Amino acid structure regularization (REFINE)
[TOC] The X-ray menu (XRAY)
[TOC] The structure fragment database (DGLOOP)
[TOC] Relational protein structure database (SCAN3D)
[TOC] Selecting database proteins (SELECT)
[TOC] Atomic parameter correlation rows (SEARCH)
[TOC] (Re-)creating the database (SEQ3D)
[TOC] 3-dimensional structure superposition (3SSP)
[TOC] Sequence manipulation (WALIGN)
[TOC] Using the graphics (GRAFIC)
[TOC] Graphics objects and items (ITMADM)
[TOC] Two dimensional graphics (GRATWO)
[TOC] Graphics enhancement options (GRAEXT)
[TOC] Colouring atoms, residues, molecules, etc. (COLOUR)
[TOC] Plotting (PLOTIT)
[TOC] Labeling atoms (LABEL)
[TOC] Very fancy graphics; molecular pornography (PORNO)
[TOC] Connolly surface (CONOLY)
[TOC] Using grid (GRID)
[TOC] Gromos related commands (GROMOS)
[TOC] Molecular dynamics analysis (ANATRA)
[TOC] ESSENTIAL DYNAMICS ANALYSIS (ESSDYN)
[TOC] ANALYZE TRAJECTORY (ANATRA)
[TOC] OTHER OPTIONS (OTHER)
[TOC] Notes for programmers
[TOC] List of include files. Common variables. Topology file.
[TOC] How to make your own manual, WWW pages, etc. (DOSELF)
[TOC] List of tools subroutines
[TOC] Bugform
[TOC] Program parameters
[TOC] Teaching module
[TOC] Overview (README)
[TOC] Appendix
[TOC] Reconstruction from stereo plots
[TOC] Distribution conditions
[TOC] Installation notes
[TOC] Frequently Asked Questions
[TOC] License
[TOC] Acknowledgements
[TOC] Disclaimer