Author: Gert Vriend
WHAT IF was written with proteins in mind. Many options are available to visualize proteins (see the menus GRAFIC for normal molecular display, GRATWO for two dimensional graphics, GRAEXT for special effects, RIBBON in PORNO for very beautiful graphics or molecular pornography, COLOUR to colour atoms, residues, molecules, etc., PSTPLT for postscript plots).
You can perform many calculations on proteins. See HBONDS for hydrogen bonds, ACCESS for accessibility calculations, CHIANG for torsion angle manipulations, BUILD to do ab-initio building, REFINE to patch up your structure after you mugged it up manually, GROMOS to interface to the GROMOS energy minimization and molecular dynamics program, GRID to interface to the GRIN and GRID potential energy calculation programs, HSSP to manipulate HSSP files (multiple sequence alignments), WALIGN for sequence operations. Model building by homology is done via the BLDPIR command in the PIRPSQ menu. The command CHECK activates a menu for protein structure verification, all thinkable and unthinkable errors will be detected, and you can get (completely automatically) a report written as if it is an article to be submitted.
The WATER menu has several options to manipulate water molecules. In the ANACON menu you will find contact analysis and bump checking options. GROMOS molecular dynamics movies can be displayed from the ANATRA menu. All superposition options, inclusive the fully automatic protein superposition module can be activated from the SUPPOS menu, however, if you want to run the automatic superposition option against the whole database, you should use the 3SSP menu. The CONOLY menu can be used to work with Connolly's surface area calculation and visualization program.
The NMR menu holds NMR specific options like multiple structure display, multiple structure superposition, multiple structure entry etc. The XRAY menu holds several XRAY specific commands, for example, MASMAP to massage electron density maps, CHKMDF to visually inspect h, k, l, F, sigma files, MAPEDT to edit envelope maps and SYMTRY for symmetry operations.
The TABLES menu holds a molecular spread sheet. All WHAT IF options that produce residue related output (e.g. accessibilities, secondary structure, packing quality, etc.) can write tables in this spread sheet. This spread sheet removes the hassle of manually comparing many sheets of paper with the output of many different programs.
The DGLOOP menu holds options to use the fragment database, for example to make loop insertions. The SEARCH menu helps you searching for complicated situations in your protein like atoms potentially involved in a hydrogen bond which actually are not, but are fully buried, or similarly complicated combined questions. The SCAN3D menu holds all options to manipulate the very special relational database. This database is best compared with the very nice (but expensive) IDITIS (tm) database system. SCAN3D is less extensive, but fully integrated.
In the CSB core do the following to use WHATIF:
Especially useful is the CHECK menu for checking many aspects of a structure. Run it on your structure only if you are having a good ego day.
The check menu does not require graphics, just type the following at the WHAT IF> prompt,
check (go to the check menu)
fulchk (run full check)
filename.pdb (the name of your pdb file)
name (a name for this object in WHAT IF)
n (don't stop here necessarily)
$more pdbout.txt (Read it and weep)
How to mutate a residue, remove contacts, and write out a new PDB file with the mutation
Last Modified: Thursday, 15-Aug-2002 10:42:00 EDT