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 dynamicsprogram, 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 hasle 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.
WHAT IF is based on a so-called SOUP. This SOUP holds all information like coordinates, database hits, parameters, atomic colours, energy values etc. The SOUP menu can be used to manipulate the SOUP.
Most graphical options are performed from the GRAFIC menu, but also options outside the GRAFIC menu can produce graphical output. For example, the SHOHBO option in the HBONDS menu will calculate hydrogen bonds and list them in the text window. However, if the graphics window has been activated (by using the command GRAFIC earlier) the hydrogen bonds are also displayed in the graphics window.
You can calculate atomic distances (DIST), clashes (BUMPS), or environments (NAYB). The results can be graphically represented (GRAFIC). Contacts with waters (WATER), buried waters, or the distance of atoms to bulk water (CABWAT) can be calculated.
You can calculate hydrogenbonds (HBONDS), and you can even optimise hydrogenbond networks (HB2NET). These can be displayed (HB2GRA), and errors in ambihuous hydrogenbonding residues can be detected ((HB2LFR).
There are many different contact analysis options (ANACON). For example, atomic contacts (CONATM) or residue based contact analysis (CONRES) can be performed and graphically represented. These graphical contact plots, like all two dimensional graphics in WHAT IF, are pickable. Saltbridges (SHOSBR) are a special case of contact analysis. The SETVDW menu allows you to use any desired Van der Waals` radius during these calculations.
The SUPPOS menu has many different superposition options. The most intelligent option probably is the fully automatic superpositioning of protein structures. In contrast to many other methods, this module does not require human intervention. Several options exist to compare covalently identical, or covalently highly similar molecules (COMPAR, EQUAL).
The NMR menu allows you to do a few operations on many covalently identical molecules at a time.
The molecular spreadsheet TABLES provide a useful tool for organising data at the residue level.
The CHIANG menu allows you to display (SHOCHI), or manipulate (SETCHI, RNGCHI) torsion angles. The TORS command allows you to do this interactively. The automatic ligand topology maker (DRGTOP) makes it possible to also interactively manipulate small molecule torsion angles.
WHAT IF provide several small molecule related options in the DRUG menu. It can read small molecules in PDB format (GETMOL), MOL2 format (GETML2), or in CSD format (GETCSD). Intefaces exist to the LIGIN and FLEXX drug docking programs, but some limited docking facilities are an integral part of WHAT IF (DENFIT, DENOPT).
The Schneider and Sander HSSP files that hold multiple sequence alignments for all known structures can be read (SHOHSP), use for variability analysis (GETHSP), or for building models (BLDHSP).
Th toy NEURAL network can be used to experiment a bit with small neural network related problems.
WHAT IF can operate ten electron density maps at a time. Maps should have the MFF format, or formatted Xplor format. Most map formats can be converted to either of these two formats by the CCP4 map converter.
The CAVITY options allows you to visualise cavities.
The CHKMDF menu allows the crystallographers to visualise reciprocal space. HKL,F,sigma files can be displayed, as well as differences between datasets.
WHAT IF provides the most extensive and most intelligent symmetry menu of all molecular modelling related packages. Most options, eg. hydrogen bond analysis, accessibility calculations, contact analysis, etc, can automatically incorporate symmetry related partners if requested.
The REFI option regularises structures that are about OK. The CRUDE option, as the name already suggests, does an extremely crude fixing of structures that have really large errors in them.
The SEARCH menu allows you to answer complicated questions like: "Where are the buried unsatisfied hydrogen bond donors/acceptors that are not involved in a hydrogen bond?". This menu allows for the flexible combination of most of WHAT IF's calculation options.
The WALIGN menu is a story in itself. It allows for several rather intelligent sequence analysis possibilities. Iterative profile alignment (PROF2D) is the basis of this menu. Correlation analysis (CORREL) helps you determine essential (functional or structural) amino acids in your sequence(s).
The GRATWO menu does two dimensional graphics. PHIPSI plots, B-factor plots (BFPLOT), etc., can be drawn and interactively inspected.
The ITMADM menu allows you to book-keep the graphical objects GETITM will get yesterdays objects (called items) back, for example.
The GRAEXT command holds some rather special graphics commands. For example with ARROW you can draw an arrow that you can than place anywhere at the screen you want. LINATM allows you to draw lines between atoms. PLUTO draws 3D plots much like the old pluto program did in 2D. CELL draws a fram around your crystallographic cell. There are also some options to draw hidden line removed, depth cueued SPLINE plots.
The PORNO menu holds the very fancy graphics options, the so-called molecular pornography. Here you find the interface to the RIBBON program and to the PLUTON program.
You can also LABEL atoms any way you want in the label menu.
The COLOUR menu holds options like COLCHG to colour by charge, COLROW to colour by search hit, COLBFT to colour by B-factor, but also options like COLBB to colour the backbone, etc.
WHAT IF also is the scientific father of the PDBFINDER databse. This PDBFINDER can be queried by many different programs, e.g. SRS. The SELECT options allow you to search for example for proteases solved at better than 2.5 A resolution that are shorter than 250 amino acids, etc.