What if main body

A license to use WHAT IF freely for all purposes except redistributing or publishing it or parts of it in any form can be obtained from:

Dr. G. Vriend EMBL Meyerhofstrasse 1 69117 Heidelberg West Germany (Internet: "VRIEND@EMBL-Heidelberg.DE")

The license costs are:

$250,-  for universities and other non-profit organisations.
$0,-    annual fee for universities and other non-profit organisations.
$5000,- for industry and other profit making organisations.
$0,-    annual fee for industry and other profit making organisations.
$250,-  per distribution. Both for profit and non-profit organisations;
        (the first distribution is included in the lisence costs).
        updates via the computer network are free of charge.
This includes a tape with the entire program, all command files, source codes, object files, help files, executables, and special graphics software. Also included are installation notes, a copy of the writeup, and the source codes needed to run the additional programs. (NOT those additional programs themselves).

Additional programs

Several parts of WHAT IF consist of software which I obtained from elsewhere. In those cases where I promissed not to re-distribute, I will NOT do so. However, if you can prove that you have permission from the original authors of this additional software to use their products, I will supply you with every line of (my) code needed to run these programs (including auto-installation files and the lines you need to change in these programs from other people).

Prices mentioned for the products mentioned below are my best guess at this moment. For real pricing info please contact the vendors.

These additional software products / data files are :

Free software

Free software that can be used in conjunction with WHAT IF is available by anonymous FTP from the WHAT IF distribution machine:, directory /whatif/support. This includes a complete setup for LaTeX and xfig.

PDB files

PDB-files. If you want to use WHAT IF's 3D-database you need PDB files. (These are the Brookhave Protein Data Bank coordinate files for proteins and DNA molecules. I am not allowed to re-distribute these files, but the derived data needed for database operations is part of the distribution.
PDB files are distributed by:

Worldwide except Japan and Australia:

Protein Data Bank
Chemistry Department 
Brookhaven National Laboratory
Upton, New York 11973, USA


CSIRO Central Information Service
P.O. Box 89, East Melbourne
Victoria 3002, Australia


Institute for Protein Research
Osaka University
Yamadaoka, 3-2, Suita,
Osaka 565, Japan

Costs ($250,$250)

Also several other sites allow PDB files to be FTP-ed from their servers.


DSSP determines helix, sheet, turn and coil contents of protein structures. If you show proof that you have this program, you will also receive the code in WHAT IF needed to use DSSP.

Only a few options in WHAT IF do not work in absence of DSSP. These are of course the secundary structure evaluation, but also SPLINE the subroutine that generates nice smooth ribbon drawings of the way the protein is folded, the mutation quality control, etc.

DSSP is written by Kabsch and Sander. Contact Dr. C. Sander at the EMBL Meyerhoffstrasse 1 69117 Heidelberg West Germany ($1100,- $0,-)


GROMOS can be used to do energy minimizations and molecular dynamics. WHAT IF will run perfectly without GROMOS, but energy minimization and molecular dynamics are an important and powerful tool in molecular modeling. GROMOS can be obtained from:

University of Groningen 
Nijenborgh 16
9747 AG groningen
The Netherlands
tel 31-50-634320

and/or from

Prof. W. van Gunsteren
Department of ...
ETH Zurich
($10.000,- $200,-)
We have the right to redistribute even the GROMOS source code, provided you are a lisence holder. If you have your GROMOS lisence already for several months, you might already be on our list, otherwise, send a copy of the agreement between you and BIOMOS.


The program GRID can be used to create potential energy maps. WHAT IF contains a PRE-GRIN/GRID GRID user interface. This interface is included. However, you will have to ask Dr. P.J. Goodford for the program(s).

GRID can be obtained from:

Dr. P.J. Goodford,
West Way House
Elms Parade
Oxford OX2 9LL
($200,- - ...)
(see also chapter on GRIN/GRID)


Several programs from this library will be included, because some WHAT IF option use them explicitly, but all other programs can be obtained from B. Dijkstra in Groningen.
CFB crystallographic library
Prof. B.Dijkstra
Dept. Chem Phys,
Univ. Groningen
Nijenborg 16
9747 AG Groningen
The Netherlands


The fancy small molecule plotting program PLUTON is available from

Dr. T. Spek
Dept. Cryst. and Struct. Chem
Hugo R. Kruijt gebouw
Padualaan 8
NL 3584 CH Utrecht
The Netherlands
($ 1.000,-, Pc version free; Hfl 0.0,-)
free updates over FTP


The fancy ribbon and CPK program RIBBONS was written by Mike Carson at the university of alabama. This program is available ($1000,-; $250,-). If you have a RIBBONS lisence, we can give you a copy that has been modified to work better together with WHAT IF. Mike Carson University of Alabama at Birmington Center of Macromolecular Crystallography 252 BHS 79 THT University Station Birmingham, AL 35294 USA (... - $250,-)


The scatterplot program SCATTER is written by Rob Hooft. It can be obtained free of cost from anonymous FTP at