From: gwilliam@mrc-crc.ac.uk (Gary Williams x3294)
Newsgroups: sci.nanotech
Subject: Public Domain molecular modelling packages
Date: 23 Jan 93 03:36:31 GMT
Organization: MRC Human Genome Resource Centre


The following list of programs may interest those of you who expressed
an interest in public domain molecular modelling/molecular dynamics
packages. 

I haven't followed up any of these programs, so I look forward to
hearing on sci.nanotech from anyone who gets them up and running. 

This list is about 6 months old, so some of the information may be no
longer valid. 

You should note that you get what you pay for :-) 
As has already been remarked in this news-group, there are many
excellent packages for a few hundred pounds/dollars/marks/yen/ecu. 

There was also a question about formats for storing molecular structures
in files.  There are many conventions, but nearly all good packages
should understand the Brookhaven format (also called the PDB format). 

----------------------------------------------------------------------

[ Based on a list from cristy@dupont.com < Cristy > , which asked for
 systems for displaying Molecular Dynamics, MD for short ]

a. Flex is a public domain package written by Michael Pique, at The Scripps
   Research Institute, La Jolla, CA. Flex is stored as a compressed,
   tar'ed archive (about 3.4MB) at perutz.scripps.edu [137.131.152.27], in
   pub/flex. It displays molecular models and MD trajectories.

b. MacMolecule (for Macintosh). I searched with Archie, and the most
   promising place is sumex-aim.stanford.edu (info-mac/app, and
   info-mac/art/qt for a demo)

c. If you are running on an SGI, try MD-DISPLAY, from Terry
   Lybrand (lybrand@milton.u.washington.edu).

d. Duncan McRee <dem@scripps.edu> has something called XtalView.  It is a
   crystallography package that does visualize molecules and much more.
   It uses the XView toolkit.

e. landman@hal.physics.wayne.edu:

   I am writing my own visualization code right now.  I look at MD output
   (a specific format, easy to alter for the subroutine) on PC's.  My
   program has hooks into GKS.  If your friend has access to Phigs for X
   (PEX) and fortran bindings, I would be happy to share my evolving code
   (free of charge).  Right now it can display supercells of up to 65
   atoms (easy to change), and up to 100 time steps, drawing nearest
   neighbor bonds between 2 defining nn radii.  It works acceptably fast
   on a 10Mhz 286.

f. icsg0001@caesar.cs.montana.edu:

   I did a project on Molecular Visualization for my Master's Thesis, using
   UNIX/X11/Motif which generates a simple point and space-filling model.

g. KGNGRAF by IBM.

h. ditolla@itnsg1.cineca.it:

   I'm working on molecular dynamic too.  A friend of mine and I have
   developed a program to display an MD run dynamically on Silicon
   Graphics.  We are working to improve it, but it doesn't work under X,
   we are using the graphi. lib. of the Silicon Gr. because they are much
   faster then X.  When we'll end it we'll post on the news info about
   where to get it with ftp. (Will be free software).

i. XBall V2.0: written by David Nedde. Call daven@maxine.wpi.edu.

j. XMol:  an X Window System program that uses OSF/Motif  for  the
   display and  analysis  of  molecular  model data.  Data from several
   common file formats can be read and written; current formats include:
   Alchemy, CHEMLAB-II, Gaussian, MOLSIM, MOPAC, PDB, and MSCI's XYZ
   format (which has been designed  for  simplicity  in  translating to
   and from other formats). XMol also allows for conversion between
   several of these formats.
   Xmol is available as ftp.msc.edu:pub/xmol/xmol.tar


-- 
GARY WILLIAMS,  Computing Services Section,  Janet:       G.Williams@UK.AC.CRC
MRC-CRC & Human Genome Mapping Centre,       Internet:    G.Williams@CRC.AC.UK
Watford Rd, HARROW, Middx, HA1 3UJ, UK
Tel 081-869 3294   Fax 081-423 1275