Freeware Molecular Modeling and Visualization Kit

Harry Mangalam mangalam at SALK-SC2.SDSC.EDU
Mon Mar 1 12:51:40 EST 1993

Mehmet Kayaalp writes:
>I searched the list archive created last year, under keywords
>simulation, model, and visual. Except the DEC's one, which is
>probably not for free even for research, I could not find any software
>running on ULTRIX/UNIX using X-windows. If you know any software
>for modeling molecular structure (visually) and which can be
>controlled from another high level program preferably Prolog
>(but C++, or C are OK) via a suitable interface, I would
>be very glad to hear about that. If this software package
>has also capability to animate the interactions at the atomic
>level (in other words the 3D objects can be moved dynamically
>on the display), my all requirements would be satisfied.

  Open Molecule, a commercial product (by the Phils Mercurio (SDSC) and
Cohen (Scripps) and sold by ANDATACO (619 453-9191) for about $1000 will do
what you want, I believe.  It will run on a vanilla SPARC, (but would like
an accelerator board for decent performance). 
   However, you specified freeware.  Therefore you will be relieved to know
that Open Molecule is derived from FLEX, a freeware piece of work by Mike
Pique, also of Scripps (mp at scripps.edu).  This is _not_ commercial grade
software, but might be all that you need.  It can be FTP'ed from:
perutz.scripps.edu ( from pub/flex.  In various incarnations
and compilations, FLEX supports Xlib, sunview, phigs, XGL, and DORE (sp?). 
   Rob Locher <locher at iastate.edu> has already gone tried to get FLEX up and 
running, so you might give him a call as well to see how he fared.

   If you have access to an SGI machine, you might give Jerry Greeberg at
SDSC a call.  He has developed a package (MDMovie) that, while the
interface is a bit crude, does amazing stuff.  It figured in the Wilma
Olsen's Science article on DNA conformation.  It specifically is designed
for molecular DYNAMICS.  You can also use it to sample MD data from a
running process on a Cray or other compute server via socket calls and
display it 'real time' on the SGI (it uses GL calls and therefore is
specific for SGI machines (at least until other manufacturers start
supporting Open GL)

Good Luck, Harry

Harry Mangalam                                   Vox:(619) 453-4100, x250
Dept of Biocomputing                                   Fax:(619) 552-1546
The Salk Institute                        1'   mangalam at salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                   2'        hjm at salk-sgi.sdsc.edu
La Jolla CA 92037                         3'         mangalam at salk.bitnet

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