Molecular Graphics

Harry Mangalam mangalam at SALK-SC2.SDSC.EDU
Thu May 20 14:11:38 EST 1993

>We are looking for molecular graphics software in public domain that can
>3D protein structures on UNIX workstations (Sun, Decstation, etc.). We have
>used flex from the Scripps Research institute, and would like to know if there
>are other
>packages that are more suitable to our needs. Any information or reference
>is appreciated.

Point your gopher at Dashing Dan Jocobson's gopher:,
port 70

 and check out the item:  FTP Sites For Biology  

   I can think of a few other ones offhand.  Ribbon from UBC (needs an SGI
or some form of SGI-compatible GL package).  Raster3D (from ?).  
   I have some info at home about (not free but very) cheap for academics
molecular software that will run on a variety of platforms, Suns included
(and the new DEC Alpha/Kubota graphic machines, I believe with Open GL). 
I'll post it tomorrow (remind me if I don't).

   Sculpt (again for SGIs - can you tell my orientation?) will be released
very soon (not PD, but freely available) See below:

The program is called SCULPT and was written by Mark Surles, (PhD out of
Chapel Hill NC with Jane Richardson) presently at the San Diego
Supercomputer Center (619 534 8323, surles at and even for a jaded
techno junkie like myself, it was a jaw-dropper.  

   The program (now running only on SGIs (with the compute code running
locally or on a Cray, although he just said that the code ran about as fast
on an Indigo Elan as it did on the YMP - he hadn't had time to optimize it
on the Cray)) will display up at least 1000 atoms and allow you to pick an
attachment point on the peptide with the mouse and then pull it into the
conformation that you wish, after having 'pinned' the atoms that you don't
want to move.  This would be would be very nice, but what is even more
amazing is that it does a real time (10 - 2 updates/sec) minimization as
you move the peptide chain around, displaying repulsions in red hemispheres
and attractions ones in blue.  Obviously there have been some
approximations and suppositions made for the sake of speed, but overall it
is an astonishing piece of work.

There are beginning to be a few useable ones for the PC as well (viewers
mainly not real molecular modellers), some PD, some commercial, but
available to academics very cheaply or free.  The exception to the last
parentheical remark is AutoDesk's Hyperchem which will run on a 486 fast
enough to model some very simple molecules, but the compute code can run on
an SGI (in fact there is a version that is entirely SGI-specific) or other
fast cpu to generate the image data that can be viewed on the PC.

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