IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

More info on SCULPT / dancing proteins/user-draggable peptides

Harry Mangalam mangalam at SALK-SC2.SDSC.EDU
Thu Mar 18 17:24:19 EST 1993


Hi,
   I got a few queries, so I thought I'd post to the net again.

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 sdsc.edu) 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.
   The only problem is that the interface is still quite rough; not to say
that it's bad - on the contrary, it's extraordinarily good!  It just
doesn't have all the bells and whistles that a commercial program would (or
the support - it's just him and he's trying to improve it).  The other
problem is that the import facility is a bit nervous; if the file isn't in
perfect pdb format, you have to dive into it and modify it to some magic
recipe.  The final problem is that it cannot be distributed freely just yet
because it depends for some of it's speed on the Harwell Sparse Matrix
Library from NAG which requires a license.  If you have such a license or
would be willing to purchase it, you can probably get the program.

Talk to him if you're interested - I'm just a flabbergasted onlooker.
Cheers
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






More information about the Bio-soft mailing list

Send comments to us at archive@iubioarchive.bio.net