dancing proteins/user-draggable peptides

Harry Mangalam mangalam at SALK-SC2.SDSC.EDU
Wed Mar 17 12:54:28 EST 1993

Cross post from Info-GCG:

Alicia Martinez writes:
>                    Maybe you could give me some advice on the problem I
>deal with at  this moment. We're looking for a  graphics package for the
>Silicon  Graphics  Indigo being  able  to  MANIPULATE PROTEINS  without
>knowing  their coordinates.  It is,  we  would like  to make  a sort  of
>animation  by taking  initially  a  well-known conformation  (previously
>computed) and then gradually, moving it as a plastic model, bending some
>parts, change  its shape  to force  it to  have another  conformation. I
>don't have  any computation for each  one of the intermediate  steps and
>the final geometry, so the entire  process is going to be done manually,
>as you could  do to a physical spheres-and-sticks  representation of the
>molecule.  The aim  of  such animation  is  to record  a  video tape  to
>illustrate a certain theory about protein behaviour. Do you know if this
>is possible to  accomplish now with any graphics package???  Are they so

   Strangely enough, I saw a program demo yesterday that may be of
interest.  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 5100) 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)) 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 and I'm not
sure about it's availability, but I believe that it will be relatively
cheap to academics.


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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