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
>evolved???
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.
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
