VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 24 2002 - 11:33:52 CDT

Hi Sanjeev,
   Hmm, I've just run MSMS myself on 1FPY and I get the same result, no
surface. I think this is due to the way the surface calculation algorithm
works in MSMS. I re-ran the surface calculation using the atom selection
"chain A" and I got a proper surface for chain A, so I suspect that in order
to make MSMS happy you may need to create a bunch of individual
representations for each of the chains. (i.e. "chain A", "chain B", etc..)
Try that and let me know if you still need help.

By the way the new VMD 1.8 test versions contain some improvements
to the surface display code which make MSMS an even more attractive
option. The new code can display MSMS surfaces about twice as fast
as previous versions. The new code doesn't help Surf yet, that will
require more work.

Thanks,
  John Stone
  johns_at_ks.uiuc.edu

On Mon, Jun 24, 2002 at 08:10:32AM +0530, Sanjeev B.S. wrote:
> Hello,
> I am using the stable 1.7 version of VMD on a Redhat7.3 with
> NVidia GeForce2 MX200 card (with nvidia driver). When I load a huge PDB
> (1FPY) and try to generate surface, everything disappears! Is there a
> trick by which I can get it done? (The PDB is huge, ~45,000 atoms).
> Thanks in advance for any suggestions.
>
> Wish good day wishes,
> -Sanjeev 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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