VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 08 2004 - 17:20:52 CST

Jerry,
  I've spent some time trying to track down this problem but haven't
had any luck just yet. The crash doesn't occur with the same code on
the other platforms I tested though it does on the new 64-bit x86_64
Linux port of VMD. Do you get the crash if you load the file locally
rather than via the RCSB PDB accession code? It could just be something
bad in the 'webpdb' plugin, if so I hope to find it soon as I test it
with some other debugging tools. Let us know if you find anything
else that gives trouble in the new Athlon64/Opteron version of VMD.

Thanks,
  John

On Sat, Mar 06, 2004 at 12:09:07AM -0500, Jerry Ebalunode wrote:
> Hi John,
> Thanks a lot for allowing me early acces to this release. I just put
> together this amd 64 workstation this Tuesday mainly for modeling
> purposes. I am really glad to have access to a copy favorite modeling
> software (VMD) that would run on my new workstation. The release worked
> really nice for an alpha version. However there are some issues in
> opening webpdb files that I just discoverd. Let me explain.
> When you run "vmd 1crn" or "vmd 1bj7" , vmd downloads the web pdb of
> either these pdb codes and displays it just fine. But when you run "vmd 1epw" or
> " vmd 1sft" vmd crashes on trying to display the pdb. I can't trace why
> it crashes. Is there a way to do this.
> It seems this alpha release has problems in displaying large molecules
> (i.e., thousands of atoms in pdb file) that are downloaded from the PDB
> ftp site on my workstation, like PDB assertion codes 1SFT or 1EPW. On the
> other it works fine on small molecules (i.e., fewer atoms in pdb file) like
> 1CRN or 1BJ7).
> This problem is not seen when loading larger pdb files that are locally
> present (i.e. I can display my prepared system for MD simulation and the
> size of this system is 71023 atoms)
> However, I can not blame this problem entirely on VMD until someone else
> has been able to reproduce this problem on an athlon amd 64 workstation.
> Thanks again for the access and I am looking forward in squashing this
> bug.
>
> Could you let me know how you built this binary, you did not to mention
> this
> in your e-mail.
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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