VMD-L Mailing List

From: Josh Ward (wardjm_at_purdue.edu)
Date: Fri Apr 16 2004 - 11:43:18 CDT

Thanks, that did capture the message. Here is what I got.

wardjm_at_pablo [5] vmd -dispdev text
Info) VMD for LINUX, version 1.8.2 (December 4, 2003)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
Found 1 plugins or data handlers in directory
        '/bio/terry4/postlab/bin-linux/lib/vmd-1.8.2/plugins/LINUX/molfile'.
vmd > load webpdb 1sps
couldn't load file "webpdb": webpdb: cannot open shared object file: No
such file or directory
vmd > mol load webpdb 1sps
  The PDB is supported by RCSB, the NSF, US PHS, NIH, NCRP, NIGMS, NLM,
and US DoE, who are not liable for the data. PDB files shall not be
sold. See ftp://ftp.rcsb.org/advisory.doc for full details.
Info) Using plugin webpdb for structure file 1sps
Info) Using plugin webpdb for coordinates from file 1sps
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file 1sps.
Info) Analyzing structure ...
Info) Atoms: 3491
Info) Residues: 374
Info) Waters: 40
Info) Segments: 1
Info) Fragments: 48 Protein: 6 Nucleic: 0
0
vmd >

So everything looks pretty normal to me. Does this mean the problem
lies between downloading the cordinates and sending them to the
display? A graphics card issue? I can load and display my local pdb
files without any problems. What would be different with the webpdb plugin?

Josh

Brian Bennion wrote:

>Hi Josh,
>
>Is it possible to run in text mode and capture the error?
>
>ie
>
>vmd -dispdev text
>
>vmd>mol load webpdb nameofprotein
>
>Tell me if this works
>
>Brian
>
>On Fri, 16 Apr 2004, Josh Ward wrote:
>
>
>
>>Is there a precedence for loading files using webpdb to crash the
>>program? I am running vmd-1.8.2 on Debian Linux. When I try to load a
>>molecule via webpdb, some messages appear in the console, but the
>>program crashes and exits too quickly to read them. I was wondering if
>>you've run across this problem yet, and hoping there is a quick fix.
>>
>>Thanks,
>>
>>Josh Ward
>>
>>
>>
>
>*****************************************************************
>**Brian Bennion, Ph.D. **
>**Computational and Systems Biology Division **
>**Biology and Biotechnology Research Program **
>**Lawrence Livermore National Laboratory **
>**P.O. Box 808, L-448 bennion1_at_llnl.gov **
>**7000 East Avenue phone: (925) 422-5722 **
>**Livermore, CA 94550 fax: (925) 424-6605 **
>*****************************************************************
>
>
>