VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Apr 16 2004 - 11:48:55 CDT

At first glance it might appear to be a graphics issue. But you checked
this pdb file by loading it up from your local machine right?

You must be running on a server type box with all the cpus you have
listed.

What is the video card your using?

Brian

On Fri, 16 Apr 2004, Josh Ward wrote:

> 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 **
> >*****************************************************************
> >
> >
> >
>

*****************************************************************
**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 **
*****************************************************************