VMD-L Mailing List

From: Josh Ward (wardjm_at_purdue.edu)
Date: Fri Apr 16 2004 - 11:59:18 CDT

And yes this is a tried and true pdb file for me.

Josh

Brian Bennion wrote:

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