VMD-L Mailing List

From: Samuel Coulbourn Flores 花山 (scflores_at_stanford.edu)
Date: Fri May 16 2008 - 16:06:17 CDT

AutoDock was involved.. once I got rid of the extra columns (all the
ones to the right of the coordinate columns) I got the cartoons to
work..

sam

On May 16, 2008, at 12:55 PM, John Stone wrote:

>
> Hi,
> I haven't nailed down the entire root of the problem, but there are
> duplicated PDB indices and other oddities in the trajectory PDB file
> you sent the link for. When VMD analyzes the structure, it is
> definitely
> encountering problems:
> Info) Analyzing structure ...
> Info) Atoms: 3446
> Info) Bonds: 3505
> Info) Residues: 3322
> Info) Waters: 0
> Info) Segments: 104
> Info) Fragments: 3322 Protein: 1 Nucleic: 0
>
> The number of segments and fragments is abnormally high, which tells
> me that something is going very wrong there. The Stride calculation
> and
> the other backbone representations are all having problems as a direct
> result of this abnormal fragmentation.
>
> Do you know how this file was produced? It definitely has some
> quirks in
> it, and these may be causing the fragmentation problem.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, May 10, 2008 at 04:16:21PM -0700, Samuel Coulbourn
> Flores ?????? wrote:
>> Hi Guys,
>>
>> I am trying to use VMD to render a multi-frame pdb structure:
>>
>> http://molmovdb.org/uploads-motion/ce754465-18297/1204232530.2000.movie.pdb
>>
>> However although I can view the animation using 'lines', 'NewCartoon'
>> doesn't work. upon startup I get a message indicating that STRIDE is
>> failing (appended below). I have compared this to the pdb structure
>> file 1GGG.pdb, which I successfully rendered and from which the above
>> was ultimately generated, and found that in terms of conventions the
>> two differ only in the order of atoms. I can't think of a painless
>> way to reorder the atoms, if atom ordering is indeed the problem.
>> Can
>> anyone help me render this file?
>>
>> Thanks
>>
>> Sam
>>
>>
>> DNab4233ea:Downloads samuelflores$ startup.command
>> 1204232530.2000.movie.pdb
>> Info) VMD for MACOSX, version 1.8.7a12 (October 5, 2007)
>> 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, 2 CPUs detected.
>> Info) OpenGL renderer: NVIDIA GeForce 8600M GT OpenGL Engine
>> Info) Features: STENCIL MTX NPOT PS GLSL(VF)
>> Info) GLSL rendering mode is NOT available.
>> Info) Textures: 2-D (4096x4096), 3-D (2048x2048x2048), Multitexture
>> (4)
>> Info) File loading in progress, please wait.
>> Info) Using plugin pdb for structure file 1204232530.2000.movie.pdb
>> Info) Using plugin pdb for coordinates from file
>> 1204232530.2000.movie.pdb
>> Info) Determining bond structure from distance search ...
>> Info) Finished with coordinate file 1204232530.2000.movie.pdb.
>> Info) Analyzing structure ...
>> Info) Atoms: 3446
>> Info) Bonds: 3505
>> Info) Residues: 3322
>> Info) Waters: 0
>> Info) Segments: 104
>> Info) Fragments: 3322 Protein: 1 Nucleic: 0
>> vmd > Info) In any publication of scientific results based in part or
>> Info) completely on the use of the program STRIDE, please reference:
>> Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary
>> structure
>> Info) assignment. Proteins: structure, function and genetics, 23,
>> 566-579.
>> IGNORED /var/folders/rW/rW6k12o6FQ0SvpszE354zk+++TI/-Tmp-/tmp.
>> 5nm9jc -
>> (less than 5 residues)
>> No valid chain in /var/folders/rW/rW6k12o6FQ0SvpszE354zk+++TI/-Tmp-/
>> tmp.5nm9jc
>> ERROR) Unable to find Stride output file: /var/folders/rW/
>> rW6k12o6FQ0SvpszE354zk+++TI/-Tmp-/tmp.4t0bWR
>> ERROR) Stride::read_stride_record: unable to read output file from
>> Stride
>> ERROR) Call to Stride program failed.
>> quit
>> Info) VMD for MACOSX, version 1.8.7a12 (October 5, 2007)
>> Info) Exiting normally.
>>
>>
>> Samuel Coulbourn Flores
>> Altman Lab
>> Department of BioEngineering
>> Stanford University
>> samuel.flores_at_aya.yale.edu
>> 650.644.8416
>>
>> ??????
>> ?????????
>> ???????????????
>> ???????????????????????????
>> ??????????????????????????????????????????????????????
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
> --
> 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
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078

Samuel Coulbourn Flores
Altman Lab
Department of BioEngineering
Stanford University
samuel.flores_at_aya.yale.edu
650.644.8416

花山
科学者
生物工学部
スタンフォ一ド大学
スタンフォ一ド、カリフォルニア、米国