VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 16 2008 - 14:55:56 CDT

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
>
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> ??????????????????????????????????????????????????????
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-- 
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