VMD-L Mailing List

From: Samuel Coulbourn Flores 花山 (scflores_at_stanford.edu)
Date: Sat May 10 2008 - 18:16:21 CDT

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

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