VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 02 2004 - 13:29:32 CST

Dear Aurore,
  In addition to the previous suggestion to use a PSF file,
this problem could also be caused by a limitation of Stride and the
PDB file format, if you have a large structure. When one tries to
display a cartoon representation of a structure with more than 99,999
atoms or a large number of residues these exceed the legal range of a
PDB file, and unfortunately since Stride uses the PDB format as its input,
it will fail to calculate the secondary structure when presented with a
PDB file exceeding the normal range of atoms and/or residues.

I'm exploring making a modification to the Stride
binaries that are packaged with VMD to partially address this limitation,
if it turns out that I can make a very limited change to the Stride source
and get the intended effect. If so, it would be fixed in a subsequent
release of VMD. For now, the best suggestion is to use an atom selection
and generate a new PDB file containing a number of atoms and residues that
fall within the limitations of Stride, then re-load this new PDB file
in a new molecule in VMD. Its ugly, but it will get you past the problem
if you're problem is caused by Stride/PDB limitations.
I hope to improve this situation substantially in upcoming revs of VMD.

If it turns out that your problem is not caused by the size of the structure,
but is related to the structure itself, then using a PSF file should definitely
help resolve the problem. Let us know if you need more help with this.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 31, 2003 at 04:43:11PM -0500, Aurore Zyto wrote:
> hi,
> I'm trying to visualize a .pdb file, consisting of a trimer of units,
> about 400 residues each (i.e. overall structure of 1200 residues).
> When using the cartoon representation, large parts are missing (which can
> be visualized by drawing lines for example).
> How large a protein can the cartoon representation "safely" handle? Is it
> a reported bug?
> Thanks
> Aurore 

-- 
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              
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