VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 03 2008 - 14:01:23 CDT

Hi,
  The PDB plugin used by VMD doesn't pay attention to the atom indices
that you've specified in your PDB file, it counts the number of atoms
for itself. It uses heuristics to determine whether or not CONECT records
can be trusted to be valid based on the atom count. If you have more
than 99999 total atoms, then one cannot use CONECT records, as the
index fields will overflow the fields in the CONECT record for some
of the atoms. The VMD PDB plugin follows the standard PDB format
to the degree possible, and although it will accept illegally formatted
PDB files, as soon as you cross over the boundary from a valid PDB to
an illegal PDB (e.g. too many atoms) the PDB plugin can no longer
gaurantee that things like the CONECT records will give correct results,
so they are ignored for such files. You'd be better off using a different
file format for very large structures where you're concerned with bonds
being correct, or you might use PDB+PSF rather than relying on CONECT records.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 03, 2008 at 11:53:37AM -0500, Paul T. Bauman wrote:
> I should have mentioned I started counting from zero, so the "ATOM"
> number is less than or equal to 99999 (i.e. I'm not violating the column
> limitation of the .pdb format).
>
> After playing a bit more, it seems that if the number of atoms are <
> 99999 (i.e. <=99998 ) then it will be fine. For some reason 99999 is
> not included.
>
> Thanks,
>
> Paul
>
> Paul T. Bauman wrote:
> >Hello,
> >
> >I'm using VMD 1.8.6 on Linux_AMD64_OPENGL. I tried looking through the
> >archive for some discussion of the following, but couldn't find it.
> >
> >I've noticed recently that if there are many atoms in my .pdb file,
> >that the "CONECT" records do not seem to be processed correctly and
> >the bonds are not plotted. Note that "autobonds" are still plotted.
> >The magic number is somewhere between 3,000 "ATOM"'s (bonds are
> >plotted) and 100,000 (greater than or equal, bonds are not plotted).
> >Is there a maximum number of "ATOM"'s that can be in the .pdb file for
> >"CONECTS" to be plotted? I only use "ATOM" and "CONECT" records in my
> >.pdb file.
> >
> >I didn't want to send the file over the list because it's pretty
> >large, but please let me know if you'd like it.
> >
> >Any assistance is most appreciated.
> >
> >Thanks,
> >
> >Paul
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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