VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 12 2006 - 11:16:21 CDT

Vlad,
  Even if you hack the PDB plugin to avoid writing out the chain
identifier, other programs may not be able to read the resulting
file since many depend on the strictest adherance to the PDB file
format specification. The PDB plugin supports reading of various
illegally formatted PDB files as a result of many MD packages writing
such files for macromolecules with more than 99,999 atoms and thousands
of waters, for example. Readding such files into other packages
is hit and miss, and you can't blame them for not reading them since
they do indeed violate the PDB format spec. The strategy that
the PDB plugin is employing once it runs out of the 9999 legal
residue number limit, is to begin emitting hexadecimal numbers.
When we exhaust the limit of hexadecimanl numbers, then we begin
printing asterisks for the residue numbers e.g. "****". If you want
to alter the behavior of the PDB plugin with regard to these
out-of-spec files, you can simply change the readpdb.h code and
modify the write_raw_pdb_record() routine therein, increase the
plugin version number, recompile, and then load into your VMD and
you can have it do anything you like. If Leap has an alternative
way of dealing with PDB files containing > 9999 residues, let me know...

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 12, 2006 at 05:56:16PM +0200, Vlad Cojocaru wrote:
> Dear VMD developers,
>
> Is there a way to change the pdb output from vmd such as to allow
> residue numbers greater than 9999 and to eliminate the X chain identifier?
>
> I am trying to save a number of pdb files by selecting "water within 5
> of protein" and the pdb output has strange residue numbers such as
> X34ef5. The problem with these pdb files is that whenever I try to load
> them in other programs, the residues are not recognized anymore. This is
> especially painful if I want to use the created pdb files back into the
> Leap program from Amber ...
>
> Best wishes
> vlad
>
> --
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg, Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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