VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 01 2006 - 12:36:29 CDT

David,
  I already see a couple of things that could cause STRIDE to refuse
to process the molecule from the mol2 file, as loaded by the current mol2
plugin in VMD:
  - The current VMD mol2 plugin is using the mol2 ATOM section substructure
    names as residue names, which isn't really appropriate. In your file,
    these are the 3 char residue names concatenated with a serial number.
    Needless to say, STRIDE isn't going to like those.

  - The current mol2 plugin isn't reading the SUBSTRUCTURE section, and so
    it isn't picking up the RESIDUE substructure records, which contain
    chain information, and so this isn't getting into VMD presently.

>From what I see, it appears that in the short term you're going to best
off loading the PDB version of your structure, at least until I have a
chance to write the necessary mol2 reader code to process the SUBSTRUCTURE
section instead of using the ATOM substructure IDs.

  John

On Wed, May 31, 2006 at 10:55:47AM -0500, John Stone wrote:
>
> David,
> Can you send me an example mol2 file that gives you this problem?
> Most likely the issue is related to the atom names ued in the file.
> STRIDE expects PDB style atom names, so it may not be a problem with the
> mol2 file itself, but rather with the atom names contained therein.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, May 31, 2006 at 09:11:33PM +1000, David Chalmers wrote:
> > Dear VMD list,
> >
> > I worked around this problem, but it seems like q quirk. The NewCartoon and
> > Cartoon rendering methods do not work when I read in a protein as a mol2
> > file (I get a ribbon but no sheets and helices). If I convert the same file
> > to pdb format then it works fine. I am using VMD 1.8.3, so this may have
> > been fixed.
> >
> > Regards
> >
> > David
> > ________________________________________________________________________
> >
> > David Chalmers Lab: 9903 9110
> > Victorian College of Pharmacy Fax: 9903 9582
> > 381 Royal Pde, Parkville, Vic 3053. Australia
> > David.Chalmers_at_vcp.monash.edu.au
> > ________________________________________________________________________
> >
>
> --
> 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 

-- 
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