VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 16 2005 - 16:37:21 CDT

Vivek,
  Digging deeper, it appears that your GRASP .srf file contains a large
range of negative or out-of-range vertex indices, which is clearly a
problem. The only file format documentation I've got is for the
original "format=1" file described at the Honig lab, so it's tough to
determine how/why your file got the way it is. If you can tell me
more about what specific code emitted this file, what version, etc,
that'll be very helpful.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 16, 2005 at 04:08:13PM -0500, John Stone wrote:
> Vivek,
> I've tracked down the problem to a vertex index of 0 (-1 when it gets
> to VMD) in the SRF file. My belief was previously that GRASP produced
> files with 1-based indices, and indeed this is the first surface file
> I've seen with a zero-valued vertex index, so I'm not sure what that means.
> In any case, it should be easy to fix or workaround. I should have a new
> graspplugin ready in a day or so.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Sep 16, 2005 at 06:38:33PM +0300, vivek sharma wrote:
> > Hello John,
> >
> > Atleast the srf file loads finely in GRASP, but doesnot work in VMD. The
> > files are attached. Thanks very much for the help.
> >
> > br,
> >
> > Vivek
> >
> > Quoting John Stone <johns_at_ks.uiuc.edu>:
> >
> > >
> > > Vivek,
> > > It sounds like your grid/srf files may not be compatible with our
> > > readers for those formats. Can you send me a copy of the two files that
> > > fail to load so I can take a look at them?
> > >
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Fri, Sep 16, 2005 at 09:52:45AM +0300, vivek sharma wrote:
> > > > Hello John,
> > > >
> > > > Situation is:
> > > >
> > > > I am loading a pdb in VMD (using 1.8.3 both Win and Linux), it goes
> > > fine.
> > > > Now, I would like to load the *.grd (binary potential map file from
> > > > Insight/Delphi calc.) and I am doing it by selecting the molecule in
> > > VMD
> > > > Main (already loaded pdb) and using 'Load Data into Molecule'. BUt, it
> > >
> > > > doesnot go fine and error in console is:
> > > >
> > > > Improperly formatted file header: uplbl
> > > > ERROR) Unable to open file with plugin of type grd
> > > >
> > > > Actually, I searched the mailing list with this and found few emails,
> > > but
> > > > couldn't understand how to get it done. Any help will be great.
> > > >
> > > > Secondly, I also have a *.srf (GRASP surface file generated by
> > > > Insight/Delphi calculation), when I load it in VMD by selecting file
> > > > type 'grasp' from Molecule file browser, VMD does something for
> > > sometime
> > > > but dies with a core dump.
> > > >
> > > > Am I doing the stuff right or is there anything wrong? ANy suggestions
> > >
> > > > will be great.
> > > >
> > > > Thanks in advance,
> > > >
> > > > br,
> > > >
> > > > Vivek
> > > >
> > > >
> > > > --
> > > > VIVEK SHARMA
> > > > HBG BI
> > > > "Better to understand a little than to misunderstand a lot." (?)
> > >
> > > --
> > > 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
> > >
> >
> >
> > --
> > VIVEK SHARMA
> > HBG BI
> > "Better to understand a little than to misunderstand a lot." (?)
>
>
>
> --
> 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