From: vivek sharma (vivek.sharma_at_helsinki.fi)
Date: Mon Sep 19 2005 - 00:09:52 CDT

Hello John,

Thanks for all details. Actually, I will try to look into the problem once
again and will get back to you.

br,

Vivek

Quoting John Stone <johns_at_ks.uiuc.edu>:

> 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
>

-- 
VIVEK SHARMA
HBG BI
"Better to understand a little than to misunderstand a lot." (?)