VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 23 2005 - 13:44:32 CST

Peter,
  Sounds like the .vmd_tri file just contains a huge number of VMD
"draw triangle ..." commands. If so, then you may need to figure out
what sort of surface files Pymol will read. You might be able to get Pymol
to read the .vmd_tri file directly with a bit of Python scripting, but
that's not presently an area of expertise for me. Maybe you can ask
Warren about that, he or one of the other Pymol users may already
have something that works with HOLE. If not, then you could probably
hack your VMD by redefining the "draw" Tcl proc and cause it to convert
the HOLE triangle set into a file that Pymol can read. Either way you're
going to have to find a particular surface file format that Pymol can read
and write some script code to emit that format from VMD, or to read into it
from within Pymol, whichever you're more comfortable with. Assuming that
the .vmd_tri file does in fact contain a huge sequence of "draw" commands,
I think that hacking the VMD 'draw' proc for your purpose would be the
easiest solution.

  John
  

On Mon, Feb 21, 2005 at 10:38:58PM +0100, Peter Holm wrote:
> Hi John and thanks a lot for your suggestions!
> Exporting to Pymol would be my number one choice. The surface is simply read in by "source holeobject.vmd_tri" hence I guess its some kind of triangulated object? Any ideas? If not I can send you the file tomorrow when I'm back at my lab computer.
> Cheers
> Peter
>
> ****************************************************
> Peter Holm, Ph.D. Student
> Molecular Biophysics
> Center for Chemistry and Chemical Engineering
> Lund University
> P.O.B. 124
> SE-22100 Lund
> SWEDEN
>
> Telephone numbers
> Office: +46-(0)46-2221448
> Mobile: +46-(0)709-625451
> Fax: +46-(0)46-2224692
> E-mail: peter.holm_at_mbfys.lu.se
> http://www.mbfys.lu.se
> ****************************************************
>
>
> ----- Original Message -----
> From: John Stone <johns_at_ks.uiuc.edu>
> Date: Monday, February 21, 2005 6:58 pm
> Subject: Re: vmd-l: VMD object exported to Pymol
>
> >
> > Peter,
> > VMD has distanced-based atom selections which would be the easiest
> > method to select the appropriate atoms for drawing. If you don't have
> > any easily selectable reference atoms to use for the "within" atom
> > selection,you might find it easier to use "exwithin" on to
> > deselect parts you know
> > you only want to see in ribbon representations. Lastly, if
> > neither of those
> > commands are convenient, you can write a simple tcl script to
> > generate a
> > list of atom indices within a given distance of the HOLE sphere
> > set, then
> > use a macro or a tcl script to make a new representation for the
> > residuesof interest.
> >
> > There might be a way to export the HOLE surface to Pymol depending
> > on what
> > method you're using to get it into VMD in the first place. If you
> > tell me
> > how you're loading the HOLE surface I could give you further
> > suggestionsin this direction.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Feb 21, 2005 at 02:47:52PM +0100, Peter Holm wrote:
> > > Dear list readers,
> > >
> > > I have an object created a VMD surface object by the HOLE
> > program suite (http://d2o.biop.ox.ac.uk:38080/).
> > > I would like to visualise certain amino acid residues in a
> > corresponding pdb file in close proximity to the surface produced
> > while keeping residues further away than say 10Å as ribbons or
> > similar clean visualisation. I know how to do the latter in Pymol
> > but I is it possible to convert a HOLE/VMD surface to be read by
> > Pymol or is the problem possible to solve in VMD alone?
> > >
> > > Many thanks in advance
> > >
> > > Sincerely
> > >
> > > Peter
> > >
> > > ******************************************************
> > > Peter Holm, Ph.D. Student
> > > Molecular Biophysics
> > > Center for Chemistry and Chemical Engineering
> > > Lund University
> > > P.O.B. 124
> > > SE-22100 Lund
> > > SWEDEN
> > > Lab: +46-(0)46-2221448 Cell: +46-(0)709-625451
> > > Fax: +46-(0)46-2224692 http://www.mbfys.lu.se
> > > E-mail: peter.holm_at_mbfys.lu.se
> > > ******************************************************
> > >
> >
> > --
> > 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