VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 21 2005 - 11:58:32 CST

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 residues
of 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 suggestions
in 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
> ******************************************************
> 

-- 
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