VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 27 2005 - 10:01:45 CDT

Peter,
  If you want to load the existing .vert and .face files into VMD, you
can use the recently added MSMS plugin, by upgrading the plugins in your
VMD installation. If on the other hand, you've got the molecular structure
for which those .vert and .face files were created, you could just as easly
run MSMS from within VMD, and then you don't have to update your plugins.
When displaying an MSMS surface in VMD, the coloring methods that are available
are all based on atomic information. If you want to color by electrostatic
potential, you'll need to first calculate a potential map. This can be done
using the APBS plugin or with the PME potential plugin, for example.
If you're having trouble using the "MSMS" representation in VMD let us know.
That's the most convenient way to view MSMS surfaces, reading the .vert and
.face files is really only useful if you have a huge structure that takes
several minutes for MSMS to create a surface for.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 27, 2005 at 02:19:22PM +0200, Peter Holm wrote:
> Dear VMD users,
>
> OK, so my previous installation problem is solved. Now I wish to read in an MSMS triangulated object into VMD but can not find how to do this. I have created two objects in MSMS called foo.vert and foo.face.
> These are both long lists of text. Should they be read directly into VMD somehow?
>
> Furthermore, when displaying a pdb-file according to MSMS nothing is shown and when displaying as charge the whole molecule has the same colour. Have I missed to install some libraries?
>
> Many thanks in advance for advice!
>
> Best regards
>
> Peter
>
> ****************************************************
> Peter Holm, Ph.D.
> 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
> ****************************************************
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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