VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 25 2005 - 18:10:50 CDT

Hi,
  You can run MSMS by hand and generate the .face and .vert files which
can be read by the MSMS plugin. This works ok if you're not using any of the
built-in coloring methods used by VMD and just want the surface itself.
(the association between the original atom and the resulting MSMS vertex
 is lost when you load the surface from these files...)
This plugin is primarily useful if you have a truly monsterous MSMS
surface you want to show and you're happy using a solid color. If you want
to use the other coloring schemes, it's currently best to stick with
calculating the surface on-the-fly in VMD since it'll have more information.
I hope to improve this situation in a future rev of the plugins and VMD.

In order to use the msmsplugin, you must install the plugin update package
as described on the plugin page:
  http://www.ks.uiuc.edu/Research/vmd/plugins/183update2/
If you follow those directions, you should get some status messages
indicating that VMD found the updated plugins. Do you get such messages
when you run VMD? If not, that's why it isn't loading the MSMS .vert or
.face files. You should be able to check and see that "msms" is listed
among the available file types in your VMD.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 25, 2005 at 10:52:29AM +0200, floquet_at_icsn.cnrs-gif.fr wrote:
> Hello,
>
> two questions :
>
> 1 ) Is it possible to keep information from MSMS calculations in VMD, this is by
> writting all the accessible surface data in one file ?
>
> 2 ) How to re-read the vertices and faces files in VMD ? I updated my plugins
> but ...
>
> More precisely, i would like to calculate the accessible surface of one protein
> pocket during a trajectory (e.g. a dcd file).
>
> Many thanks for your help !
>
> Nico
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program. 

-- 
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