VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 05 2004 - 14:18:33 CDT

Dear James,
  It would appear that MSMS didn't emit any geometry for your structure.
Do you have a large structure or a collection of atoms which are spaced
far apart? MSMS doesn't do so well when presented with sparse sets of
atoms. We're also running MSMS 2.5.5 here, and in it works normally in
the cases we've run here, so it could be that it doesn't like your
structure for some reason. If you export a PDB file and run MSMS on it
manually, do you get a surface that way?

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 05, 2004 at 05:29:29PM +0100, james tomomi macdonald wrote:
> Hi,
>
> I'm having problems with msms. I've downloaded msms 2.5.5 and installed
> in in my path, however when i try and use the msms representation in vmd
> 1.8.2 I get the following output:
>
> Info) Starting MSMS with: 'msms -no_area -socketPort 1357 &'
> INPUT 1391 spheres 0 collision only, radii 1.000 to 1.900
> PARAM Probe_radius 1.500 density 1.500
> REDUCED SURFACE ...
> RS component 0 identified 1159 1157 1156
> MSMS END
> Info) Done with MSMS surface.
>
> but no surface display in my window!
>
> If anyone could be any help I would be very grateful.
>
> Cheer,
>
> James. 

-- 
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              
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