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From: james tomomi macdonald (j.macdonald_at_mail.cryst.bbk.ac.uk)
Date: Mon Jul 05 2004 - 16:02:12 CDT
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Hi John,
For some reason, after having left it a while, it has now decided to
start working on exactly the same structure and same VMD session! I'm
sure i didn't change anything in the meantime - very odd.
Anyway, thanks and sorry for the unnecessary bother.
James.
On Mon, 2004-07-05 at 20:18, John Stone wrote:
> 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.
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