VMD-L Mailing List

From: Tyler Luchko (tluchko_at_gpu.srv.ualberta.ca)
Date: Mon Dec 16 2002 - 18:48:45 CST

Hello,

recently I have been working with vmd 1.8 using the surf and msms
representations for a couple of different proteins. I have noticed
problems with both surf and msms.

In surf there appears to be two problems. The first is that some atoms
do not appear to be sent to surf. I believe that something similar to
this has already been sent to the mailing list. Turing on both the surf
and line/VDW representations at the same time shows atoms outside the
calculated surface that seem to be completely ignored. In some cases this
can leave large holes in the molecule. The second problem is that phantom
atom surfaces are created. That is, when surf is called a surface for an
atom (that never existed and is completely removed from the molecule)
appears. This does not always appear in the same location for difference
selections.

In MSMS the problem seems to be that the program simply won't work with
molecules where I have changed the default radii and have a subset of the
atoms present. In this case I have used a script to generate the exposed
surface of a single tubulin in a microtubule. In other words, only the
surface atoms for about 1/2 of the protein are present in the file. At
this point MSMS works fine. When I change the radii of the atoms to use
that in the AMBER 94 VDW parameters MSMS gives me

Info) Starting MSMS with: '/users/tluchko/bin/msms -no_area -socketPort
1359 > /dev/tty &'
INPUT 1764 spheres 0 collision only, radii 0.200 to 2.000
PARAM Probe_radius 1.500 density 1.500
REDUCED SURFACE ...
    RS component 0 identified 1587 1560 1588
MSMS END
Info) Done with MSMS surface.

and no surface. This seems to work fine in all other representations.

In both cases the same files are being used and are typically fairly
large (from 3000+ to 500 000+ in one case). If these are not bugs but an
error on my part I would be grateful for any recommendations you can
provide.

Thank you,

Tyler

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