VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 18 2002 - 09:11:52 CST

Hi Tyler,
  If you can send me a molecule that exercises the bugs you're
seeing, along with a VMD saved state file that contains the
right Surf or MSMS settings, I can use that to send bug reports
to the authors of these programs, where applicable, or see if there
might be a bug in VMD itself. I don't know how much we can get done
for Surf, as the author has moved on to other things, but the author
of MSMS is very responsive and willing to work with us on bugs.
If your files are too big for email, let me know and we can arrange
something else.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 16, 2002 at 05:48:45PM -0700, Tyler Luchko wrote:
> 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
>
> ________TyLer_LuchKo__::__MaSters_StuDent__->>__DePartMent_Of_PhysIcs_________
> _______UnIVerSiTy_Of_AlBerTa__->>__EdMonTon__->>__AlBerTa__->>__CanADa________
> ____http://Phys.UAlBerTa.Ca/______________________tluchko@Phys.UAlBerTa.Ca____
> _______________________780-492-5519__(But_SomeTimes_3552)_____________________
>
> 

-- 
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