VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 17 2007 - 01:35:38 CST

Hi,
  In order to use the MSMS representation on a Windows PC,
you must first download and install MSMS on your computer.
MSMS is available from Scripps here:
  http://www.scripps.edu/~sanner/html/msms_home.html

Once you've downloaded MSMS and installed it somewhere, then you
need to set the MSMSSERVER system environment variable using
your Windows control panel. The environment variable should be
set to the full path of the executable, e.g.:
  c:\program files\msms\msms.exe
Once this is done, and you've saved the newly added
environment variable in your control panel settings, the next
time you start VMD, it will know where to find MSMS and will
run it automatically to calculate the solvent surface. MSMS runs
much faster than Surf, so downloading and using it is very desirable.

For measuring solvent accessible surface area, you'll
want to use the "measure sasa" command. There isn't a
graphical interface for this yet, since there are so many
ways to use this command, but there are a number of past emails
on this subject in the VMD-L archive that you can reference to
help you get started. Let us know if you have more questions
on this.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 17, 2007 at 04:21:52PM +1100, Peter Hains wrote:
> Hi all,
>
> I am trying to get the MSMS representation to work on a Windows
> machine (Win XP SP2). I am using VMD 1.8.5. I have looked over the
> manuals and mail archive, but I can't find anything useful. The
> manual does have an esoteric reference to the environment variable
> (pg 63, section 5.1.16) for MSMSSERVER, but I'm afraid I can't work
> out what it the author is directing me to do....
>
> I also want to work out the solvent accessible area for certain
> residues in my structure. I was going to use the 'sasa' command for
> this. I haven't worked out how to do this as yet, but I should be
> fine. Can anybody suggest another way of determining solvent
> accessibility, other than VMD that doesn't involve a command line
> interface? ie. some Windows program? I can cope with command line
> interfaces, but I'm afraid I'm a point and click person at heart.
>
> Thanks for any advice,
>
> Peter
> 

-- 
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