VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 22 2003 - 14:56:05 CST

Hi,
  The user's guide has some examples on how to do distance based
atom selections, including some fairly complex ones:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8/ug/node85.html#SECTION00838200000000000000
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8/ug/node77.html#4476
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8/ug/node179.html#12437

Regarding MSMS, what do you get if you do this from within a running
VMD session:
  puts $env(MSMSSERVER)

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 22, 2003 at 02:45:36PM -0600, phubbard_at_post.its.mcw.edu wrote:
> Hello,
>
> Thanks for the quick reply. With reagrds to defining a subset - distance
> would be the best (I have used this method in InsightII and it works
> well). Could you please tell me how I do this as I've had limited
> experience with VMD (just the point 'n' click stuff).
>
> With regards to MSMS: I've tried the following
>
> paul_at_iris10 % > msms
> MSMS 2.4.1 started on iris10
> Copyright M.F. Sanner (1994)
> Compilation flags -O2 -Olimit 660 -xansi -DVERBOSE -DTIMING -DFUNCPROTO
> -fullwarn -mips2
> MSMS: No input stream specified
> paul_at_iris10 % > which msms
> /usr10/local/bin/msms
> paul_at_iris10 % > setenv MSMSSERVER /usr10/local/bin/msms
> paul_at_iris10 % > vmd
>
>
> Info) Starting MSMS with: '/usr10/local/bin/msms -no_area -socketPort 1357
> > /dev/tty &'
> Info) Waiting for MSMS server ...
> Info) Waiting for MSMS server ...
> Info) Waiting for MSMS server ...
> Info) Waiting for MSMS server ...
> ERROR) Could not connect to MSMS server. Please check that the program
> '/usr10/local/bin/msms' exists and is executable, or set the environment
> variableMSMSSERVER to point to the correct binary.
> Info) Could not compute MSMS surface
> Info) Done with MSMS surface.
>
> Thanks
>
> AGS
>
> >
> > Hi,
> > For the atom selection, one possibility would be to do a distance
> > based atom selection, another would be to use any other properties of
> > the structure that you're aware of to select just the atoms in the
> > binding site, by index or residue range, chain, or any other useful
> > fields that would help you distinguish the atoms at the binding site
> > from the rest.
> >
> > In order to get MSMS to work, VMD needs to be able to find it in your
> > path. If it cannot, then another way is to set the environment variable
> > MSMSSERVER to the actual binary, i.e.:
> > setenv MSMSSERVER /usr/local/bin/msms
> >
> > Let us know if you need more help.
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Jan 22, 2003 at 02:01:37PM -0600, phubbard_at_post.its.mcw.edu
> > wrote:
> >> Hi all,
> >>
> >> I have 2 pdb files, one of the protein, and one of a ligand bound to
> >> the protein. Could someone please tell me how I can define a subset of
> >> atoms in the protein that line the binding site, and have a surface
> >> rendered for just that part of the protein.
> >>
> >> P.S: I have MSMS 2.4.1 instatlled, but VMD (1.8) doesn't recognize it
> >> -
> >>
> >> Info) Starting MSMS with: 'msms -no_area -socketPort 1357 > /dev/tty
> >> &' Info) Waiting for MSMS server ...
> >> Info) Waiting for MSMS server ...
> >> Info) Waiting for MSMS server ...
> >> Info) Waiting for MSMS server ...
> >> ERROR) Could not connect to MSMS server. Please check that the
> >> program 'msms' exists and is executable, or set the environment
> >> variableMSMSSERVER to point to the correct binary.
> >> Info) Could not compute MSMS surface
> >> Info) Done with MSMS surface.
> >>
> >> Any tips on how to fix it.
> >>
> >> Thanks
> >>
> >> AGS
> >>
> >
> > --
> > 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
>
> 

-- 
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