VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 08 2007 - 13:47:34 CDT

Hi,
  Changes to VMD itself shouldn't have had significant effects
on the surfaces returned by Surf or MSMS, since VMD simply provides
Surf and MSMS with the atomic coordinates and radii. It is
entirely up to Surf and MSMS as to what the resulting surface
for a given set of atom coordinates and radii are.

That said however, if you're working with structure files that don't
provide atomic radii, then you may see small differences in the
resulting surfaces only because the new versions of VMD use a more
sophisticated method of guessing atomic radii for atoms than older
versions did. As such, the radii sent to Surf and MSMS will be very
slightly different than before.

The behavior of Surf and MSMS in regards to non-contacting structure
should be independent of the VMD version, and would only depend on
the version of Surf or MSMS you're using. The Surf version included
with VMD hasn't changed in years since it is not currently in active
development by Prof. A. Varshney or his students, AFAIK.

If you want to use the old atomic radii assignments (which were
less accurate), you can override the radii guessed by
VMD and provide your own using the '$sel set radius' command.

You can tweak, scale, or entirely replace the atomic radii in any
loaded VMD structure using the '$sel set radius' command, to get
any desired effect you like.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Apr 08, 2007 at 02:22:11PM -0400, dimka wrote:
> I've also noticed that newer version of VMD has trouble displaying
> surface (both with Surf and MSMS) of residues that are *not*
> connected, or another words, not in contact. A way of getting around
> that is by drawing surfaces of residues that are not in contact by
> different selections.
>
> -d
>
> On 3/29/07, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >Harish,
> > Perhaps I wasn't clear, but you have to download an install MSMS
> >separately from VMD. While we are allowed to distribute Surf along
> >with VMD, MSMS must be separately downloaded and installed. You can
> >get MSMS from Scripps here:
> > http://www.scripps.edu/~sanner/html/msms_home.html
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, Mar 29, 2007 at 07:09:43PM -0400, hl332_at_drexel.edu wrote:
> >> Hi John,
> >> Thanks for your suggestion and i tried even MSMS but it didnt work
> >either giving this error message:
> >> ==========================================
> >> vmd > Info) Starting MSMS with: 'msms -no_area -socketPort 1357 &'
> >> sh: msms: command not found
> >> 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' e
> >> xists and is executable, or set the environment variable MSMSSERVER to
> >point to
> >> the correct binary.
> >> Info) Could not compute MSMS surface
> >> Info) Done with MSMS surface.
> >> =========================================
> >>
> >> regards
> >> Harish
> >> -------------------------------------------------
> >> Harish Vashisth (Ph.D Candidate)
> >> CAT-361,Chemical & Biological Engg.
> >> Drexel University, Philadelphia, PA
> >> office: 215-895-5823
> >>
> >> ----- Original Message -----
> >> From: John Stone <johns_at_ks.uiuc.edu>
> >> Date: Thursday, March 29, 2007 5:10 pm
> >> Subject: Re: vmd-l: 'SURF' representation problem
> >>
> >> > Hi,
> >> > Have you tried using MSMS instead? MSMS is much newer than Surf
> >> > and is supported by the people at Scripps. Surf hasn't been
> >> > maintainedfor many years now and the version we provide with VMD
> >> > just has various
> >> > bug fixes that we've added ourselves. Give MSMS a try and let us know
> >> > if you still need help.
> >> >
> >> > Cheers,
> >> > John Stone
> >> > vmd_at_ks.uiuc.edu
> >> >
> >> >
> >> > On Thu, Mar 29, 2007 at 05:04:02PM -0400, hl332_at_drexel.edu wrote:
> >> > > Hi,
> >> > > I have been trying to draw my protein and several of its
> >> > residues using surface representation 'SURF' but for some reason it
> >> > displays only a small portion as surf not the whole protein. The
> >> > following commands are executed in vmd console:
> >> > > =================================
> >> > >
> >> > > vmd > Reading 4716 atoms..done
> >> > > Probe radius = 1.400
> >> > > Constructing solvent-accessible surface ..
> >> > > Max edge length = 1.200
> >> > > Malloc of zero or illegal length!!
> >> > > length = 0
> >> > > Malloc of zero or illegal length!!
> >> > > length = 0
> >> > > ...........compute_tri_plane_int(): denom close to zero 0.000000
> >> > > .....................................
> >> > > Total Triangles 255214 Total constraints 228706
> >> > > Max Neighbors per atom 90 Average Neighbors per atom 48.4958
> >> > > Surface construction + writing time 4.94 seconds
> >> > > done
> >> > > Info) This surface is made with SURF from UNC-Chapel Hill. The
> >> > reference is:
> >> > > Info) A. Varshney, F. P. Brooks, W. V. Wright, Linearly Scalable
> >> > Computation> Info) of Smooth Molecular Surfaces, IEEE Comp.
> >> > Graphics and Applications,
> >> > > Info) v. 14 (1994) pp. 19-25.
> >> > > Info) Reading Surf geometry output file...
> >> > > Info) Read Surf output file, processing geometry...
> >> > > Info) Done.
> >> > > ========================================
> >> > >
> >> > > regards
> >> > > Harish
> >> > >
> >> > > -------------------------------------------------
> >> > > Harish Vashisth (Ph.D Candidate)
> >> > > CAT-361,Chemical & Biological Engg.
> >> > > Drexel University, Philadelphia, PA
> >> > > office: 215-895-5823
> >> >
> >> > --
> >> > 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
> > 

-- 
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