VMD-L Mailing List

From: dimka (newyorkdimka_at_gmail.com)
Date: Sun Apr 08 2007 - 13:22:11 CDT

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
>