VMD-L Mailing List

From: Peter Holm (Peter.Holm_at_mbfys.lu.se)
Date: Mon Jun 27 2005 - 10:37:57 CDT

OK, plugins updated even though I do have the coordinate file. But I still can't display the MSMS surface. So here's what I did:

1) Converted .pdb to .xyzr
2) Started VMD 1.8.3
3) Within VMD console:

vmd > msms -if foo.xyzr -of test
MSMS 2.5.5 started on xxxxx.yyyyy.lu.se
Copyright M.F. Sanner (1994)
Compilation flags -O3 -mips3 -xansi -DVERBOSE -DTIMING -DFUNCPROTO -fullwarn
INPUT foo.xyzr 2892 spheres 0 collision only, radii 1.400 to 2.000
PARAM Probe_radius 1.500 density 1.000
REDUCED SURFACE ...
    RS component 0 identified 796 803 802
    3 free edge(s) found in component 0
    RS component #faces #edges #free_edges #vertices genus
         0 3136 4704 3 1435 69
    Time Reduced Surface real: 0.19 user: 0.18 sys: 0.00
ANALYTICAL SOLVENT EXCLUDED SURFACE...
    Component 0
        Time Surface real: 0.04 user: 0.03 sys: 0.00
        Time Singularities real: 0.02 user: 0.02 sys: 0.00
    SES comp. #fac. #edg. #s_edg. #vert. #s_vert. R_h C_h genus
         0 9602 19377 210 9762 360 0 9 12

ANALYTICAL SURFACE AREA :
    Comp. probe_radius, reent, toric, contact SES SAS
      0 1.500 4196.562 6201.302 5345.952 15743.814 17477.615
TRIANGULATION...
    Component 0
    component#, vertices, edges, faces, genus, density
        0 17790 53436 35624 12 1.130
        Time Triangulation real: 0.15 user: 0.15 sys: 0.01
NUMERICAL VOLUMES AND AREA
    Comp. probe_radius SES_volume SES_area)
       0 1.50 49635.516 15128.468
    Total ses_volume: 49635.516
MSMS terminated normally
Total Time real: 0.63 user: 0.59 sys: 0.01
vmd >

So, now I'v got the files test.vert and test.face
and my coordinate file foo.pdb.

I can load the pdb-file into VMD but it doesn't visualise the MSMS output when I choose "Drawing method" MSMS in the Graphical Representations. I also tried loading the .vert and .face files via File-New Molecule in the VMD mail window but VMD don't accept that. What am I doing wrong?

Thanks in advance!

Best regards

Peter

----- Original Message -----
From: John Stone <johns_at_ks.uiuc.edu>
Date: Monday, June 27, 2005 5:01 pm
Subject: Re: vmd-l: MSMS

>
> Peter,
> If you want to load the existing .vert and .face files into VMD, you
> can use the recently added MSMS plugin, by upgrading the plugins in
> yourVMD installation. If on the other hand, you've got the
> molecular structure
> for which those .vert and .face files were created, you could just
> as easly
> run MSMS from within VMD, and then you don't have to update your
> plugins.When displaying an MSMS surface in VMD, the coloring
> methods that are available
> are all based on atomic information. If you want to color by
> electrostaticpotential, you'll need to first calculate a potential
> map. This can be done
> using the APBS plugin or with the PME potential plugin, for example.
> If you're having trouble using the "MSMS" representation in VMD let
> us know.
> That's the most convenient way to view MSMS surfaces, reading the
> .vert and
> .face files is really only useful if you have a huge structure that
> takesseveral minutes for MSMS to create a surface for.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jun 27, 2005 at 02:19:22PM +0200, Peter Holm wrote:
> > Dear VMD users,
> >
> > OK, so my previous installation problem is solved. Now I wish to
> read in an MSMS triangulated object into VMD but can not find how
> to do this. I have created two objects in MSMS called foo.vert and
> foo.face.> These are both long lists of text. Should they be read
> directly into VMD somehow?
> >
> > Furthermore, when displaying a pdb-file according to MSMS nothing
> is shown and when displaying as charge the whole molecule has the
> same colour. Have I missed to install some libraries?
> >
> > Many thanks in advance for advice!
> >
> > Best regards
> >
> > Peter
> >
> > ****************************************************
> > Peter Holm, Ph.D.
> > Molecular Biophysics
> > Center for Chemistry and Chemical Engineering
> > Lund University
> > P.O.B. 124
> > SE-22100 Lund
> > SWEDEN
> >
> > Telephone numbers
> > Office: +46-(0)46-2221448
> > Mobile: +46-(0)709-625451
> > Fax: +46-(0)46-2224692
> > E-mail: peter.holm_at_mbfys.lu.se
> > http://www.mbfys.lu.se
> > ****************************************************
> >
>
> --
> 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
>