From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 08 2010 - 14:32:10 CST

Hi,
  PSF files don't contain surfaces either. They contain additional
information beyond what is contained in a PDB, but they too are purely
focused on storing atomic data. As I mentioned before, if you want to
load pre-defined surface meshes into VMD, you'd want to use a file format
such as STL or the MSMS face/vert file formats for this purpose. If you
just want to _display_ a molecular surface, you can have VMD call MSMS or
Surf to compute a solvent accessible surface for a group of selected atoms.
>From what you've been saying in your previous emails I took your questions
to indicate that you have an existing triangle mesh representing some
surface already...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 08, 2010 at 02:47:43PM -0500, Fatemesadat Emami wrote:
> Hi John,
> What if I create .psf files because I have already lammps dcd files
> obtained from simulation. Then I have to name my surface elements again.
> Do you have any sample of a .psf files for a system including a surface?
> Is there any webpage explaining the exact format of a psf file?
> Thanks for your time
> Fatima
> On Mon, Mar 8, 2010 at 11:05 AM, Fatemesadat Emami <fe2_at_zips.uakron.edu>
> wrote:
>
> Thank you John
>
>
> On Mon, Mar 8, 2010 at 11:04 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> If you wish to display a surface in addition to the atoms, you could
> either have VMD draw the surface with "draw" or "graphics" commands
> (your program could emit the appropriate commands to a text file that
> you
> could then load into VMD), or you could emit the surface as an STL
> or MSMS file, or another geometric file format that VMD can read.
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Mar 08, 2010 at 10:57:02AM -0500, Fatemesadat Emami wrote:
> > Thank you very much John,
> >
> > Then I won't be able to load my system into vmd from pdb files,
> is that
> > right?
> >
> > Thank you again,
> > Fatima
> >
> > On Mon, Mar 8, 2010 at 10:25 AM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> >
> > Hi,
> > The PDB file format spec is available here:
> > http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html
> >
> > Unless I misunderstand what you mean by "surface", no there is
> not
> > a way to represent a polygon mesh or other geometric surface in
> a
> > PDB file. PDB files only contain atoms, associated structure
> data,
> > and information about the crystallography methods used to
> determine
> > the structure, etc.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Mar 08, 2010 at 09:59:14AM -0500, Fatemesadat Emami
> wrote:
> > > Hi vmd users,
> > > I am creating pdb files (with my own code) from the
> Material Studio
> > > coordinate files. I have a surface in my system that I do
> not know
> > how to
> > > name its elements in the pdb file. I was wondering if
> anybody can
> > give me
> > > an idea of how I have to include a surface in a pdb file
> or how I
> > can find
> > > a sample for such a sys?
> > > Many Thanks
> > > Fatima
> > >
> > > --
> > > Yours Sincerely,
> > > Fateme Sadat Emami
> > > Nano Scale Laboratory
> > > Polymer Engineering Department
> > --
> > 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
> >
> > --
> > Yours Sincerely,
> > Fateme Sadat Emami
> > Nano Scale Laboratory
> > Polymer Engineering Department
>
> --
> 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
>
> --
> Yours Sincerely,
> Fateme Sadat Emami
> Nano Scale Laboratory
> Polymer Engineering Department
>
> --
> Yours Sincerely,
> Fateme Sadat Emami
> Nano Scale Laboratory
> Polymer Engineering Department

-- 
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