From: Fatemesadat Emami (fe2_at_zips.uakron.edu)
Date: Mon Mar 08 2010 - 10:05:36 CST

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