VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 08 2010 - 10:04:00 CST

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