VMD-L Mailing List

From: Fatemesadat Emami (fe2_at_zips.uakron.edu)
Date: Mon Mar 08 2010 - 09:57:02 CST

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