VMD-L Mailing List

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Wed May 05 2010 - 18:53:30 CDT

Hi Fatima,
Sorry for getting in this thread this late, I think there is an
extension in VMD that helps you in building a surface, i think it is
called inorganic builder. Had i known about this i would not have had to
use material studio to build my SiO2 structure.

I don't use pdb for my system (DNA on SiO2) as pdb does not contain
connectivity information, i use mol2 files.

i hope this helps,
Taufik

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 <mailto: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
> <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:johns_at_ks.uiuc.edu>
> Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/
> <http://www.ks.uiuc.edu/%7Ejohns/> 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 <mailto:johns_at_ks.uiuc.edu>
> Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/
> <http://www.ks.uiuc.edu/%7Ejohns/> 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