VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 20 2010 - 10:52:25 CDT

Hi,
  The Unix versions of VMD also support the old "mol urlload" command,
e.g. to load a PDB you'd do this:
  mol urlload pdb http://www.ks.uiuc.edu/~johns/files/brH.pdb

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 16, 2010 at 08:58:22PM -0400, Axel Kohlmeyer wrote:
> ian,
>
> On Fri, Jul 16, 2010 at 7:46 PM, Ian Stokes-Rees
> <ijstokes_at_hkl.hms.harvard.edu> wrote:
> >  We have several variations of the PDB that we have modified for our own
> > use, and also have a mirror of SCOP.  It would be nice if there were
> > some easy way to load PDB files from these "alternative" sources.  Is
> > there straightforward way for me to modify VMD to enable this functionality?
>
> yes, you'd just have to write a few little wrappers in tcl.
>
> you can download practically any URL to a local file with the
> following script code.
>
> vmdhttpcopy http://some.web.server/path/to/file.pdb tmpfile.pdb
>
> and then load it with:
>
> mol new tmpfile.pdb
>
> with a little bit of extra Tk script magic you can have
> a nice GUI around it. or download an index, parse it
> and then provide a list of available file etc.
>
> cheers,
> axel.
>
>
> > Another perspective is that we have a web-based protein study portal and
> > would like to send users VMD script files which can fetch all files from
> > URLs, or just use SCOP codes to fetch the files.  It would be great if
> > we could do this without having to ship all PDB files to users from the
> > web browser, but instead just the script which references web-based PDB
> > files (or a URL source from which PBDs should be fetched).
> >
> > Cheers,
> >
> > Ian
> >
> > --
> > Ian Stokes-Rees, PhD                       W: http://abitibi.sbgrid.org
> > ijstokes_at_hkl.hms.harvard.edu               T: +1.617.432.5608 x75
> > NEBioGrid, Harvard Medical School          C: +1.617.331.5993
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA. 

-- 
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