VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jul 16 2010 - 19:58:22 CDT

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.