From: Axel Kohlmeyer (
Date: Fri Jul 16 2010 - 19:58:22 CDT


On Fri, Jul 16, 2010 at 7:46 PM, Ian Stokes-Rees
<> 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.


> 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:
>               T: +1.617.432.5608 x75
> NEBioGrid, Harvard Medical School          C: +1.617.331.5993

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.