VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 24 2007 - 11:27:22 CDT

Hi Amarda,
  Are you downloading the files yourself (e.g. in your own scripts)
or are you getting them via 'mol new' and friends? At present the
webpdbplugin deals with this kind of situation by returning a molecule
containing zero atoms, so if you're using the 'mol new' method to
get the structures, you could simply test whether you got an empty
molecule after the load completes. If you can tell me more about
the particular symptom you're experiencing I might be able to improve
the behavior of the webpdb plugin or give you further suggestions.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 24, 2007 at 09:23:44AM -0500, Amarda Shehu wrote:
>
> Hello,
>
> I am trying to load pdb files automatically from the rcsb website through
> vmd. I notice that once in a while the connection times out.
>
> Is there any way to catch this when it happens and reset the connection? I
> am trying to write tcl code to do this automatically.
>
> -Amarda Shehu 

-- 
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