From: John Stone (
Date: Tue Apr 24 2007 - 13:44:13 CDT

Hi Amarda,
  It almost sounds like you're having some sort of intermittent
network problems which are causing the symptoms you describe. I do a lot
of testing of VMD using structures downloaded via the web but I rarely
have timeouts etc, but then I may just be "lucky" or we may have a better
route to the RCSB web site. When these hangs occur, are you able to
use a web browser or similar tool to access the RCSB site, or do they
also hang? I'm just trying to determine if the problem is even solvable
from within VMD or if it is something systemic such as an unresponsive
DNS server causing hostname lookups to hang or fail, etc.

If you're doing a lot of PDB structure processing, you may find it to be
much more efficient to simply create a local mirror of the entire PDB
on your system there. We have done this ourselves for some of the large
PDB structure processing jobs we run as a means of achieving higher
performance and to avoid loading the UIUC network (and the RCSB web server).
If you're doing a large number of structure loads over the web, the RSCB
web server might even be intentionally throttling your connection.
A full copy of the PDB structure data is well under 100GB, and it's easy
to mirror the RCSB site using rsync scripts once every few weeks.
If you want, I can give you a copy of the rync script I use here.

If you prefer to continue loading the data via the web connection,
then I'll likely want to see how your script works, as I may be able
to give you some Tcl code to make it more robust.

  John Stone

On Tue, Apr 24, 2007 at 11:39:03AM -0500, Amarda Shehu wrote:
> No, I am not using 'mol new' - but 'mol pdbload pdb_code'
> At the moment I resorted to a similar hack - making a selection that when
> checked for the number of atoms, has 0 atoms.
> Besides the connection timeout problem, sometimes - for reasons I do not
> understand yet - the loading of a particular pdb fails, even though the
> pdb code is a valid one. I use the same check for 0 number of atoms to
> detect this.
> The more serious problem is hanging from the vmd console - after a
> timeout - when the execution will not go to the next line.
> In this case I have resorted to a manual restart, saving certain counter
> values to ensure that the loading of pdb structures starts from where the
> execution left off.
> -Amarda
> On Tue, 24 Apr 2007, John Stone wrote:
> >
> >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
> >
> >
> >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: Phone: 217-244-3349
> > WWW: Fax: 217-244-6078
> >

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:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078