VMD-L Mailing List

From: Amarda Shehu (shehua_at_cs.rice.edu)
Date: Tue Apr 24 2007 - 13:55:24 CDT

I do attempt a lot of connections, in the order of thousands. However, I
just finished loading up all the info I wanted. We have had some network
issues lately, since we are undergoing some upgrades, but in any case I am
done with this particular step.

On the other hand, I would be interested in having a mirror of the PDB on
one of my machines and rsync often to get the latest. If you can show me
how to do this, I would appreciate it.

-Amarda

On Tue, 24 Apr 2007, John Stone wrote:

> 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.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> 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
>>> 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
>>>
>
> --
> 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
>