[Chimera-users] About direct fetc hing biological assemblies into Chimera

[Tom Goddard]

Hi Darrell,

  The new Chimera fetch PDB biounit code does an ftp fetch of a url that looks like

	ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates/all/391d.pdb1.gz

using urlretrieve() from the Python urllib module.  Here’s the code

http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/FetchBioUnit/fetch_biounit.py
http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/chimera/fetch.py

  Tom


On Jun 12, 2014, at 12:56 PM, Hurt, Darrell (NIH/NIAID) [E]  wrote:

> Hi Tom,
> 
> Thanks again for adding this functionality. I'm running the script on a
> server behind a firewall. Can you tell me the address(es) (and port(s), if
> applicable) that must be available to my server if I want to use this new
> direct fetching of biological assemblies?
> 
> Thanks,
> Darrell
> 
> 
> -- 
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
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> 
> On 6/3/14 2:52 PM, "Tom Goddard" wrote:
> 
>> Hi Darrell, Boaz,
>> 
>> I made a few improvement to the fetching of PDB biological unit files
>> that will be in tonight¹s daily build.
>> 
>> 1) Made fetching biounit give each assembly a separate top level model id
>> number and separate color.  Before all the assemblies were grouped
>> together in Model Panel, and now each assembly is on a separate line in
>> Model Panel.
>> 
>> 2) Renamed biounit file type and prefix from pdbbuID to biounitID.  So
>> use Chimera command ³open biounitID:1hho².
>> 
>> 3) Allowed specifing a specific biounit by number using pdb id plus "."
>> followed by number, eg. 3fad.2.  This works in the Fetch by Id dialog and
>> on the command-line.  Also to fetch a few different biounits you can use
>> 3xyz.1.3.8 with each . specifying another assembly number.  Used "."
>> instead of comma since commas separate multiple identifiers in the fetch
>> dialog.
>> 
>> 	Tom
>> 
>> 
>> On Jun 3, 2014, at 5:52 AM, Boaz Shaanan  wrote:
>> 
>>> Hi Tom,
>>> 
>>> This is a nice addition but can you ALSO give the option of fetching
>>> just one of the biological assemblies? It is my experience that
>>> biological assemblies for a particular pdb entry consist of one correct
>>> assembly, in the sense of biological function corresponding to the
>>> description given by the depositors and other assemblies. I usually flip
>>> between the assemblies on the RCSB website before deciding which one to
>>> fetch. With your new addition this of course can all be done now in
>>> Chimera but if possible, I'd rather not waste time and disk space with
>>> meaningless assemblies. What do you think?
>>> 
>>>  Cheers,
>>> 
>>>        Boaz   
>> 
> 
>