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

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Thu Jun 12 15:35:02 PDT 2014


Fantastic! Thank you!


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

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----- Original Message -----
From: Tom Goddard [mailto:goddard at sonic.net]
Sent: Thursday, June 12, 2014 06:22 PM
To: Hurt, Darrell (NIH/NIAID) [E]
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>; Boaz Shaanan <bshaanan at bgu.ac.il>
Subject: Re: [Chimera-users] About direct fetc hing biological assemblies into Chimera

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
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office: 301-402-0095
> Mobile: 301-758-3559Web: BCBB Home Page
> <http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb
> .aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit <https://twitter.com/niaidbioit>
> 
> 
> Disclaimer: The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be used
> by anyone who is not the original intended recipient. If you have received
> this e-mail in error please inform the sender and delete it from your
> mailbox or any other storage devices. National Institute of Allergy and
> Infectious Diseases shall not accept liability for any statements made
> that are sender's own and not expressly made on behalf of the NIAID by one
> of its representatives.
> 
> 
> 
> 
> 
> 
> 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   
>> 
> 
> 




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