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

Tom Goddard goddard at sonic.net
Mon Jun 16 09:45:12 PDT 2014


Thanks Darrell,

  I’ve fixed the code so that fetching pdb biounit files uses the lower-case 4-letter id.  Fix will be in tonight’s daily build.  Oddly for some entries upper and lower case work, while for others, only lowercase works.

	Tom


On Jun 16, 2014, at 9:27 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:

> Hi Tom,
> 
> Thanks again for this. I found that when I specify a PDB using uppercase
> letters via a script, the command doesn't work. But lowercase letters do
> work. I catch it in my script, but you may want to build this into the
> command for other users, kind of like how regular PDB fetch does it.
> 
> 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>
> 
> 
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> 
> 
> 
> 
> 
> 
> On 6/12/14 6:35 PM, "Hurt, Darrell (NIH/NIAID) [E]"
>  wrote:
> 
>> Fantastic! Thank you!
>> 
>> 
>> 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 301-758-3559
>> http://bioinformatics.niaid.nih.gov (Within NIH)
>> http://exon.niaid.nih.gov (Public)
>> 
>> 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.
>> 
>> ----- Original Message -----
>> From: Tom Goddard 
>> 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/fet
>> ch_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/bc
>>> bb
>>> .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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