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

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Mon Jun 16 09:27:14 PDT 2014


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
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On 6/12/14 6:35 PM, "Hurt, Darrell (NIH/NIAID) [E]"
<darrellh at niaid.nih.gov> 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
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>by one of its representatives.
>
>----- 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/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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