[Chimera-users] Fetch biological unit?

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Mon Jun 2 19:11:55 PDT 2014


Hi Tom,

Wow! Thanks. I'll give it a try tomorrow. This may really help!

Cheers,
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 6/2/14 7:53 PM, "Tom Goddard" <goddard at sonic.net> wrote:

>Hi Darrell,
>
>  I added a Chimera Fetch dialog entry ³PDB biounit² that will fetch all
>the biological assembly files for a pdb id ‹ there can be more than one.
>Also they can be fetched using the Chimera command:
>
>	open pdbbuID:2bbv
>
>  Will be in tonight¹s daily build.
>
>	Tom
>
>
>On Jun 2, 2014, at 2:19 PM, Hurt, Darrell (NIH/NIAID) [E]  wrote:
>
>> Hi Elaine,
>> 
>> No problem. We'll work around it. I just wanted you to know that
>>someone else was interested in it, too.
>> 
>> :)
>> 
>> 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: 301-758-3559
>> Web: BCBB Home 
>>Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Page
>>s/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.
>> 
>> From: Elaine Meng
>> Reply-To: 
>>"chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> BB"
>><chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
>> Date: Monday, June 2, 2014 5:18 PM
>> To: Darrell Hurt <>
>> Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> BB"
>><chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
>> Subject: Re: [Chimera-users] Fetch biological unit?
>> 
>> Hi Darrell!
>> Sorry, there isn't any PDB biological unit fetch Š one has to download
>>them from the RCSB website, then open "manually" in Chimera.  We have
>>discussed changing from PQS to PISA in the fetch interface (trac ticket
>>#10237), but it hasn't been done.
>> Best regards,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> On Jun 2, 2014, at 10:18 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote:
>> 
>> Hi Chimera friends,
>> The PQS server still works well for downloading the biological unit,
>>but (as noted) it doesn't have every structure in it. The PDB itself
>>provides the biological unit(s) for download in their weird ".pdb1",
>>".pdb2", etc. format for every entry in the database (even if it is
>>redundant). Is there a way to grab those files from the PDB itself using
>>the Chimera interface? The repository is in:
>> ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates
>> Thanks,
>> Darrell
>> 
>> 
>> 
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>




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