[Chimera-users] Fetch biological unit?

Tom Goddard goddard at sonic.net
Mon Jun 2 16:53:06 PDT 2014

Hi Darrell,

  I added a Chimera Fetch dialog entry “PDB biounit” 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 tonight’s daily build.


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)
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> 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 … 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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