[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.

	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/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.
> 
> 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
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




More information about the Chimera-users mailing list