[Chimera-users] Fetch biological unit?

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Mon Jun 2 14:19:58 PDT 2014


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
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From: Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>>
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 <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>>
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]" <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>> 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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