[Chimera-users] biounit

Arthur Szabo agszabo at outlook.com
Mon Aug 14 15:19:07 PDT 2017


Elaine

Thank you

A follow up question. PDB 4V9D is a structure of a bacterial ribosome. Some 35Mb.

Can this be handled, or is the size to large to download.
I tried to fetch it by PDB index, but it just seemed to stall or was way too large.

Regards

arthur

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Monday, August 14, 2017 4:42 PM
To: Arthur Szabo <agszabo at outlook.com>
Cc: chimera-users at cgl.ucsf.edu BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] biounit

Hi Arthur,
The main PDB fetch is the contents of the crystallographic asymmetric unit, whereas the biological unit is the known or guessed biologically relevant assembly based on that structure.  Sometimes they are the same, but often they’re not… this page at the RCSB PDB has a good explanation:

<https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies>

I see that the link I had in the Chimera manual to explain “biounit” no longer works, so I’ll update it to use the link above instead.  The current terminology is “biological assembly,” which makes more sense.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Aug 14, 2017, at 12:52 PM, Arthur Szabo <agszabo at outlook.com> wrote:
> 
> When one fetches structures from the PDB data base what is the difference between fetching using the PDB  only selection and the pdb biounit selection? 
> Arthur G. Szabo




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