[Chimera-users] Chimera-users Digest, Vol 134, Issue 4

Boaz Shaanan bshaanan at bgu.ac.il
Tue Jun 3 11:59:38 PDT 2014

Thanks a lot Tom, 

 This is wonderful.  I'll try it as soon as it's on the site.


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710

Message: 7
Date: Tue, 3 Jun 2014 11:52:46 -0700
From: Tom Goddard <goddard at sonic.net>
To: Boaz Shaanan <bshaanan at bgu.ac.il>,  "Hurt, Darrell (NIH/NIAID) [E]"
        <darrellh at niaid.nih.gov>
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] About direct fetching biological
        assemblies      into Chimera
Message-ID: <2FF03268-945D-4B45-B2BE-1A7B17370069 at sonic.net>
Content-Type: text/plain; charset=windows-1252

Hi Darrell, Boaz,

  I made a few improvement to the fetching of PDB biological unit files that will be in tonight?s daily build.

1) Made fetching biounit give each assembly a separate top level model id number and separate color.  Before all the assemblies were grouped together in Model Panel, and now each assembly is on a separate line in Model Panel.

2) Renamed biounit file type and prefix from pdbbuID to biounitID.  So use Chimera command ?open biounitID:1hho?.

3) Allowed specifing a specific biounit by number using pdb id plus "." followed by number, eg. 3fad.2.  This works in the Fetch by Id dialog and on the command-line.  Also to fetch a few different biounits you can use 3xyz.1.3.8 with each . specifying another assembly number.  Used "." instead of comma since commas separate multiple identifiers in the fetch dialog.


On Jun 3, 2014, at 5:52 AM, Boaz Shaanan <bshaanan at bgu.ac.il> wrote:

> Hi Tom,
> This is a nice addition but can you ALSO give the option of fetching just one of the biological assemblies? It is my experience that biological assemblies for a particular pdb entry consist of one correct assembly, in the sense of biological function corresponding to the description given by the depositors and other assemblies. I usually flip between the assemblies on the RCSB website before deciding which one to fetch. With your new addition this of course can all be done now in Chimera but if possible, I'd rather not waste time and disk space with meaningless assemblies. What do you think?
>   Cheers,
>         Boaz


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