[Chimera-users] About direct fetching biological assemblies into Chimera

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Thu Jun 12 12:56:04 PDT 2014

Hi Tom,

Thanks again for adding this functionality. I'm running the script on a
server behind a firewall. Can you tell me the address(es) (and port(s), if
applicable) that must be available to my server if I want to use this new
direct fetching of biological assemblies?


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559Web: BCBB Home Page
Twitter: @niaidbioit <https://twitter.com/niaidbioit>

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On 6/3/14 2:52 PM, "Tom Goddard" <goddard at sonic.net> wrote:

>Hi Darrell, Boaz,
>  I made a few improvement to the fetching of PDB biological unit files
>that will be in tonight¹s 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 ³open biounitID:1hho².
>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
>	Tom
>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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