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

[Hurt, Darrell (NIH/NIAID) [E]]

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?

Thanks,
Darrell


-- 
Darrell Hurt, Ph.D.
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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
>dialog.
>
>	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   
>