[Chimera-users] Splitting an pdb with multiple proteins

[Jochen Baßler]

Hi Eric,

Yes,  the new release candidate is having all the important information in
the reply log file and it is shown below as Elaine indicated.
Thank you for this new feature. Maybe one could extend this a bit further?
Since these informations  are already imported, one could implement them
into the "select Chain" menu, which one can access via the model panel?
Then it would be very easy to click or select a protein of interest.

Thanks for the feedback and the information. (The only bad point is that
this new version is not running on my mac wit OSX 10.7, So I have to update
also hereŠ)

Best wishes

Jochen



From:  Eric Pettersen <pett at cgl.ucsf.edu>
Reply-To:  Mailing List <chimera-users at cgl.ucsf.edu>
Date:  Friday, 10June, 2016 6:54 PM
To:  J B <jochen.bassler at bzh.uni-heidelberg.de>
Cc:  Mailing List <chimera-users at cgl.ucsf.edu>
Subject:  Re: [Chimera-users] Splitting an pdb with multiple proteins

Hi Jochen,
Support for chain descriptions coming from mmCIF files (rather than PDB
files) was only added after the 1.10.2 release.  Please try the current 1.11
release candidate and see how that works.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

On Jun 10, 2016, at 1:36 AM, Jochen Baßler wrote:

> Dear Elaine, Eric,
> 
> Thanks a lot for your fast replay.
> I imported 3jct and 5hau to test your suggestions, but the reply log just
> contained :
> 
> [MMLIB:WARNING] monomer description not found in zipfile for '4SU'
> [MMLIB:WARNING] monomer description not found in zipfile for '5MC'
> 
> How can I activate the status message?
> With the mouse I can see the chain number near the mouse pointer, but there is
> no information below at the main window.
> 
> (I am running chimera version 1.10.2)
> 
> Best wishes
> 
> Jochen
> 
> 
> From:  Eric Pettersen <pett at cgl.ucsf.edu>
> Date:  Friday, 10June, 2016 1:51 AM
> To:  "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Cc:  J B <jochen.bassler at bzh.uni-heidelberg.de>
> Subject:  Re: [Chimera-users] Splitting an pdb with multiple proteins
> 
> It is also listed in the reply log as the structure is opened.
> 
> ‹Eric
> 
> Eric Pettersen
> UCSF Computer Graphics Lab
> 
> 
>> On Jun 9, 2016, at 4:49 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Jochen,
>> This information is already imported, and when you mouse over the chain, it
>> is shown in the ³status message² area across the bottom of the Chimera
>> window.  
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html>
>> 
>> I tested just now, and the information is retained and can be shown in the
>> same way after ³split² is used.  However, it is not automatically used as the
>> model names.
>> I hope this helps,
>> 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 9, 2016, at 4:05 AM, Jochen Baßler
>>> <jochen.bassler at bzh.uni-heidelberg.de> wrote:
>>> 
>>> Hi,
>>> 
>>> I´m frequently looking at pdb´s that contain multiple chains, like ribosomes
>>> or preribosomes (e.g. Pdb  3JCT).
>>> Is there a way to import the information from the pdb database, which tells
>>> you the name of the chains?
>>> Chain A = rpl2
>>> Chain B = Rpl4 etc.
>>> Cool would be to split the pdb into multiple models that have the name from
>>> the pdb database.
>>> (It is quite annoying to have a pdb with nearly 60 different chains and you
>>> have to spend half a day to rename the chains or to create individual
>>> models, before analyzing the structure)
>>> 
>>> Thanks for suggestions and solutions
>>> 
>>> Best wishes
>>> 
>>> Jochen
>>> 
>> 
>> _______________________________________________
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>> 
> 



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