[Chimera-users] Splitting an pdb with multiple proteins

Jochen Baßler jochen.bassler at bzh.uni-heidelberg.de
Mon Jun 13 10:32:29 PDT 2016


Hi Eric,

Great job! Thanks a lot.

Best wishes

Jochen


From:  Eric Pettersen <pett at cgl.ucsf.edu>
Reply-To:  "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Date:  Monday 13 June 2016 19:21
To:  Jochen Baßler <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,
Since it was pretty easy I went ahead and implemented your suggestion.  It
will be in the next daily build and release candidate.

‹Eric

Eric Pettersen
UCSF Computer Graphics Lab

> On Jun 13, 2016, at 1:30 AM, Jochen Baßler
> <jochen.bassler at bzh.uni-heidelberg.de> wrote:
> 
> 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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