[Chimera-users] Splitting an pdb with multiple proteins

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 13 11:00:42 PDT 2016


I should clarify that I implemented it in the dialog that the “select chain(s)…” button in the model panel shows.  That was easy.  I didn’t implement it in the main Select->Chain menu, since the code modifications would be considerably more complicated.  The latter is still worth doing but won’t happen immediately.

—Eric

> On Jun 13, 2016, at 10:21 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> 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 <mailto: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 here…)
>> 
>> Best wishes
>> 
>> Jochen
>> 
>> 
>> 
>> From: Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>>
>> Reply-To: Mailing List <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>
>> Date: Friday, 10June, 2016 6:54 PM
>> To: J B <jochen.bassler at bzh.uni-heidelberg.de <mailto:jochen.bassler at bzh.uni-heidelberg.de>>
>> Cc: Mailing List <chimera-users at cgl.ucsf.edu <mailto: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 <mailto:pett at cgl.ucsf.edu>>
>>> Date: Friday, 10June, 2016 1:51 AM
>>> To: "chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> BB" <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>
>>> Cc: J B <jochen.bassler at bzh.uni-heidelberg.de <mailto: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 <mailto: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 “status message” area across the bottom of the Chimera window.  
>>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/chimerawindow.html <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 “split” 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 <mailto: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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