[Chimera-users] Splitting an pdb with multiple proteins
pett at cgl.ucsf.edu
Fri Jun 10 09:54:18 PDT 2016
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.
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
> 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 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 “status message” area across the bottom of the Chimera window.
>> 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 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:
>>> 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
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