On Jun 13, 2016, at 1:30 AM, Jochen Baßler <jochen.bassler@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@cgl.ucsf.edu>
Reply-To: Mailing List <chimera-users@cgl.ucsf.edu>
Date: Friday, 10June, 2016 6:54 PM
To: J B <jochen.bassler@bzh.uni-heidelberg.de>
Cc: Mailing List <chimera-users@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@cgl.ucsf.edu>
Date: Friday, 10June, 2016 1:51 AM
To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu>
Cc: J B <jochen.bassler@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@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>

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@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

_______________________________________________
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

_______________________________________________
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users