[chimerax-users] Help please on how to create a homodimer with different chain IDs using sym command

[Elaine Meng]

Dear Scott,
That's great!  We like to hear that ChimeraX is used in teaching.  To get the dimer, I guess you used 

open 2zhg
sym #1 assembly 1

(since "sym #1" merely reports the assemblies available and does not add the other half).

Then, the first half is model #1 containing chains A,B and the second half is model #2 also containing chains A,B.  You can see you have two models in the "Models" panel on the right.  Thus you can refer to the two A chains separately in the command line as  #1/A and #2/A, or the entire models as #1 and #2.

Command-line specification:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

An alternative is to fetch the biounit directly, e.g. 

open 2zhg from pdbe_bio maxassemblies 1

In that case the DNA chains are A and AA  and the protein ones are B and BA.  You can see this information in the Log when the file is opened.  For explanation of fetching and its options:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch>

Unless including private data, it's better to send questions to chimerax-users at cgl.ucsf.edu (CC'd here) rather than to me personally... then others may benefit, and the messages are kept in a searchable archive.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 10, 2020, at 9:43 AM, Scott White <S.A.WHITE at bham.ac.uk> wrote:
> 
> Dear Elaine,
> 
> I am using ChimeraX for teaching. I want to be able to instruct how to create a homodimer, but to manipulate the separate chains, eg colour them differently.
> 
> example:
> open 2zhg (asu, one half of a homodimer)
> sym #1 (create the other half)
> 
> but both polypeptide chains are labelled Chain A. If I select "sel \a" I get the whole model. If I use right-mouse-button select by clicking, I get the atom in both chains selected.
> 
> How can I manipulate the two polypeptide chains independently? I've tried playing with the various sym options, but I can't get that to work. I have tried using "split" command, but that splits the polypeptide and DNA chains into separate submodels, as expected. It won't split the two chains A into a A and C, for example.
> 
> Any guidance please?
> 
> I know I could save the file and use a file editor such as vi, but this is a class for students and I was hoping to do it all by ChimeraX.
> 
> I'm working with ChimeraX version 1.0
> 
> thanks for your help,
> Scott