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@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@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