Hi Tiglath,
That message means exactly what it says: Modeller cannot handle templates with multi-character chain IDs.

I see that when you use

open pdbe_bio:3r2p

... then you get one chain A and one chain AA (two characters, = multi-character, so can't be used as Modeller template).  This is shown in the Log when you open the structure.  Not sure why PDBe chose to name the second chain as AA, but you can change it to a single character instead, for example to B with "setattr":

setattr /AA chain chain_id B

Sometimes (but not in this case) you might need two commands to change the chain ID instead of one, as explained in this recent post:
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-October/001565.html>

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

> On Oct 26, 2020, at 3:02 PM, Moradkhan, Tiglath A <tmoradkhan@csus.edu> wrote:
>
> Hi Elaine
> OK. Thank you for the help. I have one more question. So I'm building a C-terminal dimer model of human Apo A-I using 3R2P as a template model (a C-terminal truncated x-ray crystal structure of the protein). I loaded the biological assembly (a dimer) in ChimeraX and used the Sequence viewer to get the template-query alignment. But when I try to run Modeller, it gives me the following message: "Modeller cannot handle templates with multi-character chain IDs". Am I missing something here?
> I would be very grateful for your help.
> Thanks
> Tiglath