Hi Elaine, Thanks for the quick response. I read through the link to to the guide and it has given me an idea. I’ll update one way or the other when I get it finished. Thanks again for your help over the many years - love using Chimera! Best regards, Jim

On Apr 4, 2023, at 12:39 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Jim, As far as I know the other way (A to A and B to B separately) is not even possible, if each A-B dimer is a single model in Chimera, since subparts of the same model are not moved separately by matchmaker.

mm #0:.a:.b #1:.a:.b pair ss

Tested on 4hvp and 1hiv, Reply Log gives RMSD over more residue pairs than present in A or B alone. The "pair ss" option allows giving multiple chains per model, which will be paired in order, as explained here:

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#pairing>

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

...

On Apr 4, 2023, at 4:16 AM, James Nettles via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

I’m asking a question that has been asked and answered before in 2009 - but not with exact solution that I would like.

I have a relatively small homo dimer( <200 residue) and would like to fit with a homo dimer of the almost same sequence but slightly different conformations. I would like to fit the dimers as a pair (A/B to A/B) rather than A to A and B to B separately.

In other word, I’m wanting to spread the deviation across both monomer units of the dimer in a single step rather than fitting separately and then recombining.

I know Chimera isn’t formally supported any more, but I’m running this on an old machine with an old OS , so ChimeraX isn’t an option here.

Thanks so much in advance - this group has always bee fabulous over the years.

Best regards,

Jim