[Chimera-users] Aligning homdimers

[Elaine Meng]

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 at 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