[Chimera-users] Aligning homdimers
James Nettles
nettlesconsulting at gmail.com
Tue Apr 4 10:02:24 PDT 2023
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 at 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 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
>
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