[chimerax-users] mmcif assemblies for alphafold prediction

[Elaine Meng]

Hi Heather,
I don't know what you mean by "similar to 4 and 6."  The mmCIF information is for describing and applying symmetries, not making an asymmetric assembly.

Assuming that your ultimate goal is to generate such an assembly of your AlphaFold-predicted monomeric chain structures:  If you have an assembly structure of some other similar proteins in that arrangement, you can open copies of your alphafold predictions and superimpose these copies onto the corresponding subunits of the known assembly (e.g. with "align" or "matchmaker" ... probably the latter, as it is easier if it works for your specific situation), then close that known assembly, leaving your approximately modeled assembly of AlphaFold models.

Matchmaker tool and command
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html>

align command
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.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 29, 2021, at 6:53 PM, Noriega, Heather via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> I am trying to create an asymmetrical assembly similar to 4 and 6 with an alphafold prediction. There are no mmCIF assemblies connected with this prediction, is there a way to add the assemblies, if so how? Or is there another way to create this figure without the assembly?
> Thank you,
> Heather Noriega
> PhD-Pharmaceutical Science student 
> Howard University
> heather.noriega at bison.howard.edu
> 520-203-1883