[chimerax-users] Create Complete Oligomers

[Elaine Meng]

Dear Samuel,
(A) One possibility is to just fit the monomer prediction onto each chain of the trimer experimental structure.  It is very easy to do this in ChimeraX, just use commands:

open 3un9
alphafold match #1
close #1

See "alphafold match"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#fetch>

You would need to inspect the resulting #2 model to see if this approach is good enough for you -- since you are going to use MD, it should take care of any small clashes.   You may want to combine the models #2.1, 2.2, 2.3 into a single model:

combine #2 model #3
close #2

...then save #3 to PDB or whatever you were planning to do.

(B) The other possibility is to run a new alphafold calculation of the trimer.  However, I do not know if that total size is feasible (maybe takes too long to work).  Approach (A) is probably good enough for you as the model is not severely clashing, and you are planning to use MD anyway.   But if you want to try alphafold prediction of multimers, see:

ChimeraX Alphafold tool ( menu Tools... Structure Prediction... AlphaFold), "Predict" option
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict>

...or command "alphafold predict"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#predict>

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

> On Sep 9, 2022, at 5:07 AM, Samuel Kyobe via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX
> 
> We have a protein NLRX1 which functions as a trimer, however only the terminal component of this trimer has been experimentally resolved (3UN9) and in alpha fold the complete monomer of NLRX1 has been predicted (Q86UT6).
> 
> Is it possible to build a complete trimer of NLRX1 starting with the partial X-ray resolved structure as a reference using ChimeraX and the alphafold model. 
> 
> We would like to use the complete structure for MD studies.
> 
> Thank you
> 
> Samuel