[chimerax-users] Using ChimeraX to predict protein-protein interaction/binding via Alphafold.

[Elaine Meng]

Hi William,
The "&" is wrong -- that symbol is for intersection, and the intersection between the two different models is nothing (none of the atoms are in both #1 and #2 at the same time).  I.e. to specify both models together try #1,2 instead:

alphafold predict #1,2

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#combinations>

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


> On Oct 5, 2022, at 6:44 AM, Tan, Wei Ren via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear Sir/Mdm,
>  
> Sorry to disturb you with regards to this matter, as I am unable to find any resources online, or on your YouTube channel to solve my problem. I am William, a medical student at King’s College London, UK, who have been using your software, ChimeraX, for the past few months to elucidate possible protein structure for one of the protein I am currently studying. I have faced a problem with predicting a protein interaction between a heterodimer (6z1n) and a novel protein that I am studying now. When I loaded both pdbs, I am unable to run the alphafold via the command:
>  
> alphafold predict #1&#2 (where #1 is 6z1n and #2 is my protein of interest)
>  
> Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead?
>  
> Thank you very much and sorry to disturb you!
>  
> Sincerely Yours,
> William Tan