[chimerax-users] alphafold contacts output

[Elaine Meng]

> On Sep 27, 2022, at 1:59 PM, McClean, Phillip <phillip.mcclean at ndsu.edu> wrote:
> 
> Hi Elaine, 
> 
> I am using output data from alphafold2 multimer as provided by Colabfold.  Following the video (https://www.youtube.com/watch?v=TMcjEecFHaI&t=6s), I use the following command:
> 
> 
> alphafold contacts /b to /c distance 8
> 
> For my complex, the links at the distance are all blue (good results).  What is confusing is that the distance of some of the contacts are greater than 8 angstroms.  Those distances are between backbone carbon atoms, I assume.  The fact that the command asks for amino acid pairs that are less than 8 angstroms apart suggest that other atoms than those in the backbone are less than 8 angstroms.  Is my conclusion correct.
> 
> Thanks as always for the advise.
> 
> Phil

Hi Phil,
Yes, your conclusion is correct - the distance cutoff applies to any atom in the residue within any atom in the other residue, whereas the pseudobond is drawn between alpha-carbons, as mentioned here:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts>

We generally recommend sending questions to chimerax-users at cgl.ucsf.edu (CC'd here) since many heads are better than my one, unless you are including some data that needs to remain private.

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