Thx Elaine for the reassurance about the contacts output. I will send me questions to via the question portal next time.
Phil ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, September 27, 2022 5:35 PM To: McClean, Phillip phillip.mcclean@ndsu.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: alphafold contacts output
On Sep 27, 2022, at 1:59 PM, McClean, Phillip phillip.mcclean@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@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