Hello ChimeraX Users,

I would like to analyze protein/nucleic acid complexes from the PDB by comparing the protein/nucleic acid chain interactions in each. Ideally I would like to know:

The number of interactions < 4.0 A that the nucleic acid makes with neighboring protein chains
If possible, output a list of those interactions to a text file
Even better, generate a 2D interaction map

I tried contacts (#1/A | #1/B) #1/C cutoff 4.0 saveFile contacts_ABC.txt for the first bullet (with a few permutations when it didn't work), but received the error "expected a keyword."

Has anyone successfully determined something like this in ChimeraX?

Thanks for the input!

Shawn R

Rutgers University