[chimerax-users] Use values printed from Log inside a script (e.g. RMSD)

[Steven Truong]

Dear ChimeraX Admins,

I was hoping to use the “rmsd” command in ChimeraX to measure distances between models within a .py script. 

Is there a way to use the output of “rmsd” (or generally any other output in Log) within the script? For example, if rmsd > 2 Angstroms, then do X. 

Ultimately, I am attempting to align chains between models. Because my protein is asymmetric, chain A on Model #1 might actually be chain B on Model #2. I was hoping to use “rmsd” to map one chain to the other. Is it a better idea to do this in another program and re-write chain IDs in the .PDB file? If so, what other program would be better at making RMSD calculations between .PDB chains?

Thank you,
Steven Truong
Cambridge University