VMD-L Mailing List

From: Kevin Lin (klin665_at_uchicago.edu)
Date: Tue Nov 21 2023 - 18:08:58 CST

Hello,

I currently have a simulation of a protein in a waterbox. I'm looking to identify residues on the protein surface throughout the simulation using the measure sasa command. I am aware that the sasa command returns a surface area value for each selection I input it, which I'm currently giving residues. So far, I'm seeing values between 300 and up to over 1000. Is there a suggested threshold for a sasa cutoff value to identify which residues are on the surface, or is there a better way to do this?

Any tips would be greatly appreciated!

Thanks!