VMD-L Mailing List

From: Roni Saiba (ronis_at_imsc.res.in)
Date: Tue Nov 21 2023 - 22:02:41 CST

Giving individual residues as selection will cause higher values of
SASA as surrounding residues are not considered. If you add the
"-restrict $restrict_sel", where $restrict_sel is the selction
hindering full solvent access to the residue you will get lower values.

Quoting Kevin Lin <klin665_at_uchicago.edu>:

> 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!