Hi Jianghai, As I understand it, PISA ignores the explicit hydrogens (if any) and uses united-atom radii for the heavy atoms when calculating solvent-accessible surface areas and thermodynamic parameters. It says a little bit about that here, although they use the term "enhanced" rather than "united-atom": <https://www.ebi.ac.uk/pdbe/pisa/pi_tips.html> Best, Elaine
On Aug 28, 2026, at 11:39 AM, jianghai.zhu--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks, Elaine, for clarifying some of the details.
I understand that the SASA difference between calculations with and without hydrogens is small. And it is true that many people only care about comparisons. However, technically speaking, the surface area calculated without hydrogens is NOT the true "solvent accessible area". I don't think there is a name for it. I do appreciate that in PISA, it always compensates for hydrogens when no explicit hydrogens are present in the structure; therefore, one gets the same answer with or without hydrogens in the pdb file. No confusion there. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/