There are other programs that calculate electrostatic potential in a more quantitative manner (APBS, DelPhi, others), but they also all give a big 3D grid of many points and are normally used for visual analysis by coloring molecular surfaces. So usually people show the electrostatic effect of some mutation by side-by-side image comparison of the coloring of the mutated protein next to the coloring of the wild-type protein, which you could also do with ChimeraX. I don't know if you are trying to get some single number that tells you something, but that is not how "potential" exists -- it is a 3D spatially varying quantity. Elaine
On Nov 5, 2024, at 6:03 PM, mishra.ananya.163--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thank you very much for your clear and thorough response!
I appreciate your explanation that the electrostatic potential map in ChimeraX is best interpreted through surface coloring. Given this, I was wondering if you might recommend any other software that is more suitable for generating quantitative values for surface electrostatic potential within specified regions of a protein.
My project focuses on investigating how mutations in certain proteins affect their physical properties, including surface electrostatic potential. Access to such quantitative data would be incredibly valuable for my analysis.
Thank you again for your guidance and any advice you might have. Wishing you a wonderful day ahead!
Warm regards, Ananya _______________________________________________ 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/