Thanks, Eric! It's good to bring people's attention to the problem of missing atoms when calculating electrostatic potential. I think we have some warnings in the Log when there are missing parts, but probably many people disregard them. Besides using AlphaFold, Chimera and ChimeraX also have a Dock Prep tool that can fill in truncated amino acid sidechains using a rotamer library, and a Modeller interface to fill in missing loops where the backbone is also missing. AlphaFold may do a better job on the exact placement, however; I have not done a detailed comparison. ChimeraX can also use a potential map from APBS, DelPhi, etc. for coloring, but the built-in calculation is just the simple Coulombic one. A LONG time ago I made a page informally discussing surface coloring with simple Coulombic ESP vs. maps calculated with the full Poisson-Boltzmann approach: <https://www.cgl.ucsf.edu/home/meng/grpmt/esp-compare/esp-compare.html> Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 6, 2024, at 1:52 PM, Eric Martz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
You may be interested in seeing this comparison of electrostatic potential maps generated by ChimeraX, iCn3D, and PyMOL:
https://proteopedia.org/wiki/index.php/Electrostatic_potential_maps and the related topic
https://proteopedia.org/wiki/index.php/Missing_residues_and_incomplete_sidec... which suggests using AlphaFold models for electrostatic potential maps when the empirical model lacks sidechains of charged amino acids on its surface (very common).
-Eric Martz http://martz.molviz.org _______________________________________________ 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/