Dear Elaine,

Dock Prep: Very nice! I ran it on 1bl8 and confirmed that it filled in missing sidechain atoms on 20 residues, and added hydrogens. I'll add mention of it in my articles linked below. Thanks for calling it to my attention!

Also I appreciate your 2009 Coulombic coloring comparison. I'll also link that.

-Eric

On Friday, December 6, 2024 at 09:23:19 PM EST, Elaine Meng <meng@cgl.ucsf.edu> wrote:


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_sidechains
> 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
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