For nonstandard residues such as most ligands, you would have to manually modify atom type(s) with either the Build Structure tool or the "setattr" command. Attribute name is "idatm_type", see <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#atom> <https://rbvi.ucsf.edu/chimerax/docs/user/atomtypes.html> Elaine
On Jan 25, 2026, at 9:04 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, See the Add Hydrogens (or addh command) help page. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/addhydrogens.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/addh.html>
No it does not calculate pKa shifts. It gives each functional group the standard protonation for that group and after that, looks at what H-bonds are geometrically possible given the nearby functional groups. The only protonation states that might be guessed from using other nearby atoms (metals etc.) are for cysteine and histidine sidechains.
If you want to force a different protonation state than what you get from ChimeraX defaults, you have to use a more complicated method by manually changing the residue name and/or atom types.
See the name options in the above manual pages about how to specify protonation states by using residue names HID, HIE, HIP, ASH, GLH, CYM.
I hope this helps, 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 Jan 24, 2026, at 7:34 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users!
I have a question about the protonation of ligands in the complex. When I protonate only a ligand (using addh :LIG) I see in the log that it takes into account the hydrogen bonds.
Does it mean that it defines the protonation state of each titratable group based on its local chemical environment of binding pocket? If so, is it possible to manually define the total charge of the ligand (and protonate it according to it)?
Many thanks in advance!
Enrico _______________________________________________ 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/
_______________________________________________ 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/