Dear Chang Woon, There is no choice of different pH values when adding hydrogens in ChimeraX. You would need to use some other program or web server. Maybe this web server that runs PDB2PQR with PROPKA (predicts pkas of protein residues) and your specified pH, although I don't know if it gives you a PDB file output. Since it's the first part of an APBS calculation it might not give you the intermediate files. You could try it: <https://server.poissonboltzmann.org/pdb2pqr> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Dec 18, 2023, at 6:35 AM, Chang Jang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX help,

I am using ChimeraX 1.6.1. Would anyone know how to "set or change and check" a pH level of a protein or a system from the software?

Thanks, Chang Woon