[Chimera-users] create automatically all alternative protonation states of protein

Thomas Evangelidis tevang3 at gmail.com
Tue Mar 19 07:59:14 PDT 2019


I want to write a script that will read a protein-ligand complex, will find
all residues with alternative protonation states within a radius from the
ligand, and will write to separate pdb files all combinations of
alternative protonations or the protein's binding site. Is this possible in
Chimera? I saw at the documentation of addh command that there is not a way
to specify explicitly which residues to protonate and how (e.g. I can
protonate all ASP to ASH but not ASP34 to ASH34 and keep ASP52 as it is).

Thanks in advance.



Dr Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
Brno, Czech Republic

email: tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/
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