[Chimera-users] Add Hydrogens - non standard residue - protonation state

Subha Kalyaanamoorthy kalyaana at ualberta.ca
Thu Aug 18 15:22:22 PDT 2016

Hi There,

Can anybody please suggest me how to use 'setattr' (or any other function)
to assign a protonation state for an atom in a non-standard residue.

I have a ligand and I am using a python script to add hydrogens and charge
to the ligand molecule using chimera no-gui. I see that chimera adds an
extra hydrogen to a nitrogen atom in the ligand and assigns a charge of +1
to the molecule. Removing this hydrogen using GUI is simple but not
practical for large set of molecules. So, it would be helpful if somebody
suggest me a command-line to set specific protonation states for atoms (in
non-standard residue).

Thanks and Best Regards,
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