[phenixbb] Protonation of a symmetry-related His in Zn coordination sphere

Pavel Afonine pafonine at lbl.gov
Fri Nov 16 05:19:40 PST 2018

Hi Priit,

> I have a structure in which one of the His-residues of a Zn coordination sphere is from a symmetry-related protein chain. I specified the symmetry in an edits file so the coordination sphere is nice and plays well in refinement.

glad to hear it works!

> I now added hydrogens to the model, but the His from the other chain does not get protonated correctly.

Sounds like a bug in Reduce or ReadySet. Can you please send us inputs, 

> I assume reduce doesn’t detect the presence of the symmetry-related Zn.


> It protonates NE, while that is the atom that interacts with Zn, but ND should be protonated instead. What would be the best way to fix this?

Send us inputs and we might be able to help you keep going.

> And another question on the same matter: is it possible to specify a LINK in PDB between these atoms?

Phenix doesn't care about LINKs as they are one of least reliable and 
least validated records in PDB.
Perhaps you can do it manually, but don't expect the program respect them.


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