[phenixbb] Error with Phenix refine after adding ligand

Oleg Sobolev osobolev at lbl.gov
Tue Jan 23 10:41:24 PST 2018

Hi Main-Chee,

> The ligand that I am adding is a malonate, and the 3-letter chemical code
> is MLI. I add the ligand using Coot and it fit perfectly into the electron
> density map.

I suspect this is when you ended up with a model with two oxygens sitting
on top of each other. Since you already identified oxygens in question it
would be easy to check if Coot introduced them before you run any Phenix
program. In this case I would address this question to Coot developers.

Best regards,
Oleg Sobolev.
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