green peaks around your supposed Mg's mean that something heavier than Mg is in fact presented. Try Ca2+ ? Oleg -----Original Message----- From: "Almudena Ponce Salvatierra" Sent: Thursday, August 4, 2016 10:00am To: "[email protected]" , "[email protected]" Subject: [phenixbb] Mg is driving me crazy _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] all, I am refining a structure that showed two positive peaks larger than 8 sigma. I assigned them as Mg ions, since I have them in the crystallization condition and also because it make sense, according to where they are located. However when I refine there's still all this green blob around the already properly placed Mg ions. I don't know why, they don't show large thermal factors or anything suspicious... I'm refining individual sites, individual adps, and TLS groups. The resolution I am talking about is 2.5 A. Any thoughts on this? Thank you very much Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany