[phenixbb] Mg is driving me crazy

luzuok luzuokun at 126.com
Mon Aug 8 19:38:37 PDT 2016

Dear Almudena,

Have you placed water molecules around the magnesium? It's a coordination complex.



Lu Zuokun, Ph.D. Candidate
College of Life Science, Nankai University

在 2016-08-04 22:00:35,"Almudena Ponce Salvatierra" <maps.farma at gmail.com> 写道:

Dear 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 Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
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