[phenixbb] Phenix Refine Place Elemental Ions

Xiao Lei xiaoleiusc at gmail.com
Sat Jan 30 09:11:25 PST 2016

Hi Phenixbb members,

I have a dataset of 2.7A resolution and solved by molecular replacement.
Now I am refining my structure using Phenix Refine (Fedora; Version
1.10.1). I'd like to try "place elemental ions" option in the GUI.

I read the Phenix refine manual and it says: " to enable this option,
simply enter a list of the elements to search for; this will also enable
solvent picking as a first step. This option is not recommended if you have
data worse than 3.0A resolution, and works best with anomalous data."

I have questions about this: 1. In my crystallization condition I have 80
mM CaCl2 and 5mM MgCl2. How should I enter the ions to search for into the
GUI? Should I enter "Ca; Mg" or "Ca and Mg" or "Calcium and Magnesium" ? I
wonder how the Phenix Refine can really differentiate Ca or Mg in the map.

2. Phenix Refine says the place elemental ion option works best with
anomalous data, does the anomalous completeness needs to be over 80% to
consider anomalous data? Tough I did not do MIR or Selenium which produces
anomalous signals for phase,  Phenix Xtriage  shows my data has anomalous
completeness around 70% (I even do not know what caused the anomalous
signal in my dataset).  Does this help Phenix Refine to locate elemental

Thanks ahead.
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