[phenixbb] Phenix Refine Place Elemental Ions

Pavel Afonine pafonine at lbl.gov
Sat Jan 30 09:25:29 PST 2016


> 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 would try
Ca, Mg
Ca Mg
and then check log file to see if that was recognized

> I wonder how the Phenix Refine can really differentiate Ca or Mg in 
> the map.

It will need anomalous signal from anomalous data.

> 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?

If it doesn't say this then this is probably not a hard requirement.

>   Does this help Phenix Refine to locate elemental ions?

If your data is truly anomalous and anomalous signal is present then it 
should help refinement to locate ions.

I would just try and see what happens.


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