Phenix Refine Place Elemental Ions
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 ions? Thanks ahead.
Hello,
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 or 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. Pavel
participants (2)
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Pavel Afonine
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Xiao Lei