I am following this topic.

http://www.phenix-online.org/pipermail/phenixbb/2014-April/020622.html.

Here is the point I am not clear. If I am using phenix.refine to generate LLG map, how do I pick the anomalous group since I have not placed them in the model yet? By the way, when I choose ion_placement and specify Br, the result comes with no Br.

Let me make my situation clear first.

I want to find whether the Br-containing ligand is seen in my protein which I have a high resolution structure available.

I have data collected at Br wavelength, peak or higher position. Phenix.xtriage reported that the anomalous signal is present to about 4A. However, both AutoSol or MR-SAD cannot identify the Br position. Simply say, AutoSol or MR-SAD can not generate any solution. Well, of course, the simple answer would be that there is no such ligand cocrystallized. 

Anyway, I am trying to see if the anomalous difference map or LLG(generated by phenix.maps, this would be the initial one I assume) can tell me anything more useful.

So, my question on this topic would be what is a better way you guys would recommend to identify these Br-ligands? By the way, I did have the native datasets for the same protein with ligand.

Thanks!

Charles 

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Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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