[phenixbb] following on the anomalous map

CPMAS Chen cpmasmit at gmail.com
Sun Aug 24 06:46:01 PDT 2014

Hi, All Phenix users,

I am following this topic.


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.





Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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