Hi, All

Is it possible that I have anomalous and LLG peak, but I have no difference density peak? In this case, is that because the model I have is not good enough or the diffraction data at this site of the model is missing?

Thanks!

Charles 

On Mon, Sep 8, 2014 at 1:23 PM, Pavel Afonine <pafonine@lbl.gov> wrote:

On Mon, Sep 8, 2014 at 9:58 AM, CPMAS Chen <cpmasmit@gmail.com> wrote:

A difference map is used to identify whether there is anything not-modeled, say some ligands, ions. Then when I generate anomalous difference map, I should not put the ligand(which contains Br) in the model, right? Or in phenix, after I put the Br-ligand in the model, I should not see the anomalous difference density at the site, right?

An "anomalous difference map" is a map of the anomalous differences DANO (Fobs(+) - Fobs(-)).  It's independent of  Fcalc, so it doesn't matter if you put the ligand in or not. 

This is not quite an accurate statement. To calculate a Fourier map one requires amplitudes and phases. (Fobs(+) - Fobs(-)) are the amplitudes for the anomalous difference map. The phases come from Fcalc (actually from Fmodel), one way or another.

Pavel

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Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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