[phenixbb] anomalous difference map

Jason phenix.upitt at gmail.com
Fri Mar 25 21:20:23 PDT 2011

Hello Everyone,

I have an old question about how to create anomalous difference map.

1) Synchrotron Fluorescence scan indicates the heavy atom definitely
presents in my protein (my control is a second protein with the same ligand
showed no absorbance spectrum)
2) xds processed mtz file
3) Data resolution ~ 3 angstron
3) molecular replacement solved apo structure protein.pdb using
4) phenix.maps to generate anomalous map (phenix.refine will also generate
it, but let's leave it aside for the moment)


When I load the mtz file to phenix.maps GUI, the mtz label pulldown menu
indicates 4 possible choices for the column to use:(1) IMEAN, SIGIMEAN
(2) I(+),  sigI(+),  I(-), sigI(-) merged (3) F(+), sigF(+), F(-), sigF(-)
merged (4) F, sigF, Dano SigDano. I have tried the choices of (2) (3) and
(4). However, there is barely any anomalous signal at 4sigma, which makes me
wondering if something is not right. The first thing coming to my mind is
the mtz labels: I(+),  sigI(+),  I(-), sigI(-) merged. What does merged
mean? Could this be the reason? Other issues that could causing the trouble?
Thank you all.

Structural Biology Department
University of Pittsburgh
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