[phenixbb] anomalous difference map

Kris Tesh kris.tesh at att.net
Mon Mar 28 07:48:57 PDT 2011

To follow up a little more thoroughly, the fluorescence scan indicates presence 
of the element, but not position.  I would guess that your solution about your 
crystal contains the heavy atom or that the heavy atom is weakly bound in 
numberous non-identical positions on the protein.
A way to check oversome this is to back-soak your crystal to remove unbound 
heavy atom.  This can be done very quick to get replace the solution or longer 
to try to remove the weakly bound sites.  The only issue is the removal of the 
sites you want...so, you will need to be patient and set up trials with 
different back-soak times (usually done by adding heavy atom to drop, removing 
part of liquor, replacing non-metal liquor, mounting several crystals from the 
drop, noting the time of the back-soak).
Good luck,
 Kris F. Tesh, Ph. D.
Department of Biology and Biochemistry
University of Houston 

From: Jason <phenix.upitt at gmail.com>
To: phenixbb at phenix-online.org
Sent: Fri, March 25, 2011 11:20:23 PM
Subject: [phenixbb] anomalous difference map

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 phenix.refine
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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