[phenixbb] anomalous difference map
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).
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
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
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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