I just looked at a previous thread by Dale Tronrud that explains this.
here it is:
Re: [ccp4bb] Fo-Fo Difference Map
Dale Tronrud
Mon, 03 May 2010 16:19:46 -0700
I've struggled with getting CCP4 to calculate Fo-Fo maps, since I
usually use other software. The tricks are that the data sets have to
be scaled to each other in reciprocal space, and the maps calculated
with the same cell constants (which will be a lie for at least one of
them). The procedure I used the last time I did this was
1) Create a master mtz file with F-holo, F-apo, Fc-apo, Phic-apo.
Use "Reflection Data Utilities", "Merge Mtz Files (Cad)". Don't
include the H, K, and L columns explicitly, despite the default.
2) Scale F-holo and F-apo. Use "Experimental Phasing", "Data
Preparation", "Scale and Analyse Data Sets", "Scale refinement using
Scaleit". Don't include anomalous differences unless your interest
is in changing anomalous scatterers. My notes indicate that Fhscal
works better but does not have anisotropic scaling. If your two data
sets do not differ anisotropically try Fhscal.
3) Enter Coot.
a) Load apo coordinates.
b) Open mtz, calculate map F-holo, phic-apo. This is done with
File.Open Mtz,mmCIF, fcf or phs...
c) Open mtz, calculate map F-apo, phic-apo
d) Calculate difference map. Extensions.Maps... . Make a
Difference Map...
e) Find difference map peaks.
The greater the difference in cell constants the greater the "noise" in
the map. I think the high resolution cutoff for the maps should be
2 A delta/(A+delta) where A is the cell edge with the largest change,
and delta is the amount of change (in Angstrom).
Basically a 1A change for a 100A edge would require a 2A resolution
limit. A 5A change would imply a 10A cutoff and a very boring map. I
would appreciate feedback on this procedure, if you find it hard to
understand or it doesn't work. Certainly the Phenix solution looks
simpler. Dale Tronrud
Replacing the Coot step by FFT works too.
vincent
Le 2/28/11 5:26 PM, Scott Pegan a écrit :
Trying to calculate a difference map from a dataset downloaded from
the RCSB and one I have. The following applies:
Object find the difference between two bound ligands of the same
structure in the same space group.
My following work path has been:
1) Convert mmCIF to mtz (RCSB data set)
2) Use CAD to combine them
3) Use FFT to generate the diff map
If I remember correctly, I think I am missing a scaling step
somewhere. Any thoughts?
Scott
--
Scott D. Pegan, Ph.D.
Assistant Professor
Chemistry & Biochemistry
University of Denver
Office: 303 871 2533
Fax: 303 871 2254
--
Vincent Chaptal
Institut de Biologie et Chimie des Protéines
Drug Resistance modulation and mechanism
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 16
