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
On 05/03/10 15:27, Yi-Liang Liu wrote:
> Hi Everyone,
>
> I've checked the previous posts about how to generate the difference map
> from two crystals with different cell constants. I tried MAPMAN to
> generate this map but I never got luck on this. It turned out to show
> "Maps have different cell constants" every time. Does anyone know what
> is the step-by-step process to generate such kind of map. Thanks.
>
> Best,
>
> Lucas
