xmerge
NAME
xmerge - Merge and scale two data files.
USAGE
xmerge data1.fin data2.fin
DESCRIPTION
data2.fin is merged and scaled to data1.fin. The data in
file 2 is scaled to match that in file1. The data in
data1.fin is referred to as f1 and that in data2.fin is f2.
crystal info needed: cell.
METHOD
The data is scaled into n bins based on sin(theta)/lambda2.
Two scaling methods are available: single and anisotropic.
In single scaling, a single parameter is used to scale the
data in each bin such that
sum(f1)=sum(f2)*scale.
If Bijovet pairs exist, they are averaged for scaling pur-
poses. In anisotropic scaling first single parameter scaling
is done and then a 6 parameter scaling such that the scaling
parameter is a function of the three crystal indices. This
helps minimize errors due to differential absorption, etc.
The formula used for the scale factor s at each h,k,l is:
s = h*h*a11 + k*k*a22 + l*l*a33 + h*k*a12 + h*l*a13 + k*l*a23
where a is found by a least-squares fitting procedure. The
fitting procedure may fail if too few data are used. In
this case you have two choices: decrease the number of bins
to put more data in each bin or use single parameter scal-
ing.
OPERATION
Fin File 1
The "standard" data set, as the second fin file is
scaled to this one. Normally use your best native data
here.
Fin File 2
The fine file containing the data to be scaled to fin
file 1. Normally derivative or mutant data.
Output File
The merged and scaled data. The name should indicate
which data was used to make this file. (See example
below.)
Output type
You can output your data in either fin or df format.
fin format merges f1 and f2 (Bijovet's = f+ and f-) in
the input fin file so that the output fin file also has
only two fields. All fields are preserved in a df file
so that Bijvoet information is preserved for both input
files. Since df files can always be turned into a fin
file with xdftofin, this is the more useful of the two
options.
Output
Reflections in common means that reflection must be in
both file1 and file2. All reflections are all of those
in file 1 and those in common in file2. If a reflec-
tion is in file2 but not in file 1 it is not used or
output.
Number of bins
The data is divided into bins based on
sin(theta)/lambda squared. This slider sets the number
of bins with 10 as the default. Not that dividing by
the square does not put equal numbers of reflections
into the bins as would sin(theta)/lambda cubed, but
provides a better distribution in reciprocal space. If
there are too few reflections in a bin the number of
bins should be decreased to put more reflections in
each bin. For anisotropic scaling about 500 reflec-
tions per bin are good with 50 being a good minimum.
Too many bins will decrease the signal by scaling away
any differences, and too few may not adequately scale
the two data sets. Note: On sliders, if you edit the
number with the keyboard, be sure to hit <CR> to regis-
ter the new value.
Sigma Cut
The data is excluded from the scaling equations if its
amplitude is less than sigma cut times the sigma of
the amplitude. Usually makes little difference
because these data are weak anyway.
Scaling type
Sets the scaling method used as explained above.
Anisotropic scaling is actually single scaling followed
by anisotropic scaling. If there are too few reflec-
tions for anisotropic scaling you will get errors. In
this case decrease the number of bins or use single
scaling.
Graph
Two results are graphed in the graphics window: delta,
the abs(f1 - s*f2) ( dashed line) and the R-factor
abs(f1 -f2*s)/f1 (solid line) for each shell. For a
heavy atom derivative the delta should start high and
decrease with resolution. If it starts to increase,
this may mean that the derivative is non-isomorphous
past this resolution. The R-factor should smoothly
change with each bin. If not then use fewer bins.
History File
The history file contains in addition to the normal
information a list of the scale, r-factor, abs delta
for each resolution bin.
EXAMPLES
To scale a native data set to a derivative data set:
xmerge ccpnat4.fin ccppt1.fin ccpnat4pt1.df
You can use this file as input to xfft to make a patterson
map which can be contoured with xcontur.
Advanced Example
In some instances you may wish to scale data in a single fin
file to itself. For example, if you wish to scale Bijvoet
pairs. In this case, you must first split the file and then
remerge and scale. For example, to scale unscaled.fin to
scaled.fin ( remember a fin file is records of
h,k,l,f+,s(f+),f-,s(f-)) you can use the following commands:
awk '{print $1,$2,$3,$4,$5,$4,$5}' unscaled.fin > unscaled_fp.fin
awk '{print $1,$2,$3,$6,$7,$6,$7}' unscaled.fin > unscaled_fm.fin
xmerge unscaled_fp.fin unscaled_fm.fin scaled.fin
VERSION
Release 3.2 of XtalView
SEE ALSO
xtalview(1), xcontur(1), xfft(1)