makescalein: automatically scale multiple sets of data
makescalein ("make-scale-in") makes an input file for scalepack based on
a set of ".x" files.
In the directory containing the ".x" files you want to scale together, type
makescalein [options] [file name pattern]
This will:
- Scan all ".x" files (if any are given on the command line, only those
will be read), and classify them into data sets.
- Read the first ".x" file to get default resolution limits and symmetry.
If the GUI is enabled (the default) it will then pop up a dialog
allowing you to change some major parameters of the scalepack program.
On clicking "OK", the program will create a scalepack input file. The
default name for that file is "scale_all.in".
Once the input file is prepared, "mkscalein" will run scalepack (once or more
than once, based on the parameters), and show a report of the results.
"mkscalein" can be asked not to run scalepack (i.e. only prepare the
input files) by specifying the command line option "norun".
If you prefer "theta angles" over "resolutions", please see the
resomode configuration variable.
Options
- norun
-
Inhibits the actual scalepack run, terminating the program right after the
scalepack input file has been written
- nogui or gui
-
Switches the GUI off or on. Default is on. If the gui mode is switched
off, no windows will be popped up, and all options are read from the
command line only.
- prefix=xxx
-
Sets the filename prefix. Default "scale_all"
- spacegroup=xxx
-
Sets the space group for merging.
- system=xxx
-
Sets the crystal system for unit cell refinement.
- scalerestrain=number
-
Sets the restraint strength between scale factors of successive
frames. This should be a number that is approximately the expected
fractional change of the scale factor. Default is 0.002, configurable
via the configuration file.
- dircos or nodircos
-
Switches direction cosines on or off. Default is off. If direction cosines
are requested, no scaling and no merging is performed.
- merge or nomerge
-
Switches merging of data on or off. Default is on. If direction cosines
are requested, no scaling and no merging is performed and this switch has
no effect. Please note that scalepack uses a special weighting scheme that
may result in slightly better data than plain merging. Use the "nomerge"
flag therefore only with care.
- resolution=number,number
-
Selects the low- and high-resolution cutoff in Angstroms.
- anomalous or noanomalous
-
If "anomalous" Friedel pairs are output separately.
If "noanomalous" Friedel pairs will be merged.
- errormodel or noerrormodel
-
If "errormodel" is specified, the error model will be refined in a final cycle.
This should only be done if there are no unknown sources of differences
in intensity (e.g. significant absorption). The default is "noerrormodel".
- defaultscale=number
-
Sets the default factor with which all reflection intensities should be scaled.
The default value is 10.0. If reflections with sigma=0 are produced, this
number should be reduced. This parameter can also be used to scale datasets
with different exposure times together.
Bugs
Please note that most "scalepack" versions can only scale 10 sets of
images at a time. This limitation is not present if scaling is
inhibited (using "outside scaling" and direction cosines).
