Man page of X-GEN
Section: X-GEN Commands (1)
Updated: April 2005
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X-GEN - scalem
"scalem" is the one-step X-GEN post-processing functionality. It reads in the
output of "reduce" or "mrmerge", i.e. a MULTIREF file containing multiple
observations of the reflections in a set of diffraction data, and determines
scaling functions that minimize the squared differences among the intensities
of the symmetry-related observations. The scaling and outlier-rejection
steps in this process are carried out in several steps.
In the first step, the scaling is a simple linear least-squares minimization
employing one scaling parameter per scaling group. It then performs an
outlier rejection on the scaled data. Subsequently it scales the data using
a somewhat more sophisticated scaling algorithm, in which the single-parameter
scale parameters are combined with one set of spherical-harmonic parameters
for each data run. It then does another round of outlier rejection, restoring
to the list of possibly included observations the observations that had been
deleted on the previous pass. A third cycle of scaling is then performed with
spherical harmonics and with incorporation of nonlinear scaling algorithms if
the linear algorithm becomes unstable. If the redundancy in the data is
sufficiently high, a fourth round of scaling is performed with the
After these rounds of scaling, a set of statistical indicia are computed
that characterize the data, and the spacegroup of the data is revalidated.
At that point the scaled data have been massaged adequately. Therefore the
data are written out in six different ASCII formats:
1. the traditional X-GEN MULIST format;
2. a format suitable for input to SHELX and XPREP;
3. a format suitable for input to CNS;
4. a format suitable for input to XPLOR v.3.1.
5. a format compatible with the output.sca format from SCALEPACK,
with Friedel-mates kept separate.
6. a format compatible with the output.sca format from SCALEPACK,
with Friedel-mates merged.
Accordingly the standard behavior of scalem is equivalent to running
running the individual X-GEN post-processing programs "scalek",
"reject", "stats", "spaceg", and "makemu" in the following sequence:
1. scalek -ktp1
2. reject -bf0.015
3. scalek -ktgp1
4. reject -bf0.015
5. scalek -ktghp1
6. scalek -ktghnp1
7. stats -n
9. makemu -a
If the redundancy is low, the sixth step is removed, and the
and the "stats" step will not have the -n flag set.
Most of these Booleans and switches for "scalem" correspond to options in
the individual X-GEN post-processing programs, and the descriptions in the
"parent" documents are in some cases more complete than those given here.
If specified, "scalem" will open a file with environment
variable name CHECKREFL each time that it does an outlier
rejection and will write out a moderately detailed log of
how the rejection is done to that file. This is equivalent
to the -c flag to "reject".
In the final output files, write out structure amplitudes
rather than intensities. This is the equivalent of the -f
flag to "makemu".
During outlier rejection, if an observation is flagged for
a reflection with exactly two observation, then delete both
observations. This is the equivalent of the -k flag in "reject".
If specified, "scalem" will only write out multiply-observed
reflections. This is the equivalent of the -m flag to "makemu".
If specified, "scalem" will set the intensities of reflections
for which <I> is less than zero to zero just before it writes
them out. This is the equivalent of the -n flag to "makemu".
If specified, "scalem" will refrain from writing out a list
of missing reflections. Otherwise it will print out a list of all
reflections that are not contained in the input MULTIREF but which
lie within the resolution range associated with that MULTIREF.
This is equivalent to the -o option to "makemu".
If specified, "scalem" will preserve the sin(theta)
dependence of the input scale factors rather than correcting
for it. This is equivalent to the -p option to "makemu".
During scaling, merge the top and bottom of the detector
together rather than calculating scale factors for those two
halves separately. This is equivalent to the -t option to "scalek".
If specified, "scalem" will output the ASCII results in
sin(theta)/lambda order rather than in hkl order. This is
equivalent to the -t option to "makemu".
If specified, "scalem" will compute the variances of the
merged reflections according to an alternate approach
described in the "makemu" documentation. This option is
equivalent to the "-v" option to "makemu".
If specified, "scalem" will print out substantially more
information to the log file during each stage of the post-
processing effort than would otherwise happen. This is equivalent
to the "-v" flags to "scalek", "reject", "stats", and "spaceg".
If specified, the initial scaling effort will be based on a
Wilson-statistics analysis of the input data rather than by
setting the starting scale factors to 1. This is equivalent
to the -w flag to "scalek".
During outlier rejection, inflate the observation sigmas by a
machine-error term. This is equivalent to the -m flag in "reject".
This specifies the minimum average redundancy for the
dataset as a whole, below which the Friedel-separated scaling
step will be skipped. The default value of <val> is 4.
Specifies the number of resolution bins into which the
data will be broken for calculations of completeness and
redundancy and for shell R-factor calculations during the
statistics calculations. This is equivalent to the "-b" flag to
"stats". The default is 10 for datasets with more than 27000
observations; it ranges between 4 and 9 for smaller datasets.
During outlier rejection, we will attempt to delete a
fraction of the data equal to <val>. This is equivalent to the
"-f" flag to "reject". Default value: 0.015.
This specifies the minimum <I> value for a reflection such
that it can be included in the scaling process. It is therefore
equivalent to the "-i" option in "scalek".
This specifies the value of |I - <I>| / sigma used during
outlier rejection to determine whether an observation should be
considered for deletion. It is therefore equivalent to the "-q<val>"
option to "reject".
This specifies an overall scale factor for the ASCII
output files. It is thus equivalent to the /-s/ option to makemu.
Scale, reject outliers, and produce ASCII output
from a MULTIREF.
- scalem -tvg0.01
Perform post-processing with the ASCII output in
sin(theta)/lambda order, verbose log files, deleting
roughly 1% of the data during outlier-rejection.
Report bugs to Andy Howard at email@example.com or 312-567-5881.
Copyright © 2002, Illinois Institute of Technology.
See the file 'LICENSE' for information on usage and redistribution
of this file, and for a DISCLAIMER OF ALL WARRANTIES
- REPORTING BUGS
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Time: 02:08:09 GMT, October 03, 2005