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Man page of X-GEN
X-GEN
Section: X-GEN Commands (1)
Updated: April 2005
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NAME
X-GEN - scalek
SYNOPSIS
scalek
[-abdefghjlknrtvwx] [-c<val> . . . ]
DESCRIPTION
"scalek" is the X-GEN scaling 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.
- -a
-
Use all observations, even those coming from scaling
groups for which non input scale factor was provided. This is
default ONLY if no scale-input file is specified.
- -b
-
Scale using a nonlinear, Simplex algorithm with the scale
factors and (if requested) spherical harmonic parameters acting as
the adjustable parameters in the Simplex algorithm. If this is not
specified the ordinary diagonal linear least-squares approach is
taken. The Simplex scaling is MUCH slower than the diagonal linear
least-squares, and should not be used on large datasets unless you
are willing to wait for ten minutes or more.
- -d
-
Scale using a spherical harmonic expansion in the
diffraction vectors of the input observations. A total of ten
parameters per data run will be calculated, along with the
conventional scaling parameters that are calculated on a finer grid.
- -e
-
Scale using a spherical harmonic expansion in the
exit-beam vectors of the input observations. A total of nine
parameters per data run will be calculated, along with the
conventional scaling parameters that are calculated on a finer grid.
- -f
-
The weight factor used in scaling is the inverse of the
variance of each observation. Normally the variance is computed
as the sum of the observation's own variance and a term
proportional to the square of the Rsym of the scaling group:
this term represents the variance in the scale factor itself.
If this Boolean is on, the scale-factor variance term is set to
zero; this has the effect of up-weighting contributions from
poorly-determined scaling groups but it leaves the scaling
problem somewhat stabler.
- -g
-
Scale using a spherical harmonic expansion in the
diffraction vectors of the input observations, but with the term
that would multiply (sx^2 + sy^2 + sz^2) set to zero.
- -h
-
Start the scaling process by performing diagonal linear
least-squares determinations of the scaling parameters.
If this approach reaches a stage where the overall R value
is going up rather than down, it will switch to a Simplex
nonlinear optimization. If this switch and -b are both
specified, this one takes precedence.
- -j
-
Stop cycling once the scaling functions converge to within
the convergence criterion. This is the default, and is the
converse of the "-k" flag.
- -k
-
Continue cycling for as many cycles as the user has requested,
even if the scaling parameters and symmetry R values have converged.
- -l
-
Do _not_ perform spherical-harmonic scaling in any of the
variants available in this package. This is the default.
- -n
-
Treat Bijvoet-related reflections (e.g., (6,4,3) and
(-6,-4,-3)) as independent in calculating scaling factors. By
default, Bijvoet-related reflections are treated as the same
reflection.
- -r
-
Do not perform ordinary spherical-harmonic scaling.
This is the default.
- -t
-
Merge the top and bottom of the detector for scale-factor
determinations. If we do not specify this option, the top and
bottom of the detector are treated as separate scaling groups.
- -u
-
Do not merge the top and bottom of the detector for
scale-factor determinations; instead, treat the top and bottom as
separate scaling groups. This is the default.
- -v
-
If this Boolean is on, a moderate amount of additional
diagnostics beyond the default will be written to the XLOG log file
and stdout.
- -w
-
Determine the initial scale factors from a constructed
Wilson-plot rather than setting them to 1.
- -x
-
Do not switch from linear scaling to nonlinear Simplex
scaling, even if the R-factor starts to creep up. This option is
the default, and is the converse of the /-h/ option.
- -c<val>
-
This specifies the maximum number of cycles to be
-
performed. Cycling will quit early if the scaling converges
unless the "keep cycling" flag is on. Default value: 10.
- -i<val>
-
This specifies the minimum value of the mean intensity to
-
be used in scaling. Default value: 0.
- -o<val>
-
This specifies the minimum number of observations per
-
reflection required for inclusion in the scaling. Default value: 2.
- -p<val>
-
This specifies the number of parameters calculated per
-
ordinary scaling group. Legal values are 1, 2, and 3. The first
parameter is always a linear scale factor; the second and third
are terms multiplied by sin(theta) squared and sin(theta),
respectively. Default value: 1.
- -q<val>
-
This specifies 10000 times the convergence criterion. Thus
-
if you specify this value as 10, then scaling will be defined to
have converged if the largest scale-factor change since the
previous cycle is (10/10000) = 0.0001. Default value: 100.
- -s<val>
-
This specifies the fraction of the computed changes in the
-
scaling parameters that will actually be applied at the end of
each scaling cycle. Thus if this is specified as 1, the full
computed change will be applied; if it is specified as 0.05, only
0.05 * the computed change will actually be applied to the scale
factors. Default value: 1.
EXAMPLES
- scalek
-
Perform ten cycles of scaling using all reflections with
two or more observations, for which the mean intensity is
non-negative, using one parameter per scaling group and
exiting if the scale factors converge to within 0.0001:
- scalek -ktghnp1
-
Scale using spherical harmonic expansions in the
-
diffraction vectors and switching to a Simplex optimization
if the linear least-squares approach becomes unstable,
merging the top and bottom halves of the detector together
but separating Friedel mates during scaling:
REPORTING BUGS
Report bugs to Andy Howard at howard@iit.edu or 312-567-5881.
COPYRIGHT
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
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- EXAMPLES
-
- REPORTING BUGS
-
- COPYRIGHT
-
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