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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 - reduce
SYNOPSIS
reduce
[-behijkoqrsuvxz] [-a<val> ...] [runno] [minsi] [resmi] [resmax]
DESCRIPTION
"reduce" converts the output of "integrate" into a more compact
form, and can be used to filter out possibly faulty reflections.
The initial output format of integrate produces 80 bytes of
information per observation, and the output format from reduce
merges that down to 16 bytes of information per unique reflection
plus 16 additional bytes for each individual observation. Data
can be excluded from output based on agreement between
profile-fitted and summed intensities, the actual I/sigma values,
resolution range, consistency with the space-group
symmetries, and other factors.
- -b
-
Use the "best" I/sigma value; that is, look at the
profile-fitted and summation intensities for each reflection and
write out whichever one has the larger I/sigma. The resulting
MULTIREF will be partially profile-fitted, partially summed.
- -e
-
Kabsch output, i.e. choose the integration results based on
geometrical rebinning into diffraction vector space
(alpha,beta,gamma) rather than using the direct experimental
space (X,Y,omega).
- -h
-
Replace the current polarization correction with that
associated with a fully-polarized input X-ray beam, e.g. from a
synchrotron, in which the goniostat's rotation axis is in the
plane of polarization.
- -i
-
Re-index the reflections by a 3x4 matrix transformation on the
indices before output. The transformation matrix is specified in a
file with environment variable REINDEX. If the matrix is specified as
- 1
-
0 0 -1
- 0
-
-1 0 0
- 0
-
0 -1 0
-
then the output reflections will obey h(out) = h(in) - 1,
k(out) = -k(in), l(out) = -l(in).
- -j
-
Causes the output to exclude reflections in specified
resolution ranges. Typically this would be used to eliminate
reflections in ice-rings. The file containing the resolution
ranges to be eliminated is specified with the environment
variable ICERING. Each line contains a lower and an upper
resolution value in Angstroms, e.g.
-
3.67 3.63
2.24 2.20
1.93 1.89
1.48 1.44
- -k
-
If this is specified, the program will the recompute indices
of all the reflections in the UREFLS file according to the crystal
and detector parameters contained in the UPARAMS file. If any of a
reflection's indices differs from an integer by greater than the
index-error limit in the UPARAMS file (typically 0.1-0.25) the
reflection is not output. This becomes a way of filtering out
reflections that have been moved too far from their starting
position; it is probably less effective than the XYOmega filter
(below).
- -o
-
If this is specified, the program will read a file with
environment variable name REFLECTIONS as a output file from the
XENSYS / BUDDHA program SCAN rather than reading UREFLS as an
output from the integration program herein.
- -q
-
Ordinarily the "reduce" operation prints out the first 10
reflections rejected by the algorithm within each category of
rejection; after that it suppresses printout. If this Boolean is
specified, ALL rejected reflections will be printed to the log file.
- -r
-
If this is specified, the program will recompute the indices
of all reflections in the file according to the crystal and
detector parameters contained in the UPARAMS file. Unlike the
"recompute and reject" operation described under /-k/, this one
does not then reject any reflections.
- -s
-
Use intensity and sigma values obtained by simple summation
rather than by profile-fitting. In combination with the
"transformed coordinate" option; this option allows for 4
different intensity and sigma measurements: profile profile fitted
and summed, direct-space or transformed-coordinate integration.
- -u
-
This flag tells the program to /remove/ the monochromatized
polarization correction from the intensity measurements and
replace it with an unmonochromatized polarization correction.
Thus if the data were erroneously integrated with the
monochromatized polarization formula "on", this flag allows
the user to undo that erroneous correction.
- -v
-
Replace the current polarization correction with that
associated with a fully-polarized input X-ray beam,
e.g. from a synchrotron, in which the goniostat's
rotation axis is perpendicular to the plane of polarization.
- -x
-
If this is specified, the program will write out only
reflections for which
|Xob - Xp | < dX, |Yob - Yp | < dY, and |Zob - Zp | < dZ,
where (Xob ,Yob ,Zob ) is the observed centroid, (Xp ,Yp ,Zp)
is the predicted centroid, and (dX,dY,dZ) are the error limits
in (X,Y,Z) set in the UPARAMS file. Thus this provides a filter
preventing inclusion of spots whose centroids moved too far during
integration.
- -z
-
If this is specified, we recompute the indices of all
reflections in the file according to the crystal and detector
parameters contained in the UPARAMS file. If any of the
reflection's indices differs from an integer by greater than the
index-error limit specified in the UPARAMS file (typically 0.1-0.25
degrees) or if the new indices are different from the old
indices, do not output the reflection.
- -a<minfm,maxfm>
-
This specifies the range of frames over which
-
integrated data will be output. The values are given in the
form minfm,maxfm. Thus if you wish to output the data from
frame 312 to frame 381, enter "-a312,381". Default value:
no restriction imposed.
- -c<val>
-
A non-blank, nonzero value <val> here specifies that we
-
should write out a CENTROIDS file rather than a MULTIREF. The
resulting file can be used as input to the refinement
functionality, so that we can use the superior centroid-finding
and background-subtraction algorithms of "integrate" as input to
the refinement effort. The value <val> given should be the maximum
number of centroids written out in each of the roughly 400 regions
of the detector face within which output will occur; thus
specifying "7" here will cause at most 7 spots to be written out
per region, or about 2800 altogether. Default value: if "-c" is
not specified, no CENTROIDS file is created. If "-c" is specified
without a corresponding numeric argument, then 10 is the
corresponding value.
- -d<val>
-
If you specify a value <val> here, the reduction routine
-
will delete from output all reflections with
-
|Ifit - Isum | > <val>* sqrt(sigfit)^2 + sigsum)^2).
-
Default value: 4.
- -f<val>
-
A nonzero value here specifies that we should only output
-
reflections for which I/sigma is greater than that value. Thus
specifying "-2" here would cause the program to output only
reflections with I/sigma > -2. Default value: -3.
- -g<val>
-
If you specify a value <val> here, the reduction routine
-
will delete from output all reflections with
-
|Ifit - <val> * Isum | > <val> * sqrt(sigfit^2 + (G*sigsum )^2),
-
Thus if <Ifit > = <Isum > (G == 1) this option is identical to
to the -d option given above; if not, it will result in the
deletion of a slightly different list of spots. Default: no
restriction imposed.
- -l<val>
-
Inflate the Lorentz correction values by this specified
-
value so that
-
I = (Iraw / p) * (val + 1 / L) instead of I = (Iraw / p) * (1 / L).
-
The purpose of this option is to allow for an artificial expansion
of the Lorentz correction (1/L). There is some evidence with
certain kinds of data that this correction may be useful.
Default value: 0.
- -m<val>
-
Examine the data to find the dependence of <I/sigma>
-
on sin(theta)/lambda and impose a resolution cutoff at the
sin(theta)/lambda value where <I/sigma> falls to <val>.
Thus if you specify -m1.5 and the average intensity/sigma
value falls to 1.5 at a D spacing of 2.35 Angstroms,
then the data will be output only out to 2.5 Angstroms.
Default: 1.4.
- -n<val>
-
Output a combination of profile-fitted and summed data.
-
Any reflection whose I/sigma value is above <val> will have its
intensity output according to summation; any other reflection will
have its intensity output according to profile-fitting. Default:
999999, i.e. this option is not put in effect.
- -p<val>
-
Ordinarily the "reduce" operation prints out the first 10
-
reflections rejected by the algorithm within each category of
rejection; after that it suppresses printout. If a nonzero value
<val> is specified here, then for each category of rejected
reflections the program will output <val> reflections to the
log file rather than 10. Default value: 10.
- -q<val>
-
Turn on a variety of options to "reduce" depending on
-
the specified <val>. There are more than 26 run-time options
for "reduce", which is the reason this approach must be used.
The options available and their meanings are:
val Meaning Equivalent
- 1
-
Output larger I/sigma -b
- 2
-
Kabsch intensities -e
- 3
-
Input from SCAN/BUDDHA -o
- 4
-
Simple-summation output -s
- 5
-
Change polarization to synchrotron-horizontal -h
- 6
-
Omit reflections within ice-rings -j
- 7
-
Omit reflections with non-integer indices -k
- 8
-
Print all screw-axis-deleted observations -q
- 9
-
Recompute reflection indices using UPARAMS -r
- 10
-
Undo the polarization correction -u
- 11
-
Change polarization to synchrotron-vertical -v
- 12
-
Omit reflections with large (X,Y,omega) errors -x
- 13
-
Keep duplicate observations -y
- 14
-
Recompute hkl and omit if non-integer -z
-
Thus reduce -q5 -q9 would alter the polarization to that
appropriate to synchrotron data with a horizontal axis (assuming
the data had been initially integrated with a monochromator
polarization formula), and would recompute the reflection indices
based on the contents of the UPARAMS file.
- -t<val>
-
Adjust all intensity and sigma values by a
-
multiplicative value of 1 - <val>*cos(2 * pi * omega).
This corrects for certain obscure goniostat-related errors.
Default value: 0.
- -w<val>
-
Set the nominal width of the scaling groups generated by
-
the reduction step to be <val> degrees rather than the default 5
deg. The actual scaling group width will be slightly larger than
the value specified here so that we don't end up with a ragged
scaling group at the end. Thus if the data span 60 degrees and you
specify 8 degree scaling groups, the program will create 60 / 8 =
7 pairs of scaling groups, and each will be 60 / 7 = 8.57 degrees
wide. Default value: 4, 1.5, or 1, depending on how many
reflections are present in the data set (4 with fewer than 5000
reflections, 1.5 with more than 5000 reflections but a run-width
larger than 100 degrees; 1 with a run-width smaller than 100
degrees). With very long runs the nominal width is set to ensure
that there are fewer than 200 scaling groups associated with a run.
- -z<val>
-
Turn OFF a variety of options to "reduce" depending on
-
the specified <val>. There are more than 26 run-time options for
"reduce", which is the reason this approach must be used. In the
list of equivalents below, a notation like !-x would indicate
the complement of what option -x does. The options available and
their meanings are:
val Meaning Equivalent
- 1
-
Disable output of larger Isigma !-b
- 2
-
(X,Y,omega) intensities !-e
- 3
-
No SCANBUDDHA input !-o
- 4
-
Profile-fitted output !-s
- 5
-
Don't change polarization to synchrotron-horizontal !-h
- 6
-
Use reflections within ice-rings !-j
- 7
-
Keep reflections even if they have non-integer indices !-k
- 8
-
Don't print all screw-axis-deleted observations !-q
- 9
-
Don't recompute reflection indices !-r
- 10
-
Don't undo the polarization correction !-u
- 11
-
Don't correct polarization to synchrotron-vertical !-v
- 12
-
Keep reflections with large (X,Y,omega) errors !-x
- 13
-
Don't keep duplicate observations !-y
- 14
-
Don't recompute hkl and omit if non-integer !-z
-
Thus reduce -z3 -z9 would ignore data from a SCAN or BUDDHA run,
and would decline to recompute reflection indices.
-
<runnumber> This specifies the run number associated with the run.
-
Default value: 0.
- <minsigoi>
-
This specifies a machine error correction to the data.
-
If the input variance is v and the value specified here is m, then
the output variance is v + (m*I) * (m*I). Default value: 0.
- <resmin>
-
This specifies the low-resolution cutoff in
-
Angstroms, below which reflections will not be output.
Default: no restriction imposed.
- <resmax>
-
This specifies the high-resolution cutoff in Angstroms,
-
above which reflections will not be output. Default value: 0.
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
-
- REPORTING BUGS
-
- COPYRIGHT
-
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Time: 02:08:09 GMT, October 03, 2005