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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 - anal_u
SYNOPSIS
anal_u
[-ks] [-i<val>] [-f<val>] <nfmpergrp>
DESCRIPTION
"anal_u" goes through the current integrated-reflections (UREFLS)
file and breaks it up into groups of 1-20 images' worth of data. For
each group it prints to XLOG a statistical summary, containing <I>,
<I/sigma>, <sigma>, <background> and a histogram of I/sigma values.
It prints a similar summary for the entire UREFLS file as well. The
user can select how many images per group will be used and whether
to use profile-fitted or summation data.
The functionality represented in anal_u is now built into the
"integrate" program itself at the end of a data run. The only reason
a user is likely to need to run anal_u separately is if the
options captured by the version embedded in integrate fail to
deliver what he or she wants. The version that runs within
integrate is equivalent to anal_u 1.
OPTIONS
- -k
-
This toggles whether the data to be output should be the
Kabsch-geometry (local diffraction-vector-space) data
rather than the conventional (X,Y,omega)-geometry data.
- -s
-
This toggles whether the data to be output should be the
simply-summed data rather than the profile-fitted data.
- -f<val>
-
The anal_u facility estimates the fraction of reflections
-
that are fully recorded within a single image by noting
how many reflections satisfy
-
I(2nd brightest frame) < <val> * I(brightest frame),
-
so that if <val> is 0.04 and the brightest frame in a
reflection's profile has intensity=1000 and the
next-brightest has intensity = 30, then that reflection
will be defined as fully-recorded. This command specifies
the value of <val> in this equation. Default Value: 0.05.
- -i<val>
-
In computing the fraction of reflections that are fully
-
recorded in the brightest image, the Integration Statistics
facility looks only at reflections with intensities above a
sigma cutoff. This command specifies that sigma cutoff.
Default value: 3.
- <framespergroup>
-
This parameter specifies how many frames will
-
constitute a group over which anal_u's statistics will be calculated.
Thus specifying "3" here will cause the routine to break the
data into groups that are 3 frames wide. Default value: 20.
EXAMPLES
-
anal_u -ks -f0.025 4 Output statistics for a UREFLS file,
-
dividing the data into four-image groupings and using
Kabsch, simply-summed data, and treating the data as
fully-recorded if less than 2.5% of the data lie
outside the peak image.
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
-
- OPTIONS
-
- EXAMPLES
-
- REPORTING BUGS
-
- COPYRIGHT
-
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