Content-type: text/html 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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Time: 02:08:09 GMT, October 03, 2005