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 - filterc  

SYNOPSIS

filterc [-acehs] [-dval ... ]  

DESCRIPTION

"filterc" is a non-interactive filter for CENTROIDS files. It reads a CENTROIDS file and writes out another one whose environment variable name is CENOUT, from which some of the observations have been deleted. Normally only observations that have errors in h, k, l, X, Y, or phi greater than a certain value removed from the output. The error limits are the ones set in a run of "refine" or "refine1".
The resolution cutoffs, the integerness error checks, and the

(X,Y,omega) error checks in `filterc' can only be applied if a UPARAMS file exists, i.e. if the crystal and detector parameters are known. The "complement" function applies only to reflections that violate the integerness and (X,Y,omega) rules, not the other rules. Thus if filterc is invoked with -c and a reflection violates the monotonicity or sharpness criteria, it will not be output.  

OPTIONS

-c
This "complement" option does deletions, but only for observations with DO satisfy the (X,Y,omega,h) criteria for acceptance or that DO NOT satisfy the rules regarding minimum intensity, resolution limits, monotonicity, intensity, and nearness to neighbors. Violators of the (X,Y,omega,h) error rules are retained. This provides a method of separating the reflections belonging to one lattice from the ones belonging to another lattice.
-h
Compute the indices hkl and the predicted values of (X,Y,omega) for each reflection. Check the integerness of the hkl values against the index error limit and the size of the |Xp-Xob|, |Yp-Yob|, |omega(p)-omega(ob)| against the (X,Y,omega) error limits. This is the default behavior of the program.
-s
Do not check for integerness or (X,Y,omega) errors.
-d<val>
For each observed reflection, determine the relative plane spacing between it and all other reflections in the list. If that relative plane spacing is less than , delete both reflections from the list. Default: 10000 Angstroms, i.e., no restriction.
-i<val>
Delete all reflections whose intensity is smaller than <val>. Default: -10000, i.e., no restriction.
-l<val>
Lower-resolution cutoff is <val>. Default: 10000 Angstroms, i.e., no restriction.
-m<val>
Examine the omega profile of each reflection to see if it increases monotonically upward to the peak and then decreases monotonically downward. If it does not, and in particular if the fraction of the profile that violates this monotonic behavior is larger than <val>, delete the reflection. Thus if <val> = 0.1, this normalized profile:
0.01 0.10 0.09 0.45 1.0 0.7 0.15
would be allowed, because the non-monotonic "bump" (0.10 - 0.09) is only 0.01, whereas
0.01 0.20 0.09 0.45 1.0 0.7 0.15
would be disallowed. Default: 1, i.e. no restriction.
-n<val>
Delete very sharp peaks. If the second-largest element in the omega profile is smaller than <val> * the largest element, the reflection is considered too sharp and should be deleted. Default: 0, i.e. no restriction.
-u<val>
Upper-resolution cutoff. Default: 0, i.e. no restriction.
 

EXAMPLES

filterc -hm0.1
Eliminate reflections whose (X,Y,omega) or (h,k,l) errors errors are too large, and also those that are non-monotonic.
filterc -cn0.08
Eliminate reflections that do satisfy the current orientation matrix, and also those that are very sharp.
 

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