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 - editcen  

DESCRIPTION

"editcen" is a "curses"-based editor 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 which have errors in h, k, l, X, Y, or phi greater than a certain value are printed and presented to the user for deletion. The error limits are the ones set in a run of "refine1".
The resolution cutoffs, the integerness error checks, and the (X,Y,omega)

error checks (see below) 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 integerness and (X,Y,omega) rules, not the other rules. Thus if "editcen" is invoked with -c and a reflection violates the monotonicity or sharpness criteria, it will not be output.  

OPTIONS

-a
This "automatic" option specifies that deletions are performed without asking the user.
-c
This "complement" option does automatic deletions, but only for observations with DO satisfy the criteria for acceptance. Violators are retained. This provides a method of separating the reflections belonging to one lattice from the ones belonging to another lattice.
-e
This "every" option directs that every observation be presented to the user for consideration, rather than only presenting the ones violating the error criterion. The uninteresting conclusion from this is that using both "-a" and "-e" will cause all reflections to be deleted, so no output file needs to get written.
-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, then 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

editcen -hi5
Flag reflections that disagree with the current matrix sufficiently to violate the (X,Y,omega) or h error limits, and to remove reflections with intensities below 5.
editcen -cm0.1
Flag reflections that do agree with the current matrix and also those with non-monotonic omega profiles.
 

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
DESCRIPTION
OPTIONS
EXAMPLES
REPORTING BUGS
COPYRIGHT

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Time: 02:08:09 GMT, October 03, 2005