Man page of X-GEN
Section: X-GEN Commands (1)
Updated: April 2005
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X-GEN - editcen
"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.
This "automatic" option specifies that deletions
are performed without asking the user.
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
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.
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.
Do not check for integerness or (X,Y,omega) errors.
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.
Delete all reflections whose intensity is smaller
than <val>. Default: -10000, i.e., no restriction.
Lower-resolution cutoff is <val>.
Default: 10000 Angstroms, i.e., no restriction.
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.
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.
Upper-resolution cutoff. Default: 0, i.e. no restriction.
- 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.
Report bugs to Andy Howard at firstname.lastname@example.org or 312-567-5881.
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
- REPORTING BUGS
This document was created by
using the manual pages.
Time: 02:08:09 GMT, October 03, 2005