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X-GEN

Section: X-GEN Commands (1)
Updated: April 2005
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NAME

X-GEN - makemu  

SYNOPSIS

makemu [-afimnptvxyz] [-cval] [-sval] [rescut]  

DESCRIPTION

"makemu" reads a merged data set (MULTIREF file) and a scaling parameter file (SCALEIN) and uses it to generate several ASCII files containing the merged intensities or structure amplitudes. After writing the data out it also performs an analysis of the Bijvoet differences in the data: it computes an overall scale and relative temperature factor relating the primary observations (F+ or I+) to the Bijvoet observations (F- or I-) and an R-factor between the two sets. A large value of this "Bijvoet R" factor might indicate the presence of a significant anomalous signal in a data set, assuming adequate redundancy and a small overall error.

The "native" output format is the MULIST, whose format is described below.

Each line in the MULIST will contain either

h
k l I sig(I) I+ sig(I+) I- sig(I-) flag

or

h
k l F sig(F) F+ sig(F+) F- sig(F-) flag

where

I+ is the mean intensity of observations of the primary reflection and its symmetry mates; I- is the mean intensity for the Bijvoets; F+ and F- are the corresponding structure amplitudes; and sig(I), sig(I+ ), sig(I- ), sig(F), sig(F+ ), sig(F- ) are the standard deviations associated with I, I+ , I- , F, F+ , and F- , respectively.
 

The flag value ranges from 0 to 63 and is the ORing of these conditions:

bit no.
condition for off condition for on
------- ------------------- -----------------
0
acentric reflection centric reflection
1
I+ measurement made no I+ measurement
2
I- measurement made no I- measurement
3
mean intensity > 0 mean I <= 0
4
mean I+ > 0 mean I- <= 0
5
mean I- > 0 mean I- <= 0
 

Thus the possible values of the flag are:

flag
centricity <I> <I+> <I-> value
value
value value
0
acentric > 0 measured and <= 0 measured and > 0
1
centric > 0
2
acentric > 0 measured and > 0 not measured
4
acentric > 0 not measured measured and ? 0
9
centric < 0
16
acentric > 0 measured and < 0 measured and ? 0
24
acentric <= 0 measured and < 0 measured and ? 0
28
acentric <= 0 measured and < 0 not measured
32
acentric > 0 measured and ? 0 measured and < 0
40
acentric <= 0 measured and < 0 measured and > 0
42
acentric <= 0 not measured measured and < 0
56
acentric <= 0 measured and < 0 measured and < 0

The program also writes out data in five other ASCII formats to separate files, whose names and environment variables are given in the FILES section, below. The formats besides the MULIST are:

1. the "HKL" format used by XPREP and the various incarnations of
SHELX, consisting of (h,k,l,I,sigma(I),1), or (h,k,l,F,sigma(F),1) formatted as follows:
0
2 5 249.17 6.97 1
2. a format intended as input to CNS, containing a six-line header
followed by reflection lines that look like
INDEx=
0 2 5 IOBS= 249.17 SIGI= 6.97
3. a format intended for XPLOR V.3.1, with no header and data lines
that look like
INDEx
0 2 5 IOBS 249.17 SIGMa 6.97
4. a format compatible with the /output.sca/ file put out by
SCALEPACK, with the Friedel-mates merged.
5. a format compatible with the /output.sca/ file put out by
SCALEPACK, with the Friedel-mates unmerged.
 

OPTIONS

-a
Output the ASCII MULIST (and the other ASCII output files) in absolute hkl order rather than in standard X-GEN order. Thus in a monoclinic spacegroup (0,2,3) will precede (2,0,3), and in triclinic, monoclinic, or trigonal spacegroups (1,3,-7) will precede (1,3,2).
-f
This specifies that structure amplitudes ("F's") will be
written out rather than intensities. Note that the resulting square roots are taken separately for I, I+, and I-, so in general <F> will not equal 0.5 * (<F+> + <F->). Note that for this option, reflections with negative <I> will be output with <F> set to zero and sigma(<F>) set to 9999.
-i
Reindex the reflections by a 3x4 matrix transformation on
the indices before output. The transformation matrix is specified in a file with environment variable REINDEX. If the matrix is specified as 1 0 0 -1 0 -1 0 0 0 0 -1 0
then the output reflections will obey h(out) = h(in) - 1, k(out) = -k(in), l(out) = -l(in).
-m
Write out only those reflections that have two or more
observations.
-n
Set the negative mean intensity values to zero upon output
even if we are outputting intensities rather than structure amplitudes. This option is not recommended, but it is included for those who want it.
-p
Ordinarily "makemu" corrects for any alteration in the
overall sin(theta) dependence of the data that the scaling introduces. If this flag is on, this correction is NOT performed, and the sin(theta) dependence of the scaled data is preserved in the output.
-t
Write out the reflection lists in increasing order of
sin(theta) rather than in some hkl-based order.
-v
Ordinarily "makemu" determines sigma(<F>) or sigma(<I>)
according to a formula that is sensitive both to the variances of the individual observations and to the deviations of those values from their means. If this flag is set the program determines the variance strictly from the variances of the inputs, namely var(<I>) = 1. / (SUM (1. / var(Ii))
-x In the X-PLOR and CNS output files, write out the reflections
with the Friedel mates separated. This is the default behavior.
-y In the X-PLOR and CNS output files, write out the reflections
with the Friedel mates merged.
-c<val>
In the "Bijvoet R factor" calculations, use only the reflections for which I/sigma is greater than <val>. Default value: 2.
-s<val>
This value specifies the overall scale factor to be applied to the output F's or I's. Default value: 1.
<rescut>
specifies the high-resolution cutoff in Angstroms, above
which reflections will not be output. Default: no cutoff applied.
 

EXAMPLES

makemu
Output intensities (not amplitudes) with a scale factor of 1 and using all the data:
makemu -ifps0.1
Output structure amplitudes with a scale factor of 0.1 and using data only to 1.7 A, changing to the non-standard variance formula and reindexing the data based on the contents of the REINDEX file:
 

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
The flag value ranges from 0 to 63 and is the ORing of these conditions:
Thus the possible values of the flag are:
OPTIONS
EXAMPLES
REPORTING BUGS
COPYRIGHT

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