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 - spaceg  

SYNOPSIS

spaceg [-cov] [rescut]  

DESCRIPTION

"spaceg" reads a MULTIREF and SCALEIN file and analyzes the data contained therein to determine whether the spacegroup has been assigned correctly. Initially the R-merge value is calculated in the spacegroup that has already been assigned for the data. Then the measurements are transformed into each of the other 44 lattice characters, and for the best lattice character of each point group, the Rmerge value is computed. For each of the 16 unique Laue groups it determines the lattice character that best fits the primitive unit cell and calculates a lattice residual. Then it builds up an internal list of unique reflections and computes a symmetry R factor for the data according to the symmetry associated with each of several possible spacegroups that are consistent with the defined Laue group. In all it calculates Rmerge values for 24 spacegroups, namely International Tables numbers:
1,
3, 5, 16, 20, 22, 23, 75, 79, 89, 97,143,
146,150,151,155,168,177,195,196,197,207,209,211

For spacegroups 146 and 155 (R3 and R32) it computes the cell parameters and Rmerge values both with hexagonal indexings and with rhombohedral indexings. If the Rmerge values for hexagonal R3 differ from those for rhombohedral R3, something is wrong!

In the end it computes a figure of merit for each of the 24 spacegroups, based on the lattice residual and the goodness-of-fit of the scaled data. Higher-symmetry spacegroups are given lower (better) figures of merit than lower-symmetry spacegroups with similar goodness-of-fit and lattice residual values. It then sorts these results by the figure of merit and writes them out to the log file and the terminal. The weight factors for specific symmetries that are used in computing the figure of merit are subject to discussion and tweaking in the future. For example, it may list a C-centered orthorhombic unit cell as being preferable to a tetragonal primitive cell even when the real lattice is tetragonal. The code will be refined in the future.

Once the spacegroup with the best figure-of-merit is determined, the program analyzes the data for possible screw-axis absences associated with that spacegroup. Thus if spacegroup P321 (International Tables #150) is found by symmetry analysis to be the best one, then there are three noncentrosymmetric spacegroups that could really be operating: P321, P3(1)21, and P3(2)21. By examining 00L reflections with L not equal to 3n, we can distinguish between P321 and the other two. We cannot distinguish between P3(1)21 and P3(2)21 in reciprocal space. The results of this analysis are also written to the log file and the screen.

If the user asks for an output MULTIREF to be written (see below), it converts the input MULTIREF to one in which the converted spacegroup is in operation.  

OPTIONS

-c
Conditional output: An output MULTIREF in the spacegroup found to be the most probable is written, but only if that spacegroup is significantly different from the input.
-o
Unconditional output: An output MULTIREF in the most probable spacegroup is written, no matter what.
-v
Verbose mode: more output is provided. Under any circumstances, any reflection whose input (hkl) value does not produce a symmetry-mate with the manually-computed (hkl) is removed from consideration. With the "-v" flag set, the identity and properties of this "non-conforming" reflection are written out to the log file.
<rescut>
specifies the high-resolution cutoff in Angstroms,
above which reflections will not be analyzed. Default: no restriction.
 

EXAMPLES

spaceg
Determine or reverify the spacegroup of a crystal without automatically changing the spacegroup:
spaceg -c 1.8
Produce an output MULTIREF only if the spacegroup
turns out to be different from the one that had been input, while using only the data out to 1.8 Angstroms:
 

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