Man page of X-GEN
Section: X-GEN Commands (1)
Updated: April 2005
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X-GEN - spaceg
"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:
3, 5, 16, 20, 22, 23, 75, 79, 89, 97,143,
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.
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.
Unconditional output: An output MULTIREF in the most
probable spacegroup is written, no matter what.
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.
specifies the high-resolution cutoff in Angstroms,
above which reflections will not be analyzed. Default: no restriction.
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:
Report bugs to Andy Howard at email@example.com 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