Man page of X-GEN
Section: X-GEN Commands (1)
Updated: April 2005
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X-GEN - refall
"refall" performs a hands-off indexing and refinement of the crystal
and detector parameters based on a set of spots found with a "spots"
command. If the crystal has already been auto-indexed (as identified by
the fact that the initial RMS error in index is less than 0.1) the
auto-indexing is skipped. "refall" is designed to take a crystal from
a completely unindexed state to one in which the user can immediately
launch an integration.
In general, this program uses the machinery of the "refine1"
functionality (q.v.) in the following sequence (see the documentation
on the "refine1" command to see what each of these commands does):
- i 0.8 0.39 50
- j plated n tilt n swing n gamma2 n
- l a
- d resmin 999
- d resmax 0
- r a
- l a
- j plated y
- j tilt y
- f q
- r a
If the -i or -l options are invoked (see below), then during the Bravais
lattice calculation the user's specification of the spacegroup or the
crystal system is honored, provided that the user's specification yields
a good figure of merit in the Bravais calculation. If the user asks for
a tetragonal spacegroup, and tetragonal spacegroups yield an implausible
figure of merit, then the symmetry imposed will be the one with the best
figure of merit, NOT the one the user has specified.
Ask the user for confirmation of the Bravais choice before
installing it. Thus b q would replace the b and f q commands above.
Flip the sign of the stepsize to the opposite of from the
from the one intuited from the image headers.
Don't do the re-centering after the auto-indexing. Thus the
auto-indexing command above would be replaced with "i 0.8 0.39 50 1".
Don't include reflections that lie within ice-rings in auto-indexing.
The resolution ranges that constitute the ice-rings
are specified in a text file with environment variable ICERING.
If that file is absent, the ice-ring ranges are 3.97 to 3.60
Å, 3.48 to 3.40 Å, 2.70 to 2.63 Å, and
2.28 to 2.21 Å.
Ask the user to specify the spacegroup after the Bravais
determination has been completed. The specification will be the
International Tables number of the spacegroup.
Specify the centering type of the spacegroup to be <val>.
<val> = 1 is primitive; 2 is C-centered; 3 is I-centered;
4 is F-centered; 5 is H (rhombohedral indexed hexagonally);
6 is R (rhombohedral indexed rhombohedrally); 7 is A-centered
(spacegroups 38 through 41).
Specify the International Tables spacegroup to be <val>.
Values larger than 230 correspond to rhombohedral indexings
of the corresponding rhombohedral spacegroup. Thus -f155 is
R32 indexed hexagonally; -f255 is R32 indexed rhombohedrally.
As noted above, the specified spacegroup will ONLY be imposed
if it yields a good residual.
Specify the crystal system to be <val>. 1 is triclinic;
2 is monoclinic; 3 is orthorhombic; 4 is tetragonal;
5 is cubic; 6 is hexagonal or rhombohedral H;
7 is rhombohedral R. As noted above, the specified crystal
system will ONLY be imposed if it yields a good residual.
Specify the minimum RMS error as <val>. Thus
"refall -m0.15" specifies that the minimum RMS error is
0.15 rather than 0.1.
Perform a completely hands-off indexing and refinement.
- refall -as
Perform a mostly hands-off refinement in which the user is
prompted for confirmation of the Bravais calculation and
then prompted for the spacegroup.
refall -i96 Perform a hands-off refinement, but impose spacegroup 96,
i.e. P4(3)2(1)2; here the crystal system is 4, the centering
is P, there are two-folds perpendicular to the fourfold, and
there is a 4-fold screw along c and a 2-fold screw on a;
provided, though, that this symmetry yields a good Bravais lattice.
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