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


refall [-afnrs] [-cilm<val>]  


"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):

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 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




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