SHELXA
4.34 - SHELXA - Empirical Absorption Correction
Synopsis
This program
applies "absorption corrections"
by fitting the observed to the calculated intensities as in the
program DIFABS. SHELXA is intended for EMERGENCY USE ONLY,
eg. when the world's only crystal falls off the diffractometer
before there is time to make proper absorption corrections by
indexing crystal faces or by determining an absorption surface
experimentally by measuring equivalent reflections at different
azimuthal angles etc.
The following restrictions apply to the use of SHELXA:
- The structure should not be twinned (racemic twinning
is allowed), the data should have been collected from one crystal
(inter-batch scale factors should not have been refined), and
there may not be a re-orientation matrix on the HKLF instruction.
Otherwise there are no restrictions on the type of structure
(SHELXA is equally (un)suitable for proteins) or the instructions
used in the SHELXL refinement.
- It is understood that any structure determined by means
of this scientifically dubious procedure WILL NEVER BE PUBLISHED
! The anonymous author of SHELXA has no intention of ever
writing a paper about it that could be cited and thereby ruin
his reputation.
The absorption is modeled by spherical harmonic functions using
full-matrix least-squares more or less by the method of Blessing
(1995). It is not this model that should be regarded as dubious,
just the way SHELXA misuses it. Data are used for parameter determination
if the I/(I) ratios for both the observed and calculated intensities
exceed a given or assumed threshold (equal
to 5.0). The delta(U)/lambda**2 parameter specifies an artificial U/2 value that
is applied to the calculated intensities. This helps to prevent
atoms going NPD, but the default value is zero. The highest
even and odd order spherical harmonics
to employ must be specified. The refinement could be unstable if these are too high,
especially if only part of reciprocal space is sampled, eg. because
only an asymmetric unit was collected for a high symmetry structure.
Allowed values are (0,2,4,6,8) and (0,1,3,5,7) respectively.
The data may be re-processed when, for example, extra atoms are
added. However, as with DIFABS, best results are obtained if the
procedure is last run with the final ISOTROPIC model. Re-running
it after anisotropic refinement will result in a deterioration
of the structure and (most important) the R-factors. The
U fudge should not be used repetitively, because the effects will
be cumulative !
Note that all esd's estimated by SHELXL using data "corrected"
in this way will be invalid unless the number of parameters used
in the absorption model is input as the third L.S. parameter.
This number depends on the number of even/odd harmonics used
and is output by SHELXA. The program can read either standard SHELX
direction cosines (relative
to the crystal reciprocal axes), or orthogonal direction cosines
calculated by the method given in Blessing's paper.
Files read
- name.FCF file written by SHELXL-97 (using LIST 4 or LIST 6
and any combination of MERG, OMIT etc). A SHELXL-93 .FCF
file is NOT suitable because some information is missing.
- name.HKL - uncorrected reflection file written by programs XCAD4 or
PROFIT. Direction cosines are required, which MUST correspond to the
unit cell in the name.INS file.
Files written
- SHELXA.HKL - absorption corrected reflection file
- SHELXA.LST - List file giving summary of the applied corrections
- SHELXA.CIF - CIF containing relevant information