PRELIM
2.1 - PRELIM - Preparation of initial model file
The programs under this menu item should normally be run at the beginning of a structural
determination. The option AUTO-START causes an automatic execution and the
programs may be run individually at any time during the structural analysis.
- The program Import KappaCCD reads the file IMPORT.CIF written by the
Nonius/Collect program Cifin and writes out the file DREDUC.CIF (data reduction
summary) the SHELX reflection file IMPORT.HKL and the SORTAV reflection file
IMPORT_HKL.SORTAV
- The program E-STATISTICS carries out a Wilson plot, calculates
the normalised structure factors (E's) and
the statistics of the distributions of these E-values. This
sometimes provide a valuable clue as to the presence of a centre of symmetry.
NOTE however that the presence of heavy atoms, especially on special
positions, and/or extended planar ring systems in light atoms structures,
may give rise to misleading or even incorrect indications of the centricity.
A graphical display of the Wilson plot and E-distributions is given. RMS
deviations of the experimental curve (for all data) from those calculated
for NONCENTRIC, CENTRIC and HYPERCENTRIC structures is calculated. A Figure of Merit
(FOM) for the CENTRIC and ACENTRIC cases is then calculated, based on these
percentage deviations. A FOM less than 0.1 is usually conclusive.
- The program ASSIGN SPACEGROUP first of all compares equivalent reflections in
the .HKL file under all possible Laue symmetries. This provides a valuable
check that the supposed Laue symmetry is indeed correct. The program
then prints a full listing of potential
systematic absences, and attempts to assign a space group. If E-STATISTICS
has been previously run in the same session, then information about the
centricity is passed to the program. A combined Figure of Merit
(CFOM) is then calculated, based on the available information.
The lower the value of CFOM, the more likely that the assignment is correct.
A value below 10.0 indicates a satisfactory fit, while one below 1.0 indicates
the chosen space group is highly likely.
- the program INITIALISE FILES will prepare the initial model file name.INS
for a SHELXS run,
and also write the file STRUCT.CIF. This latter file contains basic
information about the crystal eg size, colour, crystal system, space group
etc, which is not stored explicitly anywhere else. For instance the structure
solution programs SIR92 and DIRDIF will read this file to obtain
information about the unit cell and space group. The STRUCT.CIF file may of
course be later modified, for example if the originally assigned space group
was incorrect.
- The option AUTO-START will run the programs E-STATISTICS, ASSIGN SPACEGROUP
and INITIALISE FILES in automatic sequence, with slightly different defaults and less
output than when run individually. It will attempt to assign a unique space group, and will optionally
run a default session of direct methods using SHELXS and open CAMERON to view the
resultant .RES file. If no .HKL file is present, but a CAD4 diffractometer file
is detected, then XCAD4 will be launched automatically.