S provides three options for the storage of the original (raw) diffractometer data from which
S can be started.
1.
With
COMPOUND.ins and
COMPOUND.hkl (or
COMPOUND.fcf) data in the
current directory
Example:
s sdemo.ins
2. With the raw shelx reflection data stored in a directory below the default (i.e.
/mnt/shxdata) location.
E.g. Shelx data (i.e. shelx.hkl and shelx.ins) for compound s1000 are stored in
/mnt/shxdata/s1000
S will find the data (shelx.ins & shelx.hkl) when started up with
s s1000
The default location can be changed by setting the environment variable SHXPATH
to the proper alternative.
3. In our local operation, CAD4 files (e.g. s1000.cad) are stored in a single directory
/mnt/cad4data (i.e. /mnt/cad4data/s1000.cad).
System S is started in this context as
s s1000
An alternative is to create an 's1000' sub-directory under 's' and copy the CAD4 data
as s1000.cad into '~s/s1000'.
System S is started as
s s1000.
10.7 - OTHER TRY-IT-YOURSELF EXAMPLES
Following are adapted (i.e. no prior space-group information given ins the '.ins' data-file)
datasets
supplied with Dr A.D. Hunter's
SHELXTL course
.
Example1:
sfun1.ins
and
sfun1.hkl
Example2:
sfun2.ins
and
sfun2.hkl
Example3:
sfun3.ins
and
sfun3.hkl
Example of an inorganic compound Cs2TiSi6O15:
csti.ins
and
csti.hkl
10.8 - How to Implement the new Space group suggested by ADDSYM
ADDSYM (either run explicitly or implicitly) will suggest an alternative spacegroup in
RED on the main S window. Addsym is invoked automatically (unless switched off) at the
start of the anisotropic refinement.
The transfer of the current structural results to the suggested space group is effected by
clicking on 'TRMX' and 'SPGR'.
The Formula and Z can be adapted when desired following this transfer.
Refinement can now proceed in the new spacegroup.
Example: Solve the 'sdemo' structure not in P21/c but in Pc (# 7). At the anisotropic
refinement stage, a message 'M/P P21/c' in RED will appear to attract attention to the
possibly missed or pseudo-symmetry.
10.9 - How to run S on a 'CIF/FCF' Dataset
System S can be invoked using a 'fcf' (and 'cif') formatted file(s) (e.g. taken from the IUCR-
Acta Cryst C Web-page) via:
s demo.fcf
S will convert the data in the .fcf file into a shelx.hkl (HKLF 4 format) file and ask for
additional missing data.
The .hkl file can be found in the subdirectory 'hklf'.
A shelx.ins file is prepared from the data available in the 'fcf' file. Since an 'fcf' file doesn't
contain information on the composition composition, this info should be given manually.
Alternatively, when both a 'CIF' and an 'FCF' (either with extension '.hkl' or '.fcf' is
available, S can we invoked with:
s demo.cif
10.10 - KappaCCD/Denzo to PLATON/SYSTEM-S interface
The KappaCCD/Denzo software provides two output file formats
1.
compound.hkl - i.e. SHELXL structured file. In order to run SYSTEM-S, an
additional
compound.ins has to be prepared.
2.
import.cif - i.e. a reflection CIF containing both reflection data, cell dimensions,
wavelength and optionally the supposed composition formula.
SYSTEM-S can be started for this dataset via
platon -s import.cif.
10.11 - SUMMARY OF S-INSTRUCTIONS
10.11.1 - ABSGAUSS
Absorption correction using a Gaussian Integration Grid.
10.11.2 - ABSTOMPA
Absorption correction following the de Meulenaer & Tompa (1965) analytical correction
technique.
10.11.3 - ASYM (VIEW)
Extensive listing and display of the averaging and completeness of the reflection data as
supplied.
The VIEW keyword invokes a display function giving a detailed view on the reciprocal
lattice (completeness etc.)
10.11.4 - AUTO
Synonymous for the No-Questions-Asked mode.
10.11.5 - DIRDIF
The method of choise for heavy atom structures.
DIRDIF may have problems with structure determinations run with an incorrect
CONTENTS formula, in particular when the number of heavy atoms is different from the