Appendix VI – The PLATON/CALC Listing Explained
The PLATON/CALC instruction invokes an extensive listing on a file with extension
.lis
with information that can be derived from the input data (preferably a
.cif). This file is
suitable to be inspected with an editor. For hardcopy on laser printers both PostScript and
PDF versions are or can be produced with extensions
.lps and
.pdf respectively. Below the
listing that is obtained for a compound named ambi will be examined. The relevant files
ambi.cif,
ambi.fcf,
ambi.lis,
ambi.ps,
ambi.pdf can be downloaded from <>. Not all
features can be illustrated with a single example. Features that are missed in the current
example will be illustrated with the relevant parts of other examples.
Cell Dimensions.The listing starts with info related to the cell dimensions and includes an
orthogonalization matrix that brings the coordinates of the atoms in an orthogonal Angstrom
scale system. Such a system is useful for simple calculations such as distances between
atoms by hand. Orthogonalization is not unique. In the literature at least three versions can
be found. The method used in PLATON is the one described in the excellent book of Dunitz
(1979).
Space Group Symmetry. The symmetry as provided on input is analyzed and converted
into a standardized list of symmetry operator, Hermann-Mauguin and Hall space group
symbols (Hall, 1981). First comes the set of symmetry operations not including the
inversion or lattice centering operators. This is essentially the group generated from a small
set of so-called generators (for P2
1
2
1
2
1
this involves just 2 of the three screw axis). This list
is expanded by inversion where applicable, taking care that translation parts are always in
the range 0 to 1. The resulting list is expanded according to the lattice centering operations.
The resulting list is used in all subsequent calculations.
ADDSYM. A default analysis is carried out to report on possibly missed higher or pseudo
symmetry with ADDSYM (an extended version of the MISSYM algorithm of Le Page
(1987, 1988)). The result of this analysis is not implemented in the rest of the calculations
but might need a more detailed analysis.
Coordinates. The structure is analyzed on the bases of predefined or optionally user-
supplied values associated with the atom types in the structure. The values used are listed.
The structure is analyzed in terms of molecular residues, in this case two, and their
coordinates listed both in terms of fractional coordinates as with Angstrom coordinates. The
atom list is sorted with various properties listed for each atom such as refinement flags and
site-occupation (population) parameter that should be 1.0 unless disordered. This value may
differ from the SHELXL site-occupation parameter value by the site symmetry number for
atoms on special positions. The coordinate list is completed for molecules on special
positions.
Summary of of the unit cell contents. The centre-of-gravity for each molecular residue is
listed along with its formula and multiplicity in the unit cell. A moiety and sum formula
with associated Z value is derived from that information. Those values may need a change
by a small integer value in complicated cases where chemistry might point to a better
presentation. In any case, when the Z value is changed also F(000), Z' and the molecular
weight have to be changed accordingly. The calculated Friedif value (Flack & Shmueli,