major disorder components and those less than 0.5 as minor disorder components. The usual
transformations on input coordinates are restricted. In general it will be necessary to supply
disordered molecules as connected sets. The calculation of distances and angles etc. will
extend only to entities involving the major disorder component or the minor disorder
component but not between them.
2.4.3 – Molecules, Residues and ARU's
The concepts of molecules and residues are related but not always synonymous with those
in the PLATON context. A residue is defined as a part of the structure that is connected by
intra-molecular bonds only and is associated with a number (residue number). A structure
may thus contain one or more residues (molecules, ions, chains or network). Residues may
be chemically equivalent or chemically distinct. An
ARU is defined as the unique
asymmetric part of a residue connected by intra-molecular bonds only. One or more
ARU's
may join by crystallographic symmetry into one residue. A particular
ARU is designated by
a code: [nijk.rr] where
n denotes the symmetry operation with respect to the basic molecule,
ijk the translation with respect to 555 and
rr the residue number. The crystal structure of
sucrose (space group P2
1
) thus consists of two molecules (e.g. [1555.01] and [2545.01]) but
only one residue.
2.4.4 - Population parameters
A distinction should be made between 'population parameters' as used in SHELXL
(indicated with
sof) and those in the CIF (indicated here with
PP) and in PLATON. Most
refinement packages refine a population parameter that is defined as
sof = PP / ssn, where
ssn is the site symmetry number. E.g. A full weight atom on an inversion center has in
general
PP=1.0 when fully occupied but
sof = 0.5 in SHELXL since
ssn = 2.
2.5 – Instruction Summary
This section provides a description of the available instructions for keyboard input. The
more common ones are also available through mouse-clicks on menu-items. The
instructions are grouped together as compound specific, calculation, plot, list and general
instructions. The logical order of the geometry calculations is intra-molecular, inter-
molecular and coordination. In the description of individual instructions below the
following applies:
- (Sub)keywords are in uppercase and user data in lower case
- Data in parentheses are optional.
- Data in [] are defaults.
- Choices are separated by a slash.
Note: parentheses in atom names (on input) are ignored except for that Ag denotes the atom
type and Ag() the individual atom. Lower case input is automatically converted to upper
case. Instruction records with a blank character in position 1 or a # are ignored. Instruction
records may be continued with data on the next line by placing the symbol = at the end of
the line.
2.5.1 - Directives Preceding all Calculations
The instructions given in this section will be necessary only in special situations.