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9.3 PLATON - ANALYSE Menu WinGX v1.64
5.2 Disorder
The program attempts to manage the problems that are encountered with several types of
disorder. Only two-fold disorder is allowed. Populations higher than 0.5 are understood as
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 both.
5.3 Molecules and Residues
The concepts of molecules and residues are related but not always synonymous within the
PLATON realm. A residue is defined as a part of the structure that is connected by intramolecular
bonds only and is associated with a number. A structure may thus contain one or
more residues. Residues may be chemically equivalent or chemically distinct. A molecule is
defined as an asymmetric part of the structure connected by intra-molecular bonds only.
Several molecules may join by crystallographic symmetry into one residue. A particular
molecule 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 structure of sucrose thus consists of two molecules (e.g. [1555.01] and [2545.01]) but
only one residue.
6. Parameter files
The atomic parameters (including unit cell parameters, coordinates and temperature
parameters) for a given structure may be input in various ways: the STANDARD
PARAMETER FILE Format (SPF), SHELX type .INS/.RES files, simple XYZ Angstrom
coordinate format, CIF, PDB, CSD-FDAT formats
The SPF-format is card image oriented. The first four characters on a card specify the nature
of the data that follow on that card. Data that are not needed for the current program are
simply skipped. All data are in free format.
6.1 The SPF format
TITL text
This text may be used for various titling purposes. It may be overridden at any time by
another TITL instruction.
CELL (wavelength) a b c alpha beta gamma
Optional wavelength and cell parameters in Å’s and degrees respectively. No CELL card is
needed for Å data input. The wavelength is used for the calculation of the linear absorption
coefficient.
CESD sig(a) sig(b) sig(c) sig(alpha) sig(beta) sig(gamma)
This optional card specifies standard deviations in the cell parameters. No CESD card is
needed for Angstrom data. The cell e.s.d. is combined with the coordinate e.s.d. for the
calculation of the e.s.d. in derived parameters.
Chapter. 9.3 PLATON 24