This page addresses questions that were recently communicated.
See also What is PLATON and how to get Started
Currently only A4 format labels are allowed on input to PLATON.
The exceptions on this rule are parentheses, underscore and symmetry extensions (see below).
Atom labels are interpreted (parsed) into three parts, each with their own meaning:
This information is used for sorting purposes and table lookup of atomic type related properties (radii etc.)
Parentheses or an underscore are required when the interpretation of the
label is not unique.
e.g. Cu(2A)a, Cu(), Cu1A_a
Other examples of valid labels:
Cu99, C999, H12"
Atom labels that do not fit in the scheme given above are converted automatically into generated labels (e.g. C#1, C#2, N#1 etc).
Note: Labelling schemes in use in macromolecular crystallography will probably require some editing to fit within the current syntax rules.
When relevant, additional planes can be defined. This should be done before any CALC instruction is given.
Example: Calculate angle (with s.u.) between (C1 C2 C3 C4) and (C5 C6 C7):
Enter the following instructions on the prompt ''>>' after the invocation of PLATON with the appropriate data file:
LSPL C1 C2 C3 C4
LSPL C5 C6 C7
The result will be in the .lis and .lps files.
Note: The number of planes given can be more than one; all n * (n - 1) / 2 inter-plane angles will be calculated.
PLATON has the option for the automatic assembly of a unique connected set of atoms and residues. This is the default behaviour with .spf & .res structured files. The underlying idea is that in the early stages of a structure determination the atom set does not necessarily form connected sets.
Alternatively, it is assumed by default that the atoms should be untouched (i.e. not moved) when data are supplied as as as .cif or .dat (CSD) structured files or when the structure is disordered. In those cases, it is assumed that the user has taken care of this issue.
The default may be changed by clicking on the 'NoMove' button prior to the first PLOT or CALC instruction. The message on the plot is just a reminder of the way the plot was assembled.