2.5.3.12 - DEFINE at1 TO at2 at3 .. atn (DASH/LDASH)
I
nclude a bond between
at1 and the center of gravity of the set
at1-atn. Such an instruction
is usually executed automatically to replace the original five 'covalent' metal to the
individual cyclo-pentadienyl carbon atom bonds by one dashed bond from the metal to the
center of gravity of the ring.
Example:
DEFINE Zn1 TO C1 C2 C3 C4 C5
2.5.3.13 - RADII BONDS ((NORMAL/TO METAL/ TO H/ALL) bt r)/LIST
Sets bonds of specified type (i.e. NORMAL, TO METAL, TO H or ALL) to another radius
(r) and number of lines (related to the value of
bt) on the bond circumference or LIST
current radii.
bt = bond type should be within the range -5 to 5. Negative values correspond
with dashed lines. r = radius (Angstrom).
Example:
RADII BONDS TO METAL 3 0.02
2.5.3.14 - ELLIPSOID (C/H/OTHER) type (lines)
Set plot type of ellipsoids. Type = 0 or 1.
2.5.3.15 - HINCLUDE/HEXCLUDE atomname1 .....
Facility to indicate H-atoms that should remain 'included' in the plot list when the general
(global) condition is 'no-Hatoms' (see
Section 1.4.1.3). The default setting is 'exclude'. A
HEXCLUDE instruction is therefore needed only to undo an earlier HINCLUDE. This
feature is useful when only a few relevant hydrogen atoms are to be shown in the ORTEP
display and the rest left out.
Example:
HINCLUDE H601 H101
2.5.4 - General Instructions
2.5.4.1 - HELP (SPGR)
This instruction provides an on-line HELP facility. The SPGR option lists all space groups
known to PLATON.
2.5.4.2 - LIST BONDS/ATOMS/SYMM/CELL/RADII
This provides for on-line inspection of BOND and ATOM tables, the current symmetry,
CELL dimensions and default radii.
2.5.4.3 - LIST IPR/PAR (ival1 (ival2))
I
nternal parameter values may be inspected with this instruction. A range will be listed when
two values are specified and the full range when none is given.
Example:
LIST PAR 3 5
2.5.4.4 - SET PAR p1 p2
This instruction is not meant for general use. It provides a facility to modify internal
parameter values, in particular those with no equivalent (sub)keyword. p1 is the parameter
number and p2 the new value.
2.5.4.5 - SET IPR p1 p2
This instruction is not meant for general use. It provides a facility to modify internal
parameter values, in particular those with no equivalent (sub)keyword. p1 is the parameter
number and p2 the new value.
2.5.4.6 - SET IGBL p1 p2
This instruction is not meant for general use. It provides a facility to modify internal global
parameter values, in particular those with no equivalent (sub)keyword. p1 is the parameter
number and p2 the new value.
2.5.4.7 - SAVE
This instruction causes the saving of subsequent instructions on a file to be executed on all
(subsequent) data sets, separated by ENDS cards, on the parameter file.
2.5.4.8 - END
This results in a normal end of program when the input file contains only one data set,
otherwise the program restarts for the next data set on the file.
2.5.4.9 - QUIT
This results in an immediate stop of the program, ignoring possible further datasets on the
input file.
2.5.4.10 - STOP
This results in an immediate stop of the program, ignoring possible further datasets on the
input file.
2.6 – Parameter File Standards
The atomic parameters (including unit cell parameters, coordinates and temperature
parameters) for a given structure may be supplied in various ways:
- CIF
- The Crystallographic Information File standard
- RES
- The SHELX .res style format
- SPF
- The Standard Parameter File format (see
Appendix I.1)
Chapter 3 – The PLUTON Tool
PLUTON is an easy-to-use interactive graphics program (now integrated in the program
PLATON). It is used as a tool for viewing, RES file modification, structure analysis and
presentation of molecular structures. Drawings of either individual molecules or assemblies
of molecules in a crystalline arrangement can be produced. PLUTON may be considered as
a completely redesigned and considerably expanded descendent of the original PLUTO
program versions by Sam Motherwell and Bill Clegg.
3.1 - Introduction to PLUTON and its Design
Drawings are produced either on a display surface (called DISPLAY) and/or as a file (called
META) saving graphics instructions for later use such the inclusion in a publication text or
to be sent to a laser printer. Coordinate input data can be either Cartesian or fractional,
originating from crystal structure determination programs such as SHELXS, refinement
programs such as SHELXL, from the Cambridge Structural Database or otherwise.
A drawing of a molecular structure as generated with PLUTON may be thought of in three
principle aspects: the content, the style and the viewpoint.
- The content of the drawing requires the definition of items such as ARU's (=
Asymmetric Residue Units,
vide infra) making up the list of molecules and anions to be
displayed, atoms within ARU's, connections between atoms (= bonds), labels, and unit
cell representation. By default, connected and possibly symmetry expanded sets of
atoms constituting molecules or ions will be assembled from the input data.
- The style of the drawing may be like a STICK model (atoms are points and bonds are
single lines joining them), a SOLID ball-and-spoke, ball-and-STRAW or ball-and-ROD
model, mainly differing in the default settings of the variable radii for atoms and bonds,
or as a space filling model with van der Waals radii assigned to each atom (also called
CPK model). The atom types may be distinguished with various patterns in the black-
and-white mode or colored to differentiate between the atom types. Drawings may be
made in parallel projection, perspective, or stereo-pair perspective. By default, a
STICK-style drawing will be generated in the PLUTON native mode or a STRAW-style
drawing in the PLUTON-auto mode.
- The view direction may be chosen with reference to molecular features such as lines
and planes defined by atoms, or with reference to the unit cell or orthogonal axial
systems. The view direction may be further modified by rotations, giving flexible
control of the viewpoint. By default a minimum overlap view is chosen.
All input to the program is free-format, using (sub)keywords and numerical data. The input
to PLUTON is normally provided in two parts: a disk file, in general produced by a program
or prepared with a text editor and containing the pertinent data on the structure at hand such
as atomic coordinates, followed by interactive input of the instructions via the keyboard or
by mouse-clicks.
In general, a small set of instructions in terms of global keywords with associated default
parameter settings will suffice to produce a drawing for the supplied data. Alternatively, all
input may be given on the disk file or entered by the keyboard.
More than one data set, separated by an ENDS card may be present on the input file. This is