Chapter 10: Drawing Style Control
The user is able to choose from three different drawing styles.
The basic syntax for style control is :-
XXXX at1 at2 el1 el2
where XXXX is LINE, BALL or ELLIPSE as required. The user may specify atoms eg C1, C2 and/or elements eg C O to be drawn in the XXXX style. The user may therefore have all three styles present at any one time within the picture. Alternatively the ALL may be used to convert the drawing style of all the atoms present to XXXX. The initial drawing style used is LINE.
The ELLIPSE drawing style is only available if the user has
that contains information on the temperature factors (isotropic
anisotropic) of the atoms concerned. The ellipse drawing style
represents atoms by their thermal ellipsoid. Note that negative eigen
values are reset at input to .001* the next largest.
If the information
available is U[iso] only, a circle is plotted whose radius
is scaled according to its value.
These subcommands can be used to specify which atoms are to be affected by the drawing style command.
Several other commands are available in addition to the basic style commands.
There are no extra commands following LINE.
RADII The user can specify the drawing radius (in angstroms) of a specified atom or element. The syntax is :-
BALL RADII C 0.8 N1 1.1
which will draw all C atoms with a radius of 0.8 angstroms, and the N1 atom with radius of 1.1 angstroms.
DEFAULT This sets all the radii to their initial covalent values. The syntax is:-
BALL RADII DEFAULT.
VANDERWAALS This sets the radii of the specified atoms/elements to the appropriate values. The syntax is BALL RADII COVALENT N. The further subcommand ALL can be used - BALL RADII IONIC ALL - to set all atoms if required.
UNFILL These are header commands and are used to specify whether the circles drawn in the BALL style are to be filled with colour or not. No arguments are required by these commands.
ELLIPSE may be followed by the sub command TYPE which enables the user to control the type of ellipse used to represent the atom. The syntax is:-
ELLIPSE TYPE at/els/all n.
Type 'n' can take any of four values :-
1 - bounding ellipse only. 2 - bounding ellipse and principal ellipses, this is the default representation. 3 - as 2 but excluding the principle axes. 4 - as 2 but with shading.
ALL ALL can be used followed by a number to set the ellipse type of all atoms in the drawing.
Note that any use of ELLIPSE TYPE will set all the atoms referred to ellipse type even if they were previously in LINE or BALL. Hence,
ELLIPSE TYPE C 2 will have all carbon atoms drawn in type 2 form. ELLIPSE TYPE ALL 4 will have all atoms drawn in type 4 form
The NEGATIVE sub command requires one argument. If atoms are
with negative temperature factors the atoms temperature factor
using the value specified by ELLIPSE NEGATIVE u. The default
value of u
This is used to specify the size of the ellipsoid probability envelope displayed. It is followed by a percentage value.