For the "full Monte" see
http://www.stolaf.edu/people/hansonr/jmol/test/poly/poly.htm
:)
Proposed for the documentation:
polyhedra
Jmol supports polyhedral representation of molecular structures,
including tetrahedra, octahedra, and many other geometric forms.
Centers. Potential polyhedra centers are defined either by the
currently selected set of atoms or by explicitly indicating an atom
expression within the polyhedra command.
polyhedra (chlorine)
polyhedra (atomno=1) 2.0
polyhedra (atomno=1 or atomno=3) 4
select (atomno < 3); polyhedra 4
Vertices. From this set of centers, polyhedra can be formed based upon
a specified number of bonds (e.g., polyhedra 6) or upon a maximum
distance expressed as a decimal number (e.g., polyhedra 2.0). In
addition, you can add the keyword "TO" and a second atom expression to
indicate that only atoms matching this expression should be selected
for vertices. The default is to use bonds, but if a radius and a
number of bonds is indicate, then the number of "bonds" simply means
the number of vertices within this radius, actually "bonded" or not.
polyhedra (silicon) TO (oxygen) 4
polyhedra (zinc) TO (oxygen or nitrogen) 5.0
Options. Several additional options may be used to adjust the
appearance of the polygons.
These include:
COLLAPSED
Collapse the polygon into the center atom, as though all the volume
had been removed, leaving only a "skin." This allows visualization of
the central atom.
EDGES
Highlight the edges of the polyhedra.
FRONTEDGES
Highlight only the front edges of the polyhedra (Useful when color is
translucent.)
MAXFACTOR [decimal number] (default 1.85)
Determines the cutoff point used to determine faces. Vertex-vertex
distances longer than this factor times the average center-vertex
distance are discarded. In certain circumstances this parameter can be
adjusted to produce better polygons.
FACECENTEROFFSET [decimal number] (default 0.25)
This absolute offset, in Angstroms, sets the position of the point at
the base of the cavity in a collapsed polygon. The value 0.0 indicates
that the base of the cavity should be the central atom and is not
recommended. Adjusting this parameter can lead to interesting
effects.
Additional commands that can be invoked after polygons have been
created include the following. Note that each can include a specified
atom set or use the current selection so as to operate only on
specific polyhedra based on their center atoms.
polyhedra ON/OFF{default: ON}
Show or hide polyhedra whose central atom is selected.
polyhedra DELETE
Delete the polyhedra associated with central atoms that
are selected.
polyhedra EDGES
As above
polyhedra FRONTEDGES
As above
polyhedra NOEDGES
Turns off edges
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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