Re: [Jmol-users] Re: Polyhedra connections

[Bob H. <ha...@st...>]

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, ha...@st..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:ha...@st...
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge."  - Albert Einstein