I have incorporated this into
http://www.stolaf.edu/people/hansonr/jmol/docs/#.polyhedra
Since I couldn't get translucent to work myself, I left that info out for now.
Bob
Miguel wrote:
can you remind us of the command for that?
Polyhedra are constructed using the selected set of atoms as the centers.
Either bond connectivity or distance can be used to specify the vertices.
If you specify distance then you can also specify a set of atoms that are
valid as the vertices. This set of valid vertex atoms must be specified in
parentheses. (I don't recall, but I don't think this vertex-set selection
works for 'polyhedra bonds').
If you have exactly 4 vertices and the center is on the inside of the 4
planes formed by those vertices then you become a tetrahedron.
If you have exactly 6 vertices and you are on the correct side of the
planes formed by those vertices then you become an octahedron.
Change color on the selected polyhedra.
color polyhedra hotpink
Making the polyhedra translucent is valuable because you can see the atoms
inside the polyhedra.
color polyhedra translucent orange
You can explicitly make the edges stand out a bit more to emphasize the
polyhedra. You can either turn on all the edges, or only the front edges
polyhedra edges|frontedges|noedges
Showing only the front edges may help when using translucent polyhedra.
load "samples/crystals/kaolinite_small.mol"
#turn on polyhedra based upon bond connectivity
polyhedra bonds
select atomno > 75
# change the color of some
color polyhedra blue
select atomno > 50 && atomno < 100
# make some translucent
color polyhedra translucent yellow
polyhedra frontedges
load samples/crystals/kaolinite_big_noconnect.pdb
# make polyhedra where aluminum is at the center
select aluminum
# and oxygens within 2.0 angstroms are at the vertices
polyhedra 2.0 (oxygen)
Miguel
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Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN
55057
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