Jmol-developers,
Before I forget -- my VPN is down, so I can't show you this, but I'd like to
get people thinking about it. I hit on the idea today of being able to
manipulate crystal symmetry operations in Jmol. Then I realized that all we
needed were a few simple matrix operations and a matrix variable. So now we
have 3x3 and 4x4 matrices in Jmol as variables that can be multiplied,
inverted, applied to points, and such. They look like this:
x = [[1,2,3],[4,5,6],[7,8,9]]
(same as in JavaScript, though here we are restricted specifically to 3x3
and 4x4 matrices)
This is interesting, because 3x3 matrices are rotations and inversions, and
4x4 matrices are rotations+inversions+translations. So what's really
interesting is that by manipulating 4x4 matricies, you can apply *and
manipulate* crystal symmetry operations such as rotation-inversions, glide
planes, and such. I think it works pretty well:
for Jmol 11.9.3:
load quartz.cif packed
print symop(2) # gives the 4x4 matrix for symmetry operation 2
print symop(-2, "array") # details about the inverse of symmetry operation 2
x = symop(2) # assigns the matrix to a variable
y = x * {1/1, 0, 0} # the point in space that the fractional coordinate {1
0 0} maps to
print x*x # the symmetry operation applied twice
print symop(x*x,"description") # description of that -- something like "C3
axis"
draw symop 2 # draw that operation
draw symop -2 # draw its inverse
draw symop @{symop(2) * symop(2)} # draw its second application
and this is the really interesting part:
draw symop @{symop(2) * symop(3)} # draw the product of the two operations
print symop(symop(2) * symop(3), "description") # its description
I'm hoping someone out there in Jmol land is interested in this and will
find something interesting to do with it. I'd like to work with someone to
perfect it. The first application I can think of is an extension to the
symmetry pop-up menu item that would read "all mirror planes" "all glide
planes" etc...
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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