Miguel wrote:
Miguel, is this the sort of thing you are talking about
wanting to be able to do in Jmol?
From something like this:
4.910 4.910 5.402
90.000 90.000 120.000
SPGR =154 P 32 2 1 OPT = 1
1 Si1 0.48078 0.48078 0.00000
2 O2 0.15018 0.41459 0.11650
going to something like the first model at
http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm
Be advised that we got an 'ArrayIndexOutOfBoundsException' in Normix3D the
first time that I followed this link
Thanks. What happened the second time?
You asked if this is the kind of thing that I want to be able to do ...
I think so ... but this seems to be a much fancier version of what I was
thinking.
I was thinking something more like ... start with 1 NaCl and grow a 4x4x4
crystal.
But I assume that the ideas are the same.
right, well, the point is that usually you don't have cartesian
coordinates, so we would have to install all the symmetry knowledge
contained in that space group designation.
From an implementation perspective, my thought was that you started with a
model, you applied the 'crystal 3 3 3 <otherParameters>' command ... and
you created a new model.
right -- something like that. It's what's behind that simple command
that's the real trick:
-molecular vs unit cell depiction (whether you combine pieces from one
end of the unit cell with those from the other so as to complete molecules
-turning space-group designations into symmetry elements
-applying the symmetry elements (which are often redundant) to
generate derived atom positions.
-building in the necessary space-group information. On this we might
be in luck: http://cci.lbl.gov/sginfo/
SgInfo is library of ANSI C routines
* for the generation of symmetry matrices
[that's us]
* easy on-line access to a total of 530 settings of all space
groups listed in the International Tables Volume I (1952) (ITVI) and
Volume A (1983) (ITVA)
[ooooh, that's useful]
and... jackpot!
http://cctbx.sourceforge.net/
Here's the kind of function I like to see already present in open
source (if not Java) from
http://cci.lbl.gov/publications/download/iucrcompcomm_jan2003.pdf
quartz_structure = xray.structure(
special_position_settings=crystal.special_position_settings(
crystal_symmetry=crystal.symmetry(
unit_cell=(5.01,5.01,5.47,90,90,120),
space_group_symbol="P6222"
)
),
scatterers=flex.xray_scatterer([
xray.scatterer(
label="Si",
site=(1/2.,1/2.,1/3.),
u=0.2),
xray.scatterer(
label="O",
site=(0.197,-0.197,0.83333),
u=0)])
)
yeah, that's it!
Bob
--
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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