I'm trying to compose a general web page that would allow
users to construct a unit cell packing diagram using a CIF and
whatever strategy they would like to pursue. My first attempt is at:
http://macxray.chem.upenn.edu/cells/3159SG.html
To develop this, tho, two changes would be nice:
(1) right now, a symop, for example, -X, 1/2+Y, 1/2-Z, that would put
a molecule in a neighboring unit cell with a negative X-coordinate is
adjusted by Jmol so the co-ordinates are all positive. I would prefer
that the symop -X, 1/2+Y, 1/2-Z actually put the molecule at a
negative X! This is important if I have an external program that
tells me there is a hydrogen bond between symop X, Y, Z and symop -X,
1/2+Y, 1/2-Z. I would like to be able to draw those specific
molecules with Jmol.
(2) could the command load "" {3 3 3} be changed to also accommodate
negative co-ordinates? That is instead of loading cells 555 thru 777
with 555 being the base cell, it would be nice if it loaded cells 444
thru 666 with 555 being the base cell. Again, this change would make
Jmol agreeable with other output that has, e.g., a hydrogen bond to a
molecule at -1+X, 1/2-Y, 1/2+Z.
And finally that page referenced above was written for space group
P2(1)/c and those four specific symops. Is it possible to communicate
from the CIF the number of symops and their x, y, z expressions so a
general page could be written that does not know the symops
beforehand? Is this something that can be done by javascript?
Pat Carroll
Chem Dept
U of Penn
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