[cctbxbb] Problems with conversion from conventional to primitive cell
Jörg-Rüdiger Hill
Joerg-Ruediger.Hill at scienomics.com
Thu Nov 24 02:12:31 PST 2005
Dear All,
I am trying to convert from a conventional cell to a primitive cell using
cctbx, but I am having some problems. What I do is the following:
1) I construct a spaceGroup object using the space group symbol
2) I retrieve the change of basis operator using z2p_op() from the space
group object
3) I apply this operator to the conventional cell
4) I take a list of symmetry unique atoms and apply the operator to their
fractional coordinates
At this point I have a primitive cell which agrees exactly with what I get
from other codes. The problem comes when I am trying to construct all atoms
from the symmetry unique ones. I do this by the following procedure:
5) I take the space group object and call its change_basis() method with
the z2p_op() operator
6) I loop over all order_z() symmetry operations in the space group applying
the operation to the fractional coordinates making sure that I don't
create two atoms at the same position
The whole procedure works well, e. g., for cubic crystals. However, if I
take a hexagonal crystal (e. g., Cr2O3, R -3 c) the crystal build by steps
5 and 6 above is not correct. In this case the conventional cell has a=b != c,
alpha=beta=90, and gamma=120, but the primitive cell has a=b=c and
alpha=beta=gamma. I have tried to add ":R" to the space group symbol and
constructing a new spaceGroup object in step 5 above, but that does not make
any difference. What do I have to do to build the crystal in this case or
what is wrong with my procedure ?
Best Regards,
Jörg-Rüdiger Hill
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