This is a tutorial for indexing, structure solution and subsequent refinement of urea from powder data that I wrote for a powder diffraction course at the University of Bern, Switzerland. If you use it for any other than your own purpose, please cite accordingly.
For the structure refinement, it has to be ensured that sites do not slip off diagonal mirror planes. For this purpose, equations have to be set up. Access to the "International Tables for Crystallography, Volume A: Space-group symmetry" helps a lot.
The following input is needed:
site O1 x 0.01 y 0.01 z 0.01 occ O 1.0 beq 4
site C3 x 0.02 y 0.02 z 0.02 occ C 1.0 beq 4
site N2_A x 0.03 y 0.03 z 0.03 occ N 1.0 beq 4
site H1_A x 0.04 y 0.04 z 0.04 occ H 1.0 beq 4
site H2_A x 0.05 y 0.05 z 0.05 occ H 1.0 beq 4
site N2_B x 0.06 y 0.06 z 0.06 occ N 1.0 beq 4
site H1_B x 0.07 y 0.07 z 0.07 occ H 1.0 beq 4
site H2_B x 0.08 y 0.08 z 0.08 occ H 1.0 beq 4
rigid
z_matrix O1
z_matrix C3 O1 1.258
z_matrix N2_A C3 1.342 O1 121.53
z_matrix H1_A N2_A 0.876 C3 118.83 O1 180
z_matrix H2_A N2_A 0.868 C3 -117.22 O1 180
z_matrix N2_B C3 1.342 N2_A 116.95 O1 180
z_matrix H1_B N2_B 0.876 C3 118.83 O1 180
z_matrix H2_B N2_B 0.868 C3 -117.22 O1 180
rotate rot_a 0 qa 1 qb 0 qc 0
rotate rot_b 0 qa 0 qb 1 qc 0
rotate rot_c 0 qa 0 qb 0 qc 1
translate
ta t_a 0.01
tb t_b 0.01
tc t_c 0.01
The instructions and data can be found here:
http://topas.dur.ac.uk/topaswiki/lib/exe/fetch.php?media=urea.zip