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--- //[[alan.coelho@bigpond.com|Alan Coelho]] 2017/08/28 04:08//
The following example runs stand-alone; ie. no data files necessary. The rotation and translation coordinates are determined in one refinement Cycle.
Atoms types given for occupancy is for display purposes.
/*
Rigid Body - Matching to a known fragment
Determining rotation and translation parameters for a known fragment
The known-fragment is in fractional coordinates.
Doing the same for a fragment in Cartesian coordinates is possible by changing the lattice angles to 90 degrees and adjusting the lattice parameter lengths.
*/
only_penalties
continue_after_convergence
yobs_eqn !aac.xy = 1; min 10 max 20 del 0.02
STR(p1)
a 6.54131
b 7.75969
c 9.13579
al 96.18524
be 107.23760
ga 101.40126
view_structure
' Known Fragment
site Al1 x 0.24949` y 0.20782` z 0.41049` occ Al+3 1 beq 1
site O1 x 0.54370` y 0.19252` z 0.43481` occ O-2 1 beq 1
site O2 x -0.04471` y 0.22313` z 0.38619` occ O-2 1 beq 1
site O3 x 0.25944` y 0.35365` z 0.25728` occ O-2 1 beq 1
site O4 x 0.23953` y 0.06199` z 0.56370` occ O-2 1 beq 1
site O5 x 0.35706` y 0.41500` z 0.56828` occ O-2 1 beq 1
site O6 x 0.14191` y 0.00063` z 0.25270` occ O-2 1 beq 1
' Rigid body to fit to known fragment
site wAl1 x 0 y 0 z 0 occ Zr 1 beq 1
site wO1 x 0 y 0 z 0 occ C 1 beq 1
site wO2 x 0 y 0 z 0 occ C 1 beq 1
site wO3 x 0 y 0 z 0 occ C 1 beq 1
site wO4 x 0 y 0 z 0 occ C 1 beq 1
site wO5 x 0 y 0 z 0 occ C 1 beq 1
site wO6 x 0 y 0 z 0 occ C 1 beq 1
rigid
Octahedra(wAl1, wO1, wO2, wO3, wO4, wO5, wO6, 1.9)
macro VA { val_on_continue = Rand(-180, 180); }
rotate @ 0 VA qa 1
rotate @ 0 VA qb 1
rotate @ 0 VA qc 1
translate
ta @ 0
tb @ 0
tc @ 0
' Probably not necessary to include all of these
Distance_Restrain(Al1 wAl1, 0,0,0,1)
Distance_Restrain(O1 wO1, 0,0,0,1)
Distance_Restrain(O2 wO2, 0,0,0,1)
Distance_Restrain(O3 wO3, 0,0,0,1)
Distance_Restrain(O4 wO4, 0,0,0,1)
Distance_Restrain(O5 wO5, 0,0,0,1)
Distance_Restrain(O6 wO6, 0,0,0,1)
The following should be seen from the GUI after running the above:
{{::rigid-match.jpg}}