rigid_body_-_matching_to_a_known_fragment
— 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_body_-_matching_to_a_known_fragment.txt · Last modified: 2022/11/03 15:08 by 127.0.0.1