rigid_body_-_matching_to_a_known_fragment
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— | rigid_body_-_matching_to_a_known_fragment [2022/11/03 15:08] (current) – external edit 127.0.0.1 | ||
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+ | --- // | ||
+ | |||
+ | The following example runs stand-alone; | ||
+ | |||
+ | Atoms types given for occupancy is for display purposes. | ||
+ | |||
+ | < | ||
+ | /* | ||
+ | Rigid Body - Matching to 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 | ||
+ | |||
+ | | ||
+ | a | ||
+ | b | ||
+ | c | ||
+ | al | ||
+ | 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 | ||
+ | site O2 x -0.04471` y 0.22313` z 0.38619` occ O-2 1 beq 1 | ||
+ | site O3 | ||
+ | site O4 | ||
+ | site O5 | ||
+ | site O6 | ||
+ | |||
+ | ' 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 | ||
+ | | ||
+ | |||
+ | macro VA { val_on_continue = Rand(-180, 180); } | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | | ||
+ | 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: | ||
+ | |||
+ | {{:: | ||