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The translation and rotation parameters of a known rigid body fragment with a unit cell can be determined by refining a rigid body against the known fragment. Consider the known fragment to comprise of two C atoms with sites named wC1 and wC2. Then create two more sites called C1 and C2 as follows:

only_penalties
continue_after_convergence	
xdd...
	str...		
		site wC1... occ C 0
		site wC2... occ C 0
		...
		site C1...
		site C2...
		...
		rigid
			z_matrix C1...
                        z_matrix C2...
			rotate @...
				rand_xyz 2
			translate 
				tx ... val_on_continue = Val + Rand(-2, 2);
				ty ... val_on_continue = Val + Rand(-2, 2);
				tz ... val_on_continue = Val + Rand(-2, 2);
 
		Distance_Restrain("C1 wC1", 0, 0, 0, 1)
		Distance_Restrain("C2 wC2", 0, 0, 0, 1)

Here the known site positions start with 'w'; these sites are not part of the rigid body. The sites named C1 and C2 are part of the rigid nody and only the rotate and translate parameters of the rigid body are refined. Note, the use of only_penalties. Also note that setting occupancies to zero means that the site can be used in penalties but it won’t take part in structure factor calculations if observed data were to be refined against.

Refinement would then fit the rigid body against the known site positions.


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