Problems with Rigib body macros

CGAC

Hi, I'm Cristian

I'm working with one material that has two aromatic rings, one from a 4-nitrofenil group and the other one from a benzil group. The space group of the material is P21 and I'm planning to use rigid body macros to refine both rings. For the benzil group I not having any problems to get the values of rotation and translation for the macros Rotate_about_axies and Translate, respectively. But for the ring of the 4-nitrofenil group the result in the view structure in TOPAS looks odd.

Here it is the lines of the INP file that I'm using:

only_penalties
continue_after_convergence

yobs_eqn aac = 1; min 10 max 20 del 0.01 'Dummy file

str
space_group P1211
	a   4.824579_0.001199
	b   12.478312_0.002960
	c   15.087978_0.005490
	be   97.18336_0.01500

	'Anillo nitrofenilo
	site wC7 num_posns  2 x  0.4682 y  0.0339 z  -0.0446 occ C  1 beq 1
	site wC8 num_posns  2 x  0.2109 y  0.0869 z  -0.0475 occ C  1 beq 1
	site wC9 num_posns  2 x  -0.0008 y  0.0696 z  -0.1174 occ C  1 beq 1
	site wC10 num_posns  2 x  0.0475 y -0.0022 z 0.1847 occ C  1 beq 1
	site wC11 num_posns  2 x   0.3002 y  -0.0567 z  -0.1834 occ C  1 beq 1
	site wC12 num_posns  2 x  0.5099 y  -0.0382 z  -0.113 occ C  1 beq 1

	site C7 num_posns  2 x  0 y  0 z  0 occ C  1 beq 1
	site C8 num_posns  2 x  0 y  0 z  0 occ C  1 beq 1
	site C9 num_posns  2 x  0 y  0 z  0 occ C  1 beq 1
	site C10 num_posns  2 x 0 y 0 z 0 occ C  1 beq 1
	site C11 num_posns  2 x  0 y  0 z  0 occ C  1 beq 1
	site C12 num_posns  2 x  0 y  0 z  0 occ C  1 beq 1

	rigid
	 z_matrix C7
	 z_matrix C8 C7 1.387
	 z_matrix C9 C8 1.384 C7 121.183
	 z_matrix C10 C9 1.377 C8 118.743 C7 0.28
	 z_matrix C11 C10 1.377 C9 121.863 C8 0.19
	Rotate_about_axies(rx1  23.41153`, ry1 -7.37915`, rz1  122.71870`)
	Translate(ta1  0.06617`, tb1  0.10524`, tc1  0.38480`)


	Distance_Restrain(wC7 C7, 0, 0.00, 0, 1)
	Distance_Restrain(wC8 C8, 0, 0.00, 0, 1)
	Distance_Restrain(wC9 C9, 0, 0.00, 0, 1)
	Distance_Restrain(wC10 C10, 0, 0.00, 0, 1)
	Distance_Restrain(wC11 C11, 0, 0.00, 0, 1)
	Distance_Restrain(wC12 C12, 0, 0.00, 0, 1)

	view_structure
           'end

I really appreciate if anyone can tell me why that happened and how to fixed.
Thanks in advance,
CGAC.

johnsoevans

Are you trying to match a rigid body to a known fragment?
One common problem when doing this is specific atoms you're trying to match. For example the site being generated by the rigid body (C) might be a different symmetry equivalent to the site listed (wC), so a large distance away.
In general you can only get around this by specifying the full atom name using: Distance_Restrain("C1 wC1", 0, 0, 0, 1). Here the numbers detail the symmetry operator used to generate the atom and the unit cell in which it sits.
There's a work around to this discussed on the wiki.

CGAC

johnsoevans
Hi John,

Yes, I'm trying to match a rigid body to a known fragment. Today looked once again the data and I noticed that the z coordenate of the atom wC10 was wrong, that is why I couldn't match a rigid body with the fragment properly. I already fix that and everything is working well with the macro.

Thanks!