giulioisacco
Hi there,
Is there a way to specify the equivalent position of the atoms in a rigid body or in a restraint? I have this molecule that is cut in two by a mirror plane, and I would like to include N1:4, C1:4, N1:5, C2:5, C3:5, C4:4, C5:5 in the same Z-matrix. Is that possible? These are the lines I wrote in the input file:
rigid
load z_matrix {
N1:4
C1:4 N1:4 !c1n1 1.331`
N1:5 C1:4 =c1n1; N2 !n3c5n2 114.9`
C2:4 N1:4 !c2n1 1.382` C1:4 !c2n1c1 104.5` N1:5 !c2n1c1n1 -1.0`
C2:5 N1:5 =c2n1; C1:4 =c2n1c1; N1:4 =c2n1c1n1;
C3:4 C2:4 !c3c2 1.384` N1:4 !c3c2n1 131.0` C1:4 !c3c2n1c1 -179.1`
C3:5 C2:5 =c3c2; N1:4 =c3c2n1; C1:4 =c3c2n1c1;
C4:4 C3:4 !c4c3 1.390` C2:4 !c4c3c2 117.7` N1:4 !c4c3c2n1 178.4`
C4:5 C3:5 =c4c3; C2:5 =c4c3c2; N1:5 =c4c3c2n1;
}
But of course Topas can’t find site N1:4 or any other site expressed in such way. What’s the right syntax to do that? If I can’t do it, I guess I will have to insert a rigid body with half occupancy forcing the equivalent half occupied atoms to have the same position, I think. It just sounds more complicated to me.
If not in a Z-matrix, can I specify the equivalent position in a distance/angle restraint? That would be generally useful. I had a case where I had to restrain the distances and the angles in a coordination polyhedron. Not all the ligands were part of the asymmetric unit and since I wasn't sure about what Topas was doing with my restraints I did the refinement with GSAS.
Thank you for your help.
Giulio
alancoelho
Hi Giulio
The equivalent position cant be used in a rigid body as the rotate/translate commands would invalidate the symmetry of the space group.
You can use sites_geometry restraint which is in z-matrix form, see test_examples\sites_geometry_1.inp and sites_geometry_2.inp.
sites_geometry uses site_to_restrain (see Technical_Reference.PDF) and the equivalent positions can be got at; its syntax is:
[site_to_restrain $site [ #ep [ #n1 #n2 #n3 ] ] ]...
where ep is the equivalent position and n1, n2 and n3 the lattice vector translations which defaults to 0,0,0.
Or maybe look in the Technical_Reference.PDF for atomic_interaction, ai_exclude_eq_0 and ai_only_eq_0.
If you get stuck then e-mail me.
cheers
alan