Subject:

**How to constrain atoms part of a rigid body to special positions?**
Hello,

I am dealing with the Rietveld refinement of a metal-organic framework which has cubic symmetry (Fm-3m) and contains tetrafluoroterephtalic acid as a linker.

The linker is defined by five crystallographically independent atoms (named O2, C1, C2, C3 and F), three of which should sit in special positions: O2 (x, 0, z), C1 (x, 0, x) and C2 (x, 0, x).

I have set up the following rigid group:

With such a rigid group, the position of C2 is constrained to be the following: Linktrans1, 0, Linktrans1

The problem arises when I try to constrain the y coordinate for both O2 and C1 to be 0 and the x and z coordinates for C1 to have the same value.

I have tried to create and refine parameters, but these seem to conflict with the rigid body.

Is there a way of getting around this issue?

Thanks,

Marco

I am dealing with the Rietveld refinement of a metal-organic framework which has cubic symmetry (Fm-3m) and contains tetrafluoroterephtalic acid as a linker.

The linker is defined by five crystallographically independent atoms (named O2, C1, C2, C3 and F), three of which should sit in special positions: O2 (x, 0, z), C1 (x, 0, x) and C2 (x, 0, x).

I have set up the following rigid group:

**rigid**

z_matrix C2

z_matrix C3 C2 1.39

z_matrix F C3 1.35 C2 120

z_matrix C1 C2 1.48 C3 120 F 0

z_matrix O2 C1 1.30 C2 120 C3 = torsion;

prm torsion 43.27588` max 90 min 0

prm Linkrot1 -179.98276`_LIMIT_MIN_-180 max 180 min -180

prm Linkrot2 -180.00000`_LIMIT_MIN_-180 max 180 min -180

prm Linkrot3 14.92436` max 180 min -180

prm Linktrans1 0.20673`

prm !Linktrans2 0

rotate @ =Linkrot1; qx 1

rotate @ =Linkrot2; qy 1

rotate @ =Linkrot3; qz 1

Translate( @ =Linktrans1; , =Linktrans2; , @ =Linktrans1; )z_matrix C2

z_matrix C3 C2 1.39

z_matrix F C3 1.35 C2 120

z_matrix C1 C2 1.48 C3 120 F 0

z_matrix O2 C1 1.30 C2 120 C3 = torsion;

prm torsion 43.27588` max 90 min 0

prm Linkrot1 -179.98276`_LIMIT_MIN_-180 max 180 min -180

prm Linkrot2 -180.00000`_LIMIT_MIN_-180 max 180 min -180

prm Linkrot3 14.92436` max 180 min -180

prm Linktrans1 0.20673`

prm !Linktrans2 0

rotate @ =Linkrot1; qx 1

rotate @ =Linkrot2; qy 1

rotate @ =Linkrot3; qz 1

Translate( @ =Linktrans1; , =Linktrans2; , @ =Linktrans1; )

With such a rigid group, the position of C2 is constrained to be the following: Linktrans1, 0, Linktrans1

The problem arises when I try to constrain the y coordinate for both O2 and C1 to be 0 and the x and z coordinates for C1 to have the same value.

I have tried to create and refine parameters, but these seem to conflict with the rigid body.

Is there a way of getting around this issue?

Thanks,

Marco