Frequently Asked Questions

Chapter 7: Refinement

: 7.1: What infomation does Crystals need for least squares refinement?; 7.2: Refinement instructions; 7.3: How do I add restraints?

7.1: What infomation does Crystals need for least squares refinement?

List 1 - Cell

List 2 - Symmetry

List 3 - Scattering factors

List 4 - Weighting scheme (default - unit weights)

List 5 - Parameters (model)

List 6 - Observations (reflections) AND/OR List 16 - Observations (restraints)

List 12 - Refinement instructions

List 23 - Refinement options

List 28 - Reflection acceptance criteria (default - all)

List 29 - Asymmetric unit contents

7.2: Refinement instructions

List 12 can be entered in the following manner:

 \LIST 12
 FULL I(1,X'S,U'S) C(7,X'S) O(1,Y) O(1,U[ISO]) UNTIL C(6)
 GROUP C(1) UNTIL C(6)
 END

This example refines the position and Uij's of I(1), the position of C(7), the y-coordinate of O(1) and the isotropic thermal parameters of atoms O(1) until C(6) based on the order they appear in list 5. It also refines the positions of atoms C(1) to C(6) as a rigid-body.

Alternatively, choose Guided I{Automatic from the Refinement menu to run a script which automatically writes List 12 and refines the structure based on its assessment of the current state of progress.

7.3: How do I add restraints?

Restraints are set up using list 16.

For easy generation of simple restraints select two, three or more atoms in the model window. Right click on one of the group and choose an option from the pop-up restraints sub-menu. Any restraints generated in this way will be appended to the existing restraint instructions in list 16.

An example List 16 could be:

 \LIST 16
 DIST  1.39 , .01 =      C(1) to C(2)
 DIST  0.0  , .01 = MEAN C(3) to C(4), C(4) to C(5)
 VIBR  0.0  , .01 =      C(6) to C(7)
 U(IJ) 0.0  , .02 =      C(8) to C(9)
 PLANAR                  C(1) until C(6)
 SUM                     K(1,OCC), K(2,OCC), K(3,OCC)
 LIMIT                   U[11] U[22] U[33]
 END

The first instruction restrains the bond C(1) to C(2) to be 1.39 angstroms with an e.s.d. of .01 angstroms.

The second instruction is a similarity restraint which restrains the difference between two bonds (C3-C4 and C4-C5) to be zero with an e.s.d of .01 angstroms.

The third restrains the difference between the mean square displacement of each atom along the direction of a bond to be zero, with an e.s.d of .01. Isotropically refined atoms will also be dealt with correctly.

The U(IJ) restraint between C(8) and C(9) restrains the difference between the corresponding Uij components to be zero with an e.s.d of .02.

The planar restraint restrains atoms C(1) to C(6) (based on the list 5 order) to be planar. The e.s.d defaults to 0.01.

The sum restraint holds the sum of the specified parameters (in this case the occupancy of three postassium atoms) to be constant during the refinement. The default e.s.d is 0.0001. This is useful where disordered atoms occupy more than two sites, since in these cases the total occupancy cannot be held constant using constraints.

The limit restraint attempts to limit the shift of the specified parameters to zero (in this case all the Uii anisotropic parameters). This is useful for controlling refinements of poor starting models. The default e.s.d is 0.01. Lowering it to 0.001 will effectively fix the parameter, and raising it to 10 will have almost no effect unless the shift due to the X-ray observations is huge.