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Crystals PrimerChapter 16: Advanced Refinements
CRYSTALS was originally conceived as a refinement program, and continuing
developments have maintained it as one of the best. The following examples
illustrate some common situations. Remember that constraints are set in LIST
12, and restraints in LIST 16. They can be combined in almost any resonable
fashion. An important principle to remember in building constraints is
that it is not parameters which are refined, but sfifts in
parameters. Parameters cn be linked to have the same shift, even if the
staring values are (and will remain) different.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 16.1: Mixed isotropic and anisotropic refinement!\LIST 12 !BLOCK SCALE X'S !CONTINUE C(1,U'S) UNTIL O(42) !CONTINUE P(1,U[ISO]) UNTIL F(6) !END !\LIST 22 !END
These commands define a single matrix block containing the overall
scale factor, the positions for
all atoms, the anisotropic temperature factors for the first group of
atoms, and isotropic for the second. The command LIST 22 converts the
symbolic LIST 12 into an internal format, and checks for
syntactic consistency. It should always be issued if LIST 12 is complex, so
that potential errors can be detected before least squares are started. It
also informs the user of the space
which will be needed for the matrix in the .DSC file. It is generated
internally if the user forgets.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 16.2: Large structuresThe user can refine different groups of parameters is sucessive refinement cycles, by issuing a new LIST 12 command between each cycle. It is also possible to define a multi block refinement, a very effective method if the blocks are carefully chosen. Each block should contain correlated parameters. As a rough guide, the following groups of parameters are in general highly correlated and should be refined in the same block if possible : 1. Temperature factors, scale factors, the extinction parameter, the polarity parameter and the enantiopole parameter. 2. Coordinates of bonded atoms. 3. Nonorthogonal coordinates of the same atom. 4. U(11), U(22) and U(33) of the same atom.
If it is necessary to split the temperature factors and scale factor into different blocks, their interactions must not be neglected but be allowed for by using a 'dummy overall isotropic temperature factor'. In this case, the scale factor and the dummy temperature factor must be put into a block of order 2 by themselves, and the program will make the appropriate corrections to all the temperature factors. !\LIST 12 !BLOCK X'S !BLOCK U'S SCALE !END
This defines a two block matrix. The scale factor should be with the temperature factors. !\LIST 12 !BLOCK C(1,X'S,U'S) UNTIL O(36) !BLOCK C(37,X'S,U'S) UNTIL N(61) !BLOCK SCALE DU[ISO] !END
This defines a three block matrix for a structure containing two
uncorrelated (i.e. not related by pseudo symmetry) fragments or molecules.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 16.3: Tied parametersParameters can be tied individually, on a per atom basis, or for whole groups of atoms. !\LIST 12 !FULL X'S !EQUIVALENCE C(10,OCC) CL(11,OCC) CL(12,OCC) !RIDE C(17,X'S) H(171,X'S) H(172,X'S) H(173,X'S) !LINK C(1,X'S,U[ISO]) UNTIL C(13) AND !CONTINUE C(101,X'S,U[ISO]) UNTIL C(113) !EQUIV K(1,OCC) NA(1,OCC) !WEIGHT 1 NA(1,OCC)
The first command IMPLIES the positions of all atoms. Subsequent commands
EXPLICITLY refer to parameters, and over ride the implicit definitions. The
second command
ties the occupancies of the atoms in dichloromethane. The
third defines a methyl group with riding hydrogen positions. The fourth,
which continues onto the next line, ties all the parameters in one group with the
corresponding parameters in the second. The final equivalence ties the two
occupancies, but the weight card negates the shift applied to sodium. The
total of their occupancies is therefore constant.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 16.4: Rigid groups refinementInitial refinements of large or disordered structures are best done by defining groups of atoms with well known geometries as rigid groups. The geometry of the groups should first be idealised with \REGULAR. Each atom may not occur in more than one group, though restraints can be applied to any atoms, in or out of groups. \LIST 12 FULL FE(1,X'S) P(1,X'S) CL(1,X'S) CL(2,X'S) CONTINUE U'S GROUP C(1) UNTIL C(5) RIDE C(1,U'S) UNTIL C(5) GROUP C(6) UNTIL C(11) RIDE C(6,U'S) UNTIL C(11) GROUP C(12) UNTIL C(17) RIDE C(12,U'S) UNTIL C(17) GROUP C(18) UNTIL C(23) RIDE C(18,U'S) UNTIL C(23) END
Four groups are refined together with 4 other atom positions and all
the anisotropic temperature factors. Each GROUP is given linked
anisotropic temperature shifts. They do not have to have the same
starting temperature factor values.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 16.5: PseudosymmetryWhen a structure contains whole groups of highly correlated coordinates, for example when a symmetry operator is lowered by generating atoms and removing a symmetry operator, the refinement will be unstable. This can often be controlled with: \LIST 16 LIMIT .1 X LIMIT .1 Y LIMIT .1 Z END \LIST 12 FULL COMBINE C(1,X'S) UNTIL C(23) AND C(101,X'S) UNTIL C(123) END
The LIMIT restraints prevent wild divergence on the first round of least
squares, and the COMBINE card combines the parameters from the original
fragment with those from the generated fragment  see the reference
Manual.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 16.6: Absolute ConfigurationCRYSTALS permits the refinement of either the Rogers eta or the Flack x parameter. The Flack parameter is more stable, and has a physical interpretation throughout its permitted range (0 to 1). Its refinement seems to be robust against DIFABS treatment, but does require an extinction correction to be applied if necessary, and may also require the inclusion of very weak refections. Note that these are often systematically overestimated. The listing file for a cycle of refinement including the Flack parameter contains a list of 'enantiomer sensitive' reflections. F+ is Fcalc for the current model, F for the inverse, and Fo is the observed value. Fo should tend to F+ or F. If it is consistently stronger or weaker, suspect the data collection. If the material is expected to be chirally pure, once the hand has
been determined x should be set to 0.0, and enantio removed from LIST
12 and turned off in LIST 23. If the material is twinned, enantio must
remain in the refinement.
Interpretation of the Flack Parameter
Flack e.s.d interpretation ~0.0 <.05 Hand is correct ~1.0 <.05 Hand need inverting ~0.5 <.05 Well characterised twin. ~0.0 >0.5 Hand undertermined ~1.0 >0.5 Hand undertermined ~0.5 >0.5 Twinning undertermined
[Top] [Index] Manuals generated on Wednesday 27 April 2011 16.7: Enantiomorphic Space GroupsP 61  P 65 P 41  P 43 P 62  P 64 P 41 2 2  P 43 2 2 P 61 2 2  P 65 2 2 P 41 21 1  P 43 21 1 P 62 2 2  P 64 2 2 P 41 3 2  P 43 3 2 P 31  P 32 P 31 1 2  P 32 1 2 P 31 2 1  P 32 2 1

© Copyright Chemical Crystallography Laboratory, Oxford, 2011. Comments or queries to Richard Cooper  richard.cooper@chem.ox.ac.uk Telephone +44 1865 285019. This page last changed on Wednesday 27 April 2011.