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Crystals PrimerChapter 5: The Model
The refinable parameters that define the model are kept in LIST 5.
These consist of atomic parameters, and overall parameters such as
scale factors and extinction.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 5.1: Direct MethodsCRYSTALS contains no code for direct methods, but can prepare data for other programs. It can also submit batch jobs for the other programs. SIR and the recompiled version of SHELXS (distributed in CRYSTALS with their authors permission) produce atom lists compatible with CRYSTALS. To create the files in Command mode, issue: !\FOREIGN progname !END
To prepare for Direct Methods in SCRIPT mode, issue: !\SCRIPT STRUCTUR
[Top] [Index] Manuals generated on Wednesday 8 November 2006 5.2: Inputting a trial modelIn interactive mode the files produced by the Direct Methods programs may be read into CRYSTALS with !\SCRIPT INEMAP
If a SCRIPT is not used to input the trial structure, the SIR output file can be used as it is, but the SHELXS.CRY file must be edited to standard CRYSTALS LIST 5 format. e.g. !\LIST 5 !READ NATOM = 3 !ATOM C 1 X=.23 .37 .45 !ATOM C 2 X=.31 Y=.06 .78 !ATOM O 6 OCC=.5 X=0.5 0 .25 !END
Note that the parameters x, y, z are in sequence, so only the first keyword is
requires, and that the parameters for atoms on special positions are not coded
(as required by SHELX),
and that there are defaults of 1.0 for occupancies, and 0.05 for Uiso.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 5.3: Modifying the ModelThe model from SIR may already have some real atom type assigned to each peak. SHELXS names all atoms as type 'Q'. The SHELXS.CRY file may be edited with a system editor, or the atoms can be edited inside CRYSTALS. In Command mode use \EDIT e.g. !\EDIT !CHANGE FIRST(TYPE) UNTIL LAST C !RENAME C(4) O(1), C(5) N(1) !DELETE C(42) UNTIL C(54) C(17) !END
This sequence changes the type of all atoms (FIRST UNTIL LAST) from 'Q' to 'C', and then changes C(4) to O(1), etc. deletes atom C(17) and a group of atoms. There is also a SCRIPT to help with editing parameters. \SCRIPT EDLIST5 guide you through an edit, and \SCRIPT PLOT uses the graphical editor. !\SCRIPT PLOT
[Top] [Index] Manuals generated on Wednesday 8 November 2006 5.4: Atom identifiersAtom identifiers consist of two parts, a letter string (TYPE) which is used to associate the atom with atomic properties (form factor, radius etc), and a SERIAL number in parentheses. The total identifier should be unique for each atom. Two special identifiers, FIRST and LAST refer to the first and last atoms in the atom list, and must not have serial numbers. Groups of atoms may be referenced with: atomid1 UNTIL atomid2
[Top] [Index] Manuals generated on Wednesday 8 November 2006 5.5: Atom parameter identifiersAtomic parameters are specified in an analogous way. The name of the parameter being operated on is included with the atom serial number inside the parentheses. The parameter being changed above is TYPE. e.g. !BLOCK C(2,X,Y,Z) UNTIL C(23) !BLOCK C(2,X'S,U'S) UNTIL C(23) !BLOCK U[ISO]
Permitted model parameters are: Overall parameters SCALE OU[ISO] DU[ISO] POLARITY ENANTIO EXTPARAM Atomic parameters OCC U[ISO] X Y Z U[11] U[22] U[33] U[23] U[13] U[12] Abbreviated parameters X'S Indicating X,Y,Z U'S Indicating U[11],U[22],U[33],U[23],U[13],U[12] UII'S Indicating U[11],U[22],U[33] UIJ'S Indicating U[23],U[13],U[12] Special abbreviations FIRST LAST ALL
Batch, layer and twin scale factors are also permitted.
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© Copyright Chemical Crystallography Laboratory, Oxford, 2006.
Comments or queries to David Watkin -
david.watkin@chem.ox.ac.uk Telephone +44 1865 285019.
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