Crystals Primer

Chapter 5: The Model

5.1: Direct Methods

5.2: Inputting a trial model

5.3: Modifying the Model

5.4: Atom identifiers

5.5: Atom parameter identifiers

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.
 

CRYSTALS 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

In interactive mode the files produced by the Direct Methods programs may be read into CRYSTALS with

      !\SCRIPT  INEMAP

The SCRIPT INEMAP can also be used for manual input of coordinates.

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.
 

The 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

Atom 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

This 'UNTIL' sequence causes the requested operation (detetion in the example above) to be performed on all the atoms in the atom list (LIST 5) between and including atomid1 and atomid2. A thoughtfull naming of the atoms and ordering of the atom list can save a lot of typing later. Symmetry operators can also be included in an atom specification.
 

Atomic 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]

The first example specifies a least squares matrix block for the x, y and z parameters for atoms C(2) until and including C(23). In example 2, the parameters X'S and U'S are permitted abbreviations for X,Y,Z and similarly for the anisotropic temperature factor components. A parameter appearing without an atom identifier (U[ISO] in example 3) implies the named parameter for all atoms.

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.