Crystals Primer

Chapter 7: Preparation Of The Model

: 7.1: \Peaks; 7.2: \Collect & \Regroup; 7.3: \Edit; 7.4: \Molax, \Regularise, \Aniso

This may be the input from SIR etc, from finding additional atoms in Fourier maps, or modifying the existing model (with \PEAKS, \EDIT, \COLLECT, \REGROUP, \REGULARISE, \MOLAX, \HYDROGENS, or \ANISO). These involve operations on LIST 5.

It is a good idea to assign a final atom numbering scheme as soon as
possible in the analysis. This will save a lot of hastle later.

7.1: \Peaks

This command converts the output from a Fourier peak search (held as a LIST 10) into a parameter list, LIST 5. It associates any new PEAKS with existing atoms. It can also be used for Fourier refinement, and for rejecting duplicate atoms, e.g. after changing space group.

7.2: \Collect & \Regroup

These commands assist in assembling molecules from peaks lists. REGROUP applies symmetry and reorders the atoms in LIST 5, COLLECT only applies symmetry. Both can be made to work with all atoms in LIST 5, or only operate on peaks of type Q. These are powerful utilities and can save a lot of manual editing.

  e.g.
      !\PEAK
      !END
      !\COLLECT
      !SELECT TYPE = PEAK
      !END
      !\SCRIPT PLOT
      !\REGROUP
      !SELECT SEQUENCE=YES
      !END

These commands take peaks from the latest Fourier map and try to collect atoms of TYPE 'Q' (i.e. new peaks) so that they are within bonding distance of existing atoms. The PLOT script displays the structure and permits the renaming of peaks and atoms, and the exclusion of spurious peaks. REGROUP tries to number the atoms so that adjacent ones have sequential serial numbers.

7.3: \Edit

The CRYSTALS editor, \EDIT, is designed to perform crystallograhic edits on the atom parameters, in LIST 5. If anything needs to be done on groups of atoms, \EDIT is likely to be more convenient than using a text editor on the parameter list.

  e.g.
     !\EDIT
     !CHANGE    FIRST(U[ISO])  UNTIL  C(10)  .03
     !EXECUTE
     !CHANGE    Si(3,OCC) .667   Si(103,OCC)   .333
     !SUBTRACT  .25 FIRST(Y) UNTIL LAST
     !ADD       C(30,SERIAL) UNTIL LAST 100
     !TRANSFORM -1 0 0, 0 -1 0, 0 0 -1 FIRST UNTIL LAST
     !SELECT    TYPE NE PEAK
     !DELETE    S(14)
     !UEQUIV    C(16) C(23) UNTIL LAST
     !ANISO     Pb(1)
     !KEEP      C(1) C(3) C(5) C(7) UNTIL LAST
     !END

The directive EXECUTE forces immediate execution of preceeding commands. The directive CONTINUE is available for building long lines, and QUIT abandons the edit without saving the results. The original values are unchanged.

7.4: \Molax, \Regularise, \Aniso

These commands are used to examine the geometry of the model. They can also be used to force certain geometries onto the model. MOLAX computes best planes and lines (molecular axes), REGULARISE compares and regularises structures or structural fragments, and ANISO helps with the analysis of the thermal parameters.