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Crystals PrimerChapter 7: Preparation Of The ModelThis 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.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 7.1: \PeaksThis 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.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 7.2: \Collect & \RegroupThese 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
[Top] [Index] Manuals generated on Wednesday 8 November 2006 7.3: \EditThe 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.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 7.4: \Molax, \Regularise, \AnisoThese 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.
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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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