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Crystals PrimerChapter 10: Molecular Geometry
Details of the molecular geometry can be computed in CRYSTALS. Most
calculations send a summary to the screen, and a detailed listing to the
printer file. Some will also produce a .PCH file (fixed format ASCII) suitable
for incorporation into publications in either tabular of 'cif' format.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 10.1: Distances and anglesThe user has a lot of fine control over the distance-angle routine, which should help minimise unwanted output. For many cases the default settings are suitable. A text file suitable for editing into documents may also be produced !\DISTANCE !END
[Top] [Index] Manuals generated on Wednesday 8 November 2006 10.2: Best planes, lines and dihedral anglesPlanes, lines and the angles between them are computed with MOLAX (molecular axes). This routine also produces simple plots. !\MOLAX !ATOM FIRST UNTIL LAST !PLANE !EXEC !ATOM C(1) UNTIL C(6) P(1) !PLANE !EXEC !ATOM P(1) FE(1) P(2) !LINE !ATOM P(3) FE(1) C(17) !LINE !ANGLE 3 AND 4 !END
This task computes the best plane through the whole structure, through a
P-phenyl group, and lines through two groups of atoms. The corresponding
vector (plane normal or line axis)
is stored for each PLANE or LINE calculation. The ANGLE directive
requests the angle between the 3rd and 4th vectors, i.e. the two lines.
EXEC, as in EDIT, forces immediate execution of the preceeding directive.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 10.3: Torsion anglesTorsion angles are computed with !\TORSION !ATOM C(1) C(2) C(3) C(4) !ATOM C(6) C(7) C(8) C(9) UNTIL C(11) !END
This computes one torsion atom in the first command, and 3 in the second.
The output can be sent to a text file.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 10.4: Thermal analysisDuring the course of refinement, CRYSTALS keep a watch on the thermal parameters and issues warnings if they go too small or too aspherical. However, it is often instructive for the user to examine both the principal axes and the TLS molecular motion tensors, in association with a Cameron thermal ellipsoid plot. !\ANISO !ATOM FIRST UNTIL LAST !AXES !EXEC !ATOM C(1) UNTIL C(6) P(1) !TLS !END
These commands compute the principal axes of all the atoms, and then do a
TLS analysis on the P-phenyl group. EXEC forces immediate execution of the
preceeding commands.
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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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