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Crystals PrimerChapter 1: Getting StartedThe main CRYSTALS documentation is the CRYSTALS REFERENCE MANUAL
(http://www.xtl.ox.ac.uk/crystalsmanual.html), which
is more or less complete and definitive.
This Primer gives an introduction to the main features.
A more detailed introduction to the program
is available in the GUIDE (http://www.xtl.ox.ac.uk/guide.html).
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.1: Background to structure analysisNo two crystal structure analyses follow exactly the same path, so
that it is impossible to give a definitive step-by-step procedure for
the general case. The principal causes for deviation from a linear
process are: Most of these situations can readily be recognised by a chemist with
some crystallographic experience, and so for the moment it is necessary
for some one to remain in control of each structure analysis
Principal Stages of analysis
The principal steps in structure analysis are: Data collection. Transfer of data from diffractometer to user's computer. Data pre-processing. This is diffractometer-specific and performed with a dedicated program. Data reduction. This is the Lp and possibly absorption corrections. May be included in the pre-processing, or done by CRYSTALS. Structure Solution. Usually done by direct methods (SIR or SHELXS), even for heavy atom structures. E-map evaluation, usually done by inspection with CRYSTALS/CAMERON. Structure development. Atoms not revealed by direct methods may be revealed by Fourier refinement in CRYSTALS Structure refinement, by least squares. First isotropic and then anisotropic temperature factors for the non-hydrogen atoms. Hydrogen atom location, from a difference Fourier, by geometric prediction, or a combination. Final refinement, possibly including extinction, final difference synthesis, production of tables and diagrams.
Using CRYSTALS
On any computer, it is recommended to create a dedicated directory sub-directory or folder for each separate structure. Keep the primary data from the diffractometer in this folder, together with the files created during the analysis. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.2: FilesCRYSTALS uses a many files during a structure analysis. Under most
operating systems the user can choose the filenames. Under DOS they are
pre-defined.
*.DSC
: The binary database for the structure being refined. DO NOT try
to edit or print it
*.LOG
: A log of all the data operations done with CRYSTALS. This
file could be renamed and edited for use as an instruction file for a
future job.
*.LIn
: A 132 column listing file recording all the output from CRYSTALS. Under
VMS the name is *.LIS(n).
*.PCH
: 80 column card image file of data for archiving or transfer to other
programs.
INITIAL.*
: Files produced during initial data processing, and perhaps important
when the structure is being written up.
EXPORT.DAT
: A file (optionally) written at the end of every job, containing atom
parameters and refinement directives.
Preparations for the analysis
Before you start using CRYSTALS, you will need to know (or have in a suitable file) the following: Unit cell parameters and standard deviations. Chemical formula. Space group symbol. Number of formula units in the unit cell Crystal colour and approximate size and shape. Minimum/maximum index ranges during data collection and cell determination. Minimum/maximum theta ranges during data collection and cell determination. The name of the file containig the reflection data.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.3: Reflection DataAs an introduction to the system, it is assumed that the reflections
have been pre-processed and are in SHELX 'HKLF 4' format, ie each line
of the file contains h,k,l, Fsq and sigma(Fsq) in fixed columns. You will need
to know the FORMAT of the data (a FORTRAN convention). If the pre-processor
documentation specifies the output format use it, otherwise study the
following example.
If there are decimal points in the numbers, they count as a column but
are not important for the FORMAT statement. e.g. 1234567890123456789012345678 (column number) 1 -2 13 186135 465.4 (reflection 1 -2 13, Fsq=186135, sigma=465.4) 10 3 0 145 17 (reflection 10 3 0, Fsq=145, sigma=17) The FORTRAN format for this data is: (3F4.0,2F8.0) |
© 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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