Chapter 1: Getting Started
The main CRYSTALS documentation is the CRYSTALS REFERENCE MANUAL
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-1.html).
No 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:
Direct Methods fails to yield a recognisable structure. Direct Methods yields a partial structure Fourier refinement fails to complete the structure There is disorder in the structure There is unexpected solvent (possibly disordered) Difference maps fail to locate all the H atoms, and their positions cannot be simply predicted.
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
Data collection. Transfer of data from diffractometer to users 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.
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.
*.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.
If the data has been preprocessed by some other system, you will also need to know:
The merging 'R' factor (Rint)
As 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)