Chemical Crystallography

+ Frequently Asked Questions

- Crystals Primer

1. Getting Started

2. Example Of A Simple Structure

3. Overview

4. Basic Data Input

5. The Model

6. Fourier Maps

7. Preparation Of The Model

8. Refinement

9. Seeing The Structure

10. Molecular Geometry

11. Publication Listings

12. Cif Files

13. Documentation

14. The Data Base

15. Tailoring The Program

16. Advanced Refinements

17. Scripts

18. Data Lists And Instructions

+ Crystals User Guide

+ Crystals Manual

+ Cameron Manual

+ Index

Fri Jun 2 2000

Crystals Primer

Chapter 1: Getting Started

1.1: Background to structure analysis

1.2: Files

1.3: Reflection Data


The main CRYSTALS documentation is the CRYSTALS REFERENCE MANUAL (, 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 (

1.1: Background to structure analysis

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

Principal Stages of analysis
The principal steps in structure analysis are:

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.

1.2: Files

CRYSTALS 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.


If the data has been preprocessed by some other system, you will also need to know:
The merging 'R' factor (Rint)


1.3: Reflection Data

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.
      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