Crystals Reference Manual
Contents:
- Definitions And Conventions
- The Crystals Database
- Initial Data Input
- Scope of the Initial Data Input section.
- Abbreviated startup command - QUICKSTART
- Input of the cell parameters - LIST 1
- Printing the cell parameters
- Input of the unit cell parameter errors - LIST 31
- Printing the cell variance-covariance matrix
- Space Group input - \SPACEGROUP
- Input of the symmetry data - LIST 2
- Printing the symmetry information
- Input of molecular composition \COMPOSITION
- Input of the atomic scattering factors - \LIST 3
- Printing the scattering factors
- Input of the crystal and data collection details - LIST 13
- Printing the experimental conditions, LIST 13
- Input of Structural Formula as a SMILES string - LIST 18
- Printing the SMILES string, LIST 18
- Punching the SMILES string, LIST 18
- Input of the contents of the asymmetric unit - LIST 29
- Printing the contents of the asymmetric unit, LIST 29
- Input of General Crystallographic Data - LIST 30
- Printing the general information, LIST 30
- Reflection Data Input
- Scope of the Reflection Data Input section of the Reference Manual
- Reflection Data
- Simple input of F or Fsq data - LIST 6
- Creation of LIST 7 from LIST 6 - COPY 6 7
- Printing LIST 6
- Punching LIST 6
- Advanced input of F or Fsq data - LIST 6
- Reflection Parameter Coefficients
- Storage of reflection data
- Compressed reflection data
- Intensity Data - HKLI
- Intensity Decay Curves \LIST 27
- Printing the decay curve
- Data Reduction - Lp
- Systematic absence removal - \SYSTEMATIC
- Sorting of the reflection data - \SORT
- Merging equivalent reflections - \MERGE
- Theta-dependent Absorption Correction - \THETABS
- WILSON PLOT - \WILSON
- THLIM - \THLIM
- SIGMADIST - \SIGMADIST
- Atomic And Structural Parameters
- Scope of the atomic and structural parameters Section
- Specifications of atoms and other parameters
- Input of atoms and other parameters - LIST 5
- Printing and punching list 5
- Editing structural parameters - \EDIT
- Reorganisation of lists 5 and 10 - \REGROUP
- Repositioning of atoms - \COLLECT
- Shifting the molecule to a permitted alternative origin - \ORIGIN
- Conversion of temperature factors - \CONVERT
- Hydrogen placing - \HYDROGENS
- Perhydrogenation - \PERHYDRO
- Hydrogen re-numbering - \HNAME
- Regularisation of atomic groups - \REGULARISE
- Map two atomic groups together - \MATCH
- Calculation of interatomic bonds - \BONDCALC
- Bonding information - \LIST 40
- Bonding information - \BONDING
- Printing of LIST 40
- Creating a null LIST 40
- Printing of LIST 41
- Structure Factors And Least Squares
- Scope of the structure factors and least squares section
- Refinement
- Special positions
- Atomic parameter refinement
- Overall parameter refinement
- Scale factor definitions
- Structure factor calculation control list - LIST 23
- Printing the SLFS control list
- Special position constraints - \SPECIAL
- Printing the special position information
- Refinement directives - LIST 12
- Obsolete Refinement directives
- Defining the least squares matrix
- Printing of LIST 12
- Creating a null LIST 12
- Processing of LIST 12
- Restraints - LIST 16
- Parameter, atom, bond and angle specifications
- General restraints
- General restraints
- Debugging restraints
- Printing the contents of LIST 16
- Creating a null LIST 16
- The special restraints - LIST 17
- Printing and punching LIST 17
- Creating a null LIST 17
- Checking restraints - CHECK
- Weighting schemes for refinement- LIST 4
- Weighting for refinement against Fo
- Weighting for refinement against Fsq
- Weights stored in LIST 6
- Weighting schemes
- Dunitz Seiler weighting - scheme 13
- Chebychev weighting schemes 10, 11
- Robust-resistant weighting schemes 14, 15
- Statistical Weights, 16
- Auto-Statistical Weights, 17
- Printing LIST 4
- Weighting the reflections - WEIGHT
- Reflection restriction list - LIST 28
- Creating a null LIST 28
- Printing the contents of LIST 28
- Structure Factor Least Squares Calculations - \SFLS
- Definitions
- Unstable refinements
- Sorting of LIST 6 for structure factor calculations
- Processing of the refinement directives
- Analysis of residuals - \ANALYSE
- Least squares absorption correction - \DIFABS
- Internal workings
- Fourier Routines
- Scope of the Fourier section of the user guide
- Input of the Fourier section limits - LIST 14
- Printing the contents of LIST 14
- Compute Fourier limits from the symmetry
- Fourier calculations - \FOURIER
- Calculation of superposition minimum functions
- Processing of the peaks list - LIST 10
- Printing the contents of LIST 10
- Elimination of duplicated entries in LISTS 5 and 10 - \PEAKS
- Slant fourier calculations - \SLANT
- Analysis Of Results
- Scope of this section of the user guide
- Analysis of residuals - \ANALYSE
- Create esd list - \ESD
- Output VcV matrix of selected atoms
- Distance angles calculations - \DISTANCES
- Distance-angles symmetry operations
- Void Location - \VOIDS
- TLS analysis, best planes and lines - \GEOMETRY
- Torsion angles - \TORSION
- Absolute Configuration - \TON
- Publication listing of the atomic parameters - \PARAMETERS
- Publication listing of reflection data - \REFLECTIONS
- Summary of data lists - \SUMMARY
- Estimation of Absolute configuration - \TONSPEK
- CIF lists - \CIF
- Adding Archive files - ADDARC
- Graphics - CAMERON
- Twinned Crystals
- Matrix Calculations
- Obsolete Commands
- Secret Lists
Version 14 of CRYSTALS is based on a version (Issue 2) written by J.R. Carruthers in collaboration with J.S.Rollett during 1977-78, which was a rewrite of the 1975 CRYSTALS system implemented on the ICL 1900 series of computers. It contains significant contributions by Paul Betteridge, David Kinna, Lisa Pearce, Allen Larson, and Eric Gabe and many students and visitors to the Chemical Crystallography Laboratory, Oxford. The graphical user interface (GUI) was written by Richard Cooper as part of a Part II and D Phil project (supported by a CCDC studentship) in collaboration with Ludwig Macko and Markus Neuburger in Basel, who were working on a parallel Macintosh interface.
If publishing structures analysed using CRYSTALS, please select a suitable citation from this list:
Absolute structure determination with CRYSTALS: Cooper, R. I., Watkin, D. J., and Flack, H. D. (2016) Acta. Cryst. C72, 261-267
Use of non-atomic scattering density models: Schroder, L., Watkin, D. J., Cousson, A., Cooper, R. I., and Paulus, W. (2004) J. Appl. Cryst. 37, 545–550
Use of asymmetric restraint tools: Cooper, R. I., Thorn, A. and Watkin, D. J. (2012) J. Appl. Cryst. 45, 1057–1060
Use of restraints: Parois, P., Arnold, J., and Cooper, R. I. (2018) J. Appl. Cryst. 51
Use of resonant scattering correction to Squeeze correction: Cooper, R. I., Flack, H. D., and Watkin, D. J. (2017) Acta Crystallographica, C73, 845–853.
Use of tools for large structures. Parois, P., Cooper, R. I. and Thompson, A. L. (2015) Chemistry Central Journal, 9, 30
An old general citation: Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K., Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.
While CRYSTALS can still be executed in ‘batch mode’ (ASCII file in, ASCII file out), the major demand is now for the version running under Windows, with some small demand for the LINUX version. The GUI permits the user to continually see the structure as it develops, and to interact with it and the analysis through conventional windows features. The ‘command line’ and ‘use file’ modes have been retained for experienced users, or users wishing to explore new ideas. The ‘SCRIPTing’ language has been extended to enable full control and design of the user interface to be handled from ASCII files.