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CRYSTALS manual
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Crystals Manual
Chapter 1: Introduction To The System
[Top] [Index] Manuals generated on Wednesday 8 November 2006
1.1: Layout of this manual
This manual is organised as follows
1.0 Introduction
2.0 Definitions and Conventions
2.3 Immediate commands - tailoring the program
3.0 The CRYSTALS database
4.0 Initial Data input
5.0 Reflection data
6.0 Atoms and Parameters
7.0 Structure factors and least squares
8.0 Fourier and Patterson maps
9.0 Geometry and printing results
9.12 Graphics - CAMERON
10.0 Twinned Data
11.0 The Basic Matrix Calculator
This version of the manual, has been revised to coincide with the release of version 12.00 of CRYSTALS. This revision includes further enhancements to the graphical user interface. Opportunity has also been taken to revise some features of the underlying code. Brief details of the changes are in the web document http://www.xtl.ox.ac.uk/fixes.html. We have tried to mininise the impact on existing users, and we hope that the advantages brought about by the changes will become evident.
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1.2: Status
This version of CRYSTALS continues to be 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.
A suitable citation is:
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 on Intel processors, 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.
[Top] [Index] Manuals generated on Wednesday 8 November 2006
1.3: MAJOR CHANGES for WINDOWS
The majority of the changes (many thousand edits) are
concerned with the GUI, the screen and file output, and the internal
database.
Major changes are:
1 New .DSC file 2 Extended LIST 5 format (the model parameters) 3 New ADP handling 4 New weighting for Fsq 5 More items stored in LIST 30 6 Easier handling of twins 7 More robust creation of cifs 8 HTML versions of the manuals
The internal format of some of the lists has been extended to accommodate information needed to meet current publication requirements. There is some degree of compatibility between old format .DSC files and the new CRYSTALS. A facility in /EDIT attempts to do the internal reformatting. There is no backwards compatibility. There is full forward compatibility at the ASCII level - the old LISTS 5 (the model parameters), 6 (reflections), 12 (constraints) and 16 (restraints) can be input into the new program.
In the original version of CRYSTALS, the value of Uiso was used to indicate whether it was a real usable value (e.g. 0.055), or a flag indicating that the atom was anisotropic (e.g. 0.00).
This location in LIST 5 (the model parameters) has now been changed to a proper flag, whose value indicates what kind of information is stored after the positional parameters. This has enabled us to have more complex models for the electron distribution.
original keys:
type serial occ u[iso] x y z u[11] u[22] u[33] u[23] u[13] u[12] spare
revised keys
type serial occ FLAG x y z u[11] u[22] u[33] u[23] u[13] u[12] spare
U[ISO] spare
U[ISO] SIZE spare
U[ISO] SIZE DECLINAT AZIMUTH spare
The value of 'FLAG' is used on input of atoms to indicate what kind of
patameters will follow, and is used during calculations for the
interpretation of the parameters.
FLAG meaning parameters 'old' types of atoms: 0 Aniso ADP u[11] u[22] u[33] u[23] u[13] u[12] 1 Iso ADP U[ISO] New 'special' shapes: 2 Sphere U[ISO] SIZE 3 Line U[ISO] SIZE DECLINAT AZIMUTH 4 Ring U[ISO] SIZE DECLINAT AZIMUTH
The parameters have the following meaning for the new special shapes:
If either of these angles is input with a value greater than 5.0, it is assumed that the user has forgotten to divide by 100, which is thus done automatically.
Currently, no action is taken by CRYSTALS for special shapes lying on
positions of special site symmetry. The user must set up the appropriate
constraints in LIST 12 (section 7.11) (usually preventing the refinement
of one or more parameters), and set up the correct occupancy in LIST 5
(atomic parameters).
Since the special shapes can coexist with normal atoms, it is possible to embed normal atoms in the special shapes to give a 'peakey' electron distribtion. The sums of the occupancies will need to be constrained.
Scheme 14 (Chebychev weighting) has been made more robust to ragged distributions of delta squared. The major influence is in Fsq refinement, though there is also a small (improved) effect on F refinement.
LIST 30 (section 4.17) has been extended because of changes in the new CIF dictionary.
Although CRYSTALS has been able to handle twinned data since the program was first designed in the 1970's, the input was very general, and not easily understood. Now that area detector diffractometers are able to routinely handle TLS and TLQS twins, the input has been revised to handle these special sitautions routinely. The old format input, for twins with up to 9 components, is still available (see section 10.0)
[Introduction To The System | Definitions And Conventions | The Crystals Database | Initial Data Input | Reflection Data Input | Atomic And Structural Parameters | Structure Factors And Least Squares | Fourier Routines | Analysis Of Results | Twinned Crystals | Matrix Calculations | Obsolete Commands ]
