Chapter 1: Introduction To The System
This manual is organised as follows
1 Definitions and Conventions 2 Initial Data Input 3 Reflection data 4 Atoms and Parameters 5 Structure factors and least squares 6 Fourier and Patterson maps 7 Geometry and printing results 8 Graphics - CAMERON 9 Immediate commands - tailoring the program 10 Twinned Data 11 SCRIPTS
The current version of CRYSTALS , Issue 11, was released in 1999 for machines running WINDOWS95. It 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, Alen Larsen, and Eric Gabe and many students and visitors to the Chemical Crystallography Laboratory, Oxford.
In CRYSTALS, the course of a calculation is controlled from a master control channel, which may either be a card image file or an on-line terminal. When the data is being presented directly to the program from the terminal the program is being used in the INTERACTIVE and ON-LINE mode. When the job is initiated from a terminal but the data is read from a control file the program is being used in the ON-LINE mode, and when both initiation and control is from a control file the task is a BATCH job. A mixed mode is available in some implementations, in which control is passed from the INTERACTIVE terminal to a pre-prepared control file, and later returned to the terminal.
In all ON-LINE modes, a special subset of the output
normally sent to the printer is sent to the terminal. This
provides the user with the information that he needs
to monitor the calculation in order
to initiate the next step of the computation. In all modes
of use CRYSTALS produces a well laid out and comprehensive
line printer record of the calculation.
The opportunity has been taken to make substantial changes throughout
CRYSTALS to coincide with the release of the 32 bit version for
WINDOWS95/NT. The majority of the changes (several thousand edits) are
concerned with the screen and file output, and should not distress
Major changes are:
1 New .DSC file 2 New ADP handling 3 New weighting for Fsq 4 New items stored in LIST 30
New .DSC File
The internal format of some of the lists has been extended to accomodate 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 LISTS5,6,12 and 16 can be input into the new program.
New Temperature Factor (ADP) handling
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 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 u u u u u spare revised keys type serial occ FLAG x y z u u u u u u 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 interpretation The following table shows the interpretation of the FLAG parameter.
FLAG meaning parameters 'old' types of atoms: 0 Aniso ADP u u u u u u 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
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 (usually preventing the refinement of one or more
parameters), and set up the correct occupancy in LIST 5.
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.