Crystals Manual
Chapter 1: Introduction To The System
[Top] [Index] Manuals generated on Wed Jun 6 2001
1.1: Layout of this manual
This manual is organised as follows
1 This section 2 Definitions and Conventions 3 Immediate commands - tailoring the program 4 The CRYTSALS database 5 Initial Data Input 6 Reflection data 7 Atoms and Parameters 8 Structure factors and least squares 9 Fourier and Patterson maps 10 Geometry and printing results 11 Graphics - CAMERON 12 Twinned Data 13 SCRIPTS
This version of the manual, December 2000, has been slightly revised to coincide with the release of a major revision of CRYSTALS. This major revision includes extensive changes the the graphical user interface, and to the supporting crystallographic code. We have tried to mininise the impact on existing users, and we hope that the advatages brought about by the changes will become evident
This version 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. The graphical user interface (GUI)
was written by Richard Cooper as part of a Part II and D
Phil project (suported by a CCDC studentship) in collaboration with
Ludwig Mako and Markus Neuburger in Basel, who were working on a
paralell Macintosh interface.
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
Microsoft Windows on Intel processors, wit 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 Wed Jun 6 2001
1.2: 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
data-base.
Major changes are:
1 New .DSC file 2 New LIST 5 (refineable 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
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[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 interpretation The following table shows the interpretation of the FLAG parameter.
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:
Special U[iso]
U[iso] is related to the 'thickness' of the line, annulus or shell.
Special SIZE
SIZE is the length of the line, or the radius of the annulus or shell.
Special DECLINAT
DECLINAT is the declination angle between the line axis or annulus normal and the
z
axis of the usual CRYSTALS orthogonal coordinate system, in
degrees/100.
Special AZIMUTH
AZIMUTH is the azumuthal angle between the projection of the
line axis or annulus normal onto the x - y plane and the x
axis of the usual CRYSTALS orthogonal coordinate system, in
degrees/100.
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.
Accessing 'Special shapes'
The special shape parameters can be accessed just like any traditional
parameters. FLAG is not a refinable parameter, and should only be
changed in /EDIT if corresponding changes are to be made to the actual
parameter values. This is normally automatic if the FLAG is changed to 0
or 1. To facilitate the generation of special shpes from groups of
atoms, the following directives are available in /EDIT.
SPHERE newserial atomlist
This creates a 'shell' shape from the specified atom list. The centre of
the shell is at the centre of gravity, the size is the mean distance of
the given atoms from the centre, and the occupancy is equal to the sum of
the occupancies
of the atoms listed. U[iso] is the mean of the U[iso] or Ueqiv of the
listed atoms.
The atom TYPE is QS, with the given serial number. The
original atoms are not deleted, though they should be or their occupancy
set to zero. The atom type, QS, should be changed to something
appropriate.
RING newserial atomlist
This creates an 'annulus' shape from the specified atom list. The centre of
the ring is at the centre of gravity, the size is the mean distance of
the given atoms from the centre, and the occupancy is equal to the sum of
the occupancies
of the atoms listed. U[iso] is the mean of the U[iso] or Ueqiv of the
listed atoms.
The atom TYPE is QR, with the given serial number. The
original atoms are not deleted, though they should be or their occupancy
set to zero. The atom type, QS, should be changed to something
appropriate. The DECLINATION and AZIMUTH are computed from the
constiuent atoms.
LINE newserial atomlist
This creates an 'line' shape from the specified atom list. The centre of
the line is at the centre of gravity, the size is twice the mean distance of
the given atoms from the centre, and the occupancy is equal to the sum of
the occupancies
of the atoms listed. U[iso] is the mean of the U[iso] or Ueqiv of the
listed atoms.
The atom TYPE is QL, with the given serial number. The
original atoms are not deleted, though they should be or their occupancy
set to zero. The atom type, QS, should be changed to something
appropriate. The DECLINATION and AZIMUTH are computed from the
constiuent atoms.
REFORMAT
This instruction converts an old (non-FLAG) version of LIST 5 to the new
format.
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.
New Weighting for Fsq refinement
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.
New items stored in LIST 30
LIST 30 has benn extended because of changes in the new CIF dictionary.
Easier handling of twins
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.