CRYSTALS
15.4
CRYSTALS documentation
Contents:
Crystals User Guide
Installation
Getting Started
Organisation of data
Starting the program
Customising CRYSTALS to suit your screen size
Worked examples
Cyclo - a routine structure analysis
Video demonstration
Step one: Import cell and crystal data
Step two: Import reflection data
Step three: Initial assessment of the data
Step four: Structure solution
Step five: Check atom types
Step six: Commence refinement…
Step seven: Adding Hydrogen Atoms
Step eight: More refinement & Extinction
Step nine: Choose a nice weighting scheme
Step ten: Validation and CIF archival.
Poor Quality Data - Tetraphenylene
Background
Analysis and solution
Refinement
But what of the e.s.d’s?
Spacegroup Quiz
User Interface
Overview of the graphical user interface
The Menus
File
X-ray data
Diffractometer cifs
Input Pre-processed data
Solve
Structure
Fourier
Refinement
Results
Results -> Rotax
Graphics
Graphics -> Special
Appearance
Appearance -> Atoms
Appearance -> Model
Development
Command line
Command syntax
Frequently asked questions
Getting Started: Organisation of files.
General: Who is responsible for it?
General: Where is the manual?
General: Is there an example to work through?
General: Can I prepare commands to run CRYSTALS in batch mode (like SHELX)?
General: Is there any command line help?
General: How can I switch the left and right CRYSTALS windows?
Solving structures: How do I prepare a job for SIR92 or SHELXS?
Solving structures: It failed. How do I prepare a different job?
Solving structures: How do I import the solution back into CRYSTALS?
CAMERON: How do I see a plot of the structure?
CAMERON: Can I rotate it and label the atoms?
CAMERON: How do I delete atoms?
Fourier: How do I calculate a Fourier map to find missing atoms?
Refinement: What infomation does CRYSTALS need?
Refinement: Refinement instructions
Refinement: Occupancies of an atom or fragment split over two sites?
Refinement: How do I add restraints?
Refinement: How do you use Platon’s Squeeze from CRYSTALS?
Refinement: What are parts assemblies and groups?
Structure: How can I adjust a molecule or fragment to have ideal coordinates?
Analysis: Find the angle between a plane of atoms and a bond
Analysis: Calculate intermolecular distances
Analysis: Find LIKELY H-BONDS with donors or acceptors other the O and N
Analysis: How do I use ROTAX to test for twin laws?
Analysis: How do I add hydrogen atoms to water molecules?
Publication: Editor wants completeness of the data at 25 degrees
Publication: What’s the difference between _theta_max and _theta_full?
Publication: Diagram shows wrong enantiomer. What to do?
References: What References should I know about?
Miscellaneous: Environment variables
Crystals Reference Manual
Definitions And Conventions
Syntax of Commands
Format of Commands
Syntax of the manual
Types of Commands:
Lists
Commands
Immediate Commands
Comments
Continuation Lines
Immediate commands
\FINISH
\ ….. COMMENTS ….
\TITLE ….. A title to be printed …..
\TYPE ‘filename’
\USE source
\SCRIPT filename
\SPAWN ‘shell command’
$ ‘shell command’
\COMMANDS command
? text
\MANUAL ‘name’
\HELP ‘topic’
\RELEASE devicename filename
\OPEN devicename filename
\CLOSE devicename
\APPEND devicename filename
\FLUSH devicename
Device names
\PAUSE interval
\BENCH nparam nref
\SET LIST state
\SET WATCH number
\SET FILE type
\SET GENERATE state
\SET EXPORT state
\SET UEQUIV state
\SET PAUSE value
\SET LOG state
\SET MIRROR state
\SET PAGE length
\SET TERMINAL device
\SET COMMUNICATION speed
\SET TIME state
\SET PRINTER state
\SET MONITOR state
\SET OPENMESSAGE state
\SET MESSAGE state
\SET SRQ state
\SET RATIO state
Files
Errors and Warnings
Warnings
Errors
Severe Errors
Catastrophic Errors.
Programming Errors
Errors Detected During the Creation of a LIST
The Crystals Database
General List-control Directives - \DISK
\DISK
Elimination of Old Versions of LISTS - \PURGE
\PURGE
LISTS in Current use
Printed Summary of Data lists
\SUMMARY
Element and Atom names
Element Names
Atom names
Symmetry equivalent atoms
Foreign Program Links
\FOREIGN
Initial Data Input
Scope of the Initial Data Input section.
Abbreviated startup command - QUICKSTART
\QUICKSTART
Input of the cell parameters - LIST 1
\LIST 1
Printing the cell parameters
\PRINT 1
\PUNCH 1
Input of the unit cell parameter errors - LIST 31
\LIST 31
Printing the cell variance-covariance matrix
\PRINT 31
Space Group input - \SPACEGROUP
\SPACEGROUP
Input of the symmetry data - LIST 2
\LIST 2
Printing the symmetry information
\PRINT 2
Input of molecular composition \COMPOSITION
\COMPOSITION
Input of the atomic scattering factors - \LIST 3
\LIST 3
Printing the scattering factors
\PRINT 3
Input of the crystal and data collection details - LIST 13
\LIST 13
Printing the experimental conditions, LIST 13
\PRINT 13
Input of Structural Formula as a SMILES string - LIST 18
\LIST 18
Printing the SMILES string, LIST 18
\PRINT 18
Punching the SMILES string, LIST 18
\PUNCH 18
Input of the contents of the asymmetric unit - LIST 29
\LIST 29
Printing the contents of the asymmetric unit, LIST 29
\PRINT 29
Input of General Crystallographic Data - LIST 30
\LIST 30
INTERVAL=
Printing the general information, LIST 30
\PRINT 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
\PRINT 6 mode
Punching LIST 6
\PUNCH 6 mode
Advanced input of F or Fsq data - LIST 6
Reflection Parameter Coefficients
Special Reflection storage
Recognised reflection coefficients
Storage of reflection data
Compressed reflection data
Intensity Data - HKLI
\HKLI
Intensity Decay Curves \LIST 27
\LIST 27
Printing the decay curve
\PRINT 27
Data Reduction - Lp
\LP
Systematic absence removal - \SYSTEMATIC
\SYSTEMATIC
Sorting of the reflection data - \SORT
\SORT
Merging equivalent reflections - \MERGE
WEIGHTING SCHEMES FOR THE DATA MERGE
Standard deviations produced by the merge
\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
ATOM SPECIFICATION
ATOMIC PARAMETER SPECIFICATION
OVERALL PARAMETER SPECIFICATION
Input of atoms and other parameters - LIST 5
\LIST 5
Further examples of parameter input
Printing and punching list 5
\PRINT 5
\PUNCH 5 mode
Summary display of LIST 5 - \DISPLAY
\DISPLAY LEVEL=
Editing structural parameters - \EDIT
\EDIT INPUTLIST OUTPUTLIST
Reorganisation of lists 5 and 10 - \REGROUP
\REGROUP INPUTLIST= OUTPUTLIST=
Repositioning of atoms - \COLLECT
\COLLECT INPUTLIST= OUTPUTLIST=
Shifting the molecule to a permitted alternative origin - \ORIGIN
\ORIGIN INPUTLIST= OUTPUTLIST= MODE=
Conversion of temperature factors - \CONVERT
\CONVERT INPUTLIST= OUTPUTLIST= CROSSTERMS=
Hydrogen placing - \HYDROGENS
\HYDROGENS INPUTLIST= OUTPUTLIST=
Perhydrogenation - \PERHYDRO
\PERHYDRO INPUTLIST= OUTPUTLIST=
Hydrogen re-numbering - \HNAME
Regularisation of atomic groups - \REGULARISE
Input for REGULARISE
Output from REGULARISE
Method of calculation
\REGULARISE MODE
Uses of \REGULARISE
Map two atomic groups together - \MATCH
Calculation of interatomic bonds - \BONDCALC
Method of calculation
Bonding information - \LIST 40
Bonding information - \BONDING
Printing of LIST 40
\PRINT 40
\SUMMARY 40
\PUNCH 40
\PUNCH 40 B
Creating a null LIST 40
Printing of LIST 41
\PRINT 41
\SUMMARY 41
Structure Factors And Least Squares
Scope of the structure factors and least squares section
Refinement
Correlations in Refinement
F or Fsq refinement?
Hydrogen Atom Refinement
Special positions
Atomic parameter refinement
Overall parameter refinement
Scale factor definitions
Structure factor calculation control list - LIST 23
\LIST 23
Printing the SLFS control list
\PRINT 23
Special position constraints - \SPECIAL
\SPECIAL ACTION= UPDATE= TOLERANCE=
Printing the special position information
Refinement directives - LIST 12
\LIST 12
Obsolete Refinement directives
Defining the least squares matrix
Printing of LIST 12
\PRINT 12
\SUMMARY 12
\PUNCH 12
Creating a null LIST 12
\CLEAR 12
Processing of LIST 12
\LIST 22
Restraints - LIST 16
Parameter, atom, bond and angle specifications
\LIST 16
General restraints
General restraints
Debugging restraints
Printing the contents of LIST 16
\PRINT 16
\SUMMARY LIST 16
\PUNCH 16
Creating a null LIST 16
\CLEAR 16
The special restraints - LIST 17
\LIST 17
Printing and punching LIST 17
\PRINT 17
\SUMMARY LIST 17
\PUNCH 17
Creating a null LIST 17
\CLEAR 17
Checking restraints - CHECK
\CHECK LEVEL=
Weighting schemes for refinement- LIST 4
Weighting for refinement against Fo
Weighting for refinement against Fsq
\LIST 4
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
\PRINT 4
Weighting the reflections - WEIGHT
\WEIGHT INPUT= FACTOR=
Reflection restriction list - LIST 28
\LIST 28
Creating a null LIST 28
Printing the contents of LIST 28
\PRINT 28
Structure Factor Least Squares Calculations - \SFLS
Definitions
Unstable refinements
Sorting of LIST 6 for structure factor calculations
\SFLS
Processing of the refinement directives
Analysis of residuals - \ANALYSE
\ANALYSE INPUT=
Least squares absorption correction - \DIFABS
\DIFABS ACTION= MODE= INPUT=
Internal workings
Parameter esds - LIST 9
Refinement parameter map - LIST 22
The least squares matrix - LIST 11
Printing the contents of LIST 11
Least squares shift list - LIST 24
Restraints in internal format - LIST 26
Fourier Routines
Scope of the Fourier section of the user guide
Input of the Fourier section limits - LIST 14
\LIST 14
Printing the contents of LIST 14
\PRINT 14
Compute Fourier limits from the symmetry
Fourier calculations - \FOURIER
\FOURIER INPUT=
Calculation of superposition minimum functions
Processing of the peaks list - LIST 10
Printing the contents of LIST 10
\PRINT 10
Elimination of duplicated entries in LISTS 5 and 10 - \PEAKS
\PEAKS INPUTLIST= OUTPUTLIST=
Slant fourier calculations - \SLANT
\SLANT INPUT=
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
\DISTANCES INPUTLIST=
Distance-angles symmetry operations
Void Location - \VOIDS
\VOIDS INPUTLIST=
TLS analysis, best planes and lines - \GEOMETRY
\GEOMETRY INPUTLIST=
Torsion angles - \TORSION
\TORSION INPUTLIST=
Absolute Configuration - \TON
\TON
Publication listing of the atomic parameters - \PARAMETERS
\PARAMETERS
Publication listing of reflection data - \REFLECTIONS
\REFLECTIONS INPUT=
Summary of data lists - \SUMMARY
\SUMMARY OF= TYPE= LEVEL=
Estimation of Absolute configuration - \TONSPEK
\TONSPEK INPUT= TYPE= PLOT= PUNCH= FILTER1= … FILTER5= WEIGHT=
CIF lists - \CIF
\CIF
Adding Archive files - ADDARC
ADDARC filename
Graphics - CAMERON
CAMERON
Twinned Crystals
Twinning - introduction
TLQS twins
TLS twins
Twinning Problems
Twinning - Initial clues
Twinning - Data collection and processing
Twinning - Structure solution
Twinning - Structure Refinement
Twin Data stored by CRYSTALS
Twinning - LISTS affected
Twin List 5
Twin List 6
TWIN LIST 13
Twin List 12
Twin List 16
SORTING TWINNED STRUCTURE DATA - \REORDER
\REORDER
Twins - backward compatability
Twins - Worked Example
Twinning - Mathematical aspects
Matrix Calculations
The Basic Matrix Calculator \MATRIX
\MATRIX
Obsolete Commands
Obsolete Commands
Least squares best planes and lines - \MOLAX
\MOLAX INPUTLIST=
Thermal displacement parameter analysis - \ANISO
\ANISO INPUTLIST
Principal atomic displacement directions - \AXES
\AXES INPUTLIST=
Structure factors for a group of trial models - \TRIAL
\TRIAL
Secret Lists
Secret LISTS
Storage of intermediate results and the status of a refinement - LIST 39
Cameron Manual
Introduction
HOW TO CONTROL THE PROGRAM
Command Groups
ERROR HANDLING
Abandon
Edit
Help
The HELP facility
Mouse Activation
General Input Syntax
How To Get Started
Data Input
Input of CRYSTALS List 5 files
INPUT
Outputting Data
OUTPUT
Editing The Atom List
RENAME
RETYPE
Obeying Files
OBEY
Archiving And Retrieving Views
ARCHIVE
RETRIEVE
Graphical Output Devices
SCREEN
HARDCOPY
View Direction Control
BASIC CONTROL
XROT
YROT
ZROT
ROT
CURSOR
ORIENTATION COMMANDS
PLANE
FACE
ALONG
VERTICAL
HORIZONTAL
BISECT
Other related commands
VIEW
COPY
MATRIX
STEREO
NOSTEREO
PHOTOGRAPHS
PHOTO
Include And Exclude
INCLUDE
EXCLUDE
Further related commands
MASK
UNMASK
SWITCH
Generation of Dummy atoms
DUMMY
Example
Drawing Style Control
LINE
BALL
ELLIPSE
ALL
FRAGMENT
GROUP
LINE commands.
BALL commands.
ELLIPSE commands
Connectivity Control
CONNECT
CONNECT
JOIN
REMOVE
DISCONNECT
Miscellaneous CONNECT commands
TAPER
THICKNESS
TOLERANCE
Control Of Colour
COLOUR
Example
Atom Labelling
LABEL
NOLABEL
FONT
TEXT
Other Picture Controlling Commands
MAXIMISE
SCALE
Symmetry Input
Input of symmetry operators
SPACEGROUP
SYMMETRY
Example of Space Group Input
Other symmetry related operations
SETUNIT
ENANTIO
SPECIAL
Crystal Packing Commands
PACK
CELL
WINDOW
Dealing with connectivity
INTRA
INTER
KEEP
INTRA
INTER
KEEP
EXAMPLES
ENCLOSURE
Choice of enclosure “origin”
ATOM
POINT
Type of volume to be used
SPHERE
ANORTHIC
ORTHOGONAL
EXAMPLE
PACKING MORE COMPLICATED STRUCTURES
GROUP
UNPACK
Add And Move - Further Symmetry Related Commands
ADD
ATOMS
ALL
INITIAL
GROUP
EXAMPLES
MOVE
ATOMS
ALL
GROUP
INITIAL
Distance And Angle Calculations
DISTANCE
Method of Calculation
ANGLE
TORSION
Information On Data Held Within The Program
INFORMATION
Group Definitions
DEFGROUP
Example
Miscellaneous Commands
RESET
LOG
EDIT
MENUS
ISSUE
PRINT
How To Stop The Program
END
Menu Definition File
Some Useful Ideas
CRYSTALS
Crystals User Guide
Command line
View page source
Command line
The command line.
Command syntax