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
  • View page source

Crystals User Guide

Contents:

  • Installation
  • Getting Started
  • Worked examples
  • User Interface
  • Command line
  • Frequently asked questions
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