chem cryst
CRYSTALS manual
University of Oxford

chem cryst news

Crystals Manual

Chapter 4: Initial Data Input

: 4.1: Scope of the Initial Data Input section.; 4.2: Abbreviated startup command - QUICKSTART; 4.3: Input of the cell parameters - LIST 1; 4.4: Printing the cell parameters; 4.5: Input of the unit cell parameter errors - LIST 31; 4.6: Printing the cell variance-covariance matrix; 4.7: Space Group input - \SPACEGROUP; 4.8: Input of the symmetry data - LIST 2; 4.9: Printing the symmetry information; 4.10: Input of molecular composition \COMPOSITION; 4.11: Input of the atomic scattering factors - \LIST 3; 4.12: Printing the scattering factors; 4.13: Input of the crystal and data collection details - LIST 13; 4.14: Printing the experimental conditions, LIST 13; 4.15: Input of the contents of the asymmetric unit - LIST 29; 4.16: Printing the contents of the asymmetric unit, LIST 29; 4.17: Input of General Crystallographic Data - LIST 30; 4.18: Printing the general information, LIST 30

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.1: Scope of the Initial Data Input section.

The areas covered are:

  Abbreviated startup command                      QUICKSTART
  Input of the cell parameters                     LIST 1
  Input of the unit cell parameter errors          LIST 31
  Input of the space group symmetry information    SPACEGROUP
  Alternative input of the symmetry information    LIST 2
  Input of molecular contents                      COMPOSITION
  Input of the atomic scattering factors           LIST 3
  Input of the contents of the unit cell           LIST 29
  Input of the crystal and data collection details LIST 13
  Input of general crystallographic data           LIST 30

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.2: Abbreviated startup command - QUICKSTART

The command QUICKSTART is provided to assist in migration from other systems to CRYSTALS. It requires that data reduction (section 5.14) has already been done or that a simple 4-circle Lp correction be suitable, and that the reflection data are available in a fixed format file with one reflection per line. This command expands the given data into standard CRYSTALS lists, as described elsewhere in the manuals. The user is free to overwrite LISTS created by QUICKSTART by entering new LISTS manually.

  \QUICKSTART
  SPACEGROUP SYMBOL=
  CONTENTS FORMULA=
  FILE NAME=
  FORMAT EXPRESSION=
  DATA WAVELENGTH= REFLECTIONS= RATIO=
  CELL  A= B= C= ALPHA= BETA= GAMMA=
  END

For example:

  \QUICKSTART
  SPACEGROUP P 21/n
  CONTENT C 6 H 4 N O 2 CL
  FILE CRDIR:REFLECT.DAT
  FORMAT (3F3.0, 2X, 2F8.2)
  DATA 1.5418
  CELL 10.2 12.56 4.1 BETA=113.7
  END

\QUICKSTART
None of the directives may be omitted, though some parameters do have default values. CONTINUE directives may not be used.

SPACEGROUP SYMBOL=

This directive generates symmetry information from the spacegroup symbol. The syntax is exactly as describe for the command SPACEGROUP, given in section 4.7.

SYMBOL=

There is no default for the symbol, it should be a valid H-M space group symbol, e.g. 'P 21 21 21' or 'P 21/c' or 'I -4 3 m'. Use spaces to separate each of the operators.

CONTENTS FORMULA=

This directive takes the contents of the UNIT CELL (cf LIST 29 - section 4.15) and generates scattering factors (LIST 3 - section 4.11) and elemental properties (LIST 29 - section 4.15).

FORMULA= The formula for the UNIT CELL contents (NOT ASYMMETRIC UNIT - for compatibility with SIR92) is given as a list with entries of the type

        'element name' 'number of atoms'
 
  e.g. CONTENT FORMULA = C  24  H  36  O  8  N  4

The items in the list must be separated by at least one space. The number of atoms may be fractional or, if omitted, they default to 1.0.

FILE NAME=

This directive associates the file containing the reflections with the program. The special name 'COMMANDS' causes reflection data to be read from the command stream. The reflections MUST then be terminated with an 'h' value of -512, otherwise the end-of-file is sufficient.

NAME= The name of the file containing the reflections. The syntax of the name must conform to the computers operating system. See the IMMEDIATE command \SET FILE for case sensitive systems.

FORMAT EXPRESSION=

This directive controls the reading of the reflection list. The reflection file must contain the following items in the order given. Only one reflection is permitted per line. See \LIST 6 for more flexible input (section 5.3)

           h k l F and optionally sigma(F)

F and sigma(F) may be replaced by I or F-squared.

EXPRESSION= The expression is a normal FORTRAN format expression, including the open and close parentheses. The descriptor 'nX' may be used to skip unwanted columns. The indices may be I or F format. There is no default expression.

DATA WAVELENGTH= REFLECTIONS= RATIO=

WAVELENGTH= The wavelength, in Angstroms, used in selecting elemental properties. The default is 0.7107 (Molybdenum K-alpha radiation).

REFLECTIONS= A keyword to indicate whether the input data is F, F-squared or I.

       FOBS     -  Default, indicating F values being input.
       FSQUARED -  Indicating F squared values being input.
       I        -  Indicating intensity values being input.

If REFLECTIONS equals I, then an Lp correction is done assuming four circle geometry. Note that the reflections from modern diffractometers are unlikely to be stored as FOBS. Some old X-ray data and neutron data may still be given as FOBS.

RATIO= The minimum ratio of I/sigma(I) to be used in selecting reflections. Default is 3.0

CELL A= B= C= ALPHA= BETA= GAMMA= The real cell parameters. The angles default to 90.0 degrees.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.3: Input of the cell parameters - LIST 1

Either the real cell parameters or the reciprocal cell parameters may be input and the three angles be given in degrees or as their cosines. A mixed form, containing both angles and cosines is not allowed.

  \LIST 1
  REAL A= B= C= ALPHA= BETA= GAMMA=
  END

For example

  \LIST 1
  REAL 14.6 14.6 23.7 GAMMA=120
  END

\LIST 1

REAL A= B= C= ALPHA= BETA= GAMMA=

This directive introduces the real cell parameters. If this directive is present, the directive RECIPROCAL will lead to an input error, and no new LIST 1 will be generated.

A=, B=, C= These parameter are the real cell lengths along the A, B and C axes. There are no default values.

ALPHA=, BETA=, GAMMA= These parameters give the real cell angles or their cosines. The default value is 90 degrees.

RECIPROCAL A*= B*= C*= ALPHA*= BETA*= GAMMA*= This directive introduces the reciprocal cell parameters. If this directive is present, the directive REAL will lead to an input error, and no new LIST 1 will be generated.

A*=, B*=, C*= These parameters are the reciprocal cell lengths.

ALPHA*=, BETA*=, GAMMA*= These parameters give the reciprocal cell angles or their cosines. The default value is 90 degrees.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.4: Printing the cell parameters

\PRINT 1

This command lists the cell parameters, and all the other information derived from them which is stored in LIST 1. The inter-axial angles are stored in radians in LIST 1, and printed as such.

There is no command to punch LIST 1.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.5: Input of the unit cell parameter errors - LIST 31

This list contains the variance-covariance matrix of the unit cell parameters. The input consists of a multiplier which is applied to all input parameters, followed by the upper triangle of the variance-covariance matrix (21 Numbers). The units for the angles MUST be radians and those for the cell lengths are Angstroms.

  \LIST 31
  AMULT VALUE=
  MATRIX V(11)= V(12)= .. V(16)= .. V(22)= .. V(26)= .. V(66)=
  END

For example

  \LIST 31
  \ the values of the input matrix are to be multiplied
  \ by 0.000001
  AMULT 0.000001
  \ the cell is trigonal,
  \ with errors of 0.002 along 'a' and 'b', and 0.004 along 'c'
  MATRIX 4 4 1 0 0 0
  CONT     4 1 0 0 0
  CONT      16 0 0 0
  CONT         0 0 0
  CONT           0 0
  CONT             0
  END

\LIST 31

AMULT VALUE=

This directive gives the value by which all the subsequent terms are to be multiplied, and has a default of 1.0.

VALUE=

MATRIX V(11)= V(12)= . . V(16)= V(22)= . . V(66)=

This directive is used to read in the variance-covariance matrix.

If you only have the parameter e.s.d's, input the square of these for V(11), V(22) etc.

V(11)= V(12)= . . V(16)= V(22)= . .V(66)= V(11) is the variance of A , V(12) is the covariance of A and B , V(16) is the covariance of A and GAMMA , V(22) is the variance of B , and V(66) is the variance of GAMMA . The default values for V(11), V(22) and V(33) correspond to axis e.s.d's of .001 A, V(44), V(55) and V(66) to angle e.s.d's of .01 degree.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.6: Printing the cell variance-covariance matrix

\PRINT 31

This prints list 31. There is no command for punching LIST 31.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.7: Space Group input - \SPACEGROUP

The spacegroup symbol interpretation routines in CRYSTALS are derived from subroutines developed by Allen C. Larson and Eric Gabe. It is distributed with their permission. Standard CRYSTALS command input, error handling, data storage, and output has been added to the basic routines. In addition a more flexible method of specifying the unique axis in a monoclinic spacegroup is used. The routine generates a LIST 2 (symmetry information - section 4.8), and a LIST 14 (Fourier and Patterson asymmetric unit limits - section 8.2).

  \SPACEGROUP
  SYMBOL EXPRESSION=
  AXIS UNIQUE=
  END

For example

  \ Input the symbol for a cubic spacegroup
  \SPACEGROUP
  SYMBOL F d 3 m
  END
 
  \ Input the symbol for a common monoclinic spacegroup
  \SPACEGROUP
  SYMBOL P 21/c
  END
 
  \ Input the symbol for a triclinic spacegroup
  \SPACEGROUP
  SYMBOL P -1
  END

\SPACEGROUP

SYMBOL EXPRESSION=

This directive is used to specify the space group symbol.

EXPRESSION= The value of this parameter is the text making up the spacegroup symbol. At least one space character should appear between each of the axis symbols in the spacegroup symbol. e.g.

  Use  P 21 3 rather than P 213, P2 1 3, or P2 13

Failure to put spaces in the correct place in the symbol will lead to misinterpretation.

Rhombohedral cells are always assumed to be on hexagonal indexing.

AXIS UNIQUE=

This directive specifies the unique axis orientation for monoclinic spacegroups where the symbol specified contains only one axis symbol (short symbol). In other cases any information specified with this directive is ignored.

UNIQUE=

       A
       B
       C
       GENERATE - the default value.

When UNIQUE has the value A, B, or C the program uses the 'a', 'b', or 'c' axis respectively as the unique axis. When UNIQUE has the value GENERATE, the program will attempt to select the unique axis on the basis of the cell parameters currently stored in LIST 1. If this is not possible, because the angles in LIST 1 are all close too 90 degrees or there is no valid cell parameter information, the program will assume that the unique axis is 'b'.

Further examples.

  \LIST 1
  REAL 10.2 11.3 14.1 88.3 90 90
  END
  \ Input symmetry - the program will  automatically select 'a' as the
  \ unique axis based on the cell parameters.
  \SPACEGROUP
  SYMBOL P 21/M
  END

  \ Explicitly specify 'c' unique by giving the full symbol.
  \SPACEGROUP
  SYMBOL P 1 1 21/M
  END
  \
  \ Explicitly specify 'c' unique by using the UNIQUE parameter.
  \SPACEGROUP
  SYMBOL P 21/M
  AXIS UNIQUE=C
  END

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.8: Input of the symmetry data - LIST 2

The result of inputting a \SPACEGROUP command (section 4.7) is the automatic generation of a 'LIST 2' containing the explicit symmetry operators and other information that defines the spacegroup.

Direct input of this list enables the user to specify explicitly the symmetry operators to be used. The advantage of this is that they need not comply to any standard convention - the only check made by the program is to ensure that the determinant is not zero. For example, this technique may be used to enter a set of symmetry operators that contains a translation of a half along an axis - normally that cell length would be halved instead, but it may be useful in order to work consistently with a structure that undergoes a cell-doubling phase transition.

  \LIST 2
  CELL NSYMMETRIES=  LATTICE=  CENTRIC=
  SYMMETRY  X=  Y=  Z=
  SPACEGROUP LATTICE= A-AXIS= B-AXIS= C-AXIS=
  CLASS NAME=
  END

For example:

  \ the space group is B2/b
  \LIST 2
  CELL NSYM= 2, LATTICE = B
  SYM X, Y, Z
  SYM X, Y + 1/2,  - Z
  SPACEGROUP B 1 1 2/B
  CLASS MONOCLINIC
  END

The CELL directive defines the Bravais lattice type, the number of equivalent positions to be input, and whether the cell is centric or acentric. The equivalent positions are defined by SYMMETRY directives, which contain one equivalent position each, and must follow the CELL directive. The equivalent positions input should not include those related by a centre of symmetry if the lattice is defined as centric, and should not include those related by non-primitive lattice translations if the correct Bravais lattice type is given. Positions generated by the last two operations are computed by the system. The unit matrix, defining x, y, z, MUST ALWAYS be input. If a centric cell is used in a setting which does not place the centre at the origin, then ALL the operators must be given and the cell be treated as non-centric. This will of course increase the time for structure factor calculations.

Rhombohedral cells can be treated in two ways. If used with rhombohedral indexing (a=b=c, alpha=beta=gamma), the lattice type is P, primitive. If used with hexagonal indexing, the lattice type is R.

\LIST 2

CELL NSYMMETRIES= LATTICE= CENTRIC=

NSYMMETRIES= This defines the number of SYMMETRY directives that are to follow. There is no default.

LATTICE= This defines the Bravais lattice type, and must take one of the following values :

       P  -  Default value.
       I
       R
       F
       A
       B
       C

CENTRIC= This parameter defines whether the cell is centric or acentric, and must take one of the values :

       NO
       YES  -  The default value.

SYMMETRY X= Y= Z= This directive is repeated NSYMMETRIES times, and each separate occurrence defines one equivalent position in the unit cell. The parameter keywords X , Y and Z are normally omitted on this directive, and the equivalent position typed up exactly as given in international tables. The expressions may contain any of the following :

       +X or -X
       +Y or -Y
       +Z or -Z
       + or - a fractional shift.

The fractional shift may be represented by one number divided by another (e.g. 1/2 or 1/3) or by a true fraction (0.5 or 0.33333...). Apart from terminating text, spaces are optional and ignored. The terms for the new x, y and z must be separated by a comma (,) , and the whole expression may be terminated by ; if required.

SPACEGROUP LATTICE= A-AXIS= B-AXIS= C-AXIS= This directive inputs the space group symbol, and is optional for the correct working of CRYSTALS. However, some foreign programs need the symbol as input data, and they will extract it from this record. The keywords LATTICE, A-AXIS etc are normally omitted, and the full space group symbol given with spaces between the operators, e.g.

         SPACEGROUP P 1 21/C 1

CLASS NAME= This directive inputs the crystal class. It is not used by CRYSTALS, but is required for cif files.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.9: Printing the symmetry information

\PRINT 2

This prints LIST 2. There is no command for punching LIST 2.

Further examples.

  \ THE SPACE GROUP IS P1-BAR.
  \LIST 2
  CELL NSYM= 1
  SYM X, Y, Z
  SPACEGROUP P -1
  END

  \ THE SPACE GROUP IS P 321
  \LIST 2
  CELL CENTRIC= NO, NSYM= 6
  SYM X, Y, Z
  SYM -Y, X-Y, Z
  SYM Y-X, -X, Z
  SYM Y, X, -Z
  SYM -X, Y-X, -Z
  SYM X-Y, -Y, -Z
  END

  \ THE SPACE GROUP IS P 6122 (note alternative notation for fractions)
  \LIST 2
  CELL NSYM= 12, CENTRIC= NO
  SYM X,Y,Z
  SYM -X    ,   -Y  ,Z+.5
  SYM +Y, +X,1/3-Z
  SYM -Y,-X,5/6-Z
  SYM -Y, X-Y, .333333333+Z
  SYM Y, Y-X, Z+10/12
  SYM -X, Y-X, 4/6-Z
  SYM X, X-Y, 1/6-Z
  SYM Y-X, -X, Z+4/6
  SYM  X-Y, X, Z+1/6
  SYM X-Y, -Y, -Z
  SYM Y-X, Y ,  -Z+.5
  SPACEGROUP P 61 2 2
  END

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.10: Input of molecular composition \COMPOSITION

This command takes the contents of the asymmetric unit, searches the specified data files for required values, and then internally creates normal scattering factors (LIST 3 - section 4.11) and elemental properties (LIST 29 - section 4.15). NOTE LISTS 1 (see !flabel!LIST01!) and 13 (see !RLIST13
) must have been input beforehand.

  \COMPOSITION
  CONTENTS FORMULA=
  SCATTERING FILE=
  PROPERTIES FILE=
  END

For example:

  \COMPOSITION
  CONTENT C 6 H 5 N O 2.5 CL
  SCATTERING CRSCP:SCATT.DAT
  PROPERTIES CRSCP:PROPERTIES.DAT
  END

\COMPOSITION

There are three directives, none of which have default values.

CONTENTS FORMULA=

FORMULA= The formula for the UNIT CELL (NOT ASYMMETRIC UNIT) is given as a list with entries

  'element TYPE' 'number of atoms'.

The items in the list MUST be separated by at least one space. The number of atoms may be omitted, when they default to 1.0, and may be fractional.

The element TYPE must conform to the TYPE conventions described in the atom syntax, section 3.5.

SCATTERING FILE= This directive gives the name of the file to be searched for scattering factors, and must conform to the syntax of the computing system. A file CRSCP:SCATT.DAT is provided for some implementations, and contains all the scattering factors listed in Volume IV, International Tables.

PROPERTIES FILE= This directive gives the name of the file to be searched for elemental properties, and must conform to the syntax of the computing system. A file CRSCP:PROPERTIES.DAT is provided for some implementations, and contains values gleaned from various sources. The file contains references.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.11: Input of the atomic scattering factors - \LIST 3

This list contains the scattering factors that are to be used for each atomic species that may appear in the atomic parameter list (LIST 5) - see the section of the user guide on Atom and Element names).

  \LIST 3
  READ  NSCATTERERS=
  SCATTERING TYPE= F'= F''= A(1)= B(1)= A(2)= . . . B(4)= C=
  END

For example

  \LIST 3
  READ 2
  SCATT C    0    0
  CONT  1.93019  12.7188  1.87812  28.6498  1.57415  0.59645
  CONT  0.37108  65.0337  0.24637
  SCATT S 0.35 0.86  7.18742  1.43280  5.88671  0.02865
  CONT               5.15858  22.1101  1.64403  55.4561
  CONT              -3.87732
  END

The scattering factor of an atom in LIST 5 (the model parameters) is determined by its TYPE, an entry for which must exist in LIST 3.
The form factor is calculated analytically at each value of sin(theta)/lambda, s , from the relationship :

  f = sum[a(i)*exp(-b(i)*s*s)] + c       i=1 to 4.

The coefficients a(1) to a(4), b(1) to b(4) and c and the real and imaginary parts of the anomalous dispersion correction are input for each element TYPE.

\LIST 3

This is the normal calling command for the input of LIST 3.

READ NSCATTERERS=

NSCATTERERS= This must be set to the number of atomic species to be stored in LIST 3, and thus the number of SCATTERING directives to follow. There is no default value.

SCATTERING TYPE= F'= F''= A(1)= B(1)= A(2)= . . . B(4)= C= This directive provides the form factor details for one atomic species. This directive must be repeated NSCATTERERS times.

TYPE= The element TYPE must conform to the TYPE conventions described in the General Introduction. The values used for TYPE in LIST 3 will have their counterparts in the TYPEs stored for atoms in LIST 5 (the model parameters), and in the TYPEs stored for atomic species in LIST 29 (see section 4.15). There is no default for this parameter.

F'= F''= These define the real and imaginary parts of the anomalous dispersion correction for this atomic species at the appropriate wavelength. A default value of zero is assumed if these parameters are omitted.

A(1)= B(1=) A(2=) B(2)= A(3)= B(3)= A(4)= B(4)= C= These define the coefficients used to compute the scattering factor for this atomic species. There are no default values.

   For neutrons, all the A(i) and B(i) are set to zero, and C is set to
  the scattering length.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.12: Printing the scattering factors

\PRINT 3

This prints LIST 3. There is no command for punching LIST 3.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.13: Input of the crystal and data collection details - LIST 13

LIST 13 contains information about those experimental details which may be needed during structure analysis. Information only required for the generation of a cif are held in LIST 30 (section 4.17).

If no LIST 13 has been input and one is required, a default list is generated.

  \LIST 13
  CRYSTAL FRIEDELPAIRS= TWINNED= SPREAD=
  DIFFRACTION GEOMETRY= RADIATION=
  CONDITIONS WAVELENGTH= THETA(1)= THETA(2)= CONSTANTS . .
  MATRIX R(1)= R(2)= R(3)= . . . R(9)=
  TWO H= K= L= THETA= OMEGA= CHI= PHI= KAPPA= PSI=
  THREE H= K= L= THETA= OMEGA= CHI= PHI= KAPPA= PSI=
  REAL COMPONENTS= H= K= L= ANGLES=
  RECIPROCAL COMPONENTS= H= K= L= ANGLES=
  AXIS H= K= L=

For example:

  \LIST 13
  DIFF GEOM= CAD4
  COND WAVE= .7107
  MATRIX
  END

\LIST 13

This directive describes properties that relate to the whole crystal.

CRYSTAL FRIEDELPAIRS= TWINNED= SPREAD=

FRIEDELPAIRS= This parameter defines whether Friedel's law should be used during \SYSTEMATIC in data reduction. It should be set to NO for high accuracy or absolute structure determinations. If omitted, Friedel's law will be used.

       YES  -  default value.
       NO

TWINNED= This parameter is used during refinement to indicate whether the twin laws should be used. It is automatically updated if twinned reflection data is input.

       NO  -  Default value.
       YES

SPREAD= This parameter defines the type of mosaic spread in the crystal. This information is used during the calculation of an extinction correction.

       GAUSSIAN  -  Default value. Suitable for X-rays
       LORENTZIAN - Suitable for Neutrons

DIFFRACTION GEOMETRY= RADIATION=

This directive defines the experimental conditions used to collect the data.

GEOMETRY= This defines the type of data collection method used to measure the raw intensities, and determines the type of Lp correction.

       NORMAL  -  Normal beam Weissenberg geometry.
       EQUI    -  Equi-inclination Weissenberg geometry.
       ANTI    -  Anti-equi-inclination Weissenberg geometry.
       PRECESSION
       CAD4    -  Nonius CAD4 diffractometer, Eulerian angles.
       KAPPA   -  Nonius CAD4 in kappa geometry.
       ROLLETT -  Abstract machine, see page 28 , Computing Methods
                  in Crystallography.
       Y290    -  Hilger-Watts Y290 4-Circle diffractometer.
       NONE    -  Default.

RADIATION= This parameter defines the type of radiation used to collect the data.

       XRAYS  -  Default value
       NEUTRONS

CONDITIONS WAVELENGTH= THETA(1)= THETA(2)= CONSTANTS . .

This directive describes the conditions that were used when the data were collected. CONSTANTS is short for four constants.

       CONSTANT(1)= CONSTANT(2)= CONSTANT(3)= CONSTANT(4)=

WAVELENGTH= This defines the wavelength of the radiation used to collect the data. If omitted, a default value of 0.71073 is assumed,(Mo k-alpha).

THETA(1)= This defines the Bragg angle of the monochromator. If omitted, a default of 6.05 is assumed, indicating that a monochromator was used with Mo radiation

THETA(2)= This defines the angle between the plane of the monochromator and the diffracting planes of the crystal. If this parameter is omitted, a default value of 90 is assumed. This value is not used if THETA(1) is zero. Since the angle THETA(2) is fixed, the Lp correction computed using these constants is correct only for experiments where THETA(2) is a constant. This is true for equatorial geometry experiments, but is not true for equipment that uses Weissenberg or precession geometry.

CONSTANT(1)= CONSTANT(2)= CONSTANT(3)= CONSTANT(4)= These four parameters are used to input fundamental constants for the diffractometer used to collect the data. How many of the constants, and what values they should have are determined by the equipment and its setting. To determine the values required, consult your local diffractometer expert. The default values for c(1), c(2) and c(3) are the Nonius CAD4 GONCON constants, and c(4) is the theta value for the change from bisecting to fixed chi mode (and has a value of 90 degrees). These constants are important when machine geometry dependent calculations are made - for example, absorption corrections. The defaults in the program were correct for the Nonius CAD4 in the Oxford Chemical Crystallography lab on 13 October 1980.

MATRIX R(1)= R(2)= R(3)= . . . R(9)=

This directive is used to input the orientation matrix directly. If this directive is input, the directives TWO , THREE , REAL , and RECIPROCAL (detailed below) may not be used. This directive is normally used for diffractometer collected data.

R(1)= R(2)= R(3)= . . . R(9)= The elements of the matrix must be input in the order (1,1), (1,2), (1,3), (2,1), etc. The default is a unit diagonal matrix.

TWO H= K= L= THETA= OMEGA= CHI= PHI= KAPPA= PSI=

This directive is used to input the setting details required to define a diffractometer orientation matrix from two reflections. The details for the two reflections must be input on separate directives, so that this directive must be repeated twice. This directive may only be input when the GEOMETRY parameter on the DIFFRACTION directive is Y290 or CAD4 . If this directive is input, the directives THREE , REAL , RECIPROCAL , and MATRIX may not be used. The reflections should be given in the same order as in the original experiment.

H= K= L= These three parameters define the indices of the reflection that is to be used to calculate the orientation matrix.

THETA= OMEGA= CHI= PHI= KAPPA= PSI= These parameters define the setting angles for the reflection whose indices are given by H , K and L . There are no default values for THETA , OMEGA and PHI , and one of CHI or KAPPA must be input. The default values for CHI , KAPPA and PSI are zero.

THREE H= K= L= THETA= OMEGA= CHI= PHI= KAPPA= PSI=

This directive is used to input the setting details required to define a diffractometer orientation matrix from three reflections. The details for the three reflections must be input on separate directives, so that this directive must be repeated three times. This directive may only be input when the GEOMETRY parameter on the DIFFRACTION directive is Y290 or CAD4 . If this directive is input, the directives TWO , REAL , RECIPROCAL , and MATRIX may not be used.

H= K= L= THETA= OMEGA= CHI= PHI= KAPPA= PSI= These parameters are defined as for TWO above.

REAL COMPONENTS= H= K= L= ANGLES= This directive is used to define the orientation matrix for the Nonius CAD4 diffractometer from the components of the real vector along the phi axis and the setting angles of one reflection. The items COMPONENTS and ANGLES are short for:

COMPONENT(1)= COMPONENT(2)= COMPONENT(3)=

and

THETA= OMEGA= CHI= PHI= KAPPA= PSI=
If this directive is input, the directives TWO , THREE , RECIPROCAL , and MATRIX may not be used. This directive may only be input when the GEOMETRY parameter on the DIFFRACTION directive is CAD4 .

COMPONENT(1)= COMPONENT(2)= COMPONENT(3)= These three parameters provide the components of the real cell vector that is parallel to the phi axis.

H= K= L= THETA= OMEGA= CHI= PHI= KAPPA= PSI= These parameters are defined as in TWO above

RECIPROCAL COMPONENTS= H= K= L= ANGLES= This directive is used to define the orientation matrix for the Nonius CAD4 diffractometer from the components of the reciprocal vector along the phi axis and the setting angles of one reflection. The items COMPONENTS and ANGLES are short for:

COMPONENT(1)= COMPONENT(2)= COMPONENT(3)=

and

THETA= OMEGA= CHI= PHI= KAPPA= PSI=
If this directive is input, the directives TWO , THREE , REAL , and MATRIX may not be used. This directive may only be input when the GEOMETRY parameter on the DIFFRACTION directive is CAD4 .

COMPONENT(1)= COMPONENT(2)= COMPONENT(3)= These three parameters provide the components of the reciprocal cell vector that is parallel to the phi axis.

H K L THETA OMEGA CHI PHI KAPPA PSI These parameters are defined as in TWO above

AXIS H= K= L=

This directive is used to define the axis about which data were collected in Weissenberg geometry. This directive may only be given when the GEOMETRY parameter on the DIFFRACTION directive is one of NORMAL , EQUI or ANTI .

H= K= L= These three parameters define the zone axis [hkl] about which the crystal was rotated during data collection. If any of these parameters is omitted, a default value of zero is assumed.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.14: Printing the experimental conditions, LIST 13

\PRINT 13

This prints list 13. There is no command for punching LIST 13.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.15: Input of the contents of the asymmetric unit - LIST 29

To perform calculations based on elemental properties, such as Sim weighting for Fourier maps (section 8.4), connectivity calculations, absorption and density calculations, it is necessary to input the numbers and properties of the elements in the cell. This information is stored in LIST 29.

  \LIST 29
  READ  NELEMENT=
  ELEMENT TYPE= COVALENT= VANDERWAALS= IONIC= NUMBER= MUA= WEIGHT= COLOUR=
  END

For example:

  \LIST 29
  READ NELEMENT=4
  ELEMENT MO NUM=0 .5
  ELEMENT S NUM=2
  ELEMENT O NUM=3
  ELEMENT C NUM=10
  END

\LIST 29

READ NELEMENT=

NELEMENT This must be set to the number of atomic species in the asymmetric unit, and consequently the number of ELEMENT directives that are about to follow this directive. If this directive is omitted, a default value of one is assumed for NELEMENT.

ELEMENT TYPE= COVALENT= VANDERWAALS= IONIC= NUMBER= MUA= WEIGHT= Each ELEMENT directive provides the information about that atomic species in the asymmetric unit.

TYPE= The element TYPE must conform to the TYPE conventions described in the section on atom syntax, 3.5. The default value for this parameter is taken from the COMMAND file. When LIST 29 is used for Simm weighting, the TYPE is compared with the TYPEs stored in LIST 3 (section 4.11) to determine the scattering factor of the given species.

COVALENT=

VANDERWAALS=

IONIC= The radii used during geometry calculations, with a default values set in the COMMAND file. The covalent radius is incremented by 0.1 A for distance contacts, and used for defining restraint targets (see \DISTANCES). The van der Waals radius is incremented by .25A for finding non-bonded contacts, and used for defining energy restraints The ionic radius may be used during geometry calculations.

NUMBER= This parameter gives the number of atoms of the given type in the asymmetric unit. This number can be fractional, depending on the number of atoms in the cell and whether they occupy special positions, and whether they are disordered.

MUA= This is the atomic absorption coefficient x10**(-23) /cm as in INT TAB VOL III. Note that in Vol IV the units are x10**(-24). Take care to ensure that the coefficients are appropriate for the wavelength used.

WEIGHT This is the Atomic weight

COLOUR This is the colour to be used for each atom in CAMERON. The available colours are:

  BLACK BLUE    CYAN   GREEN GREY   LBLUE LGREEN LGREY  
  LRED  MAGENTA ORANGE PINK  PURPLE RED   WHITE  YELLOW

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.16: Printing the contents of the asymmetric unit, LIST 29

\PRINT 29

This prints list 29. There is no command for punching LIST 29.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.17: Input of General Crystallographic Data - LIST 30

This list holds general crystallographic information for later inclusion in the cif file. CRYSTALS contains no COMMAND for editing this list - inputting a new LIST 30 over writes any existing version. However, some CRYSTALS commands update LIST 30 as an analysis proceeds, and there is a SCRIPT which enables some details to be changed.

  \LIST 30
  DATRED     NREFMES= NREFMERG= RMERGE= NREFFRIED= RMERGFRIED= REDUCTION=
  CONDITIONS MINSIZE= MEDSIZE= MAXSIZE= NORIENT=
  CONTINUE   THORIENTMIN= THORIENTMAX= TEMPERATURE= STANDARDS= DECAY= SCANMODE=
  CONTINUE   INTERVAL= COUNT= INSTRUMENT=
  REFINEMENT R= RW= NPARAM= SIGMACUT= GOF= DELRHOMIN= DELRHOMAX=
  CONTINUE   RMSSHIFT= NREFUSED= FMINFUNC= RESTMINFUN= TOTALMINFUN= COEFFICIENT=
  INDEXRANGE HMIN= HMAX= KMIN= KMAX= LMIN= LMAX= THETAMIN= THETAMAX=
  ABSORPTION ANALMIN= ANALMAX= THETAMIN= THETAMAX= EMPMIN= EMPMAX=
  CONTINUE   DIFABSMIN= DIFABSMAX= ABSTYPE=
  GENERAL    DOBS= DCALC= F000= MU= MOLWT= FLACK= ESD= ANALYSE-CUT= 
  CONTINUE   ANALYSE-NREF= ANALYSE-R= ANALYSE-RW= SOLUTION=
  COLOUR
  SHAPE
  CIFEXTRA   CALC-SIGMA= CALC-NREF= CALC-R= CALC-RW= 
  CONTINUE   ALL-SIGMA= ALL-NREF= ALL-R= ALL-RW=
  END

For example

  \LIST 30
  CONDITIONS MINSIZE=.1 MEDSIZE=.3 MAXSIZE=.8 NORIENT=25
  CONTINUE   THORIENTMIN=15.0 THORIENTMAX=25.0
  CONTINUE   TEMPERATURE=293 STANDARDS=3 DECAY=.05 SCANMODE=2THETA/OMEGA
  CONTINUE   INSTRUMENT=MACH3
  INDEXRANGE HMIN=-12 HMAX=12 KMIN=-13 KMAX=13 LMIN=-1 LMAX=19
  COLOUR RED
  SHAPE PRISM
  END

\LIST 30

DATRED NREFMES= NREFMERG= RMERGE= NREFFRIED= RMERGFRIED= REDUCTION= Information about the data reduction process.

NREFMES= The number of reflections actually measured in the diffraction experiment

NREFMERG= Number of unique reflections remaining after merging equivalents applying Friedel's Law

RMERGE= Merging R factor (R int) applying Friedel's Law (as decimal not %)

NREFFRIED= Number of unique reflections remaining after merging equivalents without applying Friedel's Law

RMERGFRIED= Merging R factor (R int) without applying Friedel's Law (as decimal not %)

CONDITIONS MINSIZE= MEDSIZE= MAXSIZE= NORIENT= THORIENTMIN= THORIENTMAX=

CONDITIONS (continued) TEMPERATURE= STANDARDS= DECAY= SCANMODE=

CONDITIONS (continued) INTERVAL= COUNT= INSTRUMENT= Information about data collection.

MINSIZE=

MEDSIZE=

MAXSIZE= The crystal dimensions, in mm.

NORIENT= Number of orientation checking reflections.

THORIENTMIN= Minimum theta value for orientating reflections.

THORIENTMAX= Maximum theta value for orientating reflections.

TEMPERATURE= Data collection temperature, Kelvin.

STANDARDS= Number of intensity control reflections.

DECAY= Average decay in intensity, %.

SCANMODE= Data collection scan method. Options are

       2THETA/OMEGA (Default)
       OMEGA
       UNKNOWN

INTERVAL=
Intensity control reflection interval time, minutes. Used if standards are measured at a fixed time interval

COUNT= Intensity control reflection interval count. Used if standards are measured after a fixed number (count) of general reflections.

INSTRUMENT Instrument used for data collection. Known instruments are:

       UNKNOWN (default)
       CAD4
       MACH3
       KAPPACCD
       DIP
       SMART
       IPDS

REFINEMENT R= RW= NPARAM= SIGMACUT= GOF= DELRHOMIN= DELRHOMAX= RMSSHIFT=

REFINE (cont) NREFUSED= FMINFUNC= RESTMINFUNC= TOTALMINFUNC= COEFFICIENT= Information about the refinement procedure.

R= Conventional R-factor.

RW= Hamilton weighted R-factor.

The weighted R-factor stored in LIST 6 (section 5.3) and LIST 30 is that computed during a structure factor calculation. The conventional R-factor is updated by either an SFLS calculation (section 7.42) or a SUMMARY of LIST 6.

NPARAM= Number of parameters refined in last cycle.

SIGMACUT= The I/sigma(I) threshold used during refinement.

GOF= GOF, Goodness-of-Fit, S.

DELRHOMIN=

DELRHOMAX= Minimum and maximum electron density in last difference synthesis.

RMSSHIFT= R.m.s (shift/e.s.d) in last cycle of refinement.

NREFUSED= Number of reflections used in last cycle of refinement.

FMINFUNC= Minimisation function for diffraction observations.

RESTMINFUNC= Minimisation function for restraints.

TOTALMINFUNC= Total minimisation function.

COEFFICIENT= Coefficient for refinement. Alternatives are:

       F (Default)
       F**2
       UNKNOWN

INDEXRANGE HMIN= HMAX= KMIN= KMAX= LMIN= LMAX= THETAMIN= THETAMAX= Range of reflection limits during data collection.

HMIN= HMAX= KMIN= KMAX= LMIN= LMAX= Minimum and maximum values of h,k and l.

THETAMIN= THETAMAX= Minimum and maximum values of theta.

ABSORPTION ANALMIN= ANALMAX= THETAMIN= THETAMAX= EMPMIN= EMPMAX=

ABSORPTION (continued) DIFABSMIN= DIFABSMAX= ABSTYPE= Information about absorption corrections.
NOTE the keywords PSIMIN and PSIMAX have been removed. Store values as EMPMIN and EMPMAX

ANALMIN= ANALMAX= Minimum and maximum analytical corrections

THETAMIN= THETAMAX= Minimum and maximum theta dependant corrections

EMPMIN= EMPMAX= Minimum and maximum empirical corrections (usually combination of theta and psi or multi-scan for area detectors).

DIFABSMIN= DIFABSMAX= Minimum and maximum DIFABS type correction, i.e. based on residue between Fo anf Fc (see section 7.48). In the cif it is called a refdelf correction.

ABSTYPE= Type of absorption correction. Alternatives are:

       NONE (default) EMPIRICAL    GAUSSIAN     SPHERICAL
       DIFABS         MULTI-SCAN   ANALYTICAL   CYLINDRICAL
       SHELXA         SADABS       NUMERICAL
                      SORTAV       INTEGRATION
                      PSI-SCAN

GENERAL DOBS= DCALC= F000= MU= MOLWT= FLACK= ESD=

GENERAL (continued) ANALYSE-CUT= ANALYSE-NREF=

GENERAL (continue) ANALYSE-R= ANALYSE-RW= SOLUTION= General information, usually provided by CRYSTALS.

DOBS= DCALC= Observed density and that calculated by CRYSTALS.

F000= Sum of scattering factors at theta = zero.

MU= Absorption coefficient, calculated by CRYSTALS.

MOLWT= Molecular weight, calculated bt CRYSTALS.

FLACK=

ESD= The Flack parameter and its esd, if refined.

ANALYSE-CUT=

ANALYSE-NREF=

ANALYSE-R=

ANALYSE-RW= These values are updated when ever \ANALYSE is run, and can be used to record the effect of different LIST 28 schemes. Remenber that if the LIST 28 conditions are modified to include more reflections than were used in the last \SFLS calculation (section 7.42), the values of Fc for the additional reflections will be incorrect. A \SFLS calculation sets these to the same values as in REFINEMENT above.

SOLUTION= The program/procedure used for structure solution

       UNKNOWN (Default)
       SHELXS
       SIR88
       SIR92
       PATTERSON
       SIR97
       DIRDIF

COLOUR The crystal colour.

SHAPE The crystal shape.

CIFEXTRA These are filled in by the \SFLS CALC operation (section 7.42). Structure factors are computed for ALL reflections along with R and Rw - LIST 28 is ignored (LIST 28, reflection filtering, see section 2.14LIST28). R and Rw are also computed for reflections above a given threshold.

[Top] [Index] Manuals generated on Wednesday 8 November 2006

4.18: Printing the general information, LIST 30

\PRINT 30

This prints list 30. There is no command for punching LIST 30.