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 Structural Formula as a SMILES string - LIST 18

4.16: Printing the SMILES string, LIST 18

4.17: Punching the SMILES string, LIST 18

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

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

4.20: Input of General Crystallographic Data - LIST 30

4.21: Printing the general information, LIST 30

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 the structural formula as a SMILES string  LIST 18
 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

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

       'element name' 'number of atoms'

 e.g. CONTENT FORMULA = C  24  H  36  O  8  N  4

          h k l F and optionally sigma(F)

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

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

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

 \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

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

      A
      B
      C
      GENERATE - the default value.

 \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

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.
 

      P  -  Default value.
      I
      R
      F
      A
      B
      C

      NO
      YES  -  The default value.

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

        SPACEGROUP P 1 21/C 1

 \ 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

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 4.18). 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

 'element TYPE' 'number of atoms'.

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.
 

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

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 4.20).

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

      YES  -  default value.
      NO

      NO  -  Default value.
      YES

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

      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.

      XRAYS  -  Default value
      NEUTRONS

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

This list holds the structural formula as a SMILES string

 \LIST 18
 SMILES    string.
 END

For example

list 18 smile CC(C1=CC=CC=[N]1[Ga]2345[N](N=C(S5)Nc6ccccc6)=C(C) cont C7=CC=CC=[N]73)=[N]2N=C(S4)Nc8ccccc8 smile n(o)(o)(o) end

 

To perform calculations based on elemental properties, such as Sim weighting for Fourier maps (section 8.5), 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

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

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

      2THETA/OMEGA (Default)
      OMEGA
      UNKNOWN

      UNKNOWN (default)
      CAD4
      MACH3
      KAPPACCD
      DIP
      SMART
      IPDS

      F (Default)
      F**2
      UNKNOWN

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

      UNKNOWN (Default)
      SHELXS
      SIR88
      SIR92
      PATTERSON
      SIR97
      DIRDIF