Crystals Manual

This specification defines one atom. The various parts of the expression are :

           L=    1             2                3                4
 
       P       0,0,0
       I       0,0,0      1/2,1/2,1/2
       R       0,0,0      1/3,2/3,2/3      2/3,1/3,1/3
       F       0,0,0        0,1/2,1/2      1/2, 0 ,1/2      1/2,1/2,0
       A       0,0,0        0,1/2,1/2
       B       0,0,0      1/2, 0 ,1/2
       C       0,0,0      1/2,1/2, 0
 

       1.  Centre of symmetry if 'S' negative
       2.  Symmetry operator 'S'
       3.  Non-primitve lattice translation
       4.  Whole unit cell translations 'T(X)', 'T(Y)', 'T(Z)'.
 
     i.e.
            X'=  [R(s)](+X) + t(s) + L + T(X) + T(Y) + T(Z)
     or
            X'=  [R(s)](-X) + t(s) + L + T(X) + T(Y) + T(Z)
 

       TYPE(SERIAL,1,1,0,0,0)
       TYPE(SERIAL,,,0,0,0)
       TYPE(SERIAL,1,,,,0)
       TYPE(SERIAL,,,,,)
 

       TYPE1(SERIAL1,S,L,TX,TY,TZ)  UNTIL  TYPE2(SERIAL2)
 

This definition specifies all the atoms in the current list starting with the atom TYPE1(SERIAL1) The first atom in the specification must occur before the second atom in the current parameter list, otherwise an error message will be output and the task aborted. If symmetry operators are used, they must be given for the first atom of the sequence, and will be appied to all the atoms in the sequence.

       Examples
 
                   C(1) until C(6)
 
       Six atoms lying around a centre of symmetry:
 
                   C(1) until C(3) C(1,-1) UNTIL C(3)
 

These specifications each define one atom. FIRST Refers to the first atom stored in LIST 5 (the model parameters) or LIST 10 (Fourier peaks), and LAST refers to the last atom in the list. If these are used as atom designators, no serial number may be given, but symmetry operators may be. They may be used in until sequences.

       examples
                   LAST
                   FIRST(x)
                   FIRST(-1) UNTIL C(16)  C(23) UNTIL LAST
 

This specifies all atoms in the list, can take symmetry operators or parameter names, but cannot be accompanied on the same line by any other atom specifiers.

       examples
                   ALL
                   ALL(x)
                   ALL(-1)
 

This specifies all atoms or parameters with the given residue number.

       examples
                   RESIDUE(3)
                   RESIDUE(3,X's)
 

This specifies all atoms or parameters with the given part number.

       examples
                   PART(3001)
                   PART(3001,X's)
 

The part number is constructed from two values, the assembly number and the group number.

     PART NO. = 1000 * ASSEMBLY NO. + GROUP NO.
 

The assembly number is normally zero, but a value can be given to all atoms that are involved in a particular disordered area of the structure. E.g. on a disordered methyl all the H atoms could be placed in assembly number 1.
The group number within an assembly groups together those atoms which are simultaneously occupied. E.g. on a disordered methyl, all the H atoms approximately 109 degrees apart would be given the same group number.
The part and group numbers affect the default bonds that are determined by CRYSTALS, and subsequently output in the CIF or summary file. Some bonding rules are applied in the following order of priority:

 1. An atom in assembly 0, group 0, will bond to any other nearby atom.
 2. Atoms in the same assembly, but with different, non-zero group numbers
    will not bond to each other.
 3. Atoms in different assemblies with one zero group number
    will not bond to each other.
 4. Atoms in the same assembly and group, but with a negative group number
    will not bond to symmetry related atoms in the same assembly and group.
 5. All remaining close contacts will be bonded together.
 

Rule 3 may be ignored unless you're trying to set up something very special. Rule 4 is useful if you have a group disordered across a symmetry element.
 

The following NAMES are recognised.

       X      Y      Z      OCC      U[ISO]    SPARE
       U[11]  U[22]  U[33]  U[23]    U[13]     U[12]
       X'S    U'S    UIJ'S  UII'S
 

       Examples
         X            The 'x' coordinate for all atoms
         C(9,X,Y)     The 'x' and 'y' coordinates for atom C(9)
         FIRST(X'S)   The 'x','y' and 'z' coordinates for the first atom
         FIRST(U'S) UNTIL C(23)
                      The anisotropic temperature factors for all atoms
                      up to C(23).
 

       Ugeom  = (Ui * Uj * Uk)**1/3
 
       Uarith = (Ui + Uj + Uk)/3
                                        Where Ui, Uj & Uk are the
                                        principal components of U
 
       Ugeom is the radius of the sphere with the same volume as the adp
       ellipsoid, and thus gives a good indication of the quality of the
       ellipsoid. Uarith is often closer to the value of Uiso, and so is
       useful for returning to an isotropic refinement.
 

The SPecial Shape keys are

 
       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  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
 
 

This directive specifies various parameters that refer to the structure as a whole.

This directive specifies the number of atoms, layer scale factors, element scale factors, and batch scale factors that are to follow.

The parameters for an atom, repeated NATOM times.

 KEY   shape      parameters
 
  2    Sphere     U[ISO] SIZE
  3    Line       U[ISO] SIZE  DECLINAT AZIMUTH
  4    Ring       U[ISO] SIZE  DECLINAT AZIMUTH
 
 

This directive is used to input the constants that define an index for layer scaling. The layer scale index for the reflection with indices HKL is computed from

       index = (h*p + k*q + l*r + s)
 

and the absolute value is taken if the parameter ABSOLUTE = yes.

       NO
       YES  -  Default value
 

This directive defines the layer scale factors, starting with the scale for an index of 1.

This directive defines the scale factors for the elements of a twinned structure. See the chapter on twinned structures.

This directive defines the batch scale factors.

       OFF          No monitoring occurs
       LOW          Type and serial only are displayed
       MEDIUM       Program selects level of display   (default)
       HIGH         At least the level represented by
                    'MEDIUM' listing is displayed
 

When the program selects a monitor level account is taken of the amount of relevant information for the particular directive. Thus for DELETE only 'type' and 'serial' need be displayed whereas for CHANGE all parameter values are displayed.

       OFF               No listing produced
       LOW               Type and serial listed
       MEDIUM            Type , serial , occ , u[iso] ,
                         x , y , z listed
       HIGH              All atomic parameters listed
 

  ATOM O 1 X = 0.3427 .89004 .09181
 

       NEWSERIAL = Z + OLDSERIAL
 

The sequence Z ATOM-SPECIFICATIONS can be repeated. When moving from a centrosymmetric to a non-centrosymmetric space group, for example, atoms formerly related by the centre of symmetry can be generated :

       CREATE 30 MO(1,-1) UNTIL C(15)
 
       Creates atoms MO(31) until C(45)
 

The original atoms are not deleted. The sequence Z ATOM-SPECIFICATIONS can be repeated. The new serial numbers are given by

       NEWSERIAL(1) = Z* OLDSERIAL and
       NEWSERIAL(2) = Z* OLDSERIAL +1
 

Only the atoms referenced in this directive will be kept in the list, all the others will be lost, even though they can be referenced right up until the final END. The sequence Z ATOM-SPECIFICATIONS can be repeated.
Atoms that are KEPT are moved to the top of the list, and stored in the order in which they are specified on the KEEP directive. Only one KEEP directive may be given. Use CONTINUE if one line isn't long enough for the atom sequence.

The atom specifications may contain symmetry operators, which are used to generate the coordinates of the atoms that are to be retained. 'Z' Is an optional parameter which defines the serial number of the first atom in the specification immediately following it. For each atom thereafter in the current atom specification, the serial number is incremented by one to generate the output serial number. Atoms whose serial numbers are changed in this way must be referred to in subsequent directives by their new serial numbers. If 'Z' is not given, the atoms retain their old serial numbers.

If an UNTIL sequence is used after a KEEP directive has been given, it should be used with care, since the order of the new parameter list is different from the input list.

This defines the atom in the list after which atoms that are MOVEd should be placed. (See MOVE below). If this directive is omitted, the default option places the first MOVED atom at the head of the list, and successive atoms after it. Once one AFTER directive has been given, atoms are placed behind the given atom in the order in which they are presented on MOVE directives. If no atom specification is given on this directive, subsequent MOVEs will move the atoms to the head of the list.

This directive moves atoms about in the list and places them in the position defined by the latest AFTER directive. (See the previous directive). This directive does not remove atoms from the list, but simply reorders the list. The sequence Z ATOM-SPECIFICATIONS can be repeated.

The atom specifications may contain symmetry operators, which are used to generate the coordinates of the atoms that are to be moved. 'Z' is an optional parameter which defines the serial number of the first atom in the specification immediately following it. For each atom thereafter in the current atom specification, the serial number is incremented by one to generate the output serial number. Atoms whose serial numbers are changed in this way must be referred to in subsequent directives by their new serial numbers. If no 'Z' is given, the atoms retain their old serial numbers.

If an UNTIL sequence is used after one or more MOVE directives have been given, it should be used with care, since the order of the new parameter list is different from the input list.

This directive selects and retains atoms with parameters satisfying the specified conditions. Only atoms that satisfy ALL the selection criteria, whether these are in the same or different directives, will be kept. All other atoms will be deleted from the list.

The operators allowed are :

             EQ            equal
             NE            not equal
             GT            greater than
             GE            greater than or equal to
             LT            less than
             LE            less than or equal to
 

Examples of the SELECT directive are :

       SELECT SERIAL LT 50
       SELECT OCC GT 0.5, OCC LT 1.5
       SELECT C(1,X) LT 1., C(1,X) GT 0.
       SELECT TYPE NE Q
 

This example will only retain atoms with serial numbers less than 50 and occupancies between 0.5 and 1.5. The 'X' parameter of atom c(1) must also lie between 0.0 and 1.0 oterwise it will be rejected, and any atoms of type Q will be deleted.

In the second format, a keyword corresponding to an atom parameter name (as defined in LIST 5, see section 6.3) is given, and the whole list sorted on increasing value of the specified parameter. Note that sorting on TYPE will give results depending on the 'collating sequence' of the computer. Fortunately, this generally leads to alphabetic sorting.

SORT sorts the whole list 5, and cancels any existing KEEP directives.

This directive conditionally changes the TYPES of atoms. If an atomic parameter selected by the keyword (see sort above) satisfies the conditions defined by the 'operator' and 'value' (see SELECT above), then the TYPE of the atom is changed to 'new-atom-type'.

       TYPECHANGE OCC GT 1.2 O
                               If Occ large, convert to oxygen
       TYPECHANGE U[ISO] LE 0.03 N
                               If Uiso small, convert to nitrogen
       TYPECHANGE TYPE EQ Q C
                               Convert peaks (type Q) to carbon
 

This directive assigns the given value to the named parameter for all the atoms in the atom list

       RESET OCC 1.0 ALL
       RESET OCC .5 O(1) O(2) O(3)
       RESET U[11] .05 C(27) UNTIL C(50)
 

  PARAMETER(i)  VALUE(i)
 

If ARG(i) is of this form, the specified parameter or parameters are changed to the value VALUE(i) . If PARAMETER(i) defines one or more atomic parameters, then the symmetry operators found or inserted by default are applied to the resulting set of atomic parameters. For overall parameters, no symmetry information can be provided. The VALUE associated with this argument must always be present.

The second form of ARG(i) on this directive is :

  ATOM-SPECIFICATION
 

For this form of ARG(i) , the symmetry operators given in the atom specification or assumed by default are applied, but no other atomic parameter is explicitly altered. There is no VALUE associated with ARG(i) in this format.

The two different types of argument on this directive may be used interchangeably :

       CHANGE  S(1,OCC) UNTIL O(1) .5
       CONT    C(1,-2,1) UNTIL C(12)
       CONT    C(13,X) .0179
 

Note that the anisotropic temperature factor produced by this operation is in fact still spherically symmetrical, and that the s.f.l.s. routines automatically ensure that when the temperature factor of an atom is to be refined, it is in the correct form.

Currently available values for NAME are

ELECTRON - This inserts the atomic electron count calculated from the form factor
WEIGHT - This inserts the atomic weight from LIST 29 (see section 4.15).
RESIDUE - This inserts a residue number into the 'RESIDUE' slot of list 5 replacing any previous value, such that all connected atoms have the same residue number and each molecule has a different residue number.
NCONN - This inserts the number of atoms connected to an atom, using the list of bonds.
RELAX - This inserts an ID, based upon the bonding topology and atomic types of the atoms. Atoms at topologically identical positions will be given the same ID. (e.g. the terminal F's in a CF3 group).

  \EDIT
  ROTATE 60 C(1) C(2) H(20) H(21) H(22)
  END
 

2) Turn a phenyl ring through 30 degrees around its external connecting bond, c(1) to c(20).

  \EDIT
  ROTATE 30 C(1) C(20) C(21) C(22) C(23) C(24) C(25)
  END
 

3) Rotate a residue 90 degrees about the a-direction from its centroid, QC(1) (see also CENTROID and INSERT RESIDUE directives)

  \EDIT
  INSERT RESIDUE
  CENTROID 1 RESIDUE(1)
  ROTATE 90 QC(1) 1 0 0 RESIDUE(1)
  END
 

       H
        \
       H-X-R(1)-R(2)
        /
       H
 

       H   R(1)
        \ /
         X
        / \
       H   R(2)
 

           R(1)
          /
      H- X-R(2)
          \
           R(3)
 

       H        R(2)
        \      /
         X=R(1)
        /
       H
 

         H
          \
           X=R(1)
          /
       R(2)
 

 
         X-H....R
 

  Place Hydrogen atoms on the following fragment:
 
       C(1)          C(5)
           \        /
            C(2)=C(3)
                    \
                     C(4)-Br(1)
 
      \HYDROGENS
       DISTANCE 0.99
       U[ISO]   0.06
       H33 C(1) C(2) C(3)
       AFTER C(1)
       H12 C(2) C(1) C(3)
       AFTER C(2)
       H23 C(4) Br(1) C(3)
       AFTER C(4)
       H33 C(5) C(3) C(4)
       END
 

The 3 by 3 transformation matrices generated at various stages may well be singular, especially if no rotation is defined about one of the axes. To combat possible problems with matrix inversion, a Moore-Penrose type matrix inverter is used. Even so, the user should be aware that there may be no unique solution to his problem. For example, when a planar fragment is fitted to an almost planar fragment one fit may involve inversion of the non-planar fragment. Inversion can be prevented by using Method 3. Note also that if almost planar groups are being fitted, the dilation factor perpendicular to the plane may be very large, and thus have an undesirable effect if applied to atoms far from the plane.

These 4 directives override the option specified by the MODE parameter of the REGULARISE command. The next group calculated will be treated in the specified mode. See the description of MODE for details. There are no parameters

This directive selects the method for matching the groups by giving its number from the following list:-

       Number     Method
       ------     ------
        1        Rotation  component of  rotation-dilation
                 matrix applied. ( default )
        2        Rotation-dilation  matrix  calculated and
                 applied.
        3        Pure  rotation matrix  calculated  by the
                 Kabsch method and applied. This algorithm
                 preserves chirality.
 

This directive specifies the number of atoms in the groups to be matched. It should be the first directive for each group of atoms. The appearance of a second or subsequent GROUP directive in the input initiates the calculation for the previous group.

This directive is used to specify the 'TARGET' group of atoms. The directive will carry a series of atom specifications which will define the positions of the 'TARGET' atoms and the names of any atoms to be created by the routine. Atoms which exist in LIST 5 and atoms to be created can appear in any order in the TARGET group , although the order should be such that corresponding pairs of atoms appear at the same relative positions in the 'TARGET' and 'IDEAL' groups.

This directive is used to specify a group of 'IDEAL' atoms to be taken from the stored LIST 5. Every atom on this directive must exist.

This directive is will change the co-ordinate system used to interpret any subsequent ATOM directives.

The initial co-ordinate system has orthogonal axes of unit length and is equivalent to :-

  SYSTEM  1.0  1.0  1.0  90.0  90.0  90.0
 

Values must be given for a', b', and c', the angles default to 90.0.

This directive is not yet implemented.

Three atoms of a phenyl group ( C(1), C(2) C((6)) have been located. Fill in the missing atoms from a non-dilated idealised phenyl group.

       \REGULARISE AUGMENT
       GROUP 6
       METHOD 1
       \ C(3), C(4), and C(5) do not yet exist.
       TARGET C(1) C(2) C(3) C(4) C(5) C(6)
       PHENYL
       END
 

A group of atoms is approximately octahedral. Replace them by a (posibly dilated) regular octahedron.

       \REGULARISE REPLACE
       GROUP 7
       METHOD 2
       TARGET CO(1) N(1) N(2) N(3) N(4) N(5) N(6)
       OCTAHEDRON
       END
 

Determine whether the two molecules in an asymmetric unit are related by a symmetry operation not expected for the space group. The matrix relating the molecules and the translation required to make their centroids coincide should display any additional (approximate) symmetry present. Remember that if one molecule is the enantiomer of the other, Method 3 will lead to an unsatisfactory fitting unless one molecule is inverted, (by using the operator -1 in the atom specifications e.g. FIRST(-1) UNTIL C(23). This can be done even if the space group is non-centrosymmetric ).

       \REGULARISE COMPARE
       GROUP 16
       TARGET C(101) UNTIL N(102)
       IDEAL  C(201) UNTIL N(202)
       END
 

In the example, the user has identified two sets of four non-coplanar atoms in each group e.g. C(1) with Q(103), C(3) with Q(99) etc. The transformation is then used to map the whole of the first group (C(1) until O(25)) onto the second group (Q(96) until Q(120)). Both of these groups must contain the same number of atoms, but they may be in any order. Atom Q(103) will be renamed to C(101), atom Q(100) to C(107) etc. Once all the atoms have been renamed, the list could be sorted based on the serial numbers.

       \REGULARISE
       GROUP 4
       IDEAL C(1) C(3) C(5) C(7)
       TARGET Q(103) Q(99) C(116) Q(100)
       RENAME 100
       MAP C(1) UNTIL O(25)
       ONTO Q(96) UNTIL Q(120)
       END
       \EDIT
       SORT SERIAL
       END
 

    \REGULARISE
    group 16
    target C(10) until C(26)
    ideal  C(60) until C(76)
    cameron
    map    C(51) until C(99)
    onto   C(1) until C(49)
    end
 

This produces a cameron.ini, regular.l5i and regular.oby which may be viewed by choosing Graphics->Special->Cameron (use existing...) from the menu. Then type "obey regular.oby" in Cameron to colour the molecules nicely. The TARGET and IDEAL are used to obtain the mapping. The atoms in MAP and ONTO are just the ones you want to be included. Don't read the atoms back into CRYSTALS when closing CAMERON - they're in orthogonal coordinates.