Crystals Manual

Chapter 6: Atomic And Structural Parameters

6.1: Scope of the atomic and structural parameters Section
6.2: Specifications of atoms and other parameters
6.3: Input of atoms and other parameters - LIST 5
6.4: Printing and punching list 5
6.5: Editing structural parameters - \EDIT
6.6: Reorganisation of lists 5 and 10 - \REGROUP
6.7: Repositioning of atoms - \COLLECT
6.8: Shifting the molecule to a permitted alternative origin - \ORIGIN
6.9: Conversion of temperature factors - \CONVERT
6.10: Hydrogen placing - \HYDROGENS
6.11: Perhydrogenation - \PERHYDRO
6.12: Hydrogen re-numbering - \HNAME
6.13: Regularisation of atomic groups - \REGULARISE
6.14: Map two atomic groups together - \MATCH
6.15: Calculation of interatomic bonds - \BONDCALC
6.16: Bonding information - \LIST 40
6.17: Bonding information - \BONDING
6.18: Printing of LIST 40
6.19: Creating a null LIST 40
6.20: Printing of LIST 41

[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.1: Scope of the atomic and structural parameters Section


The areas covered are:

 Specifications of atoms and other parameters
 Input of atoms and other parameters              - \LIST 5
 Re-order the atom list                           - \REGROUP
 Collect atoms together by symmetry               - \COLLECT
 Move the structure into the cell                 - \ORIGIN
 Modification of lists 5 and 10 on the disc       - \EDIT
 Applying permitted origin shifts                 - \ORIGIN
 Conversion of temperature factors                - \CONVERT
 Hydrogen placing                                 - \HYDROGENS
 Per-hydrogenation                                - \PERHYDRO
 Re-numbering hydrogen atoms                      - \HNAME
 Regularisation of groups in LIST 5               - \REGULARISE




[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.2: Specifications of atoms and other parameters

There is a consistent syntax thoughout CRYSTALS for refering to atoms and atomic parameters. This was referred to briefly in Chapter 1, and will be defined more fully here.
 

ATOM SPECIFICATION

There are three different but related ways of specifying an atom or a group of atoms.

TYPE(SERIAL,S,L,TX,TY,TZ)

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

TYPE The atom type, defined in Chapter 1 in the section on form-factors.
SERIAL The serial number, in the range 1-9999
Checking of serial numbers

Atoms of the same type are distinguished from one another by having different serial numbers. However, at no stage is a check made to ensure that there is not more than one atom in LIST 5 (atomic parameters) with the same type and serial number. If a routine is searching for an atom with a given type and serial number, the first atom found will always be taken, and any subsequent atoms with the same type and serial number will be ignored.

Serial numbers are considered to be different if they differ from each other by more than 0.0005.

S 'S' specifies a symmetry operator provided in the unit cell symmetry LIST (LIST 2 - see section 4.8). 'S' may take any value between '-NSYM' and '+NSYM', except zero, where 'NSYM' is the number of symmetry equivalent positions provided in LIST 2. if 'S' is less than zero, the coordinates of the atom stored in LIST 5 are negated (i.e. inverted through a centre of symmetry at the origin) and then multiplied by the operator specified by the absolute value of 'S' to generate the new atomic coordinates. 'S' may be less than zero even if the space group is non-centrosymmetric ( i.e. introduce a false centre), but must not be greater than 'NSYM'. The default value for 'S' is '1', specifying the first matrix in LIST 2, usually the unit matrix.
L 'L' specifies the non-primitive lattice translation that is to be added after the coordinates have been modified by the operations given by 'S'. 'L' must not be greater than the number of allowed non-primitive translations in the space group. The translations provided by 'L' depend on the lattice type and are given by :
          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


the default value of 'L' is '1', specifying no non-primitve lattice translation.

TX,TY,TZ Unit cell translation along the x,y and z directions.
The unit cell translations are added to the coordinates after the 'S' and 'L' operations have been performed. The translations may be positive or negative, but must refer to complete unit cell shifts. The default values for 'TX', 'TY' and 'TZ' are all zero, giving no unit cell translations.
The symmetry operations are applied in the order :
      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)


The format given above is a complete atom definition. For convenience the definition may sometimes be shortened. The obligatory parts are the TYPE and SERIAL. The remaining parameters, S, L, TX, TY, TZ, are optional.

An optional parameter taking its default value may be omitted, though its place must be marked by its associated comma. A series of trailing commas may be omitted.

The following are all equivalent :

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


The values of S , L , TX , TY and TZ are exactly those output and used by the distance angles routines under the headings S(I) , L , T(X) , T(Y) and T(Z) respectively. (See the section of the user guide on 'results of refinement').

When the symmetry operators are applied, the actual values of S and L are checked to see that they are reasonable. If the values found are not reasonable, an error message will be output and the job terminated.

In some cases, the symmetry operators are accepted on input, but not used by the routine. The description of the routine will state this.

UNTIL sequences When a group of atoms lie sequentially in the atom parameter list, there is an abbreviated way to refer to the group.
      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)


FIRST AND LAST

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


ALL

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)


RESIDUE

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

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


PART

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.
 

ATOMIC PARAMETER SPECIFICATION

Atomic parameters have a NAME. Some directives permit the use of the parameter name by itself, which implies that parameter for all atoms. The parameter name may be combined with an atom specifier, in which case only the parameter for that atom (or group in an UNTIL sequence) is referenced. Symmetry operators may be used. The normal drop-out rules apply.

Parameter NAMES

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).


Temperature factor definitions
Isotropic temperature factor
 The isotropic temperature factor is defined by:

       T = exp(-8*pi*pi*U[iso]*s**2)
                                       where s = sin(theta)/lambda


Anisotropic Temperature Factor
      The anisotropic temperature factor (adp) is defined by:

       T = exp(-2*pi*pi*(h*h*a'*a*u[11]
                        +k*k*b'*b'*u[22]
                        +l*l*c'*c'*u[33]
                    +2.0*k*l*b'*c'*u[23]
                    +2.0*h*l*a'*c'*u[13]
                    +2.0*h*k*a'*b'*u[12])).
                                       where x' are the reciprocal
                                       cell parameters and h, k and
                                       l are the Miller indices

Uequiv

CRYSTALS contains two definitions od Uequiv. Both definitions are acceptable to Acta. The arithmetic mean of the principle axes is often similar to the refined value of Uiso. The geometric mean is more sensitive to long or short axes, and so is more useful in publications. Ugeom is the sphere with the same volume as the ellipsoid.

      U(arith) = (U1+U2+U3)/3
      U(geom)  = (U1*U2*U3)**1/3
                                    Where Ui are the principal axes of
                                    the orthogonalised tensor.



 
CAUTION

It should be noted that if a set of anisotropic atoms are input with the FLAG key set to anything but 0, then the parameters will be interpreted as Isotropic atoms, or special shapes.
 

Uequiv Two expressions are available for the equivalent temperature factor (the geometric or arithmetric mean of the principal components). The Immediate Command 'SET UEQUIV' sets which definition will be used.
      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 Shapes

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 interpretation The following table shows the interpretation of the FLAG parameter.

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


The parameters have the following meaning for the new special shapes:

Special U[iso] U[iso] is related to the 'thickness' of the line, annulus or shell.
Special SIZE SIZE is the length of the line, or the radius of the annulus or shell.
Special DECLINAT DECLINAT is the declination angle between the line axis or annulus normal and the z axis of the usual CRYSTALS orthogonal coordinate system, in degrees/100.
Special AZIMUTH AZIMUTH is the azimuthal angle between the projection of the line axis or annulus normal onto the x - y plane and the x axis of the usual CRYSTALS orthogonal coordinate system, in degrees/100.

If either of these angles is input with a value greater than 5.0, it is assumed that the user has forgotten to divide by 100, which is thus done automatically.

 

OVERALL PARAMETER SPECIFICATION

Overall parameters are specified simply by their keys. The following overall parameter keys may be given :

      SCALE      OU[ISO]      DU[ISO]      POLARITY
      ENANTIO    EXTPARAM


SCALE This parameter defines the overall scale factor and has a default value of unity. It is the number by which /FC/ must be multiplied to put it onto the scale of /FO/, i.e. /Fo/ = scale*/FC/.
DU[ISO] This parameter is the dummy overall isotropic temperature factor and has a default value of 0.05.

The dummy overall temperature factor is in no way related to the overall temperature factor, and its use is explained in the input of LIST 12, which comes in the section of the user guide on 'structure factors'.

OU[ISO] This parameter is the overall isotropic temperature factor and has a default value of 0.05.
POLARITY This is the Rogers eta parameter, and is a multiplier for the imaginary part of the anomalous scattering factor. Setting the value to 1.0 (its default) has the effect of using the imaginary part of the anomalous scattering factor as given. Changing the value to -1.0 has the effect of changing the hand of the model. Setting the value at zero has the effect of removing the contribution of f". However, if contributions from f" are not required, IT IS MORE EFFICIENT to set ANOMALOUS = NO in LIST 23 (structure factor control, see section 7.7). If you need to use f", remember not to apply Friedel's law (LIST 13, section 4.13) during data reduction (section 5.14), and to include anomalous scattering (LIST 3, section 4.11 and LIST 23, section 7.7). See D. Rogers, Acta Cryst (1981), A37,734-741. POLARITY and ENANTIO should not be used simultaniously.
ENANTIO This overall parameter is the fractional contribution of F(-h) to the observed structure amplitude, and like the POLARITY parameter is sensitive to the polarity of the structure. It is defined by
       Fo**2 =(1-x)* F(h)**2 + x*F(-h)**2


where x is the ENANTIOpole parameter. A value of 0.0 means the structure stored in LIST 5 is of the correct hand. A value of 1.0 inverts the structure. Its effect on the structure factor is switched on or off by the parameter ENANTIO in LIST 23 (see section 7.7). Computations are more efficient when it is turned off. If the enantiopole is used (or refined) then Friedel's law must not be applied (LIST 13, section 4.13) and anomaloue scattering must be included (LIST 13 and LIST 23). See Howard Flack, Acta Cryst, 1983, A39, 876-881. This parameter is more robust than the POLARITY parameter. See also section in Results.

EXTPARAM This parameter is Larson's extinction parameter , r*, (equation 22 in A.C. Larson, Crystallographic Computing, 1970, 291-294, ed F.R. Ahmed, Munksgaard, Copenhagen , but with V replaced by the cell volume) and has a default value of zero.

Note that many other programs use expression (4), which cannot cope with Neutron data, and gives a value for 'g' which is about 1,000,000 times smaller than 'r*'.

       g ~= [(e**2/mc**2)**2 . lambda**3/V**2 . Tbar ] . r*


Tbar is the absorption weighted mean path length, and is assumed to be stored in LIST 6 (section 5.3) with a key of TBAR . If this key is absent, a default value of 1.0 is used. If extinction is to be included in the model, the mosaic spread should have been set in LIST 13 (section 4.13).


[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.3: Input of atoms and other parameters - LIST 5

 \LIST 5
 OVERALL SCALE= DU[ISO]= OU[ISO]= POLARITY= ENANTIO= EXTPARAM=
 READ NATOM= NLAYER= NELEMENT= NBATCH=
 either ATOM TYPE= SERIAL= OCC= FLAG= X= Y= Z= U[11]= ....U[12]=
 or     ATOM TYPE= SERIAL= OCC= FLAG= X= Y= Z= U[ISO]
 INDEX P= Q= R= S= ABSOLUTE=
 LAYERS SCALE=
 ELEMENTS SCALE=
 BATCH SCALE=


 \LIST 5
 OVERALL SCALE=0.123
 READ NATOM=2 NELEMENT=2
 ATOM PB 1 FLAG=0 .25 .25 .25 .03 .03 .03 .0 .0 .0
 ATOM C 2  X= .23 .13 .67
 ELEMENTS 0.8 0.2
 END


\LIST 5
OVERALL SCALE= DU[ISO]= OU[ISO]= POLARITY= ENANTIO= EXTPARAM=

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

SCALE= The overall scale factor, default = 1.0
DU[ISO]= The dummy overall isotropic temperature factor, default = 0.05.
OU[ISO]= The overall isotropic temperature factor, default = 0.05.
POLARITY= Rogers eta parameter (see above), default = 1.0.
ENANTIO= Flack enantiopole parameter (see above), default = 0.0.
EXTPARAM= Larson r* secondary extincion parameter, default = 0.0.
READ NATOM= NLAYER= NELEMENT= NBATCH=

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

NATOM= The number of atom directives to follow, default = 0.
NLAYER= The number of layer scale factors to follow, default = 0.
NELEMENT= The number of element scale factors to follow, default = 0.
NBATCH= The number of batch scale factors to follow, default = 0.
ATOM TYPE= SERIAL= OCC= FLAG= X= Y= Z= U[11]= ..

The parameters for an atom, repeated NATOM times.

TYPE= The atomic species, an entry for which should exist in LIST 3 (see section 4.11). There is no default value.
SERIAL= The atoms serial number. There is no default value.
OCC= This parameter defines the site occupancy EXCLUDING special position effects (i.e. is the 'chemical occupancy). The default is 1.0. Special position effects are computed by CRYSTALS and multiplied onto this parameter.
FLAG= This parameter specifies the type of temperature factor for the atom, and if it is omitted a default value of 1 is assumed. NOTE that it must be set to 0 for anisotropic atoms.
X= Y= Z= These parameters specify the atomic coordinates for the atom, for which there are no default values.
U[11]= U[22]= U[33]= U[23]= U[13]= U[12]= These parameters have different interpretations depending upon the value of FLAG

If FLAG=0

These parameters specify the anisotropic temperature factors for the atom and if they are omitted default values of zero are assumed. The order of the cross terms is obtained by dropping 1,2,3 sequentially from [123].

If FLAG=1

The first parameter specifies the isotropic temperature factor, which defaults to 0.05.

If FLAG=2,3 or 4, the six parameters represented by u[ij] have the following imterpretation:

KEY   shape      parameters

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


The parameters have the following meaning for the new special shapes:

Special U[iso] U[iso] is related to the 'thickness' of the line, annulus or shell.
Special SIZE SIZE is the length of the line, or the radius of the annulus or shell.
Special DECLINAT DECLINAT is the declination angle between the line axis or annulus normal and the z axis of the usual CRYSTALS orthogonal coordinate system, in degrees/100.
Special AZIMUTH AZIMUTH is the azimuthal angle between the projection of the line axis or annulus normal onto the x - y plane and the x axis of the usual CRYSTALS orthogonal coordinate system, in degrees/100.

If either of these angles is input with a value greater than 5.0, it is assumed that the user has forgotten to divide by 100, which is thus done automatically.

INDEX P= Q= R= S= ABSOLUTE=

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.

P= Q= R= These parameters have default values of zero.
S= This parameter has a default value of unity. The zeroth layer must have an index of 1.
ABSOLUTE=
      NO
      YES  -  Default value


LAYERS SCALE=

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

SCALE= This parameter gives the layer scale, and has a default value of 1. It is repeated NLAYER times.
ELEMENTS SCALE=

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

SCALE= This parameter gives the element scale factor, and has a default value of 1. It is repeated NELEMENT times - the number of components in the twin.
BATCH SCALE=

This directive defines the batch scale factors.

SCALE= This parameter gives the batch scale factor, and has a default value of 1. It is repeated NBATCH times. Remember to set appropriate keys in LIST 6
 
Further examples of parameter input
 ATOM TYPE=C,SERIAL=4,OCC=1,U[ISO]=0,X=0.027,Y=0.384,Z=0.725,
 CONT U[11]=0.075,U[22]=0.048,U[33]=.069
 CONT U[23]=-.007,U[13]=.043,U[12]=-.001
 ATOM C 5 U[ISO]=0.0 .108,.365,.815,.074
 CONT .051 .065 -.015 .048 -.014
 ATOM C 2 1 0.05 0.149 0.411 0.651 0 0 0 0 0 0
 ATOM C 1 X=0.094,Y=0.343,Z=0.890
 ATOM C 3 X=0.050 0.406 0.648



[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.4: Printing and punching list 5

\PRINT 5
Lists the current LIST 5 to the printer file.
\PUNCH 5 mode
Mode controls the format of the file.
        -  Punches the model parameters in CRYSTALS format.
      A -  Punches the model parameters in CRYSTALS format.
      B -  Punches the atomic parameters in XRAY format.
      C -  Punches the atomic parameters in SHELX format.
      E -  Punches atomic parameters and esds in a plain format


 

Summary display of LIST 5 - \DISPLAY
 \DISPLAY LEVEL=
 END

 \DISP HIGH
 END


This allows the user to display a summary of the contents of list 5. The output is sent to both monitor and listing channels, so the contents of list 5 can be examined on-line during interactive work. The output produced is more compact than that from PRINT 5, and various levels of detail can be selected. The command required is :-

\DISPLAY LEVEL=

DISPLAY has one optional parameter.

LEVEL
      LOW
      MEDIUM
      HIGH


The effects of this parameter are :-

LOW The names of the atoms, overall parameters, and any layer, batch, and element scales in list 5 are displayed.

MEDIUM Each atom in list 5 is displayed with its type, serial, occupancy, isotropic temperature factor ( if any ), and positional parameters. The values of the overall parameters and of any layer, batch, and element scales are displayed.

HIGH All of the parameters of each atom in list 5 are displayed. The values of the overall parameters, and of any layer, batch, and element scale factors are displayed.

 


[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.5: Editing structural parameters - \EDIT

 \EDIT INPUTLIST= OUTPUTLIST=
 EXECUTE
 SAVE
 QUIT
 MONITOR LEVEL
 LIST LEVEL
 DELETE  ATOM SPECIFICATIONS  .  .
 ATOM TYPE= SERIAL= OCC= FLAG= X= Y= Z= U11= ..
 CREATE Z ATOM-SPECIFICATION  ...
 SPLIT Z ATOM-SPECIFICATION ...
 CENTROID Z ATOM-SPECIFICATION ...
 KEEP  Z ATOM-SPECIFICATIONS ...
 AFTER  ATOM-SPECIFICATION
 MOVE Z ATOM-SPECIFICATION  ...
 SELECT ATOM-PARAMETER  OPERATOR  VALUE, . .
 SORT TYPE1 TYPE2 ...
 SORT KEYWORD
 DSORT TYPE1 TYPE2 ...
 RENAME ATOM1  ATOM2  (, ATOM1  ATOM2) ...
 TYPECHANGE KEYWORD OPERATOR VALUE NEW-ATOM-TYPE
 RESET PARAMETER-NAME VALUE ATOM-NAMES
 CHANGE  PARAMETER-SPECIFICATION VALUE ...
 ADD  VALUE PARAMETERS  ...
 SUBTRACT  VALUE  PARAMETERS  ...
 MULTIPLY  VALUE  PARAMETERS  ...
 DIVIDE  VALUE  PARAMETERS  ...
 PERTURB VALUE PARAMETERS ...
 SHIFT  V1, V2, V3   ATOM-SPECIFICATION . .
 TRANSFORM  R11, R21, R31, . . . R33  ATOM-SPECIFICATION . .
 DEORTHOGINAL  ATOM-SPECIFICATION . .
 UEQUIV  ATOM-SPECIFICATIONS  .  .
 ANISO  ATOM-SPECIFICATIONS  .  .
 INSERT IDENTIFIER
 SPHERE NEWSERIAL ATOMLIST
 RING NEWSERIAL ATOMLIST
 LINE NEWSERIAL ATOMLIST
 REFORMAT
 ROTATE ANGLE POINT VECTOR ATOM-SPECIFICATION
 ROTATE ANGLE ATOM VECTOR ATOM-SPECIFICATION
 ROTATE ANGLE ATOM1 ATOM2 ATOM-SPECIFICATION
 END


 LIST LOW
 TYPECHANGE TYPE EQ Q C
 SELECT U[ISO] LT 0.1
 ADD  0.25 X
 RENAME C(1) S(1)
 CHANGE  S(1,OCC) UNTIL O(1) .5
 KEEP  1 FIRST UNTIL LAST
 L L
 SPLIT 100 C(45)
 DELETE  C(46) UNTIL LAST
 RESET OCC 1.0 ALL



 

This is a powerful crystallographic editor for modifying a LIST 5 (the model parameters) or LIST 10 (Fourier peaks). It offers the editing facilities frequently needed for the management of atom parameters, including conditional operations and arithmetic.

EDIT is a semi-interactive command, in that each directive is computed as soon as its input is complete. Since CONTINUE can be used to extend a directive over several lines, completion is indicated be the start of a new directive, or the special directive EXECUTE.

After the terminating END, the resulting list is output to the disc. However if the list has not been changed, a new list will be created only if the list type is being changed ( e.g. 10 to 5 ). The current edited version of the list can be saved at any time to protect against future editing mistakes ( the SAVE directive ). It is also possible to abandon editing without creating a new list ( the QUIT directive ).

When used in interactive mode, a new list is created even though errors may have occured during command input unless the QUIT directive is used. In online and batch modes no new list will be created if errors occured during the edit. In this case an error message in generated.

Take care to note that some directives refer to atom or group of atoms, others refer to one or more parameters, and two (CHANGE and SELECT)will refer to either an atom specification or a parameter specification. Although atom definitions can include a series of symmetry operators, the only directives that will use them are those for which the subsequent description explicitly states that the symmetry operators are used. In all other cases, the symmetry information will be read in without any error messages and ignored. Those operations which require a single parameter type as argument (ADD, MULTIPLY etc ) will fail if composite parameters ( "U'S", etc ) are given.

\EDIT INPUTLIST OUTPUTLIST
INPUTLIST
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


OUTPUTLIST
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


END This should be the last directive in the set of modification directives.
EXECUTE This directive which has no parameters does nothing to the edited list. It is provided to allow the user to see the results of one operation ( initiated by the directive whose input is terminated by EXECUTE ) before attempting the next.
SAVE Forces the current atom list to be writen to disk.
QUIT This directive will cause the edit to be abandoned without the creation of a new list if it is followed by END . If it is followed by any other directive it is ignored.

MONITOR LEVEL This directive controls the level of monitoring of editing operations. When each operation is performed, the results can be monitored in the monitor channel and in the listing file. Four levels of monitoring are provided. The inital level and the default level used when no value is specified is 'MEDIUM'. The possible values of the parameter 'level' are :-
      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.

LIST LEVEL This directive produces a list of the current edited list in the monitor output stream and in the listing file. If KEEP has been used, the atoms which will be kept are indicated. The possible values for 'level' are :-
      OFF               No listing produced
      LOW               Type and serial listed
      MEDIUM            Type , serial , occ , u[iso] ,
                        x , y , z listed
      HIGH              All atomic parameters listed


DELETE ATOM SPECIFICATIONS . . All the specified atoms are removed from the current atomic parameter list. Deleted atoms should not be referenced by subsequent directives.
ATOM TYPE SERIAL OCC FLAG X Y Z U11 .. This directive causes the system to add an atom to the end of the edited list. The format is the same as that used in \LIST 5 (see section 6.3). Values must be provided for 'type' , 'serial' , 'x' , 'y' , and 'z' . Default values are provided for the other parameters as in \LIST 5. Example :
 ATOM O 1 X = 0.3427 .89004 .09181


CREATE Z ATOM-SPECIFICATION ... This directive applies the symmetry operators given or assumed by default in the atom specification, and creates a set of new atoms from those given. The new atoms are added at the end of the current list. The serial numbers of the new atoms are given by:
      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)


SPLIT Z ATOM-SPECIFICATION ... Two new isotropic atoms are added to the end of the atom list for every atom referenced in the atom-specification. These atoms lie on of the principal axis of the original atoms anisotropic adp ellipsoid and U[iso] set to U[meadian] of the original adp.

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


CENTROID Z ATOM-SPECIFICATION ... A new atom is created at the centroid of the specified atoms, and with a pseudo adp representing the inertial tensor (ie the 'shape' of the group). The atom TYPE is QC, and its serial Z. The sequence Z ATOM-SPECIFICATIONS can be repeated.
KEEP Z ATOM-SPECIFICATIONS ...

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.

AFTER ATOM-SPECIFICATION ...

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.

MOVE Z ATOM-SPECIFICATION ...

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.

SELECT ATOM-PARAMETER OPERATOR VALUE, . .

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.

SORT TYPE1 TYPE2 ...
SORT KEYWORD This directive has two formats, and is used to sort the atoms stored in LIST 5 into a user-defined order. The default action sorts the atoms on their types and serial numbers. The types are taken in the order found in LIST 5, and atoms of each type are grouped together. In each group the atoms are arranged by ascending serial number. The order of the types of atoms may also be determined by specifying them explicitly on the SORT directive, or by a mixture of these methods.

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.

DSORT TYPE1 TYPE2 ...
DSORT KEYWORD This directive is exactly analagous to SORT, above, except that it sorts into descending order.
RENAME ATOM1 ATOM2 (, ATOM1 ATOM2) ... This directive requires pairs of atom specifications (optionally separated by a comma). The TYPE and SERIAL of 'atom1' are changed to those of 'atom2'. Atom1 must exist in LIST 5, atom2 must NOT exist in LIST 5. An atom can be renamed repeatedly. If atom1 contains symmetry operators, these are applied to the coordinates of the renamed atom. An atom cannot be renamed to itself in a single step.
TYPECHANGE KEYWORD OPERATOR VALUE NEW-ATOM-TYPE

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


RESET PARAMETER-NAME VALUE ATOM LIST

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)


CHANGE ARG(1) ARG(2) ARG(3) . There are two possible formats for each 'ARG(i)' on this directive. the first is :
 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


ADD VALUE PARAMETERS ...
SUBTRACT VALUE PARAMETERS ...
MULTIPLY VALUE PARAMETERS ...
DIVIDE VALUE PARAMETERS ... These directives causes the 'value' to be applied to the parameter. 'PARAMETER(I)' may be an overall parameter, or a single atomic parameter of one or more atoms, as defined above. Any symmetry operators given with this directive will be ignored. Note that the parameter SERIAL is numeric, and so can be arithmetically modified.
PERTURB VALUE PARAMETERS ... This directive perturbs the specified parameters using a rnadom number generator. The VALUE is the requested rms perturbation, in the natural units of the parameters. The mean deviation applied should be approximately zero, and the rms deviation applied should be approximately that requested.
SHIFT V1, V2, V3 ATOM-SPECIFICATION . . This directive reads the three numbers of a shift vector, which must be in the same coodrinate system as the atomic parameters, and applies it to the parameters in the atom specification. This directive does not create new atoms, but simply modifies those already present. Any symmetry operators given are applied before the translation.
TRANSFORM R11, R21, R31, . . . R33 ATOM SPECIFICATION . . This directive reads the nine numbers of a transformation matrix, which must be separated by commas or spaces, and applies the matrix to the atoms given in the atom specification. This directive does not create new atoms, but simply modifies those already present. Any symmetry operators given are applied before the rotation.
DEORTHOGINAL ATOM SPECIFICATION . . This directive applies the matrix vector saved by a previous MOLAX SAVE directive to the atoms given in the atom specification. THEIR ORIGINAL COORDIANATES x,y,z MUST be in the MOLAX coordinate (Angstrom) system This directive does not create new atoms, but simply modifies those already present. Symmetry operators are not permitted.
UEQUIV ATOM SPECIFICATIONS . . The specified atoms to be converted so that they have isotropic temperature factors, U(equiv), defined by the SET UEQUIV command. IT IS NOT simply related to the diagonal elements of U(aniso). If an atom is already isotropic, no action is taken. If this directive is given with no arguments, all the atoms in the current atomic parameter list are converted to isotropic temperature factors. Physically impossible values are not rejected. Symmetry operators are ignored.
ANISO ATOM SPECIFICATIONS . . This directive causes all the specified atoms to be converted so that they have anisotropic temperature factors. If an atom is already anisotropic, no action is taken, and any symmetry operators given are ignored. If this directive is given with no arguments, all the atoms in the current atomic parameter list are converted to anisotropic temperature factors.

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.

INSERT IDENTIFIER=NAME This directive inserts the value of the named identifier into the parameter 'SPARE' in the atom list, replacing any previous value (except 'RESIDUE' which uses the 'RESIDUE' paramter in the atom list). SPARE is normally used to hold rho after Fourier maps.

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 4.18).
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).

SPHERE NEWSERIAL ATOMLIST This creates a 'shell' shape from the specified atom list. The centre of the shell is at the centre of gravity, the size is the mean distance of the given atoms from the centre, and the occupancy is equal to the sum of the occupancies of the atoms listed. U[iso] is the mean of the U[iso] or Ueqiv of the listed atoms. The atom TYPE is QS, with the given serial number. The original atoms are not deleted, though they should be or their occupancy set to zero. The atom type, QS, should be changed to something appropriate.
RING NEWSERIAL ATOMLIST This creates an 'annulus' shape from the specified atom list. The centre of the ring is at the centre of gravity, the size is the mean distance of the given atoms from the centre, and the occupancy is equal to the sum of the occupancies of the atoms listed. U[iso] is the mean of the U[iso] or Ueqiv of the listed atoms. The atom TYPE is QR, with the given serial number. The original atoms are not deleted, though they should be or their occupancy set to zero. The atom type, QS, should be changed to something appropriate. The DECLINATION and AZIMUTH are computed from the constituent atoms.
LINE NEWSERIAL ATOMLIST This creates an 'line' shape from the specified atom list. The centre of the line is at the centre of gravity, the size is twice the mean distance of the given atoms from the centre, and the occupancy is equal to the sum of the occupancies of the atoms listed. U[iso] is the mean of the U[iso] or Ueqiv of the listed atoms. The atom TYPE is QL, with the given serial number. The original atoms are not deleted, though they should be or their occupancy set to zero. The atom type, QS, should be changed to something appropriate. The DECLINATION and AZIMUTH are computed from the constituent atoms.
REFORMAT This directive converts an old (non-FLAG) version of LIST 5 (see section 6.3) to the new format (extra parameters, old U[iso] slot now used as a flag and u[11] used for u[iso]).
ROTATE This directive rotates a group of atoms a certain number of degrees around a specified vector. The rotation is carried out in orthogonal space so preserves the geometry of the group.
There are three options available: ROTATE D X Y Z VX VY VZ atom-specification
ROTATE D ATOM1 VX VY VZ atom-specification
ROTATE D ATOM1 ATOMS2 atom-specification
The first rotates the specified atoms, D degrees around the vector VX,VY,VZ keeping point X,Y,Z fixed. (X,Y,Z and VX,VY,VZ are given in crystal fractions).
The second notation uses ATOM1 instead of X,Y,Z to specify the fixed point.
The third notation uses ATOM1 to specify the fixed point and the vector from ATOM1 to ATOM2 to rotate around.
The rotation is D degrees anti-clockwise, when the specified vector is pointing towards you.
1) Rotate the hydrogens of a methyl group by sixty degrees.
 \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



[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.6: Reorganisation of lists 5 and 10 - \REGROUP

 \REGROUP INPUTLIST= OUTPUTLIST=
 SELECT MOVE= KEEP= MONITOR= SEQUENCE= SYMMETRY= TRANSLATION= GROUP=
 END


 \REGROUP
 SELECT MOVE=1.6,MONITOR=HIGH
 END


This routine offers a way of re-ordering the atoms in LIST 5 (atomic parameters) or LIST 10 (Fourier peaks), so that related atoms or peaks form a sequential group in the list, and the coordinates put the atoms as close together as possible.

THIS ROUTINE DOES NOT USE LIST 29 (atomic properties) to get bonding distances, but uses a single overall distance.

In this routine, a set of distances is calculated about each atom or peak in the list in turn. For each atom or peak in the list below the current pivot, the minimum contact distance is chosen, and if this is less than a user specified maximum, the atom or peak is moved up the list to a position directly below the pivot. ( The MOVE parameter). When more than one atom or peak is moved, their relative order is preserved as they are inserted behind the current pivot atom. As well as reordering the list, the necessary symmetry operators are applied to the positional and thermal parameters to bring the atom or peak into the same part of the unit cell as the current pivot atom. The result of this process is to bring related atoms together in the list, and to place all the atoms in the same part of the unit cell. Setting the GROUP parameter to YES causes the PART to be incremented between isolated parts of the structure.

\REGROUP INPUTLIST= OUTPUTLIST=
INPUTLIST=
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


OUTPUTLIST=
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


SELECT MOVE= KEEP= MONITOR= SEQUENCE= SYMMETRY= TRANSLATION= GROUP=
MOVE= This parameter has a default value of 2.0, and is the distance below which atoms or peaks are considered to be bonded, and are thus moved about the cell and relocated in LIST 5 (atomic parameters).

If the MOVE parameter is -ve, then a covalent radius used, and the absolute value of MOVE is used as a TOLERANCE, such that bonds are formed if D < COV1+COV2+TOLERANCE.

KEEP= This is the maximum number of atoms that the final output list can contain. If this parameter is omitted, all the atoms are output. If MOVE is used to move the atoms around, it is unwise to use the KEEP parameter,since some of the original input atoms may find their way to the bottom of the list and be eliminated. (The default value is 1000000).
MONITOR=
      LOW   -  Default value
      HIGH


If MONITOR is HIGH, then each pivot atom and its associated moved atoms are listed, as well as any deleted atoms. If MONITOR is LOW, the moved atoms are not listed.

SEQUENCE
      NO   -  Default value
      YES
      EXHYD


If SEQUENCE is YES, the outputlist is resquenced as described above.
If SEQUENCE is NO, the serial numbers of the atoms are not changed from the original list.
If SEQUECE is EXHYD the hydrogen atoms are excluded from the renumbering.

SYMMETRY= This parameter controls the use of symmetry information in the calculation of contacts, and can take three values.
      SPACEGROUP  -  Default value. The full spacegroup symmetry is used in
                                    all computations
      PATTERSON.     A centre of symmetry in introduced, and the translational
                     parts of the symmetry operators are dropped.
      NONE.          Only the identity operator is used.


TRANSLATION= This parameter controls the application of cell translations in the calculation of contacts, and can take the values YES or NO
GROUP
      NO   -  Default value
      YES


If GROUP is YES, the PART parameter for each atom is set.


[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.7: Repositioning of atoms - \COLLECT

This routine changes the atom coordinates so as to form a 'molecule' using the covalent radii given in LIST 29 (atomic properties - see section 4.18). The atom TYPE, SERIAL and order in LIST 5 (atomic parameters - see section 6.3) is not changed.

\COLLECT INPUTLIST= OUTPUTLIST=
INPUTLIST=
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


OUTPUTLIST=
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


SELECT MONITOR= TOLERANCE= TYPE= SYMMETRY= TRANSLATION=
MONITOR=
      LOW   -  Default value
      HIGH


If MONITOR is HIGH, then each pivot atom and its associated moved atoms are listed, as well as any deleted atoms. If MONITOR is LOW, only deleted atoms are listed.

TOLERANCE= The tolerance is added to the sum of the co-valent radii taken from LIST 29 (atomic properties - see section 4.18) to give a value used for determining inter-atomic bonds. The default is 0.2 A.
TYPE=
      ALL
      PEAKS
      ATOMS


If TYPE equals ALL, then the coodinates of all atoms and Q-peaks are liable to be modified by the symmetry operators in order to assemble a single fragment.
If TYPE equals PEAKS, then only the peaks are moved to bring them as close as possible to existing atoms.
If TYPE equald ATOMS, only non-Q atoms are modified

SYMMETRY= This parameter controls the use of symmetry information in the calculation of contacts, and can take three values.
      SPACEGROUP  -  Default value. The full spacegroup symmetry is used in
                                    all computations
      PATTERSON.     A centre of symmetry in introduced, and the translational
                     parts of the symmetry operators are dropped.
      NONE.          Only the identity operator is used.


TRANSLATION= This parameter controls the application of cell translations in the calculation of contacts, and can take the values YES or NO


[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.8: Shifting the molecule to a permitted alternative origin - \ORIGIN

 \ORIGIN INPUTLIST= OUTPUTLIST= MODE=
 END


Attempt to move the structure to the centre of the unit cell using the permitted origin shifts.

\ORIGIN INPUTLIST= OUTPUTLIST= MODE=


INPUTLIST=
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


OUTPUTLIST=
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


MODE=
      CENTROID   -  Default value.
      FIRST


CENTROID tries to move the centroid of LIST 5 as close to .5 .5 .5 as is permitted by the permitted origin shifts. Other connected atoms follow the centroid.

FIRST As above excpet that the first atom in LIST 5 is the target atom. This may be a user-computed partial centroid.

      \edit
      cent 100 residue 3
      move qc(100)
      end
      \origin mode=first


Currently (April 2011) the code only processes primitive triclinic, monoclinic and orthorhombic cells, using the tables in Direct Methods in Crystallography, Giacovazzo, Academic press, 1980, pp 74 and 76.


[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.9: Conversion of temperature factors - \CONVERT

 \CONVERT INPUTLIST= OUTPUTLIST= CROSSTERMS=
 END

 \CONVERT
 END


This routine will convert the temperature factors of a set of atoms into the correct form when their temperature factor, t, is given by :

       T = exp(-B[iso]*S**2)     where s = sin(theta)/lambda.

 or for an anisotropic atom :

       T = exp(-(h*h*b[11] + k*k*b[22] + l*l*b[33]
           + k*l*2*b[23] + h*l*2*b[13] + h*k*2*b[12]))


The cross terms stored in the original LIST 5 (the model parameters) may either be B[IJ] or 2*B[IJ] . (The correct form of the temperature factor, in terms of u[ii]'s and u[ij]'s, is given in the section on the input of LIST 5). After conversion, the atoms are output to the disc as a new LIST 5. Remember that if U[ISO] is non-zero, (its default at atom input is 0.05) the U[IJ] are ignored and so will not be converted.

\CONVERT INPUTLIST= OUTPUTLIST= CROSSTERMS=

This is the command which initiates the routine to convert the temperature factors.

INPUTLIST=
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


OUTPUTLIST=
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


CROSSTERMS=
      B[IJ]   -  Default value.
      2B[IJ]



[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.10: Hydrogen placing - \HYDROGENS

 \HYDROGENS INPUTLIST= OUTPUTLIST=
 DISTANCE  D
 SERIAL    N
 U[ISO]    U
 U[ISO]    NEXT   MULT
 AFTER     TYPE(SERIAL)
 PHENYL    X R(1) R(2) R(3) R(4) R(5)
 H33       X R(1) R(2)
 H23       X R(1) R(2)
 H13       X R(1) R(2) R(3)
 H22       X R(1) R(2)
 H12       X R(1) R(2)
 H11       X R(1)
 HBOND     DONOR ACCEPTOR
 END


 \HYDROGENS
 DISTANCE  1.09
 U[ISO]    NEXT   1.2
 H33     C(7) C(6) R(5)
 H22     C(14) C(15) C(13)
 END


This routine computes the coordinates of hydrogen atoms bonded to a target atom. The hybridisation of the target atom and the identifiers of atoms bonded to it must be given.

\HYDROGENS INPUTLIST= OUTPUTLIST=
INPUTLIST=
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


OUTPUTLIST=
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


DISTANCE D This sets the central atom-hydrogen atom distance to 'D' angstroms. The default value is 1.0. The current value of 'D' remains in force until another 'DISTANCE' directive is given.
SERIAL N This sets the serial number of the next hydrogen atom to be added to LIST 5 (atomic parameters) to 'N'. The default value is 1. Subsequent hydrogen atoms will have the serial numbers 'N+1', 'N+2', etc., until the next 'SERIAL' directive is input.
U[ISO] U This directive sets the isotropic temperature factor of each hydrogen atom to 'U' angstroms squared, and remains in force until another 'U[ISO]' directive is given. If no values is given for U, the next definition is used.
U[ISO] NEXT MULT This is an alternatine form of the preceding directive. It sets the isotropic temperature factor of each hydrogen atom to 'MULT' times the equivalent temperature factor of the atom it is bonded to. The default value is 1.2. The directive remains in force until another 'U[ISO]' directive is given.
AFTER TYPE(SERIAL) The hydrogen atoms generated by the placing routines are inserted in the new LIST 5 (atomic parameters) after the atom 'TYPE(SERIAL)'. This directive must appear immediately after the directive that generated the hydrogen atom coordinates, and applies only to that group of hydrogen atoms. If no 'AFTER' directive is given, the new hydrogen atoms are added at the end of the current LIST 5 (atomic parameters).
PHENYL X R(1) R(2) R(3) R(4) R(5) This generates the coordinates of the five hydrogen atoms of a phenyl group. The first atom specified must be the atom that bonds the phenyl group to the rest of the structure, and the other atoms must be in the order of connectivity.
H33 X R(1) R(2) This geneates the hydrogen atoms of a methyl group. The methyl carbon is the first atom specified, and the hydrogen atoms are generated so that one of them is trans with respect to the third atom specified, R(2).
      H
       \
      H-X-R(1)-R(2)
       /
      H


H23 X R(1) R(2) This generates the coordinates of two hydrogen atoms on an sp3 atom X.
      H   R(1)
       \ /
        X
       / \
      H   R(2)


H13 X R(1) R(2) R(3) This generates the coordinates of one hydrogen atom on an sp3 atom X.
          R(1)
         /
     H- X-R(2)
         \
          R(3)


H22 X R(1) R(2) This generates the coordinates of two hydrogen atoms on an sp2 atom X
      H        R(2)
       \      /
        X=R(1)
       /
      H


H12 X R(1) R(2) This generates the coordinates of one hydrogen atom on an sp2 atom X.
        H
         \
          X=R(1)
         /
      R(2)


H11 X R This generates the coordinates of the single hydrogen atom bonded to an SP hybridised atom.
HBOND X R This generates a single H atom 'DISTANCE' angstroms from the donor in the direction of the acceptor. X is the donor, R the acceptor.

        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



[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.11: Perhydrogenation - \PERHYDRO

 \PERHYDRO INPUTLIST= OUTPUTLIST=
 DISTANCE  D
 SERIAL    N
 U[ISO]    U
 U[ISO]    NEXT   MULT
 ACTION    MODE
 TYPE      C or N
 END


 \PERHYDRO
 U[ISO] NEXT 1.0
 END


This command scans the atomic coordinates for carbon atoms, attempts to assign their hybridisation state (on the basis of bond lengths) and then generates \HYDROGEN commands to create any necessary hydrogen atoms. Existing Hydrogen atoms are not replaced by this routine.

The generated commands may be processed internally by CRYSTALS without the user needing to see them, or they may be sent to the external files for later use. This is the default mode. If no new hydrogen atoms are generated, no new external files are created.

The external files are called DELH.DAT and PERH.DAT, with DELH containing an entry for every atom created by PERH. Executing DELH and PERH will delete existing named atoms, and recreate them geometrically.

\PERHYDRO INPUTLIST= OUTPUTLIST=
INPUTLIST=
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


OUTPUTLIST
      5   -  Default value, the atomic coordinates
      10                    the Fourier peaks search


DISTANCE D This sets the central atom-hydrogen atom distance to 'D' angstroms. The default value is 1.0. The current value of 'D' remains in force until another 'DISTANCE' directive is given.
SERIAL N This sets the serial number of the next hydrogen atom to be added to LIST 5 to 'N'. The default value is 1. Subsequent hydrogen atoms will have the serial numbers 'N+1', 'N+2', etc., until the next 'SERIAL' directive is input.
U[ISO] U This directive sets the isotropic temperature factor associated with each hydrogen atom to 'U' angstroms squared. The default value is 0.05. The directive remains in force until another 'U[ISO]' directive is given.
U[ISO] NEXT MULT This is an alternatine form of the preceding directive. It sets the isotropic temperature factor associated with each hydrogen atom to 'MULT' times the equivalent temperature factor of the atom it is bonded to. The default value is 1.2. The directive remains in force until another 'U[ISO]' directive is given.
ACTION MODE
MODE
      NORMAL
      PUNCH
      BOTH     -  Default value.


NORMAL causes internal commands to be generated and executed. PUNCH causes output to the PUNCH file only. BOTH forces both actions.

 

TYPE MODE
MODE
      C   -  Default value.
      N


C enables the program to place hydrogen atoms on carbon atoms.
N enables the program to place hydrogen atoms on nitrogen.
It is advisable to perform placement on C before N, since the hybridisation states of C are more clearly defined.

 


[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.12: Hydrogen re-numbering - \HNAME

 \HNAME INPUTLIST= OUTPUTLIST=
 END


 \HNAME
 END


This command automatically renumbers hydrogen atoms so that their serial numbers are related to the bonded non-hydrogen atom.
 


[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.13: Regularisation of atomic groups - \REGULARISE

 \REGULARISE    MODE
 COMPARE
 KEEP
 REPLACE
 AUGMENT
 METHOD NUMBER
 GROUP NUMBER
 TARGET Atom Specifications
 IDEAL  Atom Specifications
 RENAME offset number
 CAMERON
 MAP Atom Specifications
 ONTO Atom Specifications
 SYSTEM a b c alpha beta gamma
 ATOM    x    y    z
 CP-RING x
 HEXAGON x
 OCTAHEDRON x y z
 PHENYL
 SQP x y z
 SQUARE x y
 TBP x z
 TETRAHEDRON x
 END



 

 \REGULARISE REPLACE
 GROUP 6
 TARGET C(1) UNTIL C(6)
 PHENYL
 END


This routine calculates a fit between the coordinates of a group of atoms in LIST 5 (atomic parameters) and another group. The calculated fitting matrix may be used to compare the geometry of two groups, or it may be applied to transform the new coordinates which will then replace the existing group in LIST 5 (D. J. Watkin, Act Cryst (1980). A36,975).

In this section, the group of atoms in LIST 5 to whose coordinates the fit is made is referred to as the 'TARGET atoms', and the group to be fitted onto that group is referred to as the 'IDEAL atoms'.

The source of the 'IDEAL atoms' can be the LIST 5, a pre-stored idealised geometry, or values read in from the directives. Those directives that refer to LIST 5 use the usual CRYSTALS formats for atom specifications. Once a transformation has been found, this can be used as the basis for naming one fragment based on the names of another.

Input for REGULARISE

The input to REGULARISE must define the groups to be fitted together, the method used for fitting , and the use to be made of the results. The user must ensure that corresponding atoms are specified in the same positions of the 'TARGET' and 'IDEAL' group definitions, so the program knows which pairs of atoms are to be matched. It is not necessary to have co-ordinates of every atom in the TARGET fragment. The inclusion of atom specifications for which coordinates do not exist in the parameter list indicates that the procedure must generate coordinates for these atoms. This allows the user to give a type and serial to new atoms created by the procedure. Any 'atoms' without coordinates are not included in the fitting process.

The maximum number of atom IDENTIFIERS permitted on an TARGET or IDEAL directive is about 250. Note that an UNTIL sequence only counts as two identifiers. The number of implied atoms permitted is very large.

The 'IDEAL' group may be given in various ways. For calculations on a single structure, it may be extracted from the stored data in the same way as the 'TARGET' group. In this case however, all the atoms must previously exist. Alternatively, explicit co-ordinates may be given in a system defined by the user, or a predefined group may be used. In any case all the positional parameters of the atoms in the 'IDEAL' group will be known before the calculation begins. Finally, various pre-defined geometrical groups are available.

Output from REGULARISE

The output from REGULARISE includes the fragment centroids, their sums and differences and the transformation fitting the IDEAL onto the TARGET.

Method of calculation

The centroid of each fragment is moved to the origin. The atomic coordinates are converted to an orthogonal system and rotated to an 'inertial tensor' system (to help condition the L.S. matrix).

The fitting calculation is either constrained to be a pure rotation- inversion, or is a free linear transformation (rotation-diltion). If requested, the pure rotation component of the calculated rotation-dilation matrix is extracted. The calculated matrix is applied to the co-ordinated of the 'IDEAL' group, which is then converted back to crystal fractions, for comparison with the TARGET.

WARNING

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.

\REGULARISE MODE
MODE is an optional parameter.
MODE
      COMPARE      -      Default value
      KEEP
      REPLACE
      AUGMENT


The effects are :-

COMPARE The specified groups are only compared. The translations and rotations necessary to match the groups will be calculated but not applied.

KEEP The specified groups will be compared and the calculated transformations applied. The TARGET atoms are kept, and atoms whose parameters have been calculated will be stored at the end of the new LIST 5. NOTE. If KEEP is given as a keyword, it can be followed by an offset to be used for the new serial numbers

REPLACE The specified groups will be compared and the calculated transformations applied. The new atoms whose parameters have been calculated will be placed at the end of LIST 5 and the old atoms deleted form the list.

AUGMENT The specified groups will be compared and the calculated transformations applied. The TARGET atoms which actually exist in LIST 5 are retained unaltered. Parameters that have been calculated for dummy atoms (represented by a name only in the TARGET list) will be placed at the end of the new LIST 5.

For REPLACE and KEEP the 'IDEAL' coordinates define the geometry to be preserved, i.e. the model, and the 'TARGET' coordinates specify where, in what orientation and with what atom identifiers the model is to be placed. That is, the TARGET structure is replaced by the IDEAL.

KEEP Z
COMPARE
REPLACE
AUGMENT

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. If the mode is KEEP, an offset Z can be given to be added to ther SERIAL of kept atoms (default 0) otherwise there are no parameters.

METHOD NUMBER

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.
       4        Enable improper rotation in Kabsch method


GROUP NUMBER

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.

TARGET Atom Specifications

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.

IDEAL Atom Specifications

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.

SYSTEM a b c alpha beta gamma

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.

ATOM x y z This directive allows the cordinates of a single atom to be specified, in fractional co-ordinates in the current co-ordintate system. It must be followed by three decimal numbers which will be the X, Y, and Z coordinates of the atom.
RENAME offset number This directive can only be used after previous directives have been used to match one group onto another (REGULARISE COMPARE), and enables the use of the MAP and ONTO directives. The MAP list of atoms is transformed by the existing transformation matrix (which may have been computed from only a few specified atoms). Each atom is then compared with the ONTO list, and the TYPE and SERIAL of the MAP atom used to generate a TYPE and SERIAL for the closest ONTO atom.
OFFSET The serial numbers of the atoms in the group being re-named are related to those of the master group by an increment of 'OFFSET'. The default value is 100
NUMBER If the number of atoms supplied on the following MAP and ONTO directives does not match NUMBER, a warning is printed.
CAMERON This matches atoms as in RENUMBER, but only creates CAMERON files with atoms transformed into the common coordinate system.
MAP Atom Specifications This specifies the atoms whose TYPE and SERIAL are to be propogated into the ONTO atoms. The atoms can be in any order.
ONTO Atom Specifications This specifies the atoms to be renamed. The atoms may be in any order and have any TYPE, but there must be EXACTLY as many as on the MAP directive. The atoms can have any TYPE, but must have unique SERIAL numbers.
HEXAGON X The 'IDEAL' group is a regular hexagon with a side of length 'X'. The default for x is 1.0.
PHENYL The same as HEXAGON with a fixed side of 1.39.
CP-RING X The 'IDEAL' group is a regular pentagon with a side of length 'X'. The default for x is 1.4.
SQUARE X Y The 'IDEAL' group is a rectangle with atoms at (x,0,0) , (0,y,0) , (-x,0,0) , (0,-y,0) . The parameters X and Y specify the size of the group to be used.
OCTAHEDRON X Y Z The 'IDEAL' group is an octahedron with atoms at (0,0,0) , (-x,0,0) , (0,y,0) , (x,0,0) , (0,-y,0) , (0,0,z) , (0,0,-z). The parameters X, Y and Z specify the size of the octahedron. 'z' defaults to 'y' defaults to 'x' defaults to '1.0'
SQP X Y Z The 'IDEAL' group is a square pyramid with atoms at (0,0,0) , (x,0,0) , (0,y,0) , (-x,0,0) , (0,-y,0) , (0,0,z). The parameters X, Y and Z specify the size of the octahedron. 'z' defaults to 'y' defaults to 'x' defaults to '1.0'
TBP X Z The 'IDEAL' group is a trigonal bipyramid with atoms at (0,0,0) , (x,0,0) , (-x/2,0.86603x,0), (-x/2,-0.86603x,0) , (0,0,z) , (0,0,-z) . The parameters X and Z specify the scale in the xy plane and z directions.
TETRAHEDRON X The 'IDEAL' group is a regular tetrahedron with an atom at the centre. 'x' is the distance in Angstrom from the centre to an apex and defaults to '1.0'
ORIGIN

This directive is not yet implemented.

Uses of \REGULARISE

 
1 - Extending a fragment to a complete molecule

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



2 - Forcing a regular shape on a group of atoms

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


3 - Checking for an additional symmetry element

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


4 - Renaming a group of atoms A second group of atoms is given new TYPES and SERIAL numbers so that the atom names are related to a previously named group.

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


5 - Viewing matched molecules in CAMERON This does the mapping as RENAME, but doesn't rename the atoms, just outputs CAMERON input files showing the two molecules superimposed. Use as follows:
   \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.

- Comparing two structures The SYSTEM and ATOM directives enable one to compare one structure with atoms from a second structure. However, since the second structure is not part of the main model, CRYSTALS knows nothing about the connectivity. Using the KEEP z directive, the second strcuture can be added to the DSC file, enabling a complete calculation to be performed.
In the following example, O(16) is in a quite distinctly different position in the two structures, so place holder Q(16) is used during the first mapping. The input coordinates are added to the DSC file with SERIAL numbers off-set by 400.
In the second calculation O(16) of the original structure is compared with Q(416) of the input structure.
\regular keep
keep 400
group 7
old mo(1) o(11) o(12) o(13) o(14) o(15) q(16)
system 8.4830 10.1870 11.0340 105.260 95.290 95.100 909.60
atom 0.1570 0.5269 0.2514
atom 0.1356 0.5975 0.1278  
atom -0.0296 0.4567 0.2632  
atom 0.2258 0.3448 0.1750  
atom 0.1693 0.6928 0.3850  
atom 0.4211 0.5669 0.2567  
atom 0.7960 0.1904 0.1727  


\regular compare
group 7
old mo(1) o(11) until o(16)
new mo(401) until q(416)
end



 


[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.14: Map two atomic groups together - \MATCH

 \MATCH
 MAP Atom Specifications
 ONTO Atom Specifications
 RENAME n
 EQUALATOM
 METHOD
 END



 

 \MATCH
 MAP RESIDUE(1)
 ONTO RESIDUE(2)
 RENAME 100
 END


This routine uses the mapping routines in REGULARISE to compare two residues. Unlike REGULARISE itself, the user does not have to list the atoms in any special order - the routine attempts to make pairwise assigments. Initially this is done via a topographical search, and refined by minimising cartesian residuals whenever degeneracy is found. By default, the final coordinate matching is done using method 1.

MAP

The following list of atoms is the ideal fragment with ideal atom types and numbers

ONTO

The following list of atoms is the fragment ot be compared with the ideal. There must be the same number of atoms in both fragments, but not necessarily in the same order. Inclusion of any Q atoms sets the EQUALATOM flag, ie the atom types are ignored.

EQUALATOM

If this parameter is included, the atom types in the "ONTO" list are ignored - they can even be Q atoms

METHOD

One of the METHODS available in REGULARISE
The default is method 1.

RENAME n

If the mapping is succerssful, atoms in the ONTO list are given the same type as the corresponding atom in the MAP list, and the same SERIAL plus "n".

OUTPUT LIST= PUNCH=

Output takes the values OFF, LOW, MEDIUM, HIGH.

unch takes the values OFF, RESULTS

Results creates an ASCII file that could be processed by EXCEL or other spreadsheet.

Comparing lots of Z'=2 structures

If one has a single cif file containing many Z'=2 structures, the whole file can be processed structure-by-structure automatically, with automatic matching of the structures. See Structure matching: measures of similarity and pseudosymmetry. A. Collins, R. I. Cooper and D. J. Watkin. Journal of Applied Crystallography 2006;39(6):842-849.

To do this, extract the structures from the CSD saving the results to a single file using the operation 'Import CIF file' from the drop-down menu 'X-ray Data'. Before starting, ensure that a file titled "cifproc.dat" is in the same folder as the composite cif file and that it says:

/edit
mon off
list off
insert resi
sel type ne h
end
/match
output punch=results
map resi(1)
onto resi(2)
end
/purge
end



 

Output from MATCH

If the output is set to PUNCH=RESULTS, a summary of the result of each matching operation is copied to the Punch file (Usually BFILE.PCH) All the information for each match is appended to a single line. The items are "tab deliminated" to facilitate reading them into spreadsheets. The keywords are preceeded by a ":" so that an editor can be used to break the line as necessary.

Description of output:

CSD_CIF_AANHOX01  
:Centroids    (the x,y and z coordinates of both centroids)
:Axes of Inertia    (the three axes of inertia of both molecules)
:Sum dev sq   (sum of the squares of the deviations in x,y,z and delta-d)
:RMS dev   (rms deviations in x,y,z and delta-d)
:RMS bond and tors dev     
:Min and Max bond dev     
:Min and Max tors dev   
:Sum & delta Centroids   
:Transformation    (matrix transforming one molecule to the other)
:Det and trace     (of the matrix - -ve indicates inversion)
:Closeness to ideal rotation   
:Closeness to group operator   
:Combined measure of closeness   
:Rworst & Raverage   
:Symmetry   
:Pseudo   
:Operator   
:No_Atoms   
:S.G.   
:Cell  



 

Example of output

CSD_CIF_AANHOX01 
:Centroids       0.9169 0.6281 0.3346 1.0255 0.8741 0.8117 
:Axes of Inertia 59.3690 10.0284 0.1392 59.1659 10.1380 0.0762 
:Sum dev sq      0.0014 0.0014 0.0726 0.0754 
:RMS dev         0.0115 0.0114 0.0812 0.0828 
:RMS bond and tors dev 0.0040 2.3978 
:Min and Max bond dev  0.0003 0.0094 
:Min and Max tors dev  0.2952 6.1112 
:Sum & delta Centroids 0.9712 0.7511 0.5731 0.1086 0.2461 0.4771 
:Transformation 0.9662 0.1296 -0.071 -0.237 0.961 0.146 -0.476 0.292 -0.960
:Det and trace -1.0000 0.9679 
:Closeness to ideal rotation 0.21507 
:Closeness to group operator 0.21567 
:Combined measure of closeness 0.21522 
:Rworst & Raverage 0.203432098 0.186725736 10 
:Symmetry m 
:Pseudo m 
:Operator 0.11+X 0.25+Y 1.15-Z 
:No_Atoms 11 
:S.G. P N A 21 
:Cell 7.5570 11.4580 17.6020 90.0000 90.0000 90.0000



 


[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.15: Calculation of interatomic bonds - \BONDCALC

 \BONDCALC
  END



 

 \BONDCALC FORCE
 END


This routine calculates a list of unique bonds between atoms in LIST 5 including bonds to symmetry related atoms. The bonds are stored in LIST 41.

Method of calculation

The BONDCALC routine uses the atomic positions from LIST 5 (the model parameters, see 6.3) (together with cell (LIST 1, see 4.2) and spacegroup information (LIST 2, see 4.8), the covalent radii from LIST 29 (atomic properties, see 4.18), and any additional bonding information in LIST 40 to calculate a list of bonds. The algorithm and tolerances used depend upon settings in LIST 40.

LIST 41 is only updated by \BONDCALC if there has been a change to LISTS 5 or 40 OR if \BONDCALC FORCE is issued.

 


[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.16: Bonding information - \LIST 40

 \LIST 40
 DEFAULTS TOLTYPE= TOLERANCE= MAXBONDS= NOSYMMETRY= SIGCHANGE=
 READ NELEMENTS= NPAIRS= NMAKE= NBREAK=
 ELEMENT TYPE= RADIUS= MAXBONDS=
 PAIR TYPE1= TYPE2= MIN= MAX= BONDTYPE=
 MAKE TYPE= SERIAL= S= L= TX= TY= TZ=
      TYPE2= SERIAL2= S2= L2= TX2= TY2= TZ2= BONDTYPE=
 BREAK TYPE= SERIAL= S= L= TX= TY= TZ=
       TYPE2= SERIAL2= S2= L2= TX2= TY2= TZ2=
 END


DEFAULTS TOLTYPE= TOLERANCE= MAXBONDS= NOSYMMETRY= SIGCHANGE=

This directive may only appear once. It affects the algorithm used to update LIST 41.

TOLTYPE= A value of 1 (default) causes \BONDCALC to use as a threshold for bonding, the sum of the covalent radii * the tolerance given. A value of 0 causes \BONDCALC to use the sum of the covalent radii + the tolerance given (in Angstroms), as a threshold.
TOLERANCE= The tolerance to be used in the \BONDCALC calculation as a threshold for bonds. Exact use depends on the value of the TOLTYPE keyword above.
MAXBONDS= Specifies the maximum number of bonds that may be formed to an atom. The BONDCALC calculation proceeds through the list of atoms searching for bonds, according to the TOLERANCE criteria. If more than MAXBONDS bonds are found, the best MAXBONDS will be kept. Best bonds are those where the sum of the covalent radii is closest to the actual bond length. (Where a PAIR directive has been used, the best are the closest to the mean of the min and max values on the PAIR directive.) Note well: The calculation proceeds through the list of atoms, so bonds are formed from atoms near the top of the list to those lower down. While atoms lower down will still only form at most MAXBONDS bonds, they are less likely to be the 'best' bonds since they are formed from atoms higher up the list. E.g. You have an H right at the end of the list, and you set MAXBONDS=1 for H (see ELEMENT). If the first atom forms a bond to that H, then no more bonds can be formed to that H even if they are better. If the H were at the top of the list it would get the choice of which bonds to pick. This is fairly unimportant stuff, it is rare that there will be ambiguities over whether something is bonded or not. The default value of MAXBONDS is therefore 15.
NOSYMMETRY= 0 (default) searches for all symmetry related bonds. 1 ignores symmetry, will not find bonds across operators, may speed up bond bond calculation slightly.
SIGCHANGE= Number of angstroms that any atom in LIST 5 must move during refinement for it to be considered a significant change resulting in a recalculation of bonding.
READ NELEMENTS= NPAIRS= NMAKE= NBREAK= Specify the number of ELEMENT, PAIR, MAKE and BREAK directives that are to follow.
ELEMENT TYPE= RADIUS= MAXBONDS= Override the covalent radius in L29 and the MAXBONDS value on the DEFAULTS directive for a specific element.
TYPE= The element type. E.g. C
RADIUS= The covalent radius to use for this element.
MAXBONDS= The maximum number of bonds to this element.

DPAIR TYPE1= TYPE2= MIN= MAX= BONDTYPE= Override the covalent based calculation altogether.
TYPE1= An element type, e.g. C
TYPE2= An element type, e.g. O
MIN= The minimum length of a bond.
MAX= The maximum length of a bond.
BONDTYPE= The bondtype to be assigned to this bond. BONDCALC will eventually have a go at bond type assignment, if you are forced to add in extra PAIR commands then there is not much chance that the assignment will be correct so it can be specified here. Use 0 for unknown.

More than one pair of the same elements can be used at once:

e.g.
  PAIR C O 1.0 1.2 BONDTYPE=2
  PAIR C O 1.2 1.4 BONDTYPE=1


MAKE TYPE= SERIAL= S= L= TX= TY= TZ= TYPE2= SERIAL2= S2= L2= TX2= TY2= TZ2= BONDTYPE= Makes a bond between two atoms (possibly symmetry related).
TYPE= TYPE2= An element type, e.g. C.
SERIAL= SERIAL2= The serial number of the atom. (From List 5, atomic parameters).
S= S2= The number of the symmetry matrix used from List 2 (list of space group symmetry operators, see section 4.8) (default, unity = 1). Negative indicates centre of symmetry applied aswell.
L= L2= The number of the non-primitive lattice translation from List 2. (default =1, see section 4.8)
TX= TY= TZ= TX2= TY2= TZ2= Translations from asymmetric unit co-ordinates.
BONDTYPE= The bondtype to be assigned to this bond. BONDCALC will eventually have a go at bond type assignment, if you are forced to add in extra MAKE commands then there is not much chance that the assignment will be correct so it can be specified here. Use 0 for unknown.
BREAK TYPE= SERIAL= S= L= TX= TY= TZ= TYPE2= SERIAL2= S2= L2= TX2= TY2= TZ2= As for MAKE, but without the BONDTYPE keyword.

[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.17: Bonding information - \BONDING

 \BONDING ACTION
 DEFAULTS TOLTYPE= TOLERANCE= MAXBONDS= NOSYMMETRY= SIGCHANGE=
 ELEMENT TYPE= RADIUS= MAXBONDS=
 PAIR TYPE1= TYPE2= MIN= MAX= BONDTYPE=
 MAKE  atom-specification TO atom-specification bondtype
 BREAK atom-specification TO atom-specification
 END


THis is a more user-friendly alternative to inputting a LIST 40. Directive syntax is like \LIST 40 with the following exceptions:

1) ACTION. This can take two values:

      REPLACE (Default, and replace previous LIST 40 with a new on)
      EXTEND  (adds new commands to end of existing LIST 40)


2) The MAKE and BREAK directives look like this:

 MAKE C(1) TO C(4) 8
 BREAK N(1) TO H(14)


Symmetry may be specified in the standard CRYSTALS way, the numbers in parenthesis are serial,S,L,Tx,Ty,Tz (see above) the list may be truncated when the rest are default values: (serial,1,1,0,0,0):

 MAKE C(1,2,1,0,1,1) TO C(8) 4


3) The READ directive need not be given. This makes it easier to edit text files containing the command as you don't have to remember to alter the values on the READ directive.

3) The command may be given as \BONDING EXTEND, in which case it takes any directives given and adds them to the existing LIST 40.


[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.18: Printing of LIST 40

LIST 40 may be listed with either

\PRINT 40
or
\SUMMARY 40

LIST 40 may be punched with

\PUNCH 40
which will produce a standard List 40 in CRYSTALS format, or
\PUNCH 40 B
which will produce a \BONDING command which is easier to edit.

[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.19: Creating a null LIST 40

A null LIST 40, containing no extra information, may be created with

 \LIST 40
 END


or

 
 \BONDING
 END



[Top] [Index] Manuals generated on Wednesday 27 April 2011

6.20: Printing of LIST 41

LIST 41 may be listed with either

\PRINT 41
or
\SUMMARY 41

Issuing \BONDCALC when there is no LIST 40 will cause a null list 40 to be created.



© Copyright Chemical Crystallography Laboratory, Oxford, 2011. Comments or queries to Richard Cooper - richard.cooper@chem.ox.ac.uk Telephone +44 1865 285019. This page last changed on Wednesday 27 April 2011.