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: Conversion of temperature factors - \CONVERT
- 6.9: Hydrogen placing - \HYDROGENS
- 6.10: Perhydrogenation - \PERHYDRO
- 6.11: Regularisation of atomic groups - \REGULARISE
- 6.2: Specifications of atoms and other parameters
[Top] [Index] Manuals generated on Wed Jun 6 2001
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 Modification of lists 5 and 10 on the disc - \EDIT Conversion of temperature factors - \CONVERT Hydrogen placing - \HYDROGENS Per-hydrogenation - \PERHYDRO Regularisation of groups in LIST 5 - \REGULARISE
[Top] [Index] Manuals generated on Wed Jun 6 2001
6.2: Specifications of atoms and other parameters
There is a consistent syntax thoughout CRYSTALS for refering to atoms
and atomic parameters. This was refered 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 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).
'S' may take any value between '-NSYM' and
'+NSYM', except zero, where 'NSYM' is the
number of symmetry equivalent positions
provided in LIST 2 (see the section
of the user guide on 'initial data input').
if 'S' is less than zero, the coordinates
of the atom 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 in LIST 5 or LIST 10, 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)
ATOMIC PARAMETER SPECIFICATION
Atomic parameters have a NAME. Some instructions 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 azumuthal 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. If you need to use f",
remember not to
apply Friedels law (LIST 13) during data reduction,
and to include anomalous scattering (LIST 3 and
LIST 23). 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 given 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. Computations are more efficient when it is turned off. If the enantiopole is used (or refined) then Friedels law must not be applied (LIST 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.
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 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.
[Top] [Index] Manuals generated on Wed Jun 6 2001
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 cards 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. 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 azumuthal 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
Futher 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 Wed Jun 6 2001
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 atomic parameters in CRYSTALS format.
A - Punches the atomic parameters in CRYSTALS format.
B - Punches the atomic parameters in XRAY format.
C - Punches the atomic parameters in SHELX 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 instruction 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 Wed Jun 6 2001
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 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 or LIST 10.
It offers the editing facilities frequently needed
for the management of atom parameters, including conditional operations
and arithmetic.
EDIT is a semi-interactive Instruction, 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 card 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 instructions.
ATOM TYPE SERIAL OCC FLAG X Y Z U11 .. This instruction 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. 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 instruction 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-SPECIFICAIONS 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 at each end of the principal axis of the original atoms anisotropic adp ellipsoid.
The original atoms are not deleted. The sequence Z ATOM-SPECIFICAIONS 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 apd representiong the inertial tensor (ie the 'shape' of the group). The atom TYPE is QC, and its serial Z. The sequence Z ATOM-SPECIFICAIONS 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 card.
The sequence Z ATOM-SPECIFICAIONS 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 card. Only one KEEP
card 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 instructions 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 instructions 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 instruction 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 cards.
If no atom specification is given on this card, subsequent MOVEs will move
the atoms to the head of the list.
MOVE Z ATOM-SPECIFICATION ...
This instruction moves atoms about in the list and places them in the position defined by the latest AFTER directive. (See the previous directive). This instruction does not remove atoms from the list, but simply reorders the list. The sequence Z ATOM-SPECIFICAIONS 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 instructions 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 instructions 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 instruction 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 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 card, or by a mixture of these methods.
In the second format, a keyword corresponding to an atom parameter name (as defined in LIST 5) 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
instructions.
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 card. 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 card 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 card 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 instructions 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 instruction 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 instruction 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 instruction 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 instruction to the atoms given in the atom specification. THEIR ORIGINAL COORDIANATES x,y,z MUST be in the MOLAX coordinate (Angstrom) system This instruction 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 instruction 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 instruction 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 instruction inserts the value of the named identifier into the
parameter 'SPARE' in the atom list, replacing any previous value.
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.
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 constiuent 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 constiuent atoms.
REFORMAT This instruction converts an old (non-FLAG) version of LIST 5 to the new format.
[Top] [Index] Manuals generated on Wed Jun 6 2001
6.6: Reorganisation of lists 5 and 10 - \REGROUP
\REGROUP INPUTLIST= OUTPUTLIST= SELECT MOVE= KEEP= MONITOR= SEQUENCE= SYMMETRY= TRANSLATION= END
\REGROUP SELECT MOVE=1.6,MONITOR=HIGH END
This routine offers a way of re-ordering the atoms in LIST 5 or LIST 10, 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 to get bonding distances.
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.
\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=
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.
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
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.
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 Wed Jun 6 2001
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. The atom TYPE, SERIAL and order in LIST 5 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 to give a value used for determining inter-atomic bonds. The default is 0.2 A.
TYPE=
ALL
PEAKS
If TYPE equals ALL, then the coodinates of all atoms 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.
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 Wed Jun 6 2001
6.8: 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 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 instruction 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 Wed Jun 6 2001
6.9: 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 targe 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 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 preceeding 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 after the atom 'TYPE(SERIAL)'. This directive must appear immediately after the instruction 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.
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 AND R This generates the coordinates of the single hydrogen atom bonded to an SP hybridised atom.
HBOND X AND R This generates a single H atom 'DISTANCE' angstroms from the donor in the direction of the acceptor.
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 Wed Jun 6 2001
6.10: 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 instruction scans the atomic coordinates for cabon 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 PUNCH file for
manual editing and then be USEd by CRYSTALS.
\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 preceeding 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 - Default value.
BOTH
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.
P 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 Wed Jun 6 2001
6.11: Regularisation of atomic groups - \REGULARISE
\REGULARISE MODE COMPARE KEEP REPLACE AUGMENT METHOD NUMBER GROUP NUMBER TARGET Atom Specifications IDEAL 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 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.
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 card 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.
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 the 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 placed at the end of the new LIST 5.
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.
COMPARE
KEEP
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. 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.
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 instruction stream
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.
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