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Crystals ManualChapter 6: Atomic And Structural Parameters
[Top] [Index] Manuals generated on Wednesday 8 November 2006 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 Wednesday 8 November 2006 6.2: Specifications of atoms and other parametersThere 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
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)
PART NO. = 1000 * ASSEMBLY NO. + GROUP NO.
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.
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.
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
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
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*
[Top] [Index] Manuals generated on Wednesday 8 November 2006 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)
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 8 November 2006 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.
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 8 November 2006 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
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-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.
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
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
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)
The second form of ARG(i) on this directive is : ATOM-SPECIFICATION
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
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
\EDIT ROTATE 30 C(1) C(20) C(21) C(22) C(23) C(24) C(25) END
\EDIT INSERT RESIDUE CENTROID 1 RESIDUE(1) ROTATE 90 QC(1) 1 0 0 RESIDUE(1) END [Top] [Index] Manuals generated on Wednesday 8 November 2006 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).
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
SEQUENCE
NO - Default value YES
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 8 November 2006 6.7: Repositioning of atoms - \COLLECTThis routine changes the atom
coordinates so as to form a 'molecule' using the covalent radii given in
LIST 29 (atomic properties - see section 4.15). 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
TOLERANCE=
The tolerance is added to the sum of the co-valent radii
taken from LIST 29 (atomic properties - see section 4.15) to give a
value used for determining inter-atomic bonds.
The default is 0.2 A.
TYPE=
ALL PEAKS
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.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 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]))
\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
[Top] [Index] Manuals generated on Wednesday 8 November 2006 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
\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 8 November 2006 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
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.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 6.11: 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. 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. 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 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
[Top] [Index] Manuals generated on Wednesday 8 November 2006 6.12: 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 4.15), 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 8 November 2006 6.13: 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 8 November 2006 6.14: 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 8 November 2006 6.15: Printing of LIST 40LIST 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 8 November 2006 6.16: Creating a null LIST 40A null LIST 40, containing no extra information, may be created with \LIST 40 END
\BONDING END
[Top] [Index] Manuals generated on Wednesday 8 November 2006 6.17: Printing of LIST 41LIST 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.
[Introduction To The System | Definitions And Conventions | The Crystals Database | Initial Data Input | Reflection Data Input | Atomic And Structural Parameters | Structure Factors And Least Squares | Fourier Routines | Analysis Of Results | Twinned Crystals | Matrix Calculations | Obsolete Commands ] |
© Copyright Chemical Crystallography Laboratory, Oxford, 2006.
Comments or queries to David Watkin -
david.watkin@chem.ox.ac.uk Telephone +44 1865 285019.
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