Crystals Manual
Chapter 9: Analysis Of Results
- 9.1: Scope of this section of the user guide
- 9.2: Analysis of residuals - \ANALYSE
- 9.3: Distance angles calculations - \DISTANCES
- 9.4: Distance-angles symmetry operations
- 9.5: Void Location - \VOIDS
- 9.6: Least squares best planes and lines - \MOLAX
- 9.7: Torsion angles - \TORSION
- 9.8: Thermal displacement parameter analysis - \ANISO
- 9.9: Principal atomic displacement directions - \AXES
- 9.10: Publication listing of the atomic parameters - \PARAMETERS
- 9.11: Publication listing of reflection data - \REFLECTIONS
- 9.12: Summary of data lists - \SUMMARY
- 9.13: CIF lists - \CIF
- 9.14: Graphics - CAMERON
- 9.2: Analysis of residuals - \ANALYSE
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.1: Scope of this section of the user guide
Analysis of residuals ANALYSE Distance and angles calculations DISTANCES Void search VOIDS Least squares best planes MOLAX Torsion angles TORSION Thermal displacement parameter analysis ANISO Principal atomic displacement directions AXES Publication listing of the atomic parameters PARAMETERS Publication listing of the reflections REFLECTIONS Summary of data lists SUMMARY CIF files CIF Graphics CAMERON
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.2: Analysis of residuals - \ANALYSE
This analyses the residual, Fo-Fc, for systematic trends, which might
either indiacate an incomplete model, or an unsatisfactory weighting
scheme. It is described in the chapter Structure Factors and Least
Squares.
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.3: Distance angles calculations - \DISTANCES
\DISTANCES INPUTLIST= OUTPUT MONITOR= LIST= PUNCH= SELECT ALLDISTANCES= COORDINATES= SORTED= TYPE= RANGE= LIMITS DMINIMUM= DMAXIMUM= AMINIMUM= AMAXIMUM= E.S.D.S COMPUTE= CELL= INCLUDE atoms EXCLUDE atoms ONLY atoms PIVOT atoms BONDED atoms END \DIST E.S.D YES END
The distance angles routine is completely general with respect to crystal and lattice symmetry. For distances, the user may either use elemental radii specified in LIST 29, or specify minimum and maximum limits, and the program then calculates all possible contacts within these limits. All symmetry operations and unit cell translations are automatically generated. For the angles, LIST 29 or a separate set of distance limits may be used. At a given atom, angles are then calculated between all the atoms which bond to the central atom within the given limits.
The distance-angles routines can calculate the estimated standard deviations of the distances and angles that they produce. These e.s.d.'s are based upon the matrix stored in LIST 11, and as many variance and covariance terms as are present are used. (For a full matrix, therefore, the full variance-covariance matrix is used). For this reason, the calculation of e.s.d.'s takes at least ten times as long as a simple distance angles calculation.
When a set of e.s.d.'s are calculated, the variance-covariance matrix
for the cell parameters (LIST 31) may also be used.
\DISTANCES INPUTLIST=
INPUTLIST=
5 - Default value
10
The default is to use the normal atom coordinate list.
OUTPUT MONITOR= LIST= PUNCH=
MONITOR= This controls the monitoring information.
OFF - no output
DISTANCES - only monitors distances. (Default)
ANGLES - only monitors angles.
ALL - monitors distances and angles.
LIST= This controls the format of the listing.
OFF
LOW - Default
HIGH
If LIST is LOW , the default, then the listing is in a compressed format, without symmetry information. If LIST is OFF, no output is sent to the listing file unless PUNCH is PUBLISH, when a copy of the publication listing appears in the listing file.
PUNCH= This controls the output sent to the 'punch' file.
PUBLISH - Produce a listing suitable for publication.
RESTRAIN - Produce a proforma LIST 16. Use the RANGE, LIMIT, TYPE
INCLUDE and EXCLUDE parameters to restrict the restraints
produced.
CIF - Produce a listing in CIF format.
SCRIPT - Lists bonds in a easily machine readable format.
SELECT ALLDIST= COORD= SORTED= TYPE= RANGE= SYMMETRY= TRANS=
ALLDISTANCES=
NO - Default value
YES
If ALLDISTANCES is NO, the distances calculated about each atom will only be those to atoms that occur after the central atom in LIST 5. (i.e. each distance is only printed once).
If ALLDISTANCES is YES , then the distances from each atom to all the other atoms are calculated for all the atoms. (In this case, each distance will appear twice in the list).
COORDINATES=
NO - Default value
YES
If COORDINATES is YES, the transformed coordinates of each atom in a distance calculation are printed. If COORDINATES is NO, the transformed coordinates are not printed.
SORTED=
NO - Default value
YES
If SORTED is NO, the distances from the central atom are in the order in which the other atoms occur in LIST 5. If SORTED is YES , the distances are printed in order of increasing magnitude.
TYPE= This parameter indicates the type of distances which will be calculated.
ALL - Default value
INTRA
INTER
If TYPE is ALL, then all distances are printed; if TYPE is INTRA then only intramolecular distances are printed, and if TYPE is INTER then the intermolecular distances are printed (Note that the whole asymmetric unit is regarded as a 'molecule'.
RANGE= This parameter defines how the range is to be selected. Except when RANGE = LIMITS (when the lowest acceptable distance is user-specified) contacts of zero angstrom are suppressed.
COVALENT Use 'covalent' radii from LIST 29.
VANDERWAALS. Use 'VanderWaals' radii from LIST 29, but angles are
suppressed.
IONIC. Use 'ionic' radii from LIST 29.
LIMITS. Use the specified or default ranges set by the LIMIT card
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
LIMITS DMINIMUM= DMAXIMUM= AMINIMUM= AMAXIMUM=
This directive specifies the limits for the distance angles
calculations, and may only be given if RANGE = LIMITS has been specified
on a
preceeding SELECT directive.
DMINIMUM
This defines the distance below which distances are not
calculated or printed. The default is zero.
DMAXIMUM
This parameter defines the maximum distance above which distances are not
calculated or printed.
Use \COMMANDS DISTANCES to find the default value for DMAXIMUM.
All the distances that are to be calculated and printed
must lie between DMINIMUM and DMAXIMUM.
AMINIMUM
For a given central atom, other atoms which
make contacts that are less than AMINIMUM will
not be considered when the angles at the
central atom are computed.
The default is zero.
AMAXIMUM
For a given central atom, other atoms which
make contacts that are greater than AMAXIMUM
will not be considered when angles at the
central atom are computed.
The default value for AMAXIMUM is set in the COMMAND file.
AMAXIMUM And AMINIMUM define a shell about each
pivot atom outside of which angles are not computed.
E.S.D.S COMPUTE= CELL=
This directive determines whether estimated standard deviations
of the distances and angles are calculated.
COMPUTE
NO - Default value
YES
If this parameter is NO, standard deviations are not computed. Note that if e.s.d.'s are to be calculated, i.e. COMPUTE is set equal to YES , then a suitable least squares matrix (LIST 11) must be available.
CELL=
NO - Default value
YES
If this parameter is NO, the variance-covariance matrix for the cell parameters is not included when the e.s.d.'s are calculated.
INCLUDE atoms
This directive determines which atoms are included as pivot atoms
in the calculation.
The arguments may be either a type of atom , or an atom specification of
the 'type(serial)' or 'type(serial) UNTIL type(serial)' kind described
elsewhere in the manual. Only INCLUDEd atoms are used as pivots, but distances
and angles are computed to all other atoms in the current LIST 5 within
the ranges specified on the SELECT directive.
ONLY atoms
Similar to INCLUDE, except that specified atoms may be pivot or
bonded.
The arguments may be either a type of atom , or an atom specification of
the 'type(serial)' or 'type(serial) UNTIL type(serial)' kind described
elsewhere in the manual. Distances
and angles are computed only to specified atoms in the current LIST 5 within
the ranges specified on the SELECT directive.
PIVOT atoms
Similar to INCLUDE, except that atoms excluded with an EXCLUDE
directive can still be used to bond to.
The arguments may be either a type of atom , or an atom specification of
the 'type(serial)' or 'type(serial) UNTIL type(serial)' kind described
elsewhere in the manual. Distances
and angles are computed only to specified atoms in the current LIST 5 within
the ranges specified on the SELECT directive.
BONDED atoms
Similar to INCLUDE, except that non-included atoms can still be used as
pivots.
The arguments may be either a type of atom , or an atom specification of
the 'type(serial)' or 'type(serial) UNTIL type(serial)' kind described
elsewhere in the manual. Distances
and angles are computed only to specified atoms in the current LIST 5 within
the ranges specified on the SELECT directive.
EXCLUDE atoms
This directive determines which atoms are excluded as pivots in the
calculation.
The arguments may be either a type of atom , or an atom specification of
the 'type(serial)' or 'type(serial) UNTIL type(serial)' kind described
elsewhere in the manual. If EXCLUDE directives alone are used, all
atoms except those EXCLUDEd either explicitly or by
type, are used as pivot atoms in the calculation.
However, if both INCLUDE and EXCLUDE are used, the only atoms used in
the calculation will be those INCLUDEd and not EXCLUDEd.
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.4: Distance-angles symmetry operations
Accompanying each atom in a distance or angle calculation with LIST equal to HIGH are the symmetry operators that are necessary to bring the atom into the correct position in the cell to make a contact with the central atom. These symmetry operations are divided into six parts, which are indicated by five flags. These are explained in the section on Atomic and Structural Parameters.
\ \ distances from 0 to 2.5 \ angles from 0 to 2.0 \ the e.s.d.'s of the distances and angles are calculated \ distances from each atom to all other atoms are printed \ transformed coordinates are printed \ the distances are sorted in order of increasing magnitude \ \DISTANCES SELECT ALL=YES,COORD=YES,SORT=YES,RANGE=LIMITS LIMITS DMAX=2.5, AMAX=2.0 E.S.D. YES END
\DIST EXCLUDE ALL ONLY C(1) C(3) C(4) END
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.5: Void Location - \VOIDS
\VOIDS INPUTLIST= DISTANCE TOLERANCE CONTACTS RESOLUTION END \VOIDS DISTANCE 2.2 END
This utility searches for the asymmetric unit for points which lie
outside the known atoms. The 'radii' of the known atoms is independent
of type, and in an input value. A pseudo atom in inserted at every point
on a search grid outside the known atoms. The pseudo atoms are given a
'TYPE' dependant upon the number of neighbouring pseudo atoms. Atoms of
type R are at the core of large voids, type L are intermediate, and M at
the surface.
\DISTANCES INPUTLIST=
INPUTLIST=
5 - Default value
10
The default is to use the normal atom coordinate list.
DISTANCE value
This sets the radii of the knoen atoms, default 2.5A.
RESOLUTION value
This sets the sampling interval for the search grid, default 0.8 A.
CONTACT value1 value2
This sets the number of pseudo-atom contacts requuired for the core and intermediate pseudo atoms. The defaults are 27 (R type atoms), 15 (L type atoms). All other atoms are of type M.
\COLLECT and \REGROUP can be used to re-group the pseudo-atoms, and
the augmented structure can be viewed in CAMERON.
MOLAX#
Best lines and planes#
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.6: Least squares best planes and lines - \MOLAX
\MOLAX INPUTLIST= EXECUTE PUNCH ATOMS W(1) SPECIFICATION(1) W(2) SPECIFICATION(2) . PLOT PLANE LINE ANGLE NP(1) AND NP(2) EVALUATE ATOM SPECIFICATIONS . . . . REPLACE ATOM SPECIFICATIONS . . . SAVE QUIT END
\MOLAX ATOM FIRST UNTIL LAST PLANE SAVE END
MOLAX is used for computing the principal axes of inertia through groups of atoms using the routines described in Computing Methods in Crystallography, edited by J. S. Rollett, Pergamon Press, 1965, p67-68. It can be used to compute best lines and planes, and produce simple line printer plots of the atoms.
The best plane for a series of N atoms whose positions have varying reliability, such that they can be assigned weights, w(1), w(2), . . . w(n), is defined as that for which the sum of the squares of the distances (in angstroms) of the atoms from the plane, multiplied by the weights, w(i), of the atomic positions, is a minimum. Note that the normal to the 'worst plane' is the 'best line', and if masses are used for weights, then the calculation gives the principal inertial axes.
The atomic positions are taken from LIST 5, possibly modified by symmetry information, to compute inertial axes, deviations of atoms from the planes or lines, and the angles between normals to these planes or axes. Shape indices (Mingos M.P. and Rohl A.L. J Chem Soc Dalton Trans (1991) 3419) are computed.
Each time a line or plane is computed, the direction cosines of the relevent axis are stored as AXIS number 'n'. The angles between these axes can be computed. Three geometry indices are also computed. The geometry is best described by the index closest to unity. (Mingos,D.P.M & Rohl,A.L., J.Chwm.Soc. Dalton Trans (1991) pp 3419 - 3425)
Immediate execution of a directive can be forced by issuing an EXECUTE
directive.
\MOLAX INPUTLIST=
INPUTLIST=
5 - Default value
10
EXECUTE
This forces the execution of preceeding directives.
PUNCH
This card causes the orthogonal coordinates of the atoms of any plane or
line computed in following tasks to be output to the 'punch' file.
ATOMS W(1) SPECIFICATION(1) W(2) SPECIFICATION(2) .
This specifies atoms to be used in the calculation of the
best plane.
W(1) Is the weight assigned to the atoms
contained in the first atom specification, W(2) is the weight
assigned to the second group of atoms, and so on.
If W(1) is omitted, a default value of 1 is used,
but any other W(I) term applies to all the atoms following it,
until another W is found or the end of the card is
encountered.
At least one ATOM card must precede each PLANE or PLOT directive.
An ATOM card will over-rule an immediately preceeding ATOM card. If a
card is not long enough for the full atom list, use CONTINUE.
PUNCH
This card causes the orthogonal coordinates of the atoms of any plane or
line computed or EVALUATED in the current task to be output to the 'punch'
file.
PLOT
This instruction, (or PLANE or LINE)
must follow immediately after an ATOM card and
causes the calculation of inertial axes.
Details of the computation are suppressed on the Monitor,
but a line drawing projected onto the best plane is produced.
MOLAX Can thus be used as a means of displaying some or all
of the atoms in a structure.
PLANE
This instruction, (or LINE or PLOT)
must follow immediately after an ATOM card and
causes the calculation of a least squares best plane.
LINE
This instruction, (or PLANE or PLOT)
must follow immediately after an ATOM card and
causes the calculation of a least squares best line.
ANGLE NP(1) AND NP(2)
If present, thus card must follow at least
two ATOMS/PLANE (ATOMS/LINE, ATOMS/PLOT) card sequences.
It causes the program
to calculate the angle between the axes with serial numbers
NP(1) and NP(2) .
The AND must be present.
EVALUATE ATOM SPECIFICATIONS . . . .
If present, this card
must appear after a PLANE, LINE or PLOT directive,
and causes the co-ordinates of the atoms specified
to be calculated and printed with respect to the least squares axial system.
REPLACE ATOM SPECIFICATIONS . . .
if present, this card
must appear after a PLANE, LINE or PLOT directive,
and causes the co-ordinates of the atoms specified to be modified so that
they lie on the previously defined plane. The LIST 5 in core is immediately
updated, so that the new coordinates will be used for any subsequent
computation. A LIST 5 is only written to the disc on a satisfactory exit from
MOLAX.
SAVE
This card causes the latest plane defining matrix and
vector to be stored in LIST 20. A LIST 20 is only written to the disc on
a satisfactory exit from MOLAX.
QUIT
This directive abandons the calculation without modifying the disc LISTs.
\ \ these instructions a plane \ involving n(1),n(2),c(1),c(2) and n(3) and \ prints the co-ordinates of all the atoms with \ respect to this plane. the positions of the \ nitrogen atoms have double weight \ \MOLAX ATOMS 2 N(1) UNTIL N(3) 1 C(1) C(2) PLANE EVALUATE ALL \ \ this set of cards also calculates another plane, \ printing only the co-ordinates of c(5) with respect to \ the second plane. the angle between the two planes \ is then calculated \ ATOMS C(1) S(1) N(1) PLANE EVALUATE C(5) ANGLE 1 AND 2 END
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.7: Torsion angles - \TORSION
\TORSION INPUTLIST= ATOMS SPECIFICATIONS PUBLICATION PRINT= END \TORSION ATOM C(1) C(2) C(3) C(4) END
The routines described in this section calculate torsion angles which are defined as follows. The torsion angle about the bond j-k is the angle the bond k-l is rotated from the ijk plane. It is positive when, on looking from ij to kl, the rotation is clockwise.
The program uses atomic positions taken from
LIST 5. These can be
modified by the space group symmetry operators stored in LIST 2.
\TORSION INPUTLIST=
INPUTLIST
5 - Default value
10
ATOMS SPECIFICATIONS
This card specifies atoms that are to be used in the calculation
of the torsion angle. More than one ATOMS card can be given. Each
card must define at least four atoms, the torsion angle being
computed with respect to the first three atoms and each of the
subsequent ones.
PUBLICATION PRINT=
The parameter PRINT controls the publication listing, which is sent to
the file open on the CRYSTALS PUNCH unit.
NO - DEFAULT. There is no publication listing
YES There is a publication listing sent to the PUNCH file
CIF The listing is in CIF format
Example. \ the torsion angle about C(3)-C(4) is calculated \ two torsion angles about C(4)-C(5) are calculated \ \TORSION ATOMS N(2) C(3) C(4) C(5) ATOMS C(3) C(4) C(5) C(6) O(1) END
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.8: Thermal displacement parameter analysis - \ANISO
\ANISO INPUTLIST EXECUTE ATOMS ATOM SPECIFICATIONS CENTRE X=, Y=, Z= REJECT NV= LIMITS VALUE= RATIO= TLS EVALUATE ATOM SPECIFICATIONS REPLACE ATOM SPECIFICATIONS . . . SAVE QUIT AXES DISTANCES DL= AL= ANGLES AL= END
\ANISO ATOM C(1) UNTIL C(6) TLS SAVE END
This routine calculates the overall rigid-body motion tensors T, L, S (Shoemaker and Trueblood, Acta Cryst. B24, 63, 1968) by a least-squares fit to the individual anisotropic temperature factor components, together with librational corrections to bond lengths and angles.
Shoemaker and Trueblood's conventions and reductions are followed throughout; in particular, the trace of S, which is indeterminant, is set to zero. The program therefore determines 20 overall tensor components - the upper triangles of T and L together with the whole of S apart from S(33).
Even when the trace-of-S singularity has been removed, however,
the nature of the rigid body problem is such that ill-conditioned
and singular normal matrices are much more common than in
structure refinement and the program therefore proceeds via
the eigenvalues and eigenvectors of the normal matrix. In most
cases the largest and smallest eigenvalues are output for
inspection, but if the ratio of these quantities is less than
the LIMITing RATIO, a full eigenvalue/vector listing is produced. Further,
if any eigenvalue is itself less than the LIMITing VALUE, the corresponding
parameter combination is set to zero, thus removing the near-
singularity. These actions can be modified by the use of the
LIMIT and REJECT directives described below.
\ANISO INPUTLIST
INPUTLIST
5 - Default value
10
EXECUTE
This causes immediate execution of the previous directive, otherwise
instructions are executed on input of a new directive (or END).
ATOMS ATOM SPECIFICATIONS
This parameter specifies the set of atoms to be used for the following
calculation.
A subsequent atom card over rules all previous atom cards.
If the full atom specification cannot be got on one card, use CONTINUE.
The atom specifications are in the usual form with symmetry
operators and UNTIL sequences permitted. An ATOM card resets the CENTRE to
its default value, 0,0,0.
CENTRE X=, Y=, Z=
This card specifies the centre of libration,
in crystal fractions, to be used in the original derivation of
the overall motion tensors. The program derives and uses a unique
origin at a later stage in the calculations. This directive
is optional, the default centre being (0,0,0).
If a centre of (0,0,0) is given or set by default, the program computes
and uses the mean position of the given atoms, INCLUDING any which are
isotropic, even though these are not used to compute TLS. The stored CENTRE
is updated during TLS, and a second TLS computation may be performed using
this new value as CENTRE. This may help stabilise certain forms of
ill-conditioning.
REJECT NV=
Overrides normal action and sets the parameter combination
corresponding to eigenvector number nv to zero.
Eigenvectors are numbered in ascending order of their eigenvalues,
so that nv
is in the range 1 to 20 inclusive and will usually have been obtained
from a full eigenvalue/vector listing produced in
a previous run.
LIMITS VALUE= RATIO=
If an eigenvalue is less than VALUE or its size is less than
RATIO * (the next bigger), it is eliminated from the analysis.
VALUE is currently .000001 and RATIO .01 .
TLS
This causes the TLS calculation to be initiated. It MUST have been preceeded
by an ATOM card.
EVALUATE ATOM SPECIFICATIONS
This may be used after a successfull TLS calculation to list Ucalcs for
the specified atoms. The atom list is not modified.
REPLACE ATOM SPECIFICATIONS . . .
If present, his card
must appear after a TLS directive,
and causes the co-ordinates of the atoms specified to be modified so that
they have U's defined by the current T, L, and S matrices.
The LIST 5 in core is immediately
updated, so that the new coordinates will be used for any subsequent
computation if a new ATOM instruction is issued.
The updated LIST 5 is only written to the disc on a satisfactory exit from
ANISO.
SAVE
This card is optional. If it follows a TLS card, it
causes the latest L matrix and CENTRE to be stored in LIST 20. If it
follows an AXES card, the direction cosines and centre if the ellipse FOR
THE LAST ATOM are stored in LIST 20.
A LIST 20 is only written to the disc on
a satisfactory exit from ANISO.
QUIT
This directive abandons the calculation without modifying the disc LISTs.
AXES
This instruction (like \AXES) computes the principal axis lengths
and directions for the atoms specified on a preceeding ATOM card.
DISTANCES DL= AL=
This card calculates all interatomic distances less than
DL angstroms with librational corrections. If this directive is omitted,
no distances are calculated; if DL is absent, a default value of 1.8 is
inserted. If AL is present, angles between atoms separated by less than AL
angstroms are computed.
ANGLES AL=
This card calculates angles between all bonds less than AL angstroms. If this directive is omitted, no angles are calculated; if AL is absent, a default value of 1.8 is inserted.
*********************** WARNING *************************
The directive DISTANCE may only be followed by ATOM, EXECUTE, or END.
\ANISO ATOMS O(12) UNTIL LAST AXES TLS DISTANCES END
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.9: Principal atomic displacement directions - \AXES
\AXES INPUTLIST= END \AXES END
This routine calculates the magnitudes and directions of the principal axes of the atomic dispacement ellipsoid of an anisotropic atom. Atoms which are isotropic are ignored. Atoms with a negative principal axis generate a warning. The output gives the mean square displacement in angstroms squared along each of the principal axes, together with the direction cosines with respect to the orthogonalized axes and with respect to the real cell axes.
This routine can also be called from \ANISO to get the axes of specified
atoms only.
\AXES INPUTLIST=
This instruction initiates the routine for calculating the
principal atomic vibration directions, and requires no other directives.
INPUTLIST=
5 - Default value
10
The default value is 5.
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.10: Publication listing of the atomic parameters - \PARAMETERS
\PARAMETERS LAYOUT INSET= ATOM= DOUBLE= CHOOSE= FLOAT= NCHAR= NLINE= LISTAXES= COORDINATES NCHAR= NDECIMAL= SELECT= TYPE= DISPLAY= PRINT= PUNCH= U'S NCHAR= NDEC= SELECT= TYPE= DISPLAY= PRINT= PUNCH= END
\PARAMETERS LAYOUT ATOM-NAME=6,DOUBLE=YES END
This routine sends the atomic parameters to the PUNCH file in a suitable format for publication or binding into a thesis. As well as the current atomic parameters in LIST 5, the estimated standard deviations derived from the least squares normal matrix are also printed. THIS ROUTINE WILL NOT WORK if LIST 5 is modified in any way since the last round of refinement. If any changes, including renaming, are made, a futher round of refinement must be done. If you wish to preserve parameter values, and create a valid matrix without changing the parameter values, compute a refinemnt cycle but set all the shifts to zero.
\SFLS
REFINE
SHIFT GENERAL = 0.0
END
The output is in two halves, the first containing the positional coordinates and any isotropic temperature factors, and the second containing all the anisotropic temperature parameters.
For the first part, a page is split into 6 separate fields. The first field is blank, and is an offset so that the information is centred on the page. The remaining fields contain the atom type and serial number, the three positional parameters, and a temperature factor. This will be the value of U(iso) with its e.s.d for isotropic atoms, otherwise U(equiv), without an e.s.d, for anisotropic atoms. U(equiv) is not simply related to the diagonal elements of U(aniso), and may be computed as either the arithmetic or geometric mean of the principal axes of the ellipsoid. See \SET UEQUIV in the chapter on IMMEDIATE commands. The width of each type of field may be altered by the user, using respectively the INSET , ATOM-NAME , and NCHARACTER parameters. The default length of a page of this type of output is that required for A4 paper.
The second part contains the anisotropic temperature factors, and each page is split into eight fields. As for the atomic coordinates, the first field is blank and represents an offset. The second field contains the atom type and serial number, and the remaining six fields contain the components of the anisotropic temperature factors. The width of each type of field may be adjusted by the user, using respectively the INSET , ATOM-NAME and NCHARACTER parameters. If a different value for INSET or ATOM-NAME is required in the first and second parts of the output, the job must be run twice. Depending upon the width across the page, the second part of the output occupies one sheet of A4 paper either across the page or down the page.
For both types of output, the user can select double spacing down the page with the DOUBLE parameter. Similarly for each of the numeric fields, the user can choose the number of decimal places to be printed (the NDECIMAL parameter), and whether the numbers are printed as integers or in floating point with a decimal point. (The FLOATING parameter). The e.s.d.'s are printed to the same accuracy as the atomic parameters, so that if the chosen field is too small and an e.s.d. appears to be zero, it will be omitted in exactly the same way as for a parameter that has not been refined. A parameter printed with 4 decimal places might thus appear as :
0.0123(4)
OR
123(4)
Depending upon the format. In either case, the numbers are right justified in their field.
As an alternative to the user selecting the number of decimal places that should be printed, it is possible to get the program to choose the number of decimal places required for each parameter automatically. (The CHOOSE parameter). If the parameters are to be printed in floating point, the number of decimal places is chosen so that the e.s.d. Can be represented as a one digit number in the last decimal place. For numbers that are to be printed as integers, the field used is never less than that given by the NDECIMAL parameter. If the required field is larger than that defined by these instructions, a decimal point is inserted and the required number of extra digits is output. For example, if the number of decimal places required is four, but the e.s.d. is too small, it would appear as :
0.12345(6) OR 1234.5(6)
Depending upon whether floating point or integer output was required. For either type, if the parameter has not been refined, the number of decimal places is that given by the NDECIMAL instruction.
Since this routine prints the e.s.d.'s, it is vital that the least squares matrix (LIST 11) belongs to the current LIST 5. If LIST 5 has been modified in any way since the last Least Squares, this routine will abort.
When anisotropic atoms are present in LIST 5, U[EQUIV] is calculated
according to the current setting of \SET UEQUIV.
\PARAMETERS
This command initiates the routines for printing of the atomic
parameters in a suitable format for publication.
LAYOUT= INSET= ATOM= DOUBLE= CHOOSE= FLOAT= NCHAR= NLINE= LISTAXES=
This directive defines how the atomic parameters, both positional
and thermal, are to be laid out on the page.
INSET
This parameter sets the number of blank spaces on each line before the
atom type and serial number. If this parameter is omitted
a default value of 1 is assumed.
ATOM-NAME
This parameter sets the width of the field that contains the atom
type and serial number.
The characters are left justified in the field, and the format is
as follows :
TYPE(SERIAL)
The serial number is printed as an integer, and the unoccupied
spaces are filled with blanks.
If this parameter is omitted, a default value of 6 is assumed.
DOUBLE
This parameter has two possible values :
NO - DEFAULT VALUE
YES
If DOUBLE is YES each line of parameters is double spaced.
The default option if this parameter is omitted is single
spacing, with no interleaving blank lines.
CHOOSE
This parameter has two possible values :
NO
YES - DEFAULT VALUE
If CHOOSE is YES the program chooses the number of decimal places that
need to be printed for each parameter, depending upon its e.s.d..
The format of the output depends upon whether a decimal point
is being used, as explained above.
FLOATING
This parameter has two possible values :
YES - DEFAULT VALUE
NO
If FLOATING is NO , the parameters are printed as integers,
with an accuracy given either by the NDECIMAL parameters
to the directives COORDINATES and "U'S, or by the 'CHOOSE' parameter.
parameter.
NCHARACTER
This parameter indicates the total number of printing positions
on the output device.
If this parameter is omitted, a default value of 118 is assumed.
NLINE
This parameter indicates the total number of lines on the
on the output media. Set a very lartge value (1000) to get continuous
output.
LISTAXES
This parameter can have two values
YES
NO - DEFAULT VALUE
If the value is YES the principal axes of the temperature factors
are printed.
COORDINATES NCHAR= NDECIMAL= SELECT= TYPE= DISPLAY= PRINT= PUNCH=
This directive defines how the positional coordinates are to be
set out on the page.
NCHARACTER
This parameter sets the width of the field that contains the
positional coordinates. The characters are right
justified in the field, and if this parameter is omitted,
a default value of 14 is assumed.
NDECIMAL
This parameter sets the number of decimal places to be printed for
the positional parameters.
It may be partially or completely overriden by the CHOOSE
parameter, depending upon the format of the output.
If this parameter is omitted, a default value of 4 is assumed.
SELECT
This parameter selects the kinds of data to be printed, and
can have five values.
ALL - Default. All atoms are printed.
NONE - No atoms are printed.
ONLY - Only atoms with TYPEs given on a TYPE card are printed.
EXCLUDE - Atoms with TYPEs given on a TYPE card are not printed.
SEPARATE- Atoms with TYPEs given on a TYPE card are printed separately
TYPE
Used in conjunction with SELECT to determine which atom types to
INCLUDE,EXCLUDE or SEPARATE. TYPE is ignored if SELECT is ALL or NONE.
Its default value is 'H'.
DISPLAY
This parameter has two possible values
NO No output is displayed on the terminal. YES Output is displayed on the terminal.
PRINT This parameter has two possible values
NO No output is sent to the listing file YES Output is sent to the listing file
PUNCH This parameter has three possible values
NO No output is sent to the punch file YES Output is sent to the punch file CIF Output is in CIF format
U'S NCHAR= NDEC= SELECT= TYPE= DISPLAY= PRINT= PUNCH=
This directive defines how the thermal parameter are to be
set out on the page.
NCHARACTER
This parameter sets the width of the field that contains the thermal
parameters. The characters are right justified in the field, and
if this parameter is omitted, a default value of 11 is assumed.
NDECIMAL
This parameter sets the number of decimal places to be printed for
the thermal parameters.
If this parameter is omitted, a default value of 4 is assumed.
SELECT
This parameter selects the kinds of data to be printed, and
can have five values.
ALL - Default. All atoms are printed.
NONE - No atoms are printed.
ONLY - Only atoms with TYPEs given on a TYPE card are printed.
EXCLUDE - Atoms with TYPEs given on a TYPE card are not printed.
SEPARATE- Atoms with TYPEs given on a TYPE card are printed separately
TYPE
Used in conjunction with SELECT to determine which atom types to
INCLUDE,EXCLUDE or SEPARATE. TYPE is ignored if SELECT is ALL or NONE.
Its default value is 'H'.
MONITOR
This parameter has two possible values
OFF No output is displayed on the terminal. HIGH Output is displayed on the terminal.
PRINT This parameter has two possible values
NO No output is sent to the listing file YES Output is sent to the listing file
PUNCH This parameter has three possible values
NO No output is sent to the punch file YES Output is sent to the punch file CIF Output is in CIF format
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.11: Publication listing of reflection data - \REFLECTIONS
\REFLECTIONS LAYOUT NCOLUMNS= NLINES= INSET= NSPACE= SCALE= NCHARACTER= OUTPUT PRINT= PUNCH= LIST28= END
This routine prints the reflection data in LIST 6 in a suitable format for publication or binding into a thesis. The information printed falls into one or more columns, each of which contains h, k, l, /Fo/, /Fc/, and the phase angle in degrees. Each column is 18 characters wide. Although the user has no control over the contents of each column, it is possible to vary the number of blank spaces at the start of each line, the number of columns across the page, the number of spaces between successive columns, and the number of lines per page. (The INSET , NCOLUMNS , NSPACE and NLINES parameters, respectively). /Fo/ and /Fc/ are both put on the same scale of /Fc/, using the scale factor in LIST 5, and both these two numbers may be modified by a scaling constant before they are printed. (The SCALE parameter). However, all the values of both /Fo/ and /Fc/ must be less than 10000 when they are printed.
LIST 28 is used for checking whether or not to print a reflection. Remember
that if LIST 28 was used to reject some reflections when structure factors
were last calculated, removing these restrictions before printing LIST 6
will mean that some reflections will have incorrect values of Fc and phase.
\REFLECTIONS
LAYOUT NCOLUMNS= NLINES= INSET= NSPACE= SCALE= NCHARACTER=
This directive defines how the reflection data is to be printed.
NCOLUMNS=
This parameter indicates the number of columns of reflection data to be
printed across the page. If this parameter is omitted, a default value of
3 is assumed.
NLINES=
This parameter indicates how many lines should be on each page of output.
If this parameter is omitted a default value of 52 is assumed.
INSET=
This parameter indicates how many blank spaces should be inset at
the beginning of each line. If this parameter is omitted a default value
of 30 is assumed.
NSPACE=
This parameter indicates the number of spaces separating successive
columns across the page. If this parameter is omitted a default value
of 3 is assumed, which means that each column occupies 21
characters across the page.
SCALE=
This parameter indicates the scaling constant by which /Fo/ and /Fc/
should be multiplied before they are printed,
after they have been put on the same scale (the scale of /Fc/).
If this parameter is omitted, a default value of 10 is assumed.
NCHARACTER=
This parameter indicates the total number of printing positions
on the output device.
If this parameter is omitted, a default value of 120 is assumed.
OUTPUT PRINT PUNCH LIST28
This directive defines where the reflection data is to be printed.
PRINT=
This has two allowed values :-
NO No output is sent to the listing file YES Output is sent to the listing file
PUNCH= This has two allowed values :-
NO No output is sent to the punch file
YES Output is sent to the punch file
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.12: Summary of data lists - \SUMMARY
\SUMMARY OF= TYPE= LEVEL= \SUMMARY LIST 5 HIGH END \SUMMARY EVERYTHING END
This command produces a summary on the terminal of the contents of a
list. Use \PRINT if you need full details.
\SUMMARY OF= TYPE= LEVEL=
OF
LIST Default, also requires TYPE to be set
EVERYTHING
The value EVERYTHING generates a summary of all LISTS.
TYPE
This parameter requires a list type number if the previous parameter
was 'LIST"
LEVEL
Some lists may be listed in more or less detail.
OFF
LOW
MEDIUM Default
HIGH
\SUMMARY 6
Unlike all the other SUMMARIES, which only generate readable output,
SUMMARY 6 computes the conventional R on the basis of the current Fo, Fc
and LIST 28, and updates the value stored in LIST 6 and LIST30. The
weighted R is not affected.
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.13: CIF lists - \CIF
\CIF
There are no qualifiers.
See \PARAMETERS and \REFLECTIONS for the CIF printing of parameters
and reflections .
CheckCIF
CheckCIF and other validators are continuously updated to meet the
changing needs of the community. It is unlikely that a CRYSTALS .cif
will pass all checks first time, and edits may be necessary to
accomodate special situations. Some of these have been forseen, and the
.cif contains possible alternative texts as 'comments'. These can be
found by searching for the text 'choose'.
References
The SCRIPT directory contains two text files that contain information
coppied intoi the cif file. The user may edit them.
Refcif.dat
This file is copied in its entirety to the head of the cif file. If
it is edited, care must be taken to follow the rules about text
delimiters.
Reftab
This is a loosely formated file containing the references to be
transcribed into the cif.
Every reference is composed of 2 parts - a short text used as a data item in the cif, and the full reference. The two parts must be kept together, be separated from each other by a blank line, and be separated from any other item by a blank line.
n a four-digit number giving the number of references to follow.
Other text on the line is ignored.
Next items repeated 'n' times:
m a three digit number preceeded by a 'hash' symbol used as an
identifier for the reference. The numbers must be unique, not
necessarily in any order, with the largest one equal to 'n'
The full reference. References are put in the file in alphabetic
order.
Items 001 to 004 are associated with the keywords 'unknown' for the corresponding items in LIST 30, and thus enable the user to insert their own references. Don't forget to move tem to their correct alpabetical place.
e.s.d.s The esds output in CIF files try to follow the 'Rule of 19', as requesed by Acta Cryst. Syd Hall, Editor for Acta C, summarised the rule as follows:
'This method of handling the su (esd) values has been in force with Acta since about 1984 apparently. In my time it came up for discussion about two years ago (1996) and after much to-ing and fro-ing it was readopted as the preferred level of precision for su's.
What it means is as follows....
(1) if one adopts esd values to one digit precision (rule of 9) the values
5.548(1) 1.453(2) 3.921(3) 1.2287(8) are acceptable.
(2) if one permits two digits precision with a limit of 19 (rule of 19)...
5.5483(9) 1.4532(16) 3.921(3) 1.2287(8) are acceptable.
(3) if one permits two digits precision with a limit of 29 (rule of 29)...
5.5483(9) 1.4532(16) 3.9214(28) 1.2287(8) are acceptable.
The object of this approach is to provide a more consistent distribution of precision across all values. These particular matters are not really my responsibility but we try to conform to recommendation of the nomen- clature people. This is one such occasion.'
[Top] [Index] Manuals generated on Wed Jun 6 2001
9.14: Graphics - CAMERON
\CAMERON
This command starts the graphics program 'CAMERON' which is described in a separate MANUAL, and has an on-line help system. On exit from CAMERON the file CAMERON.L5 contains the atoms last displayed by CAMERON. Be careful - it could be a packing diagram!