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Crystals ManualChapter 9: Analysis Of Results
[Top] [Index] Manuals generated on Wednesday 27 April 2011 9.1: Scope of this section of the user guideAnalysis of residuals ANALYSE Distance and angles calculations DISTANCES Void search VOIDS Global Geometry (planes,lines & libration) GEOMETRY Torsion angles TORSION Absolute Configuration TON 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 Wednesday 27 April 2011 9.2: Analysis of residuals  \ANALYSEThis analyses the residual, FoFc, 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 Wednesday 27 April 2011 9.3: Distance angles calculations  \DISTANCES\DISTANCES INPUTLIST= OUTPUT MONITOR= LIST= PUNCH= HESD= SELECT ALLDIST= COORD= SORTED= TYPE= RANGE= SYMM= TRANS= 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 (see section 4.18 for input details), 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 distanceangles 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 (see section 7.51), and as many variance and covariance terms as are present are used. (For a full matrix, therefore, the full variancecovariance 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 variancecovariance matrix
for the cell parameters (LIST 31, section 4.5) may also be used.
\DISTANCES INPUTLIST=
INPUTLIST=
5  Default value 10
OUTPUT MONITOR= LIST= PUNCH= HESD=
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
PUNCH=
This controls the output sent to the 'punch' file.
PUBLISH  Produce a listing suitable for publication. HTML  Produce an HTML format listing CIF  Produce a listing in CIF format. HCIF  Produce a listing of the Hbonds in CIF format. SCRIPT  Lists bonds in a easily machine readable format. RESTRAIN  Produce a proforma LIST 16 (restraints  7.17). Use the RANGE, LIMIT, TYPE INCLUDE and EXCLUDE parameters to restrict the restraints produced. DELU  Proforma LIST 16 for delta U restraints SIMU  Proforma LIST 16 for Usimilarity restraints NONBONDED  Proforma LIST 16 with antibumping restraints HRESTRAIN  Produces a list of HC,N and O distance and angle restraints in the PUNCH file, and a list of the referenced H atoms in the SCRIPTQUEUE file. HRIDE  Produces a list of HC,N and O RIDE instructions. HCIF  Puts hydrogen bond donor and acceptors into the cif file. If hydrogen atom restraints are being generated, the following target values are used: No.H No.H U mult dist CH >4 1.5 .96 disorder 1 1 1.2 .93 C CH (acetylene) 1 2 1.2 .93 CC(H)C 1 3 1.2 .98 (C)3CH 2 1 1.2 .93 C=CH(2) 2 2 1.2 .97 (C)2C(H)2 3 1 1.5 .96 CC(H)3 NH >4 1.5 .89 NH4 or disorder 1 1 1.2 .86 NN/H 1 2 1.2 .86 (C)2NH 1 3 1.2 .89 (C)3NH 2 1 1.2 .86 CN(H)2 2 2 1.2 .89 (C)2N(H)2 3 1 1.2 .89 CH(H)3 OH 1 1 1.5 .82 OH Dist esd = 0.02 Vib esd = 0.002 Angle esd = 2.0
HESD=
This controls the output of ESDs to the CIF file.
ALL  (Default) Output all bond length and angle standard uncertainties (if requested) to the CIF (if requested), including those of bonds to fixed atoms (i.e. to atoms on special positions, or to atoms that are not refined). NONFIXED  Exclude standard uncertainties of bond distances and angles to Hydrogen atoms that have not been refined. (as required by Acta's notes for authors).
SELECT ALLDIST= COORD= SORTED= TYPE= RANGE= SYMMETRY= TRANS=
ALLDISTANCES=
NO  Default value YES
COORDINATES=
NO  Default value YES
SORTED=
NO  Default value YES
TYPE=
This parameter indicates the type of distances which will be
calculated.
ALL  Default value INTRA INTER
RANGE=
This parameter defines how the range is to be selected.
Except when RANGE = LIMITS (when the lowest acceptable distance is
userspecified) 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 specified or default ranges set by the LIMIT directive.
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 preceding 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
CELL=
NO  Default value YES
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 nonincluded 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 Wednesday 27 April 2011 9.4: Distanceangles symmetry operationsAccompanying 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 Wednesday 27 April 2011 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.
\VOIDS INPUTLIST=
INPUTLIST=
5  Default value 10
DISTANCE value
This sets the radii of the known 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 pseudoatom contacts required 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 regroup the pseudoatoms, and
the augmented structure can be viewed in CAMERON.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 9.6: TLS analysis, best planes and lines  \GEOMETRY\GEOMETRY INPUTLIST= ATOMS W(1) SPECIFICATION(1) W(2) SPECIFICATION(2) . PLANE LINE AXES TLS EXECUTE EVALUATE ATOM SPECIFICATIONS . . . . REPLACE ATOM SPECIFICATIONS . . . PUNCH SAVE DIHEDRAL NP(1) AND NP(2) QUIT CENTRE X=, Y=, Z= REJECT NV= LIMITS VALUE= RATIO= MODL L(11), L(22) L(33) L(23) L(13) L(12) MODT T(11), T(22) T(33) T(23) T(13) T(12) ZEROS DISTANCES DL= AL= ANGLES AL= PLOT END
\GEOMETRY ATOMS FIRST UNTIL LAST PLANE EXECUTE SAVE ATOMS FIRST UNTIL LAST TLS EXECUTE ANGLE 1 AND 2 EXECUTE DISTANCES END
GEOMETRY is used for computing the following global derived parameters: Centroid (centre of gravity) Inertial Tensor Best Plane Best Line Shape Indices Principal Axes of adps Librational and Translational Thermal Tensors Dihedral Angles
It replaces the old \MOLAX, \AXES and \ANISO commands PLANE & LINE are 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, p6768. 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. Each time a line or plane is computed, the direction cosines of the relevent axis are stored as AXIS number 'n'. The dihedral 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.Chem.Soc. Dalton Trans (1991) pp 3419  3425) If the three principal axes are "big, medium, small", then
TLS. This routine calculates the overall rigidbody motion tensors T, L, S (Shoemaker and Trueblood, Acta Cryst. B24, 63, 1968) by a leastsquares 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). (See also: Johnson in Crystallographic Computing, ed R.Ahmed, Munksgaard, 1970, pp 207219) Even when the traceofS singularity has been removed, however, the nature of the rigid body problem is such that illconditioned 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. If the TLS calcuation cannot be stabilised by means of these filters, the user can modify either T, L or S directly before applying the REPLACE or PUNCH commands. Though here is some danger in this, especially if the supposed rigid group is infact flexible, it may be preferable to using a model yielding negative vibrational or librational amplitudes. The direction cosines of the principal axis of L are stored for use in interaxis angle comutations. Immediate execution of a directive can be forced by issuing an EXECUTE
directive.
\GEOMETRY INPUTLIST=
INPUTLIST=
5  Default value 10
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 directive is
encountered.
At least one ATOM directive must precede each PLANE, LINE, TLS, AXES or
PLOT directive.
An ATOM directive will overrule an immediately preceding ATOM directive. If an
input line is not long enough for the full atom list, use CONTINUE.
PLANE
This directive, (or LINE, TLS, AXES, PLOT)
must follow immediately after an ATOM directive and
causes the calculation of a least squares best plane.
LINE
This directive, (or PLANE, TLS, AXES, PLOT)
must follow immediately after an ATOM directive and
causes the calculation of a least squares best line.
AXES
This directive (like \AXES) computes the principal axis lengths
and directions for the atoms specified on a preceding ATOM directive.
TLS
This causes the TLS calculation to be initiated. It MUST have been preceded
by an ATOM directive.
EXECUTE
This forces the execution of preceding directives.
EVALUATE ATOM SPECIFICATIONS . . . .
If present, this directive
must appear after a PLANE, LINE, TLS or PLOT directive,
and causes the coordinates or adps of the atoms specified
to be calculated and printed with respect to the current axial system.
REPLACE ATOM SPECIFICATIONS . . .
if present, this directive
must appear after a PLANE, LINE, TLS or PLOT directive,
and causes the coordinates or adps of the atoms specified to be modified so
that they conform to the most recent geometry calculation.
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
GEOMETRY.
PUNCH
This directive causes the orthogonal coordinates of the atoms of any plane or
line computed or EVALUATED in subsequent tasks to be output to the 'punch'
file. For a TLS calculation, it causes a restraint list to be output
to TLSREST.DAT
SAVE
This directive is optional. If it follows a PLANE, LINE or TLS directive, it causes the latest rotation matrix and CENTRE to be stored in the appropriate position in LIST 20. If it follows an AXES directive, 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.
DIHEDRAL NP(1) AND NP(2)
If present, thus directive must follow at least
two PLANE, LINE or TLS computations.
It causes the program
to calculate the angle between the axes with serial numbers
NP(1) and NP(2) .
The AND must be present.
QUIT
This directive abandons the calculation without modifying the disc LISTs.
CENTRE X=, Y=, Z=
This directive 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
illconditioning.
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 .
MODL L(11), L(22) L(33) L(23) L(13) L(12)
This directive enables the user to change the values of the L tensor before
EVALUATING or REPLACING the Uij. The L tensor changed is that with
respect to the inertial axes and the input centre of libration. It does
not depend upon S. All six values must be given.
MODT T(11), T(22) T(33) T(23) T(13) T(12)
This directive enables the user to change the values of the T tensor before
EVALUATING or REPLACING the Uij. The T tensor changed is that with
respect to the inertial axes and the input centre of libration, NOT the
final tensor, since this involves an interaction with S and L.
All six values must be given.
DZEROS
This directive enables the user to set the S tensor to zero before EVALUATING or REPLACING the Uij. It decouples T from L. DISTANCES DL= AL=
This directive 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 directive 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.
PLOT
This obsolete directive produces a jointhedots diagram
on the monitor or printer. It (or PLANE, LINE, TLS, AXES)
must follow immediately after an ATOM directive 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.
Examples: These instructions compute a plane involving n(1),n(2),n(3) and c(1), and prints the coordinates of all the atoms with respect to this plane. The positions of the nitrogen atoms have double weight \GEOMETRY ATOMS 2 N(1) UNTIL N(3) 1 C(1) C(2) PLANE EVALUATE ALL These instructions calculate another plane, printing only the coordinates 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) DIHEDRAL 1 AND 2 END These instructions compute a TLS tensor for the specified atoms and then set up restraints to encourage the Uij to conform to a rigid body. You might want to tighten the esd in TLSREST.dat to 0.005. \GEOM ATOM ALL TLS PUNCH EVAL ALL EX END \LIST 16 \USE TLSREST.DAT END [Top] [Index] Manuals generated on Wednesday 27 April 2011 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 jk is the angle the bond kl 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 (space
group information, see section 4.8)
\TORSION INPUTLIST=
INPUTLIST
5  Default value 10
ATOMS SPECIFICATIONS
This directive specifies atoms that are to be used in the calculation
of the torsion angle. More than one ATOMS directive can be given. Each
directive 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 Wednesday 27 April 2011 9.8: Absolute Configuration  \TON\TON END
Compute the HooftStraverSpek parameter for comparisonm with the
Flack parameter
\TON
This instruction evaluates a function of (Fo+h  Foh) and (Fo+h  Foh) for all Friedel pairs. It uses LIST 7, which must be sorted to that Friedel pairs are adjacent and with the same index signs, and with a flag to indicate if the sign has been changed in 'phase'. The data is most conveniently prepared useing the SCRIPT TON towards
the end of a refinement.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 9.9: Publication listing of the atomic parameters  \PARAMETERS\PARAMETERS LAYOUT INSET= ATOM= DOUBLE= CHOOSE= FLOAT= NCHAR= NLINE= LISTAXES= ESD= COORDINATES NCHAR= NDECIMAL= SELECT= TYPE= DISPLAY= PRINT= PUNCH= U'S NCHAR= NDEC= SELECT= TYPE= DISPLAY= PRINT= PUNCH= END
\PARAMETERS LAYOUT ATOMNAME=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 further 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 refinement cycle but set all the shifts to zero. \SFLS REFINE SHIFT GENERAL = 0.0 END
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 , ATOMNAME , 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 , ATOMNAME and NCHARACTER parameters. If a different value for INSET or ATOMNAME 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)
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 s, 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)
Since this routine prints the e.s.d.'s, it is vital that the least squares matrix (LIST 11, see section 7.51) belongs to the current LIST 5 (the model parameters). 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= ESD=
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.
ATOMNAME
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. ESDS
This parameter can take 3 values
NO YES  DEFAULT VALUE EXCLRH EXCLRH inhibits printing the e.s.ds for riding hydrogen atoms 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 directive are printed. EXCLUDE  Atoms with TYPEs given on a TYPE directive are not printed. SEPARATE Atoms with TYPEs given on a TYPE directive 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 directive are printed. EXCLUDE  Atoms with TYPEs given on a TYPE directive are not printed. SEPARATE Atoms with TYPEs given on a TYPE directive 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
[Top] [Index] Manuals generated on Wednesday 27 April 2011 9.10: Publication listing of reflection data  \REFLECTIONS\REFLECTIONS INPUT= LAYOUT NCOLUMNS= NLINES= INSET= NSPACE= SCALE= NCHARACTER= OUTPUT PRINT= PUNCH= LIST28= END
This routine prints the reflection data in LIST 6 (section 5.3) 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 INPUT=
INPUT
Indicates which reflection list to use.
6 Default 7 Alternative reflection list
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
[Top] [Index] Manuals generated on Wednesday 27 April 2011 9.11: 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
[Top] [Index] Manuals generated on Wednesday 27 April 2011 9.12: Estimation of Absolute configuration  \TONSPEK\TONSPEK CRITERION= INPUT= PLOT= END
This routine contains code kindly donated by Ton Spek for the computation of the Hooft 'y' parameter. Rob W. W. Hooft, Leo H. Straver and Anthony L. Spek, J. Appl. Cryst. (2008). 41, 96–103. It required the current LIST 6 to be comverted to a LIST 7 in which Friedel pairs are adjacent and in which Fc has been computed with the Flack 'x' parameter set to zero. The prepreparation for using this routine has been packaged into a
script available from the Analyse menu. The current value of the
Flaxk paraemter should already be stored in LIST 30.
\TONSPEK CRITERION= INPUT= PLOT=
CRITERION
If the Friedel Difference exceeds CRITERION times its standard deviation
the difference is regarded as improbably large, and the reflection is
excluded from the calculation. The default value of 999.9 effectively
includes almost all reflections.
INPUT
Indicates which reflection list to use.
6 Default 7 Alternative reflection list
[Top] [Index] Manuals generated on Wednesday 27 April 2011 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
accommodate special situations. Some of these have been foreseen, 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
copied into 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 formatted 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 fourdigit 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 preceded 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.
e.s.d.s
The esds output in CIF files try to follow the 'Rule of 19', as
requested by Acta Cryst.
Syd Hall, former 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 toing and froing 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.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 9.14: Graphics  CAMERONCAMERON
The graphics module CAMERON is part of the graphical user interface, and can only be started from the GUI. Like CRYSTALS, a subset of the possible commands are packaged up into menus, but the advanced full potential is still available from the command line. There is a separate guide for CAMERON On exit from CAMERON the current image of the structure is padded back to
CRYSTALS in the file CAMERON.L5.
This contains all and only the atoms last displayed by CAMERON.
Be careful 
it could be a packing diagram!

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