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: TLS analysis, best planes and lines - \GEOMETRY
9.7: Torsion angles - \TORSION
9.8: Absolute Configuration - \TON
9.9: Publication listing of the atomic parameters - \PARAMETERS
9.10: Publication listing of reflection data - \REFLECTIONS
9.11: Summary of data lists - \SUMMARY
9.12: Estimation of Absolute configuration - \TONSPEK
9.13: CIF lists - \CIF
9.14: Graphics - CAMERON

 

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

9.1: Scope of this section of the user guide

 Analysis 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 - \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 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 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 (see section 7.51), 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, section 4.5) 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= 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


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.
HTML - Produce an HTML format listing
CIF - Produce a listing in CIF format.
H-CIF - Produce a listing of the H-bonds 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 U-similarity restraints
NONBONDED - Proforma LIST 16 with anti-bumping restraints
H-RESTRAIN - Produces a list of H-C,N and O distance and angle restraints in the PUNCH file, and a list of the referenced H atoms in the SCRIPTQUEUE file.
H-RIDE - Produces a list of H-C,N and O RIDE instructions.
H-CIF - 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
C-H
>4            1.5      .96 disorder
1      1      1.2      .93 C C-H (acetylene)
1      2      1.2      .93 C-C(H)-C
1      3      1.2      .98 (C)3-C-H
2      1      1.2      .93 C=C-H(2)
2      2      1.2      .97 (C)2-C-(H)2
3      1      1.5      .96 C-C-(H)3
N-H
>4            1.5      .89 NH4 or disorder
1      1      1.2      .86 N-N/H
1      2      1.2      .86 (C)2-N-H
1      3      1.2      .89 (C)3-N-H
2      1      1.2      .86 C-N-(H)2
2      2      1.2      .89 (C)2-N-(H)2
3      1      1.2      .89 C-H-(H)3
O-H
1      1      1.5      .82 O-H

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



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 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


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, see section 7.51) 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 Wednesday 27 April 2011

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 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


The default is to use the normal atom coordinate list.
 

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 pseudo-atom 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 re-group the pseudo-atoms, 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, p67-68.

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
Spherical = small/big Cylindrical = 1-((medium+small)/(2.big)) discoidal = 1-2.small/(big+medium)

TLS. 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). (See also: Johnson in Crystallographic Computing, ed R.Ahmed, Munksgaard, 1970, pp 207-219)

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. 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 inter-axis 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 over-rule 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 co-ordinates 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 co-ordinates 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 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 .
 

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 join-the-dots 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 co-ordinates 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 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)
 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 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 (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 Hooft-Straver-Spek parameter for comparisonm with the Flack parameter
 

\TON

 

This instruction evaluates a function of (Fo+h - Fo-h) and (Fo+h - Fo-h) 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 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 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


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 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)


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, 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.
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.
 
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


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 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


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 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
\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 (section 2.15LIST28), and updates the value stored in LIST 6 (section 5.3) and LIST30 (section 4.20). The weighted R is not affected.

 

[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, 96103. 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 pre-preparation 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



 

PLOT When called from a SCRIPT, this flag enables plotting of the data
      NO      Default value
      FOFC    Plots the observed versus the calculated Friedel difference
      NPP     Plots the Normal Probability Plot of the Friedel differences



 


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

9.13: CIF lists - \CIF

Data can be produced in CIF format for direct deposition at CCDC or submission to journals. The required information is taken from several lists, including LIST 30 (see section 4.20). F000, Mu etc are also computed and inserted in LIST 30.
 
\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 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 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.


Items 001 to 004 are associated with the keywords 'unknown' for the corresponding items in LIST 30 (see section 4.20), and thus enable the user to insert their own references. Don't forget to move them to their correct alphabetical place.

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 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 nomenclature people. This is one such occasion.'
 


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

9.14: Graphics - CAMERON


 
CAMERON
The graphics module CAMERON is part of the graphical user interface, and can only be started from the GUI. Like CRYSTALS, a sub-set 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.