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: Least squares best planes and lines - \MOLAX

9.6: Torsion angles - \TORSION

9.7: Thermal displacement parameter analysis - \ANISO

9.8: Principal atomic displacement directions - \AXES

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: CIF lists - \CIF

9.13: Graphics - CAMERON

 Analysis of residuals                          ANALYSE
 Distance and angles calculations               DISTANCES
 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

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.
 

 

 \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
 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

      OFF         -  no output
      DISTANCES   -  only monitors distances. (Default)
      ANGLES      -  only monitors angles.
      ALL         -  monitors distances and angles.

      OFF
      LOW   -  Default
      HIGH

      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.

      NO   -  Default value
      YES

      NO   -  Default value
      YES

      NO   -  Default value
      YES

      ALL   -  Default value
      INTRA
      INTER

      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

      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.

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

      NO   -  Default value
      YES

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.
 

 
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.
 

 

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

 \MOLAX INPUTLIST=
 EXECUTE
 ATOMS  W(1)  SPECIFICATION(1)  W(2)  SPECIFICATION(2) .
 PLOT
 PLANE
 PUNCH
 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

This forces the execution of preceeding directives.
 

 
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.
 

 
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.
 

 
PUNCH

This card causes the orthogonal coordinates of the atoms of any plane or line computed in the current task to be output to the 'punch' file.
 

 
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

 \TORSION INPUTLIST=
 ATOMS  SPECIFICATIONS
 PUBLICATION  PUNCH=
 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

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 PUNCH=
 
The parameter PUNCH controls the publication listing.

      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

 \ 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

 \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

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

 \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

 \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

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)

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)

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.

 NO       No output is sent to the listing file
 YES      Output is sent to the listing file

 NO       No output is sent to the punch file
 YES      Output is sent to the punch file
 CIF      Output is in CIF format

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.

 NO       No output is sent to the listing file
 YES      Output is sent to the listing file

 NO       No output is sent to the punch file
 YES      Output is sent to the punch file
 CIF      Output is in CIF format

\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

      NO       No output is sent to the punch file
      YES      Output is sent to the punch file

 \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.
 

 

There are no qualifiers.

See \PARAMETERS and \REFLECTIONS for the CIF printing of parameters and reflections .
 

 
e.s.d.s The esds output to 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.