Chemical Crystallography Oxford: Reflection Data Input

LIST 6 will accept reflection data either as F or Fsq. For routine work, a pre-specified set of coefficients

are input and stored for each reflection.
NOTE that 'Fobs' will refer either to F or Fsq, depending on the value of F's.
The input coefficient list may be expanded for non-routine work - see section 5.7 below.

This command creates a LIST 7 as an exact copy of LIST 6 (see 5.3). The LIST 7 can then be merged using Friedel's Law to create a reflection list suitable for Fourier syntheses

\PRINT 6 mode
Mode controls the type of output.

      A - Default - The reflections are in compressed 
                    format, on the scale of Fo.
      B -           The reflections are in compressed 
                    format, on the scale of Fc.
      C -           A general print of all the data 
                    stored for each reflection.

See also \REFLECTIONS (section 9.9), which produces tables for publication.

\PUNCH 6 mode
Mode controls the format of the output.

       A - Output the reflections in a compressed format - Default.
       B - Output the reflections in 'cif' format.
       C - Output Fo, Fc, phase information in tabulated format.
       E - Output Fo and other input information in tabulated format.

LIST 6 is also output by the links to the direct methods programs. In these files, the magnitudes of Fo or Fsq are scaled so that the largest fits the format statement. The SHELX file contains Fsq, the SIR file contains Fo.

LIST 6 will accept reflection data either as F or Fsq. The data may be in free or fixed format. For routine work, a pre-specified set of parameters is stored for each reflection. This may be expanded for non-routine work by INPUT and OUTPUT coefficients.

READ NCOEFFICIENT= TYPE= F'S= NGROUP= UNIT= CHECK=

NCOEFFICIENT= Specifies the number of coefficients to be input per reflection. A list of permitted coefficients is given below. If this directive is omitted, the default is 5.
The default input coefficients are

       H K L FOBS SIGMA(F)

TYPE= This parameter determines the form of the reflections as they are read in, and must take one of the following values :

       FIXED     -  Fixed format data
       FREE      -  Free format text  -  default value
       COMPRESSED-  See 'Compressed Reflection Data' below
       COPY      -  LIST 6 is copied from the current input device to the
                    output device designated on the STORE directive with
                    the number of coefficients given on the OUTPUT and
                    COEFFICIENT directives.

F'S= This parameter is used to indicate whether Fo or Fo**2 type coefficients are being read in, and must take one of the following values :

       FSQ
       FO   -  Default value

The default value of 'FO' indicates that coefficients corresponding to Fo are being read in.

NGROUP= This parameter defines the number of reflections per line for fixed format input. (For free format input, the system can work out this information). NGROUP will be less than unity if the reflection spans several lines.

UNIT= This parameter defines the source of the reflection data that are to be input.

       HKLI   -  Default value.
       DATAFILE

HKLI indicates that the reflection data are in a separate file from the main input data. The local implementation may set up default names for this file, or the \OPEN directive can be used to connect the file to CRYSTALS.

DATAFILE indicates that the reflections follow the directives for '\LIST 6' in the normal data input stream. If this is the case, the directives for \LIST6 must be terminated by the directive END, otherwise the reflection lines will be processed as normal directives associated with the \LIST6 command, and generate a very large number of input errors.

By default, the data are assumed to come from the alternative HKLI channel.

CHECK This parameter determines whether reflections are rejected on input if they have a zero or negative value for Fo.

       YES
       NO -  Default value.

By default checking is disabled so that negative reflections are accepted on input.

CRYSTALS has a very flexible procedure for storing reflection information, enabling the user to optimise disk space use. The user must indicate to the program what information is available in the input data, and what information is to be stored. Storage space may also be reserved for data yet to be computed.

During data reduction (section 5.14), space is reserved for relevant coefficients. These coefficients (e.g. setting angles) may not be needed during structure analysis, so they are not normally preserved beyond reduction.

Special Reflection storage

The user might need to arrange special reflection storage under the following conditions:

Refinement using a partial model

If the user is experiencing difficulties with a small part of an otherwise well behaved large structure, the real and imaginary parts of the structure factors due to the well behaved part can be precomputed and stored and these atoms removed from the atom list (LIST 5). The user then only needs recompute the contributions from the varying fragment. The total Fo, Fc, real and imaginary parts are stored with the keys

       /FO/      /FC/      APART      BPART

Twinned structures

See chapter 10.0 on handling twinned data.

Recognised reflection coefficients

  Coefficients recognised are:
  H            Reflection index h
  K            Reflection index k
  L            Reflection index l
  INDICES      Packed reflection indices
  /FO/         The observed intensity, Fsq or Fo value
  /FOT/        The observed intensity, Fsq or Fo value for a twinned crystal
  /FC/         The calculated structure factor
  SIGMA(/FO/)  Standard deviation of the input observation
  SQRTW        Sqrt of weight to be given a reflection during least squares
  A-PART       Real part of structure factor
  B-PART       Imaginary part of structure factor
  PHASE        Phase angle, radians
  BATCH        An integer associated with reflections measured in batches
  BATCH/PHASE  Packed (compressed into one word) Batch and Phase
  SINTH/L**2   (Sintheta/lambda)**2
  FO/FC        Fo/Fc
  ELEMENTS     Integers corresponding to twin elements
  SERIAL       Serial number of reflection
  JCODE        reflection quality code. See RC93 manual
  RATIO        Ratio Fo**2/sigma(Fo**2)
  RATIO/JCODE  Packed ratio and jcode
  TBAR         Absorption weighted X-ray path length
  THETA        Bragg angle
  OMEGA        Setting angle
  CHI          Setting angle
  PHI          Setting angle
  KAPPA        Setting angle
  PSI          Setting angle
  CORRECTIONS  Composite correction factor for Fo
  FACTOR1      Individual correction factor for Fo
  FACTOR2      Individual correction factor for Fo
  FACTOR3      Individual correction factor for Fo
  NOTHING      A spare location for programmers use

If an output coefficient is specified without the corresponding input coefficient, it value is set to zero except for BATCH (default is 1.0) and SINTH/L**2 (value computed from cell parameters). Packed INDICES are restricted to +/- 127, packed RATIO to range 0.0 - 999.0, JCODE to range 0 - 9.

Reflections may be stored either in the structure database (the DSC file), or as external binary serial files. The latter is used mainly during data reduction (section 5.14).

When a change is made to most other data lists, they are either completely overwritten (LIST1, cell parameters), or a new list created in addition to the old list (LIST 5, atom parameters). Because the reflections are special, they are handled differently. A small piece of information (called the LIST 6 Header) is created to hold information about the rest of the reflection list, and new headers are stored each time the main body is updated. The main body of the reflection list is modified in-situ if the only changes are ones which can easily be recomputed ( e.g. Fc, phase, sqrtw), thus reducing the disk activity. If an error occurs during the updating of the body, the list becomes inaccessible to other processes, and the failing process must be re-run correctly. If the changes involve a change in size of the list, then a new body is created.

During raw data processing (Data reduction, section 5.14) the size of the reflection list can change a lot (coefficients being added or removed, reflections being merged or rejected). To prevent the .DSC file growing too large, binary serial files are used to hold the body of the reflection list. One is used for input and one for output at each stage, the roles being reversed after each stage. The header is kept in the .DSC file, and keeps track of the bodies. When data reduction is complete, the body must be copied to the .DSC file as follows:

CRYSTALS can produce files containing reflections is a 'compressed' format. This might be useful for archiving data. The compressed data is headed by the correct information for its reinput.

The file contains information for h, k, l, /FO/ or /FOT/, RATIO/JCODE and elements. For each KL pair, the K value is given for this group of reflections, then the L value for the group, followed by the H and /FO/ and other values for the first reflection, the H /FO/ and other values for the second reflection, and so on, finishing with 512, which is the terminator for this KL pair. This pattern is repeated for all the KL pairs, the terminator for the last KL pair being -512, and indicates the end of the reflection list. Take care if you try to edit these files, and note that K and L are the two constant indices for each group, while H changes most rapidly.

Raw intensity data require more processing than F or Fsq values. The instruction '\HKLI' is related to '\LIST 6', but has different default coefficients and additional directives for geometrical corrections.

In the following description, for items defined under LIST 6 above only the default value will be given.

\HKLI

READ NCOEFFICIENT= TYPE= F'S= NGROUP= UNIT= CHECK= This directive is the same as the READ directive in \LIST 6 above, except that the following parameters have different default values:

  NCOEFFICIENT= default value is 12
  TYPE= default value is FIXED
  F'S= default value is FSQ
  NGROUP= default value is 1
  UNIT= default value is HKLI

INPUT COEFFICIENT(1)= COEFFICIENT(2)= . .

This directive defines the coefficients that are to be read in. The number of coefficients is given by the NCOEFFICIENT parameter above, or its default value.
The default input coefficients are (i.e. for RC93 output):

       H K L /FO/ SIGMA(/FO/) JCODE SERIAL BATCH THETA PHI OMEGA KAPPA

STORE NCOEFFICIENT= MEDIUM= APPEND=

NCOEFFICIENT= The number of coefficients that will appear on the OUTPUT directive. The default is 9.

MEDIUM= The default value is 'FILE'. Since the reflections will be much changed during data reduction (section 5.14), the intermediate storage is usually a scratch serial file.

APPEND= The default value is 'NO'.

OUTPUT COEFFICIENT(1)= COEFFICIENT(2)= . . The default coefficients are:

       INDICES /FO/ SQRTW /FC/ BATCH/PHASE RATIO/JCODE SIGMA(/FO/)
       CORRECTIONS ELEMENTS

Note that H, K, and L are compressed into one key: 'INDICES'.

FORMAT EXPRESSION=

This directive is only valid if the TYPE parameter on the READ directive is FIXED.

EXPRESSION= If the diffractometer type indicated in LIST 13 (section 4.13) is CAD4, the default corresponds to RC93 or RC85 output, otherwise an expression must be given.

           e.g. (5X,3F4.0,F9.0,F7.0,F4.0,F9.0,F4.0,4F7.2)

Directives found in HKLI commands, but not in LIST 6 commands are:

CORRECTIONS NSCALE= NFACTOR=

NSCALE= Set to 1 or 2 to select the first or second scale factor in LIST 27 (see section !flabel!LIST27!).! The default is 2.

NFACTOR= Up to three correction per reflection to be applied to the input observations can be included in the input file. This keyword specifies how many to use.
The default is 0.

FACTORS COEFFICIENT(1)= COEFFICIENT(2)= . . The permitted coefficients are FACTOR1, FACTOR2 and FACTOR3. These are applied to the input observation before any other action (including square rooting if requested) is performed.

ABSORPTION PRINT= PHI= THETA= TUBE= PLATE= This directive controls approximate absorption corrections to be applied during input. They are only suitable if the diffractometer used is one of those permitted in LIST 13 (section 4.13).

PRINT= Permitted levels are

       FULL                  Two lines of information per reflection
       NONE    - Default     No output is produced
       PARTIAL -             Summary for each reflection

PHI=

       NO      - Default
       YES

If YES, then phi (azimuthal scan) data must follow.

THETA=

       NO      - Default
       YES

If YES, then a theta dependent correction curve must follow.

TUBE=

       NO      - Default
       YES

If YES, then orientation angles for the tube must follow.

PLATE=

       NO      - Default
       YES

If YES, then orientation angles for the plate must follow.

PHI NPHIVALUES= NPHICURVES= If phi has been set to 'YES' above, this directive sets up input and computation of azimuthal scan absorption corrections, by the method of North, Phillips and Mathews, Acta Cryst., A24, 351 (1968).

NPHIVALUES= Number of sampling points on the phi curve. These need not be equally spaced

NPHICURVES= Number of phi curves that will be entered after this directive.

PHIVALUES PHI= ..... The 'Nphivalue' phi angles of the points on the absorption curve.

PHIHKLI H= K= L= I[MAX]= The h,k,l and Imax values for the following 'Nphicurve' phi profiles, in the same order as the profiles.

PHICURVE I= ..... The 'Nphivalue' intensity values for the profile at the phi values given on the Phivalues directive. There is a Phicurve corresponding to each PHIHKLI directive.

THETA NTHETAVALUES= If theta has been set to 'YES' above this directive sets up the input for and computation of a theta dependent absorption correction. Except when the data has been corrected by a proper analytical correction, a theta dependent correction is ALWAYS recommended, since neither a phi scan, multi-scan nor DIFABS (section 7.48) will make a good theta approximation. See Int Tab, Vol II, p295 and 303 for suitable profiles.

NTHETAVALUES= The number of sampling points on the theta curve.

THETAVALUES THETA= ..... The Nthetavalues at which the curve is sampled

THETACURVE CORRECTION= ...... The Nthetavalue values of the correction factor profile.

TUBE NOTHING OMEGA= CHI= PHI= KAPPA= MU A[MAX] If TUBE has been set to 'YES' above, this directive sets up the correction for a sample in a tube, or for an acicular crystal steeply inclined to the phi axis. See J. Appl. Cryst, 8. 491, 1975. 'NOTHING' is a place-holder for internal workings.

OMEGA= CHI= PHI= KAPPA= These are the settings needed to bring the tube axis into the equatorial plane and perpendicular to the incident X-ray beam. Only one of Chi and Kappa may be given.

MU= The product of Mu and the thickness of the tube wall.

A[MAX] The maximum permitted correction. Values greater than A[max] generate a warning.

PLATE NOTHING OMEGA= CHI= PHI= KAPPA= MU A[MAX] If PLATE has been set to 'YES' above, this directive sets up the correction for an extended plate-like sample. See J. Appl. Cryst, 8. 491, 1975. 'NOTHING' is a place-holder for internal workings.

OMEGA= CHI= PHI= KAPPA= These are the settings needed to bring the plate normal into the equatorial plane and perpendicular to the incident X-ray beam. Only one of Chi and Kappa may be given.

MU= The product of Mu and the plate thickness.

A[MAX] The maximum permitted correction. Values greater than A[max] generate a warning.

If each reflection has been assigned a serial number (or some other incrementing value, such as total X-ray exposure time) then CRYSTALS can apply a correction which is linked to this value. The corrections, on the scale of Fsq, are held in LIST 27. Two correction factors can be stored, but only one used. For example, these can be the actual corrections computed from the decay of the standard reflections, and those obtained from a 3-point smoothing of the same correction data. The applied scale factor is obtained by interpolating between those given scale factors with serial numbers above and below the serial number of the current reflection. If there is a dramatic change in scale (for example due to remeasurement of some very strong reflections with attenuated X-rays), it is important not to interpolate over this discontinuity. To achieve this, a dummy scale factor is inserted at this point with scale values the same as the current scales, but with the same serial number as the first scales after the discontinuity - for example:

\LIST 27

READ NSCALE=

NSCALE= The number of SCALE directives to follow. There is no default value for this parameter.

SCALE SCALENUMBER= RAWSCALE= SMOOTHSCALE= SERIALNUMBER=

This directive is repeated once for each scale factor that is to be read in.

SCALENUMBER= This parameter indicates the number of the scale factor, starting from one. There is no default for this parameter, which currently is not used.

RAWSCALE= This parameter gives the initial scale factor, computed directly from the intensities of the standard reflections.
There is no default.

SMOOTHSCALE= This parameter gives the scale factor after the raw scale factors have been smoothed, so that a continuous curve is fitted to all the data.
There is no default.

SERIALNUMBER= This parameter gives the serial number of the first standard reflection contributing to this scale. The data reduction programs use the SERIAL to locate the correct scales to use for a given reflection.
There is no default.

\PRINT 27

This command prints the decay curve. There is no command to punch LIST 27.

The diffraction geometry, wavelength, etc. are taken from LIST 13 (section 4.13). If LIST 13 is input incorrectly, or has to be generated by the system, the message 'illegal diffraction geometry flag' will be output and the job terminated. If the user has forced the storage of Fsq values in \HKLI, it is necessary to indicate this to the Lp correction.

\LP

STORE MEDIUM= F'S=

MEDIUM= Determines the output medium.

       FILE              A serial file
       INPUT - Default   The same as the input medium
       DISC              The .DSC file.

The default output medium is the same as te input medium - usually a serial file.

F'S=

       FO      -      Default
       FSQ            Indicating that square roots were not taken at
                      input time.

This routine uses the symmetry operators in LIST 2 (section 4.8) to identify systematic absences, which are listed and rejected. It can also use the symmetry operators to transform indices to that the reflections fall into a unique part of the reciprocal lattice. The unique set is bounded by the maximum range in 'l', maximum range of 'k' given the 'l' range, and maximum range of 'h', given the 'k,l' range.

Friedel's Law may be invoked, depending on the flag in LIST 13 (section 4.13). It is important NOT to use Friedel's Law for structures which have strong anomalous scatterers, since reflections related by Friedel's law are not equivalent in this case and should not be merged together. Similarly, if orientation dependent corrections are to be made (e.g. DIFABS),original indices should be preserved. Note that in this case, only exactly equivalent reflections will be merged, and care must be taken when computing Fourier maps. See the sections on Fourier maps, !flabel!FOURIER! and DIFABS !RDIFABS
.

\SYSTEMATIC

SYSTEMATIC INPUTLIST=

INPUTLIST= 6 OR 7

STORE MEDIUM= F'S= NEWINDICES=

MEDIUM= Determines the output medium.

       FILE              A serial file
       INPUT - Default   The same as the input medium
       DISC              The .DSC file.

The default output medium is the same as the input medium - usually a serial file.

F'S=

       FO      -      Default
       FSQ            Indicating that square roots were not taken at
                      input time.

NEWINDICES= Determines whether new indices are computed.

       YES  -  Default - Permits transformation of indices.
       NO

This routine sorts the data so that the reflections are placed in a predetermined order, in which reflections with the same indices are adjacent in the list. Upon output, the reflections are arranged so that they are in groups of constant L, starting with the group with the smallest L value. Within any L group, the reflections are ordered in groups of constant K, starting with the group with the smallest K value. Within each group of constant K and L, the reflections are arranged with the smallest H value first and the largest last in ascending order.

The method of sorting is a multi-pass tree sort, in which as many reflections as possible are held in memory during each pass. If all the reflections with a given value of L cannot be in memory at the same time, the program will terminate in error.

\SORT

STORE MEDIUM

MEDIUM= Determines the output medium.

       FILE              A serial file
       INPUT - Default   The same as the input medium
       DISC              The .DSC file.

The default output medium is the same as the input medium - usually a serial file.

The merge routine takes a list of reflections and combines groups of adjacent reflections with exactly the same indices to produce a single mean structure amplitude.

\SYST (section !flabel!SYSTEMATIC!) and \SORT (section !RSORT
) produce a suitable list, and if either of them have been omitted, it is extremely likely that the list of reflections produced by the merge process will contain duplicated entries for certain reflections.

It is possible to combine equivalent reflections in several different ways, depending upon how each individual contributor is weighted when the mean is computed. Several different weighting schemes are provided, and these are described in the next section (the WEIGHT directive).

The JCODE key in the list of reflections may be input from some diffractometers (e.g. a CAD4) to indicate that the value may be inaccurate. Reflections which have JCODES that differ from unity are thought to be inaccurate and can be down-weighted or eliminated during the merge process (the JCODE directive). Note that JCODES MUST be positive and less than 10.

Although under normal circumstances LIST 6 (reflections) contains /Fo/ data rather than /Fo/**2 data, the calculations performed during the merge are done on the scale of /Fo/**2. This means that r-values are computed which refer to /Fo/**2, and that reflections can be rejected on the basis of the ratio of /Fo/**2 to its standard deviation. If for some reason the LIST 6 contains /Fo/**2 data rather than the normal /Fo/ data, it is necessary to use the "F's" parameter of the "REFLECTIONS" directive to inform the system of this fact.

During the merge process, the system calculates and then prints a set of merging r-values, which are defined as follows :

The sum variable 'i' runs over all the reflections produced by the merge process which have more than one contributor. The sum variable 'j' runs over all the contributors for each reflection produced by the merge process. <Fsq(I)> is the mean value for the reflection 'i' , while Fsq(j) is the observed value of Fsq for the contributor 'j'.

If the crystal is twinned, this will affect the merge. See chapter on twinned crystals

If the data is in Batches with different BATCH scale factors, this will affect the merge.

WEIGHTING SCHEMES FOR THE DATA MERGE

At present there are three different weighting schemes available for merging equivalent reflections. These are :

       1.      Each reflection is given equal weight (unit weights).
       2.      Weights based on a Gaussian distribution.
       3.      W(i) = 1.0/Sigma(i)**2  for each reflection.

Unit and statistical weights (schemes 1 and 3) are more or less equivalent unless some reflections have been remeasured under very different regimes ( e.g. with an attenuator set, mA turned down, different crystal)

Scheme 2 is designed to discriminate against outliers, i.e. reflections lying farther from the mean than might be expected. For this scheme, a weighted mean value of Fsq is determined iteratively, starting from unit weights. At each iteration, the weights are recomputed to discriminate against outliers and the contributing reflections are given a new weight w(i) given by :

       w(i) = exp [ (-log(a) * q(i)**2)/(b**2 * e(i)**2) ]
 
  Where
 
      q(i)  is the deviation of the particular Fsq(i) from the current average.
      e(i)  is a predicted mean deviation of the reflection 'i' from the
            current mean and is given by a function similar to that used
            in Least Squares :

e = c + d*Sig(Fsq) + g*Sig(Fsq)*/Fo/ + h*Sig(Fsq)*Fsq
a,b,c,d,g,h are 6 input parameters provided by the user
'a' and 'b' define the Gaussian distribution.
'a' is the weight to be given to a reflection which has a deviation given by 'q(i) = b*e(i)'.
Suggested values of 'a' and 'b' are 0.5 and 3.0 respectively, so that if for example, 'e(i) = 3*Sig(Fsq)' (d=3, c=g=h=0), a deviation q(i) of 6*Sig*fsq will assign a reflection a weight of 0.5.
'c' Provides the bias necessary to allow for failures in the counting statistics at low count rates.
'd' is a scaling constant.
'g' and 'h' allow for the increased dispersion of strong reflections.

  For a conventional diffractometer, suggested values for the parameters are :
 
       a = .5      b=3.0      c=1.0      d=2.0      g=.01      h=.00001

It is recommended that the Gaussian scheme be used, as it discriminates against zero or widely dispersed intensities very efficiently.

Standard deviations produced by the merge

After the equivalent reflections have been merged two different standard deviations are computed and can be output :

  SIGMA1 = Sqrt (sum [ w(i)*q(i)**2 ] / sum [ w(i) ])
              that is, the weighted r.m.s. deviation.
 
  SIGMA2 = Sqrt (sum [ w(i)*s(i)**2 ] / sum [ w(i) ])
              that is, the weighted standard deviation.

Either of these two standard deviations can be selected as an estimate of Sigma(Fsq), and perhaps be converted to a Least Squares weight. If a reflection is measured very many times, SIGMA1 should be similar to SIGMA2. It is almost always much greater.

\MERGE

MERGE=

INPUT= Either 6 or 7. Default is 6.

TWINNED=

   NO      Treat data as un-twinned
   LIST13  Treat data according to list 13 
   YES     Treat data as twinned

STORE MEDIUM=

MEDIUM= Determines the output medium.

       FILE              A serial file
       INPUT - Default   The same as the input medium
       DISC              The .DSC file.

The default output medium is the same as the input medium - usually a serial file.

REFLECTIONS NJCODE= LIST= LEVEL= F'S=

NJCODE= Specifies the number of JCODE directives to follow - default zero.

LIST= Determines the amount of information printed during the merge process.

       OFF
       MEDIUM  -  Default value
       HIGH

If LIST is 'HIGH' , all Fsq are listed with their contributors and their deviations from the computed mean. The default value of MEDIUM indicates that the merged Fsq are listed with the contributors and their deviations from the computed mean if the r.m.s. deviation exceeds LEVEL*(mean standard deviation). HIGH is equivalent to MEDIUM with LEVEL set at zero.

LEVEL= This parameter specifies the r.m.s. deviation level above which contributors are printed if LIST is equal to MEDIUM . They are printed if sigma1 exceeds level*sigma2. The default value for this parameter is 3.

F'S=

       FO      -      Default
       FSQ            Indicating that square roots were not taken at
                      input time.

JCODE NUMBER= VALUE=

This directive allows reflections whose JCODE key differs from unity to be down-weighted or eliminated from the merge. It is repeated once for each JCODE that is read in.

NUMBER= The number of the JCODE must be given. There is no default value for this parameter.

VALUE= This is the absolute weight, associated with the JCODE number, that is given to the reflection. If this parameter is omitted a default value of zero is assumed, indicating that the reflection is to be eliminated and not included in the merge at all.

REJECT RATIO= SIGMA=

This directive causes reflections whose mean intensity is less than product of the ratio and sigma to be eliminated.

RATIO= The default value for this parameter is -10. Use LIST 28 (section 7.39) to suppress the use of reflections with RATIOs below a suitable threshold.

SIGMA=

       1
       2  -  Default value

If sigma is equal to 1 the e.s.d. is the weighted r.m.s. deviation. If sigma is equal to 2 the e.s.d. is the weighted standard deviation.

WEIGHT SCHEME= NPARAMETERS= NCYCLE=

This directive determines the weighting scheme to be used in merging equivalent reflections.

SCHEME= This parameter determines which of the weighting schemes defined above is to be used in the merging of equivalent reflections, and must take one of the following values:

       1  -  Default value (unit weights)
       2                   (modified Gaussian)
       3                   (statistical)

If this parameter is omitted, unit weights are applied (scheme=1).

NPARAMETERS= This must be set to the number of parameters required to define the weighting scheme, and thus the number of values on the PARAMETERS directive to follow. The default value for this parameter is zero, as schemes 1 and 3 require no parameters.

NCYCLE= This parameter has a default value of 5 and is the number of cycles of refinement of the weighted mean if scheme 2 is being used in the merge.

PARAMETERS P ..... This directive contains NPARAMETERS values.

P= For weighting scheme 2, these parameters give the values 'a' to 'h' defined above, and describe the form of the Gaussian distribution.

Except when the data has been corrected by a proper analytical correction, a theta dependent correction is ALWAYS recommended, since neither a phi scan multi-scan nor DIFABS (section 7.48) will make a good theta approximation. See Int Tab, Vol II, p295 and 303 for suitable profiles.

Crystals Manual

Chapter 5: Reflection Data Input

5.1: Scope of the Reflection Data Input section of the Reference Manual

5.2: Reflection Data

5.3: Simple input of F or Fsq data - LIST 6

5.4: Creation of LIST 7 from LIST 6 - COPY 6 7

5.5: Printing LIST 6

5.6: Punching LIST 6

5.7: Advanced input of F or Fsq data - LIST 6

5.8: Reflection Parameter Coefficients

5.9: Storage of reflection data

5.10: Compressed reflection data

5.11: Intensity Data - HKLI

5.12: Intensity Decay Curves \LIST 27

5.13: Printing the decay curve

5.14: Data Reduction - Lp

5.15: Systematic absence removal - \SYSTEMATIC

5.16: Sorting of the reflection data - \SORT

5.17: Merging equivalent reflections - \MERGE

5.18: Theta-dependent Absorption Correction - \THETABS