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Crystals ManualChapter 5: Reflection Data Input
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.1: Scope of the Reflection Data Input section of the Reference ManualThe areas covered are: Reflection Data Simple input of F or Fsq data - \LIST 6 Advanced input of F or Fsq data - \LIST 6 Reflection Parameter Coefficients Storage of reflection data Compressed reflection files Intensity data - \HKLI Standard Decay Curves - \LIST 27 Data Reduction - \LP Systematic absence removal - \SYSTEMATIC Sorting data - \SORT Merging equivalent reflections - \MERGE Theta-dependent absorption correction - \THETABS [Top] [Index] Manuals generated on Wednesday 27 April 2011 5.2: Reflection DataFormat of reflection data
The reflection data may be embedded into the control data, but it
is more normal to hold it in a separate file, the HKLI file. This file
may have one of more reflections per line, or a reflection may span
several lines. The parameters for each reflection may be in fixed
format, i.e. right adjusted columns, or be in free-format, with
at least a single space separating items.
If fixed-format input is used, the user must supply a FORTRAN format statement. This specifies the width of the input fields, where the decimal points are, and any fields to be skipped. Even though the indices are usually integer values, CRYSTALS read them as floating point numbers. A FORTRAN 'I' format is automatically changed to an 'F' format. Note that if the input figures contain decimal points, these will over-ride values given in the format statement.
Examples - ^ represents a space.
FORMAT (3F4.0, 2F8.2) ^^^1^^12^^^3^^^47.23^^^^9.32
FORMAT (3I4, 2F8.2) ^^^1^^12^^^3^^^47.23^^^^9.32
FORMAT (3F4.0, 2F8.0) ^^^1^^12^^^3^123456.^^312.16
FORMAT (3F4.0, 3X,2F8.0) ^^^1^^12^^^3ABC^123456.^^312.16
Termination of reflection data
The reflection data themselves should be terminated with a
value less than or equal to -512 for the first value on the
final input line.
If the reflections are embedded into the control data, then correct termination is vital. Incorrect termination may lead to the program trying to read commands as reflections, producing massive error files. If the reflections are in the HKLI file, most implementations will detect the end-of-file and terminate input. F or Fsq?
CRYSTALS will accept either F or Fsq observations, signed or unsigned.
Either quantity is referred to by the name 'Fo'. If sigma values
are given, they must refer directly to the signed input F or Fsq values.
reflections are stored as Fo, and standard deviations are
transformed or approximated so that Least-Squares refinement
can be performed with either F or Fsq independent of input type. Raw
intensities, I, can be input with the HKLI command. The reflection
input routines (LIST 6 or HKLI) are the only routine able to take the
square root of the observation. See the chapter on refinement for a
brief discussion of the merits of F and FSQ refinements.
Merged or unmerged data?
CRYSTALS supports two levels of merging (averaging) simultaneously.
For Fourier syntheses it is important that all symmetry operations of
the Laue Group are applied, including Friedel's Law. For refinement it
is permitted to used un-merged data, though in general some merging is
performed. For non-centrosymmetric structures containing strong
anomalous scatterers
Friedel pairs should be kept separate, but other symmetry operations
should be applied.
The reflection list with the minimal amount of merging is the
principal reflection list, LIST 6 (section 5.3). This can
be used to create
a full-merged list for Fourier (or other) calculations, LIST 7
(section 5.4).
The user can indicate to most commands which use reflections whether
to use LIST 6 or LIST 7, but by default all use LIST 6 for backwards
compatibility.
Fourier Maps
Slant Fourier Maps
Superflip Structure Solution
The Hooft/Straver/Spek configuration parameter
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.3: Simple input of F or Fsq data - LIST 6LIST 6 will accept reflection data either as F or Fsq. For routine work, a pre-specified set of coefficients
h k l Fobs sigma(Fobs)
\LIST 6 READ F'S= FORMAT EXPRESSION= END
\ The OPEN command connects the reflection file \OPEN HKLI REFLECT.DAT \LIST 6 READ F'S=FSQ FORMAT (3F4.0, 2F8.0) END \ Close the reflection file \CLOSE HKLI
READ F'S=
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
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.4: Creation of LIST 7 from LIST 6 - COPY 6 7This 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 \COPY INPUT= OUTPUT= END
\COPY 6 7 END
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.5: Printing LIST 6The reflections can be output to listing file as follows : \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.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.6: Punching LIST 6LIST 6 can be punched as an ASCII file in several formats. \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. F's
C - Output stored information in tabulated format.
D - Output original information in tabulated format.
E - Output the reflections in 'cif' format. F^s, scale of Fo
F - Output Fo, sigma information in SHELX format.
G - SHELX output with statistically generated sigmas
H - Output the reflections in 'cif' format. F^s, scale of Fc
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.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.7: Advanced input of F or Fsq data - LIST 6LIST 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. \LIST 6 READ NCOEFFICIENT= TYPE= F'S= NGROUP= UNIT= CHECK= INPUT COEFFICIENT(1)= COEFFICIENT(2)= . . STORE NCOEFFICIENT= MEDIUM= APPEND= OUTPUT COEFFICIENT(1)= COEFFICIENT(2)= . . FORMAT EXPRESSION= MULTIPLIERS VALUE= MATRIX M11= M12= ... M33= TOLER= TWINTOLER= END
\ The OPEN command connects the reflection file \OPEN HKLI REFLECT.DAT \LIST 6 READ NCOEF=5 TYPE=FIXED UNIT=HKLI F'S=FSQ FORMAT (3F4.0, 2F8.2) INPUT H K L /FO/ SIGMA(/FO/) STORE NCOEF=7 OUTPUT INDICES /FO/ SQRTW /FC/ BATCH/PHASE RATIO/JCODE SIGMA(/FO/) END \CLOSE HKLI
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
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.
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. COEFFICIENT(1)= COEFFICIENT(2)=
Defines the coefficients and their input order. The coefficients must be
selected from the following list
H K L /FO/
SQRTW FCALC PHASE A-PART
B-PART TBAR FOT ELEMENTS
SIGMA(F) BATCH INDICES BATCH/PHASE
SINTH/L**2 FO/FC JCODE SERIAL
RATIO THETA OMEGA CHI
PHI KAPPA PSI CORRECTIONS
FACTOR1 FACTOR2 FACTOR3 RATIO/JCODE
STORE NCOEFFICIENT= MEDIUM= APPEND=
NCOEFFICIENT=
Specifies the number of coefficients to be stored per reflection. A list
of permitted coefficients is given above. If this directive is omitted,
the default is 9.
The default output coefficients are
INDICES /FO/ SQRTW /FC/ BATCH/PHASE RATIO/JCODE SIGMA(/FO/)
CORRECTIONS ELEMENTS
MEDIUM
This parameter sets the output reflection storage device. This can be a
text file, but more normally it is the database, the '.dsc' file.
See section 5.9 - 'Storage of Reflection Data'.
FILE A named or scratch ASCII serial file
INPUT A file of the same type as the input reflection source
DISK - Default - The current structure database
APPEND=
This parameter determines whether the input reflections are to replace
or be appended to existing reflections.
YES The input reflections are appended to existing reflections
NO - Default - The input reflections replace any existing reflections
OUTPUT COEFFICIENT(1)= COEFFICIENT(2)= . .
This directive defines the coefficients that are to be stored.
The number of coefficients is given by the NCOEFFICIENT parameter
above, or its default value, and the coefficients selected from the list
above.
FORMAT EXPRESSION=
This directive allows the user to define a format statement if fixed format input is being used. This directive is only valid if the TYPE parameter on the READ directive is FIXED . EXPRESSION=
This parameter defines the format to be used.
Normally this keyword is omitted, so that the directive looks
like a FORTRAN format statement, except that there must be at least
one space between the 'FORMAT' and the expression, to terminate the
directive.
Since all the data are read as real numbers, the format expression
can only contain F , E , and X field definitions - either find a good
Fortran reference book for examples, or ask someone who did
crystallography before 1990.
MULTIPLIERS VALUE=
This directive allows the user to define the multipliers to be applied to the data if they are being read in compressed format. This directive is only valid if the TYPE parameter on the READ directive is COMPRESSED . VALUE=
This parameter, whose default value is unity,
is repeated the number of times specified by the NCOEFFICIENT parameter
on the READ directive.
The order is the same as the INPUT coefficients.
MATRIX M11= M12= ...M33= TOLER= TWINTOLER=
This directive inputs a matrix to be applied to the reflection indices as they are read in. If any component of the index differs by more than TOLER from an integer, the reflection is rejected. TWINTOLER is a value, in A-2, for overlap of potentially twinned reflections. See the chapter on twinning (10.0). Mij=
The 9 elements (by row) of an index transformation matrix. The default
is a unit matrix
TOLER=
The reflection is rejected if any transformed index differs from an
integer by more than TOLER. The default is 0.1.
TWINTOLER=
The twin element tag is updated if the generated reciprocal lattice
point differs from a base lattice point by less than TWINTOLER
reciprocal Angstrom. The default is 0.001, but an ideal value will depend
upon the integration method, the mosaicity, and the lengths of the cell
edges.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.8: Reflection Parameter CoefficientsCRYSTALS 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 below 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. JCODE valuse assigned by RC93 for MACH3 data are
1 normal reflection
9 weak reflection
7 flagged strong S but not flagged D
2 deviates from expected position/peak shape, but not W
3 failed non-equal test at least once
6 flagged weak
4 reflection is bad
8 flagged strong T but not flagged D
The order of comparisons corresponds to the order of likelihood of
having a particular code.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.9: Storage of reflection dataReflections 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: \ After data reduction, make a final copy of the reflections \ and STORE THEM IN THE .DSC FILE: \LIST 6 READ TYPE=COPY END
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.10: Compressed reflection dataCRYSTALS 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.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.11: Intensity Data - HKLIRaw 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. \HKLI READ NCOEFFICIENT= TYPE= F'S= NGROUP= UNIT= CHECK= INPUT COEFFICIENT(1)= COEFFICIENT(2)= . . STORE NCOEFFICIENT= MEDIUM= APPEND= OUTPUT COEFFICIENT(1)= COEFFICIENT(2)= . . FORMAT EXPRESSION= CORRECTIONS NSCALE NFACTOR FACTORS COEFFICIENT(1)= COEFFICIENT(2)= . . ABSORPTION PRINT= PHI= THETA= TUBE= PLATE= PHI NPHIVALUES= NPHICURVES= PHIVALUES PHI= ......... PHIHKLI H= K= L= I[MAX]= PHICURVE I= ......... THETA NTHETAVALUES= THETAVALUES THETA= THETACURVE CORRECTION= ........ TUBE NOTHING OMEGA= CHI= PHI= KAPPA= MU=A[MAX]= PLATE NOTHING OMEGA= CHI= PHI= KAPPA= MU=A[MAX]= END
\ The OPEN command connects the reflection file: \OPEN HKLI REFLECT.DAT \ The HKLI instruction reads the data in: \HKLI \ There are 12 items to read: READ NCOEF=12 FORMAT=FIXED UNIT=HKLI F'S=FSQ CHECK=NO \ This is what they are: INPUT H K L /FO/ SIGMA(/FO/) JCODE SERIAL BATCH THETA PHI OMEGA KAPPA \ And this is their format: FORMAT (5X,3F4.0,F9.0,F7.0,F4.0,F9.0,F4.0,4F7.2) \ We only want to store six of them: STORE NCOEF=6 \ Specifically, these ones: OUTPUT INDICES /FO/ BATCH RATIO/JCODE SIGMA(/FO/) CORRECTIONS SERIAL \ Some absorption corrections have been measured: ABSORPTION PHI=YES THETA=YES PRINT=NONE \ Here is the theta dependent absorption curve: THETA 16 THETAVALUES CONT 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 THETACURVE CONT 3.61 3.60 3.58 3.54 3.50 3.44 3.37 3.30 CONT 3.23 3.16 3.09 3.02 2.96 2.91 2.86 2.82 \ And here is one azimuthal absorption curve containing 26 points: PHI 26 1 PHIVALUES CONT 6 16 21 26 31 36 41 61 66 76 CONT 81 86 91 96 111 121 131 136 141 146 CONT 151 156 161 166 171 176 \ This is the reflection we used for the scan: PHIHKLI -3 -1 0 28392 PHICURVE CONT 26887 25377 24608 23990 23445 23049 CONT 22867 22801 22782 22937 23104 23368 CONT 23713 24129 25669 26836 27892 28250 CONT 28291 28256 28101 28009 28204 28373 CONT 28392 28203 END \ All done. Close the hkl file. \CLOSE HKLI
\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.
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
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)
CORRECTIONS NSCALE= NFACTOR=
NSCALE=
Set to 1 or 2 to select the first or second scale factor in LIST 27
(see section 5.12).
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
THETA=
NO - Default
YES
TUBE=
NO - Default
YES
PLATE=
NO - Default
YES
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 7.50) 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.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.12: Intensity Decay Curves \LIST 27\LIST 27 READ NSCALE= SCALE SCALENUMBER= RAWSCALE= SMOOTHSCALE= SERIAL= END
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=16 SCALE 1 1.000 1.000 1 SCALE 2 1.066 1.066 4 SCALE 3 1.074 1.053 57 SCALE 4 0.997 1.018 83 SCALE 5 1.003 1.003 564 SCALE 6 0.370 0.370 564 SCALE 7 0.372 0.371 617 END
\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. [Top] [Index] Manuals generated on Wednesday 27 April 2011 5.13: Printing the decay curve[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.14: Data Reduction - LpThis command causes the Lp correction to be calculated for each reflection. 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= END
\ Apply an LP correction for the geometry stored \ in List 13. \LP END
\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.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.15: Systematic absence removal - \SYSTEMATIC\SYSTEMATIC INPUTLIST= STORE MEDIUM= F'S= NEWINDICES= FRIEDEL= END
\ Remove systematic absences and move each hkl index \ by symmetry so that they all lie in the same part of \ the reciprocal lattice: \SYST END
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 If FRIEDEL is set to "YES", Friedel's law is applied whatever the
space group. A flag is set in the 'phase' slot for each reflcetion
to indicate if the law was invoked or not. If the data is then
sorted byt not merged, Friedel pairs will be adjacent and flagged. Use
by the function "\TON" for evaluating absolute configuration.
\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.
F'S=
FO - Default
FSQ Indicating that square roots were not taken at
input time.
FRIEDEL=
No - Default
YES Indicating that Friedels law should be applied
whatever the space group.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.16: Sorting of the reflection data - \SORT\SORT INPUTLIST= STORE MEDIUM= END
\ Sort reflections into order by L, then K, then H: \SORT END
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
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.17: Merging equivalent reflections - \MERGE\MERGE INPUT= TWINNED= STORE MEDIUM= REFLECTIONS NJCODE= LIST= LEVEL= F'S= JCODE NUMBER= VALUE= REJECT RATIO= SIGMA= WEIGHT SCHEME= NPARAMETERS= NCYCLE= PARAMETERS P ..... END
\MERGE WEIGHT SCHEME=2 NPARAM=6 PARAMETERS .5 3.0 1.0 2.0 .01 .00001 END
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 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 :
R = 100*SUM[ Sd(i) ]/SUM[ M(i) ],
where 'i' runs over all reflections.
Sd(i) = SUM[ <Fsq(i)> - Fsq(j) ],
summed over 'j' contributors.
and
M(i) = SUM[ <Fsq(i)> ],
summed 'j' times for 'j' contributors.
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 :
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.
\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.
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
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
7.40) to suppress the
use of reflections with RATIOs below a suitable threshold.
SIGMA=
1
2 - Default value
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)
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.
[Top] [Index] Manuals generated on Wednesday 27 April 2011 5.18: Theta-dependent Absorption Correction - \THETABS\THETABS THETA NTHETAVALUES= THETAVALUES THETA= THETACURVE CORRECTION= ........ END
\THETABS THETA 16 THETAVALUES CONT 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 THETACURVE CONT 3.61 3.60 3.58 3.54 3.50 3.44 3.37 3.30 CONT 3.23 3.16 3.09 3.02 2.96 2.91 2.86 2.82 END
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 7.50) will make a
good theta
approximation. See Int Tab,
Vol II, p295 and 303 for suitable profiles.
THETA NTHETAVALUES=
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.
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© 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.