POINTLESS (CCP4: Supported Program)

NAME

pointless

SYNOPSIS

pointless [-c[opy]] [[HKLIN] foo_in.mtz] [XDSIN foo_in.HKL] [SCAIN foo_in.HKL] [HKLREF reference_file.mtz] [HKLOUT output_file.mtz] [XMLOUT xml_output.xml]
[Keyworded Input]

References
Input and Output files
Examples
Release Notes

DESCRIPTION

General disclaimer: this program is under continuous (or at least intermittent) development and is likely to change.

Pointless scores all the possible Laue groups consistent with the crystal class, which is based on cell dimension restraints. It does this by matching potential symmetry equivalent reflections. For chiral systems, the Laue group uniquely implies the point group. It then checks sets of reflections which may be systematically absent to suggest a possible spacegroup. There is no check for lattice centring, ie no check for whole classes of reflections having essentially zero intensity. 
[Note: strictly speaking, the program determines the Patterson group rather than the Laue group, since the Laue group is a point group, not including any lattice centring type (P,C,I,F,H,R). Lattice centring is included in the reported Laue group, and reindexing from the original setting may change the lattice type.]

The principal reflection input is taken from one or more unmerged MTZ files (HKLIN) such as those from Mosflm (or Combat), or alternatively unmerged XDS ASCII files (XDS_ASCII or INTEGRATE, XDSIN) or unmerged Scalepack files (SCAIN) (produced with the Scalepack option "nomerge original index"). Input types may be mixed.

For some crystal classes and when there is more than one input file, it is necessary to establish first that a consistent indexing convention has been used for all runs (see http://www.ccp4.ac.uk/dist/html/reindexing.html for an explanation and list). Note that if there are multiple input files and no reference file, the first input file is used as a reference for subsequent files, and this will not work correctly if this first file is indexed wrongly: the keyword TESTFIRSTFILE may be used to force a Laue group check on the first file before adding in the others.

If there is more than one input file the program checks the batch numbering schemes do not overlap, and if necessary renumbers batches.

If HKLOUT is assigned it produces a sorted reflection list (possibly after reindexing and renumbering batches) which is ready for input to SCALA.

It has other subsidiary uses described in more detail below: it can convert one format to another, check and reindex an input file to match an existing reference set of amplitudes, or apply a pre-selected reindex matrix. The command line option "-copy" (or "-c") may be used just to copy files to MTZ (equivalent to the COPY command).

Description of functions:

1. Determination of Laue group and space group (LAUEGROUP mode).

This mode is the default, if no HKLREF file is specified.

Given test data comprising unmerged observations (file(s) HKLIN, XDSIN or SCAIN), the program looks for possible symmetry based on the unit cell in order to determine the Laue group, ie the symmetry of the diffraction pattern. It then examines axial reflections (and zones for non-chiral crystals) to look for systematic absences to determine the space group.
 
If a file is assigned to HKLOUT, the reindexed file will be written out from the HKLIN file, using the selected reindexing. The hklout file is assigned to the "best" space group or point group (or the SPACEGROUP if given).

Warning Notes:

2. Testing of alternative indexing schemes (INDEX mode)

This mode is selected if an HKLREF dataset is specified.

Given a test dataset, merged or unmerged (file(s) HKLIN), and a merged or unmerged reference dataset in a known space group (file HKLREF), the program tests all possible alternative indexing schemes of the test dataset to find which one best matches the reference set. Alternative indexing schemes  arise in high symmetry space groups when the lattice symmetry is higher than the point group symmetry (eg for trigonal space groups), but may also arise in any space group from special relationships between cell parameters (eg an orthorhombic cell with a=b or more complicated examples involving cell diagonals).

If a file is assigned to HKLOUT, then the reindexed file will be written out from the HKLIN file, using the best reindexing. The hklout file is assigned to the spacegroup of the reference file.

3. Checking the centre of the diffraction pattern

It is occasionally (though rarely) possible to misindex the diffraction pattern by (say) +-1, usually on a long axis approximately parallel to the rotation axis. In this case, the centre of symmetry of the diffraction pattern is apparently not at hkl 0,0,0 as it should be. The CENTRE option does an R-factor search for the correct centre. Note that if the Laue group symmetry is wrong, this search may be less reliable: a LAUEGROUP command may be given to reset the symmetry. If the centre is wrong, the images should be re-integrated, as there will be other errors which cannot be easily corrected.

4. Reindexing

The program may also be used just to reindex or change the spacegroup, if both HKLIN and HKLOUT files are defined, and keywords SPACEGROUP and/or REINDEX are given. If the HKLIN file is a merged file, then any anomalous difference columns will be negated, and F+/- I+/- columns swapped, if the hand of the index is changed by the reduction process. Note that in this case there is no check made that the reindexing operator is consistent with the space group. Any reflections with non-integral indices after reindexing are discarded, so this may be used to select reflections corresponding to a sub-cell.

5. Converting XDS or Scalepack format to MTZ

The command line option "-copy" (or "-c") may be used just to convert and XDS or Scalepack file to the MTZ format. The NAME keyword is required, and for SCALEPACK input the CELL must be given.

Details of LAUEGROUP mode

  1. The intensity data are read from the HKLIN file(s) (or XDSIN or SCAIN). If multiple files are given, the first one is treated as a reference, and subsequent files are placed on the same indexing scheme in the same way as INDEX mode, if there are alternatives, using the symmetry from the first file (multiple files defined with wild-cards are assumed by default to have the same indexing, see ASSUMESAMEINDEXING). Note that the default is to assume that the first file has valid symmetry and indexing: the keyword TESTFIRSTFILE may be used to force a determination of the Laue group before adding subsequent files. Batch numbers are forced to be unique if necessary by incrementing them by multiples of 1000.
  2. The maximum lattice symmetry consistent with the unit cell dimensions from the HKLIN file is determined, within an angular tolerance of 2 degrees (or that given on the TOLERANCE command). Alternatively, if the command ORIGINALLATTICE is given, the lattice symmetry corresponding to the space group in the HKLIN file is used, or the LAUEGROUP command may be used to specify a particular Laue group.
  3. The data are reindexed in the asymmetric unit of the lattice symmetry (if necessary), and sorted to bring potentially equivalent observations together.
  4. The intensities are normalised to E2 , making <E2> = 1, using an overall B-factor and a further correction smoothed on resolution bins, plus a time-dependent B-factor within each run. The batch number relative to the start of the run is used as a proxy for "time", and this correction is not done if there are only a few batches in the run (< 20 batches).  Unless resolution limits are explicitly set (RESOLUTION command), an automatic high resolution limit is applied, at the approximate point where <I>/<sigmaI> < IsigLimit (default value 4.0, set with ISIGLIMIT command). It is best to exclude weak high resolution data from the scoring functions, as they contain no useful information for this purpose.
  5. All rotational symmetry elements of the lattice symmetry are first scored separately. For example, in a tetragonal lattice, the symmetry elements are: 4-fold axis along c; 2-fold axes along a, b, c, (110) and (1-10)
  6. The most useful scoring function seems to be a correlation coefficient (CC) on E2 , calculated for pairs of observations related by a particular symmetry element. Another score calculated is  Rmeas, the multiplicity-weighted R-factor. In order to allow for small samples, the CC score is converted to a likelihood, and to "significance" score or Z-score by dividing by an estimated standard deviation. This is calculated by taking many pairs of observations at the same resolution which cannot be related by symmetry, dividing them into groups of the same size as the test sample (with a maximum of 200), the score calculated for each group and their mean & standard deviation calculated. Then

    Z(score) = [Score - Mean(UnrelatedScore)]/Sigma(UnrelatedScore)]

  7. All Laue groups which are sub-groups of the lattice group are generated by combining pairs of symmetry elements (including the identity) and completing the groups. The sub-groups are then scored by combining the scores for the individual elements, counting scores for elements present in the sub-group as positive & those elements not in the sub-group as negative. 

    8. It is not clear what is the best way of combining the element scores: at present two methods are used

    1. A "likelihood" (probability) estimate: this seems to be the most useful.
    2. Combined Z-Score ("Zc" in logfile)
      The correlation coefficients are recalculated (summed) over all "for" and over all "against" elements, Z(for) and Z(against) are calculated, then NetZ = Z(for) - Z(against)

  8. The potential Laue groups are ranked according to scoring method (i), and tested for acceptance for further output and testing. A group is accepted if its likelihood score is:
    1. greater than (AcceptanceLimit * Largest likelihood score)  where AcceptanceLimit is set by the ACCEPT command [default 0.2]  
    2. the group is the original Laue group from the HKLIN file.

      3. If too many of the symmetry elements have no observations, then only the Laue group from the HKLIN file is accepted, unless the command LAUEGROUP ALL is given.

  9. All accepted Laue groups are tested for relevent systematic absences. These are scored to produce a combined score for possible space groups. 
    1. Each relevant "zone" in the lattice group is tested for absences. Zones are typically axes tested for absences due  to screws, or (in the case of non-chiral spacegroups) zones to be tested for glide planes.
    2. Observations which lie in the zone, such as along an axis, are scored by a Fourier analysis of I/sigma(I). The score used is the peak height at the appropriate point in Fourier space, eg at 1/2 for a 2(1) screw, relative to the origin: a perfect score for exact absences is thus 1.0, a score for no absences might be 0.0
    3. For each spacegroup in the Laue group a probability estimate is made from the Laue group score and the systematic absence score, and the space groups are ranked accordingly. In some case, more than one space group may have identical scores.

KEYWORDED INPUT - DESCRIPTION

Keywords are:
ACCEPT, ASSUMESAMEINDEXING, CELL, CENTRE, COPY, EXCLUDE, HKLIN, HKLOUT, HKLREF, ISIGLIMIT, LABIN, LABREF, LAUEGROUP, NAME, CHIRALITY, ORIGINALLATTICE, PARTIALS, REINDEX, RESOLUTION, SCAIN, SPACEGROUP, SYSTEMATICABSENCES, TESTFIRSTFILE, TOLERANCE, XDSIN, XMLOUT

All input is optional. Only the first four characters of each keyword are significant.

TESTFIRSTFILE

An input "reference" file (HKLREF) is always assumed to have the correct symmetry, but if there is no reference file and more the one input test file is given (HKLIN etc),  then the first defined file is used as a reference for subsequent test input files (HKLIN). By default, this first HKLIN file will be assumed to have to correct symmetry and indexing, but  this command TESTFIRSTFILE  makes the program determine the Laue group for the first file before appending subsequent files. The Laue group test will be repeated after all data files have been read. NOTESTFIRSTFILE turns off this check, and is the default.

EXCLUDE  [FILE | SERIES <series_number>] BATCH <batch range> | <batch list>

Exclude batches from all calculations and the output file. Batches may be specified as a range <b1> TO <b2>  or as a list  <b1> <b2> <b3> ...
If there are multiple HKLIN input files, specifying the batch number may be complicated by the automatic renumbering of batches which is done to make them unique.  In this case the keyword FILE (or its synonym SERIES) may be used to specify the file number or file series number in the original input file: in the absence of this keyword, the batch numbers refer to the numbers after any renumbering. Files are numbered from 1 in the order they are specified on the command line or on HKLIN commands. File series specified by wild-cards on an HKLIN command have the same file number for this purpose, but note that wild-card file series on the command line are numbered separately (since the program has no way of detecting this).

ORIGINALLATTICE

Use the original lattice symmetry from the file instead of determining the maximum lattice symmetry from the cell dimensions.

RESOLUTION [[LOW] <ResMin>] [[HIGH] <ResMax>

Resolution limits in A, either order or with keys HIGH or LOW. If this command is absent, the program imposes an automatic high resolution limit based on a minimum value for <I>/<sigmaI> within resolution shells (see ISIGLIMIT). Limits given here override the I/sigma limits.

ISIGLIMIT <minimum<I>/<sigmaI>>

Minimum value for <I>/<sigmaI> within resolution shells. This is used to set the maximum resolution for inclusion of data in the scoring. This is overridden by explicit RESOLUTION limits. Default value 6.0.

CHIRALITY CHIRAL | NONCHIRAL | CENTROSYMMETRIC

If this is NONCHIRAL the lists of possible space groups include non-chiral (or just centrosymmetric) ones as well as the chiral ones. The default is derived from the space group given in the input MTZ file.

LABREF  [F | I =]<columnlabel>

Only for MODE ALTERNATIVE (ie if HKLREF is assigned). For the reference dataset, this defines the column label for intensity or amplitude (which will be squared to an intensity). If this command is omitted, the first intensity column (or if no intensities, the first amplitude) will be used. The next column is assumed to contain the corresponding sigma.

LABIN  [F | I =]<columnlabel>

Only for MODE ALTERNATIVE (ie if HKLREF is assigned) and if the test dataset is merged. For the test dataset, this defines the column label for intensity or amplitude (which will be squared to an intensity). If this command is omitted, the first intensity column (or if no intensities, the first amplitude) will be used. The next column is assumed to contain the corresponding sigma.

LAUEGROUP  HKLIN || <Laue group name> || ALL

Select a Laue group instead of testing all possible ones, ie select one solution for further processing. A REINDEX command may be given to specify a particular reindexing operator. The keyword HKLIN indicates that the Laue group from the input HKLIN file should be used, otherwise the Laue group name.   The keyword ALL may be used to force the program to accept all possible Laue groups for systematic absence analysis, even if there appear to be insufficient symmetry-related observations to distinguish them.

SPACEGROUP  HKLIN || <Space group name>

Select a space group to write to the output HKLOUT file. A REINDEX command may be given to specify a particular reindexing operator. The keyword HKLIN indicates that the Laue group from the input HKLIN file should be used, otherwise the space group name.  In this case all that the program does is to reindex the data into the given space group and write it out.

REINDEX  [LEFTHANDED] <reindex operator>

Specify a reindex operator (in the form eg "k,h,-l"). If  a space group is specified (SPACEGROUP), then that is used, otherwise the spacegroup from the HKLIN file is changed by the reindex operator. The reindexed data are written to the HKLOUT file. Note that there is no check that the operator is sensible and consistent with the space group.

Normally this must be a right-handed operator (ie correspond to a matrix with positive determinant), and the program will fail if it is not, but the keyword LEFTHANDED allows a negative-determinant transformation to be applied. Be VERY sure that you really want to do this! It is only valid if the hand of data has been inverted by some previous mistake in the integration program, ie VERY rarely.

TOLERANCE <LatticeTolerance>

Tolerance in degrees for determination of lattice symmetry [default 2 degrees]. Tolerance is the maximum deviation from the expected angle between two-fold axes in the lattice group, eg for a putative tetragonal lattice where a~=b, the expected angle between the diagonals is 90 degrees, and the deviation   delta = 2tan^-1(a/b) - 90
When testing alternative indexing schemes to match HKLIN to HKLREF datasets, this angular tolerance is converted to a "average length" tolerance by multiplying by the average cell edge.

ACCEPT <AcceptanceLimit>

Parameters for acceptance criterion. A group is accepted if its likelihood score is greater than (AcceptanceLimit * Maximum likelihood score)  where AcceptanceLimit is set by the ACCEPT command [default 0.2] 

PARTIALS [[NO]CHECK] [TEST <lower_limit> <upper_limit>] [CORRECT <minimum_fraction>]

Set criteria for accepting complete or incomplete partials. After all parts have been assembled, the total observation is accepted if:-
  1. the CHECK flag is set [default] and the MPART flags are all consistent (these flags indicate that a set of parts is eg 1 of 3, 2 of 3, 3 of 3)
  2. if CHECK fails, then the total fraction is checked to lie between lower_limit & upper_limit [default 0.95, 1.05]
  3. if this fails, then the incomplete partial is scaled up by the total fraction if  it is > minimum_fraction [default 0.6]

COPY

Just copy input to output: useful for converting an XDS (XDSIN) file to MTZ format  (HKLOUT), or just to sort HKLIN file(s). This is equivalent to the command line option "-copy" or "-c"

CENTRE [<hgrid> <kgrid> <lgrid>]

Search for centre of symmetry in the lattice. This should be at index 0,0,0, but occasionally the pattern has been misindexed, eg by +-1 along the rotation axis. This option performs an R-factor (Rmeas) search around 0,0,0, by default for +-2 grid points in each direction  (the size of the search grid may be reset to hgrid, kgrid, lgrid here). The lowest R should be at 0,0,0. Note that if the Laue group symmetry is wrong, this search may be less reliable: a LAUEGROUP command may be given to reset the symmetry. If an HKLOUT file is specified, the reindexed data is written (even if the reindexing operator is the identity).

NAME [PROJECT <project_name>] [CRYSTAL <crystal_name>] [DATASET <dataset_name>]

Assign or reassign project/crystal/dataset names, for output file. XDS files (XDSIN) and SCALEPACK (SCAIN) do not contain this information, so the NAME command may be used to supply this, for writing to the output HKLOUT file. In the case of MTZ input, the names given here supersede those in the input file: if there are multiple files, NAME commands may be interspersed with HKLIN | XDSIN | SCAIN commands to (re)assign datasets. Note that to take effect, this command must precede the relevent HKLIN | XDSIN | SCAIN command, and the file names must be given as input commands, not on the command line.

SYSTEMATICABSENCE  ON | OFF

Usually after checking for Laue group, reflections in special zones (axes) are checked for systematic absences to try to determine the space group. If this flag is OFF, the systematic absence check is skipped, and the "best"  Laue group is accepted.

CELL <a> <b> <c> <alpha> <beta> <gamma>

Read cell dimensions. This is required for SCALEPACK unmerged input, as the cell is missing from the file. For other cases, this may be used to override the cell from the input file, but note that no check is made that the input values are appropriate (though a warning is given if they are very different from those in the file).

ASSUMESAMEINDEXING [ON | OFF]

If there are multiple input files for the test data, it may be necessary to test that the 2nd and subsequent files are on the same indexing system as the earlier files.  By default, this test is done if separate file names are given (on the command line or as HKLIN commands), but not done if the multiple input files are generated from wild-cards (eg "hklin foo_*.mtz"). This flag can be used to stop the index test ("ON"), which saves time, or to force the program to do the test ("OFF" or alternatively the command DONOTASSUMESAMEINDEXING).

HKLIN   <test data file name>

The filename for the input test data (MTZ format) may be given with this command, as an alternative to (usually) putting it on the command line (see HKLIN). Wild-cards "*" and "?" (as on the command line) may be used to specify multiple files.

XDSIN   <test data file name>

The filename for the input test data (XDS format, XDS_ASCII or INTEGRATE) may be given with this command, as an alternative to (usually) putting it on the command line, or when there are multiple input files (see XDSIN).

SCAIN   <test data file name>

The filename for the input test data (SCALEPACK format, "unmerged original indices") may be given with this command, as an alternative to (usually) putting it on the command line, or when there are multiple input files (see XDSIN). A CELL command must be given, since the file does not contain the unit cell. Note that SCALEPACK may already have removed systematic absences, invalidating the analysis here. Note that SCALEPACK files do not contain all the geometrical information from the data collection, so output MTZ files (HKLOUT) are not really suitable for further scaling in SCALA (see SCALA documentation).

HKLREF   <reference data file name>

The filename for the reference data may be given with this command, as an alternative to (usually) putting it on the command line

HKLOUT   <output file name>

The filename for the output data may be given with this command, as an alternative to (usually) putting it on the command line

XMLOUT   <xml output file name>

The filename for the XML output data may be given with this command, as an alternative to (usually) putting it on the command line

Input and output files

HKLIN

The file or files containing the test dataset. Files may be specified either on the command line with or without the optional keyword HKLIN, or as command input, keyword HKLIN.  Multiple files may be specified with "wild-cards" "*" or "?".

Lauegroup Mode. This must be an unmerged file of intensities eg from Mosflm
Compulsory columns are H, K, L, M/ISYM, BATCH, I, SIGI
Optional columns are IPR, SIGIPR, TIME, XDET, YDET, ROT, WIDTH, MPART, FRACTIONCALC, LP, FLAG, BGPKRATIOS, SCALE, SIGSCALE

If a SCALE column is present it will be applied on input.

Index or Reindex Mode. This may be unmerged (as above) or merged. Unless a column is specified in the control input, the first column of type J (intensity) or F (amplitude) will be used for comparison with the reference dataset. Amplitudes are squared to intensities on input.

XDSIN

An XDS_ASCII file (or INTEGRATE), as an alternative to HKLIN. The file must be unmerged (MERGE=FALSE). Project, Crystal and Dataset names may be given with the NAME command.

SCAIN

A SCALEPACK file, as an alternative to HKLIN. The file should be unmerged ("unmerged original indices"): a merged file can be read, but probably is not much use. Project, Crystal and Dataset names may be given with the NAME command. A CELL command must be given. Note that SCALEPACK may already have removed systematic absences, invalidating the analysis here.

HKLREF

The file containing the reference dataset for Mode 2 (alternative). This may be merged or unmerged. For a merged referenec file, unless a column is specified in the control input, the first column of type J (intensity) or F (amplitude) will be used for comparison with the reference dataset. Amplitudes are squared to intensities on input.

HKLOUT

In LAUEGROUP mode, the test dataset reindexed in the "best" space group or point group. In ALTERNATIVE mode, the test dataset with the best reindexing, in the spacegroup of the reference dataset.

XMLOUT

An XML version of the logfile is written to a file if XMLOUT is assigned. This includes a BestSolution block
eg
<BestSolution Type="pointgroup">
   <GroupName>P 2 2 2</GroupName>
   <ReindexOperator>h,k,l</ReindexOperator>
   <ReindexMatrix>      1      0      0
                        0      1      0
                        0      0      1
    </ReindexMatrix>
   <Confidence>    1.000</Confidence>
   <TotalProb>  0.567</TotalProb>
</BestSolution>

Type is "spacegroup" if a unique space group is determined, or "pointgroup" if there is an ambiguity. The reindex matrix [H] post-multiplies the row vector h (ie h' = h [H])

Examples

Simple usage, all defaults (mode Lauegroup):
 pointless [hklin] <filename.mtz>

With reference dataset (mode alternative):

pointless hklref amph_I.mtz hklin amph_scaled.mtz

With reference dataset and control input (mode alternative):

pointless hklref n20n6c1c2n6x2x14e10e7.mtz \
      hklin cd3_1_F.mtz << eof
resolution 4.0
labref  F_nat20
labin F_cd3_1
eof

Just reindexing

pointless hklin <infile> hklout <outfile> << eof
reindex k,h,-l
spacegroup P31
eof

Just copying (converting XDS file)

pointless -copy xdsin <infile> hklout <outfile>

Multiple input files

pointless hklout 12287.mtz << eof
name project JCSG crystal 12287 dataset INFL
hklin 12287_1_E1_001.mtz
name project JCSG crystal 12287 dataset LREM
hklin 12287_1_E2_001.mtz
name project JCSG crystal 12287 dataset PEAK
hklin 12287_2_001.mtz
eof

Multiple input files with exclusions
pointless << eof
#  File 1
hklin IID3_r5.mtz
#  File 2
hklin IID3_r6.mtz
exclude  batch 1             # final numbering, from file 1
exclude  file 2 batch  4     # original numbering in file 2
exclude  batch  1007 to 1008   # after re-numbering, from file 2
copy
hklout r5r6
eof

Multiple input files
pointless hklin abc_1.mtz abc_2.mtz  hklout 12287.mtz

Multiple input files with wild-card
pointless hklin abc_*_001.mtz hklout abc_1.mtz

Scalepack input
pointless scain gp6_e1_nomerge.sca

Release notes

1.2.9,10

Faster XDS reading, various bug fixes, EXCLUDE BATCH option

1.2.7

Multiple HKLIN files from HKLIN command

1.2.6

Read XDS INTEGRATE.HKL files

1.2.5

Multiple input files with wild-cards on command line ("pointless hklin abc*.mtz"), ASSUMESAMEINDEXING  option

1.2.4

Testing alternative indexing to reference (either HKLREF or first HKLIN) now uses unmerged observations instead of the reflection average, to allow for misindexing in confusing cases, where observations which are actually different may have been assigned to the same reduced reflection. Added TESTFIRSTFILE option.

1.2.3

Fix problems with reindexing relative to reference file in non-standard setting or accidental alternative indexing.
Also  "reindex" command  will change space group  if required  (eg P21 2 21 reindexed  [l,h,k] to P21 21 2)

1.2.0-2

Multiple input files, put on to the same indexing scheme with unique batch numbers.
Time-dependent B-factor normalisation (a simple-minded radiation damage correction)
SCALEPACK input (SCAIN), CELL command

1.1.5

Added XDS input (XDSIN), NAME command, COPY (& -copy) options

1.1.3, 4

Alternative indexing option now lists correct cell deviation from reference cell
Fixed bug in reading eg "reindex -h,l,k" where leading "-" were stripped

1.1.2

Fixed up systematic absence scoring so that it works properly for 6-fold screws (allow for non-independence of Fourier terms): previous versions were wrong  (to use a technical term) for 6(1) axes.
Refactor reflection reading to allow for input other than from MTZ files in future.

1.1.1...

New (and better) scoring scheme: P(CC) based on Lorentzian distribution rather than Gaussian; probabilities combined for all symmetry elements in putative Laue group in different & simpler way

1.1.0.6

Fixed bug,  hklout file was written in Laue group instead of space group under some circumstances

1.1.0.5

Tolerance in alternative indexing now based on RMS difference of base vectors, rather mean square, tolerance converted from angular value using mean cell edge. Fixed omission of resolution limits from merged HKLOUT file in reindexing.

1.1.0

New likelihood scoring scheme for Laue groups, seems to work better than Net-Zc, modified acceptance scheme to go with this.

1.0.8

XML output from Index & Centre modes

1.0.7

Reindex mode tidied up (this is when either REINDEX or SPACEGROUP commands given). Anomalous columns are swapped if necessary (probably only if LEFTHANDED option is used, not recommended). Discard fractional indices after reindexing.
CENTRE option added. Uses scaled partials if incomplete & fraction > [0.6] (PARTIALS command)

1.0.6

Use profile-fitted overloads in systematic absence test

1.0.5

XML output if xmlout is assigned

1.0.0, 1

Systematic absence analysis to choose spacegroup
Correction of various bugs

0.5.0,1,2

Alternative ways of combining Z+ & Z- (Za, Zc), remove combined RMSD printing, more input controls (ORIGINALLATTICE, LAUEGROUP, REINDEX, TOLERANCE, ACCEPT)

0.4.0

HKLOUT output added

0.3.0

Mode Alternative, labin, labref

0.2.0

User input, resolution, Isiglimit, Nonchiral