pointless [-c[opy]] [[HKLIN] foo_in.mtz]
[XDSIN foo_in.HKL] [SCAIN foo_in.HKL] [HKLREF
reference_file.mtz] [XYZIN reference_coords.pdb] [HKLOUT output_file.mtz]
Input and Output files
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 also a check for lattice
centering, ie a check for whole classes of reflections having
essentially zero intensity, including a check for obverse/inverse twinning in rhombohedral systems.
[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 (test) 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), unmerged Scalepack files (SCAIN) (produced with the Scalepack option "nomerge original index"), SHELX files (also SCAIN) or SAINT files (also SCAIN). Also free-format files containing HKL I sigI (see SCAIN). Input types may be mixed. Merged files may be checked for under-merging & for systematic absences. Files given as HKLIN will be checked for their filetype, so other types will be recognised.
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 temporary reference for subsequent files, to check for consistent indexing in cases of ambiguity.This may not work correctly if this first file is indexed in the wrong Laue group: the keyword TESTFIRSTFILE may be used to force a Laue group check on the first file before adding in the others.
For the alternative indexing check, a reference file (HKLREF, merged or unmerged) or a reference coordinate list (XYZIN)
may be given and the indexing of the test file will be checked against
this. The space group of the reference data is assumed to be correct.
If there is more than one input file the
program checks the batch numbering schemes do not overlap, and if
necessary it renumbers batches.
Multilattice files from Mosflm/FECKLESS can be read: the different
lattices are for now (pending refactoring of the data objects) are
mapped into different runs, with BATCH numbers incremented by multiples
of 1000 (in FECKLESS). By default only the first Run, corresponding to
the first Lattice, is used in symmetry determination, but all runs are
written to the output HKLOUT file. Other runs may be selected with the USE command.
If HKLOUT is assigned it
produces a sorted reflection list (possibly after reindexing and
renumbering batches) which is ready for input to AIMLESS or SCALA.
It has other subsidiary uses described in more detail below: it can convert other formats to MTZ, check and reindex an input file to match an existing reference set of amplitudes, or apply a pre-selected reindex operator. The command line option "-copy" (or "-c") may be used just to copy files to MTZ (equivalent to the COPY command).
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).
• The optimum scoring method remains to be discovered. The true solution may not have the top score, but should be close to the top
• The program will find symmetry: there is no guarantee that this symmetry is crystallographic or correct! Caveat emptor.
This mode is selected if an HKLREF dataset or an XYZIN coordinate file 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.
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.
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 reliable check made that the reindexing operator is consistent with the space group: if a SPACEGROUP command is not given, the reindexed space group will be used if it is valid, otherwise you will have to specify 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. Files containing phase columns can now be reindexed, as long as you are just changing the setting, not the space group (eg I2<->C2, P2 21 21 <-> P21 21 2 etc).
The command line option "-copy" (or "-c") may be used just to convert an XDS, Scalepack or SHELX file to the MTZ format. The NAME keyword is required, and for SCALEPACK or SHELX input the CELL must be given. For SAINT input it is recommended to give a CELL (as it may be more accurate).
A “solution” is a space group (or point group) and a reindexing operator. In INDEX mode, the solution is always chosen to give the best match to the reference file. In LAUEGROUP mode, the default is to choose the solution with the highest joint score in the Laue group search and the systematic absence test. If several non-enantiomorphic space groups have the same score (due to lack of information), then the corresponding point group is chosen (eg P222 for Laue group Pmmm). This automatic choice may be over-ridden in several ways, usually after examining the scores from an initial run.
The command CHOOSE carries out the Laue group search and the systematic absence test, but the choice of solution is specified explicitly rather than chosen automatically
CHOOSE SOLUTION <n>
Choose a Laue group solution by number in the ranked list: the systematic absence test will then be done as normal
CHOOSE LAUEGROUP <name>
Choose a Laue group solution by name, choosing the first match in the ranked list: the systematic absence test will then be done as normal
CHOOSE SPACEGROUP <name>
Choose the corresponding Laue group solution by name, choosing the first match in the ranked list, then choose the specified space group in the systematic absence test list
The command LAUEGROUP skips the Laue group search, and just uses the given Laue group, typically with a given REINDEX operator. The systematic absence test will then be done as normal.
The command SPACEGROUP skips all searches, and just uses the given space group, typically with a given REINDEX operator. This is equivalent to the operation of the CCP4 program REINDEX.
Note that when a Laue group name is needed, either the actual Laue group name (as printed) may be given, or the name of any space group in that Laue group (eg P2/m may be given as P2)
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. In a "file series" defined by an HKLIN command with wild-cards in the file name, files which cannot be read (eg because they are are still being written) are ignored, and by default acceptance of files is terminated on a file which is out of chronological order.
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.
The data are reindexed in the asymmetric unit of the lattice symmetry (if necessary), and sorted to bring potentially equivalent observations together.
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.
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). If the input file was merged, then symmetry elements implicit in the merged group are flagged as present.
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)]
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. For merged files, sub-groups of
the merged symmetry are excluded, 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.
It is not clear what is the best way of combining the element scores: at present two scores are printed
A "likelihood" (probability) estimate: this seems to be the most useful.
Combined Z-Score ("Zc" in
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)
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 greater than (AcceptanceLimit * Largest likelihood score) where AcceptanceLimit is set by the ACCEPT command [default 0.2]
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.
All accepted Laue groups are tested for relevant systematic absences. These are scored to produce a combined score for possible space groups.
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.
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. I' is an “adjusted” intensity, calculated by subtracting a small fraction (see NEIGHBOUR, default 0.02) of neighbouring intensities along the axis, to allow for possible contamination of a weak reflection by a neighbouring strong one.
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.
ACCEPT, ALLOW, ASSUMESAMEINDEXING, BLANK, CELL, CENTRE, CHOOSE, COPY, EXCLUDE, HKLIN, HKLOUT, HKLREF, ISIGLIMIT, LABIN, LABREF, LAUEGROUP, MULTIPLY, NAME, NEIGHBOUR, CHIRALITY, ORIGINALLATTICE, PARTIALS, POLARIZATION, REINDEX, RESOLUTION, RUN, SCAIN, MERGED, SETTING, SPACEGROUP, SYSTEMATICABSENCES, TESTFIRSTFILE, TOLERANCE, USE, WAVELENGTH, WILDFILE, XDSIN, XMLOUT, XYZIN
All input is optional. Only the first four characters of each keyword are significant, and keywords are case-insensitive.
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 for this purpose 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 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 or the command line have the same file number for this purpose.
Use the original lattice symmetry from the file instead of determining the maximum lattice symmetry from the cell dimensions.
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, or CC(1/2) in P1 (see ISIGLIMIT).
Limits given here override the automatic limits. Note that the
automatic limits affect only the point-group determination, and do not
apply to the systematic absence tests, nor affect the resolution in the
output file. Explicit resolution limits given here cut the data for all
purposes and restrict data in the output file.
Minimum value for <I>/<sigmaI> within resolution
shells [default value 6.0], or limit for CC(1/2) in P1 [default value
0.6]. These are used to set the maximum resolution for inclusion of
data in the scoring. This is overridden by explicit RESOLUTION
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.
Only for INDEX MODE (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, though this is not compulsory for F.
Only 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, but this not
compulsory. If the column is an I(+) or F(+), then a set of 4 columns
is expected (eg I(+), sigI(+), I(-), sig(I-)).
Specify a Laue group instead of testing all possible ones, ie set one solution for further processing in the systematic absence testing. A REINDEX command should be be given to specify a particular reindexing operator except in the case of a change of setting for the same Laue group (eg C2/m to I2/m, "LAUEGROUP I2"). 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.
Specify a space group to write to the output HKLOUT file. A REINDEX command should be given to specify a particular reindexing operator, except in the case of a change of setting for the same space group (eg C2 to I2, "SPACEGROUP I2"). 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.
Choose a Laue group solution from the ranked list in the search, usually chosen from a previous run: a solution includes the reindexing operator. The Laue group solutions are ranked by the probability score, so solution 1 is always the most probable which is chosen by default. This choice may be over-ridden with this command, either as a solution number or as a group name: the systematic absence check will then be done to try to determine the space group. The Laue group name may be given either as the name as printed or as any space group name belonging to that Laue group. This command may also be used to explicitly choose C2/m or I2/m settings for centred monoclinic system, overriding the default choice (qv SETTING), eg CHOOSE LAUEGROUP I2
Choose a space group solution from the search: first the equivalent Laue group solution is chosen from the ranked list in the search, usually selected from a previous run: a solution includes the reindexing operator. Then systematic absence check will then be done and the specified space group is chosen.
This affects only primitive orthorhombic space groups (and non-chiral I & F centred orthorhombic groups), notably P 2 2 21 (17) and P 21 21 2 (18), when a space group is being chosen based on the systematic absences, and also centred monoclinic ones (eg Laue group C 1 2/m 1), but only in the absence of a reference file (which defines the space group & setting, and overrides any other convention). In the primitive orthorhombic cases, the axis order may either be set according to the general orthorhombic (International Tables) convention from the unit cell lengths with a < b < c (CELL-BASED), or in a “reference” setting which puts the “unique” axis along c. In the first convention (CELL-BASED, the default), for example, space group 18 may be set as P 2 21 21, P 21 2 21, or P 21 21 2. If SYMMETRY-BASED is selected, then eg space group 18 always P 21 21 2 irrespective of axis lengths.
The default CELL-BASED option also affects the Laue group setting for centred monoclinic lattices: in this case the body-centred setting (I 1 2/m 1, eg space group I2) will be chosen if it leads to a less oblique cell (smaller beta angle) than the C-centred setting (C 1 2/m 2, eg space group C2). The SYMMETRY-BASED or C2 options will always select the C2 setting.
See note above.
Specify a reindex operator, either in the form eg "k,h,-l", as a
matrix, or as the equivalent real-space change of basis eg "y,x,-z".
The matrix is given in the same order as that in the XDS REIDX
ie h' = H11 h + H21 k + H31 l; k' = H12 h + H22 k + H32 l; l' = H13 h + H23 k + H33 l
Note that the real and reciprocal space operators correspond to mutually transposed matrices, eg "x-y,-y,-z" corresponds to "h,-h-k,-l".
Reciprocal space reindexing operators may include a translation (eg
h,k,l+1), real space operators may not. It is better to re-integrate
the data with the correct indexing.
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, so be careful. If no space group is specified, the reindex transformation will be applied to the input space group, but this may lead to an unrecognised space group (eg non-cyclic permutations in P 21 21 21), in which case you will have to give the space group explicitly.
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. Do not use this option unless you really know what you are doing.
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.
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]
Set criteria for accepting complete or incomplete partials. After all parts have been assembled, the total observation is accepted if:-
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)
if CHECK fails, then the total fraction is checked to lie between lower_limit & upper_limit [default 0.95, 1.05]
if this fails, then the incomplete partial is scaled up by the total fraction if it is > minimum_fraction [default 0.6]
Just copy input to output: useful for converting an XDS (XDSIN) file or SCAIN to MTZ format (HKLOUT), or just to sort HKLIN file(s). This is equivalent to the command line option "-copy" or "-c"
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).
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 for files defined with input commands, this command must precede the relevant HKLIN | XDSIN | SCAIN command: a single NAME command may be given anywhere to (re)name datasets for files defined on the command line.
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.
For the systematic absence analysis along axes, intensities are “corrected” for possible corruption by neighbouring strong reflections which may inflate the value of reflections which should be absent. This is done by subtracting a small fraction of the neighbouring intensities from each intensity, not allowing the result to be negative: this corrected I' is used in the Fourier analysis of I'/sigma(I). The default value of neighbour_fraction is 0.02,
Read cell dimensions. This is required for SCALEPACK unmerged and SHELX files, 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). It is also recommended for SAINT files, as the cell inferred from the data may not be very accurate. Note that to take effect, this command must precede the relevant HKLIN | XDSIN | SCAIN command, and the file names must be given as input commands, not on the command line.
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 within a “file series” ie a set of 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).
The filename for the input test data (MTZ format or others) may be given with this command, as an alternative to putting it on the command line (see HKLIN). Wild-cards "*" and "?" (as on the command line) may be used to specify multiple files (a “file series”). HKLIN may be used for non-MTZ files and the program will auto-detect the type.
Treat the filenames given on the HKLIN command as if they
contain wild cards to define a file series. If this command is
given without an argument, then the default template is "*_###.*,
suitable for dealing with the output from MOSFLM with the "Multiple MTZ
files" option. [This option is here mainly to get round limitations in
The filename for the input test data (XDS format, XDS_ASCII or INTEGRATE) may be given with this command, as an alternative to putting it on the command line, or when there are multiple input files (see XDSIN). HKLIN may also be used and the program will auto-detect the type.
A file in the formats from SCALEPACK, SHELX or SAINT, or in free-format (see below). HKLIN may also be used and the program will auto-detect the type. 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 except for SAINT files. Note that SCALEPACK may already have removed systematic absences, invalidating the analysis here: a warning is printed if this seems to have been done. Note that SCALEPACK files do not contain all the geometrical information from the data collection, and SHELX files contain no geometrical information, so output MTZ files (HKLOUT) are not really suitable for further scaling in AIMLESS. SAINT files have all necessary information. For merged ShelX files, a MERGED command should be given to indicate the space group (or point group) used for merging.
The filename for the reference data may be given with this command, as an alternative to putting it on the command line
The filename for the output data may be given with this command, as an alternative to putting it on the command line
The filename for the XML output data may be given with this command, as an alternative to putting it on the command line
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. HKLIN may be used for other filetypes, as alternative to
XDSIN and SCAIN: the program will automatically detect the filetype.
Multiple files may be specified with "wild-cards"
"*" or "?".
Lauegroup Mode. This should normally be an unmerged file of intensities eg from Mosflm
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.
A merged file can only be checked for under-merging ie for the true Laue group being a higher symmetry than that used for merging. A LABIN command may be given to specify the column labels for a merged file, otherwise the first column of type J (intensity) or F (amplitude) will be used.
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.
An XDS_ASCII file (or INTEGRATE): HKLIN may also be used. The file must be unmerged (MERGE=FALSE). Project, Crystal and Dataset names may be given with the NAME command.
A file in the formats from SCALEPACK, SHELX or SAINT, or in free-format (see below): HKLIN may also be used. 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 except for SAINT files. Note that SCALEPACK may already have removed systematic absences, invalidating the analysis here: a warning is printed if this seems to have been done. Note that Scala versions before 3.3.18 did not deal properly with the secondary beam correction for Phi scans.
Free-format files are recognised by a
first line beginning "COLUMNS" followed by a list of allowed item
names, in the column order they are in the file. Recognised names
are H, K, L, I, SIGI, and BATCH: the first 4 are compulsory. Following
this line, there may be optional lines CELL giving cell dimensions (an
alternative to the CELL command: one of these alternatives must be
given), and SPACEGROUP giving the space group name. Usually it is only the lattice type
(P, C, I, F, R, H) which is important. In the absence of the SPACEGROUP
information, it is assumed to be P1 and this is likely to cause failure
for centred lattices
Values on each data line must be separated by one or more spaces.Example:
COLUMNS H K L I SIGI BATCH
CELL 210.710 210.710 67.211 90.00 90.00 120.00
-48 -18 -5 -17.53 54.63 1
-47 -18 -5 39.56 42.55 1
-46 -24 -4 42.92 40.79 1
The file containing the reference dataset for Mode 2 (alternative). This may be merged or unmerged. For a merged reference 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. As an alternative, a coordinate file XYZIN may be given, in which case calculated intensities will be used as the reference.
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.
An XML version of the logfile is written to a file if XMLOUT is
assigned. This includes a BestSolution block
<GroupName>P 2 2 2</GroupName>
<ReindexMatrix> 1 0 0
0 1 0
0 0 1
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])
P.R.Evans, Scaling and assessment of data quality, Acta Cryst. D62, 72-82 (2006).
The scoring scheme has changed somewhat since this paper was written, particularly in the calculation of the probabilities
P.R.Evans, An introduction to data reduction: space-group
determination, scaling and intensity statistics, Acta Cryst. D67,
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):
hklin cd3_1_F.mtz << eof
pointless hklin <infile> hklout
<outfile> << eof
Just copying (converting XDS file)
pointless -copy xdsin <infile> hklout <outfile>
Multiple input files
12287.mtz << eof
name project JCSG crystal 12287 dataset INFL
name project JCSG crystal 12287 dataset LREM
name project JCSG crystal 12287 dataset PEAK
Multiple input files with exclusions
# File 1
# File 2
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
Multiple input files
pointless hklin abc_1.mtz abc_2.mtz hklout 12287.mtz
Multiple input files with wild-card
pointless << eof
pointless scain gp6_e1_nomerge.sca
For XDS input, flag as bad PKratio (= 99.99) & omit MISFIT observations (flagged in XDS file with SD < 0)
Multiple file series, no index checking within a series. Bug fix in XDS reading if STARTING_FRAME != 1
SETTING option, SPACEGROUP without REINDEX, fixed bug in CELL
command for MTZ files.
Corrected intensities for systematic absence analysis (NEIGHBOUR option)
Faster XDS reading, various bug fixes, EXCLUDE BATCH option, CHOOSE option
Multiple HKLIN files from HKLIN command
Read XDS INTEGRATE.HKL files
Multiple input files with wild-cards on command line ("pointless hklin abc*.mtz"), ASSUMESAMEINDEXING option
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.
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)
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
Added XDS input (XDSIN), NAME command, COPY (& -copy) options
Alternative indexing option now lists correct cell deviation from
Fixed bug in reading eg "reindex -h,l,k" where leading "-" were stripped
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)
Refactor reflection reading to allow for input other than from MTZ files in future.
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
Fixed bug, hklout file was written in Laue group instead of space group under some circumstances
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.
New likelihood scoring scheme for Laue groups, seems to work better than Net-Zc, modified acceptance scheme to go with this.
XML output from Index & Centre modes
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)
Use profile-fitted overloads in systematic absence test
XML output if xmlout is assigned
Systematic absence analysis to choose spacegroup
Correction of various bugs
Alternative ways of combining Z+ & Z- (Za, Zc), remove combined RMSD printing, more input controls (ORIGINALLATTICE, LAUEGROUP, REINDEX, TOLERANCE, ACCEPT)
HKLOUT output added
Mode Alternative, labin, labref
User input, resolution, Isiglimit, Nonchiral