REINDEX (CCP4: Supported Program)

NAME

reindex - produces an MTZ file with h k l reindexed. There are options to change the symmetry, and to reduce the reflection to the (new) asymmetric unit.

SYNOPSIS

reindex hklin foo_in.mtz hklout foo.mtz
[Keyworded input]

DESCRIPTION

Reindex reflections and/or change symmetry and/or reduce to asymmetric unit again. The input file may be:

an unmerged (multirecord) file, in which the operations are carried out on the original indices (reconstructed using the M/ISYM column of HKLIN), or
a merged file (one record per reflection), in which only reindexing is allowed. The file should not contain phase or phase coefficient columns: these will be left unchanged, and will probably be wrong. If the reflection indices are reduced to the asymmetric unit (default unless NOREDUCE is specified), 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.

This program is useful, for example when:

you have unmerged integrated data, which will need to be reduced to the asymmetric unit after reindexing, e.g. mosflm.
you have unmerged data, and you want to change to a different point group. This will have a different definition of the asymmetric unit.
you have merged data which needs to be reindexed, e.g. you might want to change h,k,l to k,h,-l in a tetragonal system. Beware, not all reindexing is appropriate, and the program does no check (e.g. reindexing l,h,k is invalid for a tetragonal crystal).

The program operates on each reflection in turn, without sorting them. Therefore, the output file will normally need to be resorted before further use (see CAD or SORTMTZ). For the reindex option, the new unit cell is determined and written to the output file. For unmerged data, the orientation data (cell and Umat) are also updated for all batches.

The following operations are carried out on each reflection:

If unmerged data (multirecord file): reconstruct original indices
Reindex if requested
Reject reflections with non-integral indices
(Optionally) reduce reflection to asymmetric unit, using new symmetry (if different). Anomalous difference, F+/- and I+/- columns will be corrected as necessary, i.e. if the hand of the index is changed by the reduction process.

KEYWORDED INPUT

Available keywords are:

END, LEFTHAND, MATCH, NOREDUCE, REINDEX, SYMMETRY

REINdex

Subkeywords HKL or AXIS (default HKL) followed by a transformation.

The transform can be given a similar way to symmetry operations (see below for examples).

Subkeyword HKL

reindex HKL k, h, -l

implies h_new = k_old, k_new = h_old, l_new = -l_old i.e. this defines a matrix to reindex the reflection data, such that

     [hn kn ln]          =  [ho ko lo] [M]

reindex HKL k, h, -l

generates a reindexing matrix:

     [M] =  [ 0  1  0]
            [ 1  0  0]
            [ 0  0 -1]

reindex HKL h, -k, -h/2-l/2

would generate a matrix:

     [M] =  [ 1.0  0.0  0.0]
            [ 0.0 -1.0  0.0]
            [-0.5  0.0 -0.5]

reindex HKL h-1, k, l

would result in all h indices being reduced by 1.

Subkeyword AXIS

If the program AXISSEARCH has been used to find possible alternative reciprocal axes, the reindexing matrix can be specified in terms of reciprocal axes, for example:

reindex AXIS a*+c*,c*,-b*

implies a*_new = a*_old+c*_old, b*_new = -c*_old, c*_new = -b*_old (which is in fact equivalent to reindex HKL h,l-k,-k)

    If     [a*new] = [M]**-1 [a*old]
           [b*new]           [b*old]
           [c*new]           [c*old]

    Since   [hn kn ln] [a*n]    =  [ho ko lo] [a*o]
                       [b*n]                  [b*o]
                       [c*n]                  [c*o]

      [hn kn ln] [M] **-1 [a*o] =     [ho ko lo] [a*o]
                          [b*o]                  [b*o]
                          [c*o]                  [c*o]

    and     [hn kn ln]          = [ho ko lo]  [M] as before

Cell dimensions will be recalculated for the redefined cell. Be careful that the index transformation preserves the hand of the axes (unless you want to invert the hand), i.e. that the matrix has a positive determinant. If it does invert the hand, the program will change the sign of all reindexing elements unless the keyword LEFTHAND is present.

If the transformation leads to fractional indices for some cases (as in the 2nd example above), these reflections will be rejected. If the reindexing operations include translations, then the orientation data in the output file will not be strictly correct.

MATCH

In some complicated cases it is easier to specify how three new reciprocal vectors should be matched onto three old ones. The program AXISSEARCH allows you to check reciprocal vector lengths and angles, and you may wish to convert a P1 cell say to one which approximately matches a C2 one with angles approximately 90 degrees. The program can deduce the reindexing matrix from this information.

    match   2h'=h +k -l  * 2k'= -h +k + l * 1l'= 1h

SYMMetry <spacegroup_name | spacegroup_number | symmetry operations>

For unmerged files, set new symmetry for reduction to asymmetric unit (after optional reindexing). Defaults to input symmetry from HKLIN file. New symmetry is written to the HKLOUT file. If the output symmetry is a lower symmetry, then all input reflections will output, but there will be a lower completeness over the asymmetric unit. If the output symmetry is a higher symmetry, then all input reflections will output, with more observations per h k l set.

For merged files, new symmetry is written to HKLOUT but reduction to asymmetric unit is turned off. This option is therefore not advisable for merged data, unless you know what you are doing.

LEFTHAND

Allow the reindexing transformation to invert the hand (EXTREMELY unwise unless you are very sure you know what you are doing!). Anomalous differences will NOT be altered by a reindexing operation inverting the hand.

NOREduce

Do not reduce merged reflections to asymmetric unit after reindexing. Reflections in unmerged files are always reduced to the asymmetric unit defined by the (new) symmetry.

END

Terminate control input, also done by end-of-file.

INPUT AND OUTPUT FILES

HKLIN: Input MTZ file. This may contain unmerged or merged reflections, depending on what you want to do, see DESCRIPTION section above.
HKLOUT: Output MTZ file, containing reindexed reflections.

EXAMPLES

unix example scripts found in $CEXAM/unix/runnable/

reindex.exam

Non-runnable examples of reindexing and sort

Data processed by MOSFLM in P1 with cell


   73.6510  126.4434  126.6338  120.6573   89.7704   89.9541

We want to convert this to P3 for scaling and merging in SCALA. As well as changing the point group, we need to reindex such that the 120 degree angle is gamma.


reindex HKLIN processed-p1.mtz HKLOUT junk.mtz <<EOF
reindex HKL k, l, h
symm P3
end
EOF

sortmtz hklin junk.mtz HKLOUT processed-p1-to-p3.mtz <<EOF
H K L M/ISYM BATCH I SIGI
EOF

Note that the data needs sorting again after reindex.

Converting P1 cell to approximate C2 form:

 #  Reindex
 reindex hklin $CCP4_SCR/P1.mtz hklout $SCRATCH/C2.mtz <<eof
        match   2h'=h +k -l  * 2k'= -h +k + l * 1l'= 1h
 eof

Changing P21 with h+l = 2n +1 absent to standard P21 form:

 #  Reindex
 reindex hklin $CCP4_SCR/bigcell.mtz hklout $SCRATCH/JUNK.mtz <<eof
        reindex h/2-l/2, k, h/2+l/2
 eof
 #  Same transformation given in terms of reciprocal axes
 #
 reindex hklin $CCP4_SCR/bigcell.mtz hklout $SCRATCH/JUNK.mtz <<eof
        reindex AXIS a*-c*,b*,a*+c*
 eof
 # Sort and reconvert to asymmetric unit again
 cad hklin1 $SCRATCH/JUNK hklout $CCP4_SCR/newcell <<eof
        LABI FILE 1 ALLIN
 eof