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.
Reindex reflections and/or change symmetry and/or reduce to asymmetric unit again. The input file may be:
This program is useful, for example when:
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:
Available keywords are:
END, LEFTHAND, MATCH, NOREDUCE, REINDEX, SYMMETRY
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).
reindex HKL k, h, -l
[hn kn ln] = [ho ko lo] [M]
reindex HKL k, h, -l
[M] = [ 0 1 0] [ 1 0 0] [ 0 0 -1]
reindex HKL h, -k, -h/2-l/2
[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
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*
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.
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
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.
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.
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.
Terminate control input, also done by end-of-file.
Data processed by MOSFLM in P1 with cell
73.6510 126.4434 126.6338 120.6573 89.7704 89.9541We 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 EOFNote 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