REINDEX (CCP4: Supported Program)
NAMEreindex - 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.
SYNOPSISreindex hklin foo_in.mtz hklout foo.mtz
DESCRIPTIONReindex reflections and/or change symmetry and reduce to asymmetric unit again. The input file may be:
This program may be useful, for example when:
It is generally better to rerun the data reduction from the beginning if you can.
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 updated for all batches.
The following operations are carried out on each reflection
Available keywords are:
END, LEFTHAND, MATCH, NOREDUCE, REINDEX, SYMMETRY
SYMMetry <spacegroup_name | spacegroup_number | symmetry operations>Set new symmetry for reduction to asymmetric unit (after optional reindexing). Defaults to input symmetry from HKLIN file.
Sub key words HKL or AXIS (default HKL) followed by a transformation.The transform can be given a similar way to symmetry operations (see below for examples).
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.
MATCHIn 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
LEFThandAllow the reindexing transformation to invert the hand (normally unwise). Anomalous differences will NOT be altered by a reindexing operation inverting the hand.
NOREduceDo not reduce reflections to asymmetric unit after reindexing: allowed for merged files only. By default, reflections are reduced to the asymmetric unit defined by the (new) symmetry.
ENDTerminate control input, also done by end-of-file.
INPUT AND OUTPUT FILES
unix example scripts found in $CEXAM/unix/runnable/
VMS versions found in $CEXAM/vms/
Non-runnable examples of reindexing and sort:
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