REFINDEX (CCP4 UNSUPPORTED PROGRAM) NAME REFINDEX REINDEX DATASET

                      REFINDEX (CCP4: Unsupported Program)

NAME

   refindex - re-index dataset maximising correlation with reference
   dataset or to the conventional setting in International Tables.

SYNOPSIS

   refindex  [HKLIN or HKLIN1 working.mtz]  [HKLREF or HKLIN2
   reference.mtz]  [HKLOUT output.mtz]

DESCRIPTION

   "refindex" automatically re-indexes an MTZ dataset, either to an
   existing reference dataset or, if no reference dataset is specified, to
   the conventional setting given in volume A of International Tables (see
   Section 9.3 of Volume A, 5th edition or later).  In the former case,
   the required re-indexing operator is first found by maximising the
   correlation coefficient between the two datasets against all possible
   re-indexings of the working dataset. In the latter case, if no working
   MTZ dataset is specified, the input cell and space group are read from
   standard input, the re-indexing operator and the transformed cell and
   space group symbol (if different) are printed, but no actual
   re-indexing is done.

   Note that in each case it is assumed that the point and space groups as
   read from the MTZ file, or the space group as read from standard input,
   are the correct ones (though interconversion between different settings
   of the same space group, such as between C2 and I2 or between
   P22[1]2[1]and P2[1]2[1]2) may be performed when re-indexing to a
   conventional cell).  In no circumstances is any attempt made to
   re-index into a different point group.  In each case, if a working MTZ
   dataset is specified and the re-indexing operator is not (h,k,l), the
   re-indexing is applied to the working dataset and the result output to
   a new file.

INPUT

   If at least one input MTZ file is specified, then nothing is read from
   standard input.  If no MTZ file is specified, the program prompts for
   the cell parameters and then the space group name or number (on a
   separate line) from standard input.  After printing the transformed
   cell, and in the case of transformation between different settings the
   transformed space group symbol, the prompt for a cell is repeated: the
   program is terminated by Ctrl-D.

INPUT AND OUTPUT FILES

   The following input and output files are used by the program:

   Input Files:

   HKLIN or HKLIN1 (optional - omit to transform input cell & space group
          to conventional cell)
          Input MTZ file containing the dataset to be re-indexed. The
          required column labels are found automatically; they must either
          be F & SIGF, or a matching pair of the form F_xxx SIGF_xxx
          (where xxx is any character string).  Only one Fobs sigma(Fobs)
          pair may be present in the file.

   HKLREF or HKLIN2 (optional - omit to re-index to conventional setting)
          Input MTZ file containing the dataset to be used as a reference.
          The required column labels are found automatically; they must
          either be F & SIGF, or a matching pair of the form F_xxx
          SIGF_xxx.  Only one Fobs sigma(Fobs) pair may be present in the
          file.

   Output Files:

   HKLOUT
          Output file that contains the re-indexed dataset.  If no
          re-indexing is needed then no output file is produced.

NOTES

   In point groups 422, 622 and 432 only one indexing is possible, so
   re-indexing to a reference dataset in these point groups does nothing.

   In crystal systems trigonal, tetragonal, hexagonal and cubic, the cell
   is unique (though the indexing may not be), so re-indexing to a
   conventional cell does nothing.

PROBLEMS

   At present the program will stop if phase or H-L coefficient columns
   are present in the HKLIN1 file.

SEE ALSO

   almn - Identifies re-indexing operator from cross-rotation function.

   othercell - Finds all possible alternative cells in all crystal
   systems.

   pointless - Automatic re-indexing to reference dataset.

   reindex - Re-indexes dataset once re-indexing operator is known.

AUTHORS

   Ian Tickle, Astex Therapeutics Ltd.
Tags: refindex (ccp4:, synopsis refindex, refindex, reindex, program), dataset, unsupported, (ccp4