REFINDEX (CCP4: Unsupported Program)


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


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


"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 P22121 and P21212) 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.


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.


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:

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


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.


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


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.


Ian Tickle, Astex Therapeutics Ltd.