REFINDEX (CCP4: Unsupported Program)
- 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]
"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.
INPUT AND OUTPUT FILES
The following input and output files are used by the program:
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 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
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
othercell - Finds all possible
alternative cells in all crystal systems.
pointless - Automatic re-indexing to
reindex - Re-indexes dataset once
re-indexing operator is known.
Ian Tickle, Astex Therapeutics Ltd.