UNIQUE (CCP4: Supported Program)

NAME

   unique - Generate a unique list of reflections

SYNOPSIS

   unique hklout foo.mtz
   [Keyworded input]

DESCRIPTION

   UNIQUE creates a unique list of reflections for a given unit cell
   with a given symmetry up to a specified high resolution limit. The
   output file can be used to complete a dataset (i.e. to give an MTZ
   file with all allowed reflections present whether or not data have
   been measured for them), and to give completeness information on
   the measured dataset. The procedure is as follows:
    1. Produce a list of the unique reflections in an MTZ file, using
       UNIQUE with the appropriate cell parameters, symmetry and
       resolution range;
    2. Use FREERFLAG to add a column of free-R flags to the MTZ file,
       to be used later for cross-validation;
    3. Add this column of free-R flags to the dataset MTZ file using
       CAD. Unmeasured data, i.e. reflections that are present in the
       column of free-R flags but not in the original dataset, are
       represented in the output of CAD as Missing Number Flag (MNF)
       entries.
    4. Run MTZDUMP on the output of CAD to get various statistics,
       including the number of missing data entries (i.e. MNFs) for
       each column of data. This gives the completeness of the dataset
       for the specified resolution range.

   A script to perform steps 1 - 3 is provided in $CETC/uniqueify (see
   below),   and   an   example   of   its   use   is  given  in
   $CEXAM/unix/runnable/unique-free-R. Note that this script only
   gives a high resolution limit to UNIQUE (see RESOLUTION keyword),
   and so the dataset is extended to the lowest possible resolution.
   This is the recommended practice.

   The 'uniqueify' script is also a part of the Convert to MTZ &
   Standardise task in the Reflection Data Utilities of the CCP4
   Graphical User Interface (CCP4I).

   If a column of free-R flags is already present in the incomplete
   dataset, then a modified procedure should be followed:
    1. Produce a list of the unique reflections using UNIQUE;
    2. Merge the output of UNIQUE with the dataset using CAD;
    3. Use the COMPLETE option of FREERFLAG to complete the free-R
       column;
    4. Remove  the surplus columns originating from UNIQUE using
       MTZUTILS;
    5. Use MTZDUMP again to analyse the dataset.

   This  sequence  is  performed  using  the  -f  switch  of the
   $CETC/uniqueify script.

   The old procedure using COMPLETE is now obsolete.

KEYWORDED INPUT

   The various data control lines are identified by keywords. Only the
   first 4 letters of each keyword are necessary.

   Compulsory

     CELL, RESOLUTION, SYMMETRY.

   Optional

     DEFAULT, LABOUT, RUN/GO/END, TITLE.

  CELL <a> <b> <c> [ <alpha> <beta> <gamma> ]

   Specify the unit cell. At least 3 numbers must be entered. Alpha,
   beta and gamma default to 90.0.

  RESOLUTION <Dmax>

   Maximum  resolution  -  either 4(sin theta/lambda)**2 or d in
   Angstrom. Unique reflections up to this limit are output to the MTZ
   file.

  SYMMETRY <Space group name or number>

   Symmetry of the output file.

  DEFAULT <default>

   <default> is a real number or missing data value (NaN) output in
   the F and SIGF columns. It defaults to NaN.

  TITLE <string>

   Title on the printer output and output MTZ file

  LABOUT <Proglab>=<Userlabel> ...

   Specify output column labels.

   The default column labels are H K L F SIGF, where F and SIGF have
   dummy values <default> (see DEFAULT keyword).

  RUN | GO | END

   Terminates keyworded input and runs the program.

INPUT AND OUTPUT FILES

   The output file is a reflection data file in standard MTZ format
   (i.e. one record/reflection) containing 5 items per reflection (see
   the LABOUT keyword for labels used).

   The  F and SIGF columns all take the <default> value (see the
   DEFAULT keyword).

PRINTER OUTPUT

   The printer output starts with details of the control data and the
   symmetry.  Limits  of the Miller indices are printed for this
   resolution range. Details of the output MTZ file followed by the
   total number of reflections tested and written out end the output.

PROGRAM FUNCTION

   The  program  UNIQUE  reads  in control data and calculates a
   reciprocal cell. From this cell the range of Miller indices for the
   required resolution range is calculated. The program then loops
   through each potential reflection and tests whether it satisfies
   the limiting conditions for this Laue group and/or whether the
   reflection is a systematic absence before outputting to the MTZ
   file.

uniqueify SCRIPT

   The full syntax of $CETC/uniqueify is:

   uniqueify [-s] [-f <label> | -p <fraction>] <input file>[.mtz]
   [<output file>]

   -s
          Keep systematic absences in the output MTZ file.

   -f <label>
          If your dataset already contains a free-R column you must
          specify this switch and give the label of the free-R column
          as it appears in the input MTZ file. uniqueify will deduce
          the style and range of flags used and preserve them when
          completing the free-R column.

   -p <fraction>
          If your dataset does not already contain a free-R column
          then you may specify the fraction of reflections to be
          tagged with each free-R indicator. <fraction> (default 0.05)
          is  passed as the argument to the FREERFRAC keyword of
          FREERFLAG (see FREERFLAG documentation).

   A VMS version ($CETC/UNIQUEIFY.COM) is also provided.

SEE ALSO

   freerflag, cad, mtzdump

AUTHOR

   A.G.W.Leslie

EXAMPLES

  Producing a set of reflection data

     unique HKLOUT x_unq.mtz << EOF
     TITLE  Unique data for protease
     LABOUT  F=FP SIGF=SIGFP
     SYMM P212121
     RESOL 1.40
     CELL 40.0 50.0 71.0
     EOF

  Statistics of completeness on a set of measured data

     #! first make the unique data
     #
     unique hklout x_unq.mtz <<eof-unique
     TITLE  Unique data for protease
     LABOUT  F=FP SIGF=SIGFP
     SYMM P212121
     RESOL 1.40
     CELL 40.0 50.0 71.0
     eof-unique
     #
     #! Now add free-R column
     #
     freerflag HKLIN x_unq.mtz HKLOUT x_unq2.mtz <<eof-freerflag
     END
     eof-freerflag
     #
     #! Now merge the free-R column of the unique file with the
     #! measured data
     #
     cad HKLIN1 x_unq2.mtz HKLIN2 p14_tru.mtz
         HKLOUT p14_tru_complete.mtz << eof-cad
     LABI FILE 1  E1=FreeR_flag
     LABI FILE 2  ALLIN
     END
     eof-cad
     #
     # ! Now run the merged file through MTZDUMP
     #
     mtzdump HKLIN p14_tru_complete.mtz << eof-mtzdump
     NREF 100
     END
     eof-mtzdump