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reflection file tools

phenix.reflection_file_converter
phenix.cns_as_mtz
phenix.mtz.dump

phenix.reflection_file_converter

Purpose phenix.reflection_file_converter is a simple utility program that allows a straightforward conversion of many reflection file formats to mtz, cns or scalepack format. Currently, combining several dataset into a single output file is not supported. Keywords Typing:

phenix.reflection_file_converter --help
results in:
Usage: phenix.reflection_file_converter [options] reflection_file ...

Options:
  -h, --help            show this help message and exit
  --unit-cell=10,10,20,90,90,120|FILENAME
                        External unit cell parameters
  --space-group=P212121|FILENAME
                        External space group symbol
  --symmetry=FILENAME   External file with symmetry information
  --weak-symmetry       symmetry on command line is weaker than symmetry found
                        in files
  --resolution=FLOAT    High resolution limit (minimum d-spacing, d_min)
  --low-resolution=FLOAT
                        Low resolution limit (maximum d-spacing, d_max)
  --label=STRING        Substring of reflection data label or number
  --non-anomalous       Averages Bijvoet mates to obtain a non-anomalous array
  --r-free-label=STRING
                        Substring of reflection data label or number
  --r-free-test-flag-value=FLOAT
                        Value in R-free array indicating assignment to free
                        set.
  --generate-r-free-flags
                        Generates a new array of random R-free flags (MTZ and
                        CNS output only).
  --use-lattice-symmetry-in-r-free-flag-generation
                        group twin/pseudo symmetry related reflections
                        together in r-free set (this is the default).
  --no-lattice-symmetry-in-r-free-flag-generation
                        opposite of --use-lattice-symmetry-in-r-free-flag-
                        generation
  --r-free-flags-fraction=FLOAT
                        Target fraction free/work reflections (default: 0.10).
  --r-free-flags-max-free=INT
                        Maximum number of free reflections (default: 2000).
  --r-free-flags-format=cns|ccp4
                        Convention for generating R-free flags
  --random-seed=INT     Seed for random number generator (affects generation
                        of R-free flags).
  --change-of-basis=STRING
                        Change-of-basis operator: h,k,l or x,y,z or
                        to_reference_setting, to_primitive_setting,
                        to_niggli_cell, to_inverse_hand
  --eliminate-invalid-indices
                        Remove indices which are invalid given the change of
                        basis desired
  --expand-to-p1        Generates all symmetrically equivalent reflections.
                        The space group symmetry is reset to P1. May be used
                        in combination with --change_to_space_group to lower
                        the symmetry.
  --change-to-space-group=SYMBOL|NUMBER
                        Changes the space group and merges equivalent
                        reflections if necessary
  --write-mtz-amplitudes
                        Converts intensities to amplitudes before writing MTZ
                        format; requires --mtz_root_label
  --write-mtz-intensities
                        Converts amplitudes to intensities before writing MTZ
                        format; requires --mtz_root_label
  --remove-negatives    Remove negative intensities or amplitudes from the
                        data set
  --massage-intensities
                        'Treat' negative intensities to get a positive
                        amplitude. |Fnew| = sqrt((Io+sqrt(Io**2
                        +2sigma**2))/2.0). Requires intensities as input and
                        the flags --mtz, --write_mtz_amplitudes and
                        --mtz_root_label.
  --scale-max=FLOAT     Scales data such that the maximum is equal to the
                        given value
  --scale-factor=FLOAT  Multiplies data with the given factor
  --sca=FILE            write data to Scalepack FILE ('--sca .' copies name of
                        input file)
  --mtz=FILE            write data to MTZ FILE ('--mtz .' copies name of input
                        file)
  --mtz-root-label=STRING
                        Root label for MTZ file (e.g. Fobs)
  --cns=FILE            write data to CNS FILE ('--cns .' copies name of input
                        file)
  --shelx=FILE          write data to SHELX FILE ('--shelx .' copies name of
                        input file)

Example: phenix.reflection_file_converter w1.sca --mtz .
Examples
  • Convert scalepack into an mtz format. Specify ouput filename (w1.mtz) and label for intensities (IP -> IP,SIGIP):

    phenix.reflection_file_converter w1.sca --mtz_root_label=IP --mtz=w1.mtz
    
  • Change basis to get data in primitive setting, merge to higher symmetry and bring to reference setting (three steps):

    phenix.reflection_file_converter c2.sca --change-of-basis=to_niggli_cell --sca=niggli.sca
    phenix.reflection_file_converter niggli.sca --change-to-space_group=R32:R --sca=r32r.sca
    phenix.reflection_file_converter r32r.sca --change-of-basis=to_reference_setting --sca=r32_hexagonal_setting.sca
    

phenix.cns_as_mtz

Purpose Converts all data in a CNS reflection file to MTZ format. Keywords Typing:

phenix.cns_as_mtz --help
results in:
Usage: phenix.cns_as_mtz [options] cns_file

Options:
  -h, --help            show this help message and exit
  --unit-cell=10,10,20,90,90,120|FILENAME
                        External unit cell parameters
  --space-group=P212121|FILENAME
                        External space group symbol
  --symmetry=FILENAME   External file with symmetry information
  -q, --quiet           suppress output

Example: phenix.cns_as_mtz scale.hkl
Example Extract unit cell parameters and space group symbol from a PDB coordinate file and reflection data from a CNS reflection file. Write MTZ file:
phenix.cns_as_mtz mad_scale.hkl --symmetry minimize.pdb

phenix.mtz.dump

Purpose Inspects an MTZ file. Optionally writes data in text format (human readable, machine readable, or spreadsheet). Keywords Typing:

phenix.mtz.dump --help
results in:
Usage: phenix.mtz.dump [options] file_name [...]

Options:
  -h, --help            show this help message and exit
  -v, --verbose         Enable CMTZ library messages.
  -c, --show-column-data
  -f KEYWORD, --column-data-format=KEYWORD
                        Valid keywords are: human_readable, machine_readable,
                        spreadsheet. Human readable is the default. The format
                        keywords can be abbreviated (e.g. -f s).
  -b, --show-batches
  --walk=ROOT_DIR       Find and process all MTZ files under ROOT_DIR