Python-based
Hierarchical
ENvironment
for
Integrated
Xtallography
Purpose
phenix.reflection_file_converter is a simple utility program that allows a straightforward conversion of many reflection file formats to mtz, cns, scalepack or shelx 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 (ignored for --shelx)
--scale_factor=FLOAT Multiplies data with the given factor (ignored for
--shelx)
--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). Data are automatically scaled if
necessary to fit into 8 column format.
Example: phenix.reflection_file_converter w1.sca --mtz .
Examples
Convert scalepack into an mtz format. Specify output filename (w1.mtz) and label for intensities (IP -> IP,SIGIP):
phenix.reflection_file_converter w1.sca --mtz_root_label=IP --mtz=w1.mtz
Convert mtz intensities into SHELX .hkl format. Specify output filename (data.hkl):
phenix.reflection_file_converter data.mtz --label=IOBS,SIGIOBS --shelx=data.hkl
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
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
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