MTools
create_population
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-d, --directory Required. Path to the directory where the new population
will be located. All future species will also go there, so
make sure there is enough space.
-n, --name Required. Name of the new population.
--help Display this help screen.
--version Display version information.
create_source
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file to which
to add the new data source.
-s, --processing_settings Required. Path to a .settings file used to
pre-process the frame or tilt series this source
should include; desktop Warp will usually
generate a previous.settings file
-n, --name Required. Name of the new data source.
--nframes Maximum number of tilts or frames to use in
refinements. Leave empty or set to 0 to use the
maximum number available.
--files Optional STAR file with a list of files to
intersect with the full list of frame or tilt
series referenced by the settings.
--help Display this help screen.
--version Display version information.
create_species
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file to which to
add the new data source.
-n, --name Required. Name of the new species.
-d, --diameter Required. Molecule diameter in Angstrom.
-s, --sym (Default: C1) Point symmetry, e.g. C1, D7, O.
--helical_units (Default: 1) Number of helical asymmetric units
(only relevant for helical symmetry).
--helical_twist Helical twist in degrees, positive = right-handed
(only relevant for helical symmetry).
--helical_rise Helical rise in Angstrom (only relevant for helical
symmetry).
--helical_height Height of the helical segment along the Z axis in
Angstrom (only relevant for helical symmetry).
-t, --temporal_samples (Default: 1) Number of temporal samples in each
particle pose's trajectory.
--half1 Required. Path to first half-map file.
--half2 Required. Path to second half-map file.
-m, --mask Required. Path to a tight binary mask file. M will
automatically expand and smooth it based on current
resolution
--angpix Override pixel size value found in half-maps.
--angpix_resample Resample half-maps and masks to this pixel size.
--lowpass Optional low-pass filter (in Angstrom), applied to
both half-maps.
--particles_relion Path to _data.star-like particle metadata from
RELION.
--particles_m Path to particle metadata from M.
--angpix_coords Override pixel size for RELION particle coordinates.
--angpix_shifts Override pixel size for RELION particle shifts.
--ignore_unmatched Don't fail if there are particles that don't match
any data sources.
--help Display this help screen.
--version Display version information.
rotate_species
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file.
-s, --species Required. Path to the .species file, or its GUID.
--angle_rot Required. First Euler angle (Rot in RELION) in degrees.
--angle_tilt Required. Second Euler angle (Tilt in RELION) in degrees.
--angle_psi Required. Third Euler angle (Psi in RELION) in degrees.
--help Display this help screen.
--version Display version information.
shift_species
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file.
-s, --species Required. Path to the .species file, or its GUID.
-x Required. Shift along the X axis in Angstrom. New map
center will be at current center + this value.
-y Required. Shift along the X axis in Angstrom. New map
center will be at current center + this value.
-z Required. Shift along Z axis in Angstrom. New map center
will be at current center + this value.
--help Display this help screen.
--version Display version information.
expand_symmetry
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file.
-s, --species Required. Path to the .species file, or its GUID.
--expand_from Symmetry to use for the expansion if it is different from
the one specified in the species (e.g. expand only one
sub-symmetry of a higher symmetry).
--expand_to Remaining symmetry that will be set as the species'
symmetry, e.g. C1 (when using --expand_from to expand only
part of the symmetry).
--helical_units (Default: 1) Number of asymmetric subunits in the helical
symmetry to expand
--helical_twist Twist of the helical symmetry to expand, in degrees
--helical_rise Rise of the helical symmetry to expand, in Angstrom
--help Display this help screen.
--version Display version information.
resample_trajectories
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file.
-s, --species Required. Path to the .species file, or its GUID.
--samples Required. The new number of samples, usually between 1
(small particles) and 3 (very large particles).
--help Display this help screen.
--version Display version information.
update_mask
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file.
-s, --species Required. Path to the .species file, or its GUID.
-m, --map Required. Path to the MRC map to be used to create the new
mask.
-t, --threshold Required. Binarization threshold to convert the input map
to a mask.
-d, --dilate (Default: 0) Dilate the binary mask by this many voxels.
-c, --center Center the species around the new mask's center of mass.
--help Display this help screen.
--version Display version information.
list_species
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file.
--help Display this help screen.
--version Display version information.
list_sources
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file.
--help Display this help screen.
--version Display version information.
add_source
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file.
-s, --source Required. Path to the .source file.
--help Display this help screen.
--version Display version information.
remove_species
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file.
-s, --species Required. Path to the .species file, or its GUID.
--help Display this help screen.
--version Display version information.
remove_source
MTools 2.0.0+db859c58158e0ac5179769d57c317a6c3b73b03d
Copyright (C) 2024 MTools
-p, --population Required. Path to the .population file.
-s, --source Required. Path to the .source file, or its GUID.
--help Display this help screen.
--version Display version information.