.. _segclassreconstruct: Segclassreconstruct ------------------- Program to compute 3D reconstruction from a single class average using a range of different helical symmetries +--------------------------------------------------+--------------------------------------------------+ | |segclassreconstruct_input.png| | |segclassreconstruct_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Class average stack | Output: Volume name | +--------------------------------------------------+--------------------------------------------------+ .. |segclassreconstruct_input.png| image:: ../gallery_images/segclassreconstruct_input.png :alt: tree :width: 4 cm :target: ../_images/segclassreconstruct_input.png .. |segclassreconstruct_output.png| image:: ../gallery_images/segclassreconstruct_output.png :alt: tree :width: 4 cm :target: ../_images/segclassreconstruct_output.png .. _making_a_segclassreconstruct_table_for_beginner: Parameters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Class average stack avgerages.hdf Class average stack: accepted file formats (hdf). Volume name recvol.hdf Output name for volumes of grid search (completion to 'name_riseXXX_rot_XXX.ext' or 'name_pitchXXX_unitno_XXX.ext\): accepted image file formats (hdf) Class number to be analyzed 3 Class number to be analyzed (1st class is 0) (accepted values min=0, max=2000). Estimated helix inner and outer diameter in Angstrom (0, 190) Generous inner and outer diameter of helix required for cylindrical mask in Angstrom (accepted values min=0, max=1500). Pixel size in Angstrom 1.163 Pixel size is an imaging parameter (accepted values min=0.001, max=100). Helical rise/rotation or pitch/number of units per turn choice rise/rotation Choose whether helical 'rise/rotation' or 'pitch/unit_number' of units per turn pairs are given for generating the helical lattice. Range of helical rise or pitch search in Angstrom (1.0, 10.0) Helical rise or pitch (Angstrom) range (from ... to ...) to be reconstructed (accepted values min=0, max=1000). Range of helical rotation in degrees or number of units per turn search (1.0, 300.0) Helical rotation (degrees) or 'number of units per turn' range (from ... to ...) to be reconstructed (accepted values min=-360, max=360). Increments of helical symmetry steps in Angstrom or degrees (1.0, 0.1) Helical rise (Angstrom) and rotation (degrees) increments to be reconstructed (accepted values min=0, max=100). ============================================================================== ============================================================================== ==================================================================================================== .. _segclassreconstruct_parameter_file_for_beginner: Sample parameter file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You may run the program in the command line by providing the parameters via a text file:: segclassreconstruct --f parameterfile.txt Where the format of the parameters is:: Class average stack = avgerages.hdf Volume name = recvol.hdf Class number to be analyzed = 3 Estimated helix inner and outer diameter in Angstrom = (0, 190) Pixel size in Angstrom = 1.163 Helical rise/rotation or pitch/number of units per turn choice = rise/rotation Range of helical rise or pitch search in Angstrom = (1.0, 10.0) Range of helical rotation in degrees or number of units per turn search = (1.0, 300.0) Increments of helical symmetry steps in Angstrom or degrees = (1.0, 0.1) .. _making_a_segclassreconstruct_table_for_intermediate: Additional parameters (intermediate level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Keep intermediate files False Keep 3D reconstruction files. Caution: depending on the size of the helical symmetry grid this can generate vast amounts of data. Montage stack of class average vs. reprojection images reprojection_montage.hdf Output montage of images from class average vs reprojection stack of 3D reconstructions: accepted image file formats (hdf) Montage stack of class average vs. reprojection power spectra power_montage.hdf Output montage of power spectra from class average and reprojection stack of 3D reconstructions: accepted image file formats (hdf) Binning option True Micrograph is reduced in size by binning. Binning factor 3 Segments are reduced in size by binning factor (accepted values min=1, max=20). Rotational symmetry 1 Additional x-fold rotational symmetry or x-number of helix start (accepted values min=1, max=100). Helix polarity polar Choose whether helix is 'polar' or 'apolar'. Polar helices have different ends at the top and bottom. Only the predominant direction within a helix will be used for the reconstruction. In apolar helices they are related by 180 degree rotation. Thus each segment can be inserted twice in the 3D reconstruction in opposite directions. Out-of-plane tilt angle 0 Out-of-plane tilt angle in degrees (0=no out-of-plane tilt) of class average view used for 3D reconstruction (accepted values min=-40, max=40). Center option True Segments are centered and rotationally aligned with respect to their helix axis MPI option True OpenMPI installed (mpirun). Number of CPUs 8 Number of processors to be used (accepted values min=1, max=1000). Temporary directory /tmp Temporary directory should have fast read and write access. ============================================================================== ============================================================================== ==================================================================================================== .. _segclassreconstruct_parameter_file_for_intermediate: Sample parameter file (intermediate level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You may run the program in the command line by providing the parameters via a text file:: segclassreconstruct --f parameterfile.txt Where the format of the parameters is:: Class average stack = avgerages.hdf Volume name = recvol.hdf Class number to be analyzed = 3 Estimated helix inner and outer diameter in Angstrom = (0, 190) Pixel size in Angstrom = 1.163 Helical rise/rotation or pitch/number of units per turn choice = rise/rotation Range of helical rise or pitch search in Angstrom = (1.0, 10.0) Range of helical rotation in degrees or number of units per turn search = (1.0, 300.0) Increments of helical symmetry steps in Angstrom or degrees = (1.0, 0.1) Keep intermediate files = False Montage stack of class average vs. reprojection images = reprojection_montage.hdf Montage stack of class average vs. reprojection power spectra = power_montage.hdf Binning option = True Binning factor = 3 Rotational symmetry = 1 Helix polarity = polar Out-of-plane tilt angle = 0 Center option = True MPI option = True Number of CPUs = 8 Temporary directory = /tmp .. _making_a_segclassreconstruct_table_for_expert: Additional parameters (expert level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Percent of image reconstruction size 50 Percent of image dimension to be used for helical reconstruction, i.e. number of views inserted in reconstruction = (100 - percent)*imagesize in Angstrom / helical rise) (accepted values min=10, max=100). Minimum number of images for 3D reconstruction 8 Minimum number of images required for 3D reconstruction. Below this value no 3D reconstruction possible (accepted values min=4, max=100). Local symmetry grid search False Local symmetry grid search fixes the number of images that are inserted in each reconstruction ============================================================================== ============================================================================== ==================================================================================================== .. _segclassreconstruct_parameter_file_for_expert: Sample parameter file (expert level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You may run the program in the command line by providing the parameters via a text file:: segclassreconstruct --f parameterfile.txt Where the format of the parameters is:: Class average stack = avgerages.hdf Volume name = recvol.hdf Class number to be analyzed = 3 Estimated helix inner and outer diameter in Angstrom = (0, 190) Pixel size in Angstrom = 1.163 Helical rise/rotation or pitch/number of units per turn choice = rise/rotation Range of helical rise or pitch search in Angstrom = (1.0, 10.0) Range of helical rotation in degrees or number of units per turn search = (1.0, 300.0) Increments of helical symmetry steps in Angstrom or degrees = (1.0, 0.1) Keep intermediate files = False Montage stack of class average vs. reprojection images = reprojection_montage.hdf Montage stack of class average vs. reprojection power spectra = power_montage.hdf Binning option = True Binning factor = 3 Rotational symmetry = 1 Helix polarity = polar Out-of-plane tilt angle = 0 Percent of image reconstruction size = 50 Minimum number of images for 3D reconstruction = 8 Local symmetry grid search = False Center option = True MPI option = True Number of CPUs = 8 Temporary directory = /tmp .. _using_segclassreconstruct_on_cmdline: Command line options ~~~~~~~~~~~~~~~~~~~~~~~ When invoking segclassreconstruct, you may specify any of these options:: usage: segclassreconstruct [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--keep_intermediate_files] [--binning_option] [--local_symmetry_grid_search] [--center_option] [--mpi_option] [input_output [input_output ...]] Program to compute 3D reconstruction from a single class average using a range of different helical symmetries positional arguments: input_output Input and output files optional arguments: -h, --help show this help message and exit --g, --GUI GUI option: read input parameters from GUI --p, --promptuser Prompt user option: read input parameters from prompt --f FILENAME, --parameterfile FILENAME File option: read input parameters from FILENAME --c, --cmd Command line parameter option: read only boolean input parameters from command line and all other parameters will be assigned from other sources --l LOGFILENAME, --logfile LOGFILENAME Output logfile name as specified --d DIRECTORY_NAME, --directory DIRECTORY_NAME Output directory name as specified --version show program's version number and exit --keep_intermediate_files, --kee Keep 3D reconstruction files. Caution: depending on the size of the helical symmetry grid this can generate vast amounts of data. (default: False) --binning_option, --bin Micrograph is reduced in size by binning. (default: False) --local_symmetry_grid_search, --loc Local symmetry grid search fixes the number of images that are inserted in each reconstruction (default: False) --center_option, --cen Segments are centered and rotationally aligned with respect to their helix axis (default: False) --mpi_option, --mpi OpenMPI installed (mpirun). (default: False) Program flow ~~~~~~~~~~~~~~~~~~~~ #. prepare_segclassreconstruct: Prepare 3D reconstruction #. reconstruct_volumes_for_each_symmetry_pair: Reconstruct_helically symmetric volumes from class average #. enter_grid_values_in_database: Enter grid values in database Functions ~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 segclassreconstruct_functions