.. _segclassmodel: Segclassmodel ------------- Program to assign a series of 3D models to class averages +--------------------------------------------------+--------------------------------------------------+ | |segclassmodel_input.png| | |segclassmodel_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Reference volumes | Output: Class average stack | +--------------------------------------------------+--------------------------------------------------+ .. |segclassmodel_input.png| image:: ../gallery_images/segclassmodel_input.png :alt: tree :width: 4 cm :target: ../_images/segclassmodel_input.png .. |segclassmodel_output.png| image:: ../gallery_images/segclassmodel_output.png :alt: tree :width: 4 cm :target: ../_images/segclassmodel_output.png .. _making_a_segclassmodel_table_for_beginner: Parameters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Reference volumes recvol???.hdf Input 3D reconstructions: to be reprojected and used for projection matching with provided classes. They should be generated using segmentrefine3d or segclassreconstruct because they require 'rise/rotation' and 'point_sym' entries in their header. Class average stack avgerages.hdf Class average stack: accepted file formats (hdf). spring.db file spring.db Program requires a combined spring.db from segment (and optional: micctfdetermine). An updated spring.db will be created in the working directory. Pixel size in Angstrom 1.163 Pixel size is an imaging parameter (accepted values min=0.001, max=100). Estimated helix width and height in Angstrom (200, 600) Generous width and height measure of helix required for rectangular mask (accepted values min=20, max=1500). ============================================================================== ============================================================================== ==================================================================================================== .. _segclassmodel_parameter_file_for_beginner: Sample parameter file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You may run the program in the command line by providing the parameters via a text file:: segclassmodel --f parameterfile.txt Where the format of the parameters is:: Reference volumes = recvol???.hdf Class average stack = avgerages.hdf spring.db file = spring.db Pixel size in Angstrom = 1.163 Estimated helix width and height in Angstrom = (200, 600) .. _making_a_segclassmodel_table_for_intermediate: Additional parameters (intermediate level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Number of projections azimuthal/out-of-plane angle (90, 7) Number of projections (e.g. 90 azimuthal projections per 360 degrees - projection every four degrees, out-of-plane tilt 7 projections from -12 to 12 degrees to be searched for 3D reconstruction. High- and maximum resolution reconstructions will be further refined by 5 * number of specified azimuthal and out-of-plane angles (accepted values min=1, max=1000). Out-of-plane tilt angle range (-12, 12) Expected out-of-plane tilt angle in degrees (0=no out-of-plane tilt) of helices used for 3D reconstruction (accepted values min=-40, max=40). Keep intermediate files False Keep reprojection stack of models. Limit in-plane rotation True Restricts in-plane rotation alignment. Delta in-plane rotation angle 10.0 Rotational alignment is being performed within +/- delta angle from 0 and 180 degrees (delta=0 means only 0/180 are checked, delta=180 means no rotational restraint) (accepted values min=0, max=180). X and Y translation range in Angstrom (50, 50) Translational range of alignment search perpendicular and along helix axis (X: off-center helical axis, Y: (minimum y-range=helical rise/2) (accepted values min=0, max=1000). Internal binning factor 2 In order to speed up alignments images can be optionally binned (accepted values min=1, max=20). High-pass filter option False Option to high-pass filter images before alignment or band-pass filter in combination with low-pass filter. Low-pass filter option True Option to low-pass filter images before alignment or band-pass filter in combination with high-pass filter. High and low-pass filter cutoffs in 1/Angstrom (0.001, 0.09) Filter design for high- and low-pass filter with cutoffs in 1/Angstrom. Maximum spatial frequency is 1/(2*pixelsize) (accepted values min=0, max=1). 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. ============================================================================== ============================================================================== ==================================================================================================== .. _segclassmodel_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:: segclassmodel --f parameterfile.txt Where the format of the parameters is:: Reference volumes = recvol???.hdf Class average stack = avgerages.hdf spring.db file = spring.db Number of projections azimuthal/out-of-plane angle = (90, 7) Out-of-plane tilt angle range = (-12, 12) Keep intermediate files = False Pixel size in Angstrom = 1.163 Estimated helix width and height in Angstrom = (200, 600) Limit in-plane rotation = True Delta in-plane rotation angle = 10.0 X and Y translation range in Angstrom = (50, 50) Internal binning factor = 2 High-pass filter option = False Low-pass filter option = True High and low-pass filter cutoffs in 1/Angstrom = (0.001, 0.09) MPI option = True Number of CPUs = 8 Temporary directory = /tmp .. _making_a_segclassmodel_table_for_expert: Additional parameters (expert level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Classes select option False Choose whether to select any particular classes. Include or exclude classes include Choose whether to 'include' or 'exclude' specified classes. Classes list 1-9, 11, 13 List of comma-separated class ids, e.g. '1-10, 12, 14' (1st class is 0). B-Factor 0 B-Factor in 1/Angstrom^2 to be applied to images. Zero no modulation of frequencies. Negative B-factors enhance high-resolution frequencies. Positive B-factors dampen high-resolution frequencies (accepted values min=-50000, max=50000). Custom filter option False Option to custom filter images before alignment. Custom-built filter file filter_function.dat Custom-built filter function with two columns (normalized spatial frequency 0 - 0.5, Fourier filter coefficients between 0 - 1): accepted file formats (txt, .dat). ============================================================================== ============================================================================== ==================================================================================================== .. _segclassmodel_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:: segclassmodel --f parameterfile.txt Where the format of the parameters is:: Reference volumes = recvol???.hdf Class average stack = avgerages.hdf spring.db file = spring.db Classes select option = False Include or exclude classes = include Classes list = 1-9, 11, 13 Number of projections azimuthal/out-of-plane angle = (90, 7) Out-of-plane tilt angle range = (-12, 12) Keep intermediate files = False Pixel size in Angstrom = 1.163 Estimated helix width and height in Angstrom = (200, 600) Limit in-plane rotation = True Delta in-plane rotation angle = 10.0 X and Y translation range in Angstrom = (50, 50) Internal binning factor = 2 High-pass filter option = False Low-pass filter option = True High and low-pass filter cutoffs in 1/Angstrom = (0.001, 0.09) B-Factor = 0 Custom filter option = False Custom-built filter file = filter_function.dat MPI option = True Number of CPUs = 8 Temporary directory = /tmp .. _using_segclassmodel_on_cmdline: Command line options ~~~~~~~~~~~~~~~~~~~~~~~ When invoking segclassmodel, you may specify any of these options:: usage: segclassmodel [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--classes_select_option] [--keep_intermediate_files] [--limit_in-plane_rotation] [--high-pass_filter_option] [--low-pass_filter_option] [--custom_filter_option] [--mpi_option] [input_output [input_output ...]] Program to assign a series of 3D models to class averages 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 --classes_select_option, --cla Choose whether to select any particular classes. (default: False) --keep_intermediate_files, --kee Keep reprojection stack of models. (default: False) --limit_in-plane_rotation, --lim Restricts in-plane rotation alignment. (default: False) --high-pass_filter_option, --hig Option to high-pass filter images before alignment or band-pass filter in combination with low-pass filter. (default: False) --low-pass_filter_option, --low Option to low-pass filter images before alignment or band-pass filter in combination with high-pass filter. (default: False) --custom_filter_option, --cus Option to custom filter images before alignment. (default: False) --mpi_option, --mpi OpenMPI installed (mpirun). (default: False) Program flow ~~~~~~~~~~~~~~~~~~~~ #. prepare_models: Prepare provided models for 3D reprojection #. launch_segmentalign2d_to_match_classes_against_projections: Aligns class averages to model reprojections Functions ~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 segclassmodel_functions