Segclassreconstruct¶
Program to compute 3D reconstruction from a single class average using a range of different helical symmetries
Input: Class average stack
Output: Volume name
Parameters¶
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). |
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)
Additional parameters (intermediate level)¶
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. |
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
Additional parameters (expert level)¶
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 |
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
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