Segclassmodel¶
Program to assign a series of 3D models to class averages
Input: Reference volumes
Output: Class average stack
Parameters¶
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). |
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)
Additional parameters (intermediate level)¶
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. |
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
Additional parameters (expert level)¶
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). |
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
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