Micrograph Movie Alignment: Align frames of micrograph movies with Unblur & Summovie.

Usage in command line

sxunblur.py  unblur_path  input_micrograph_pattern  output_directory  --summovie_path=SUMMOVIE_PATH  --selection_list=SELECTION_LIST  --nr_frames=NUM_OF_FRAMES  --pixel_size=PIXEL_SIZE  --voltage=VOLTAGE  --exposure_per_frame=EXPOSURE  --pre_exposure=EXPOSURE  --nr_threads=NUM_OF_THREADS  --save_frames  --skip_dose_filter  --expert_mode  --shift_initial=SHIFT  --shift_radius=SHIFT_RADISU  --b_factor=B_FACTOR  --fourier_vertical=VERTICAL_MASK  --fourier_horizontal=HORIZONTAL_MASK  --shift_threshold=SHIFT_THRESHOLD  --iterations=ITERATIONS  --dont_restore_noise  --verbose

sxunblur exists only in non-MPI version.

Run Unblur with dose-filtering, and then run Summovie without dose-filtering.

sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' outdir_unblur --summovie_path=~/my_app/summovie --nr_frames=25 --pixel_size=1.19 --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0 --nr_threads=1

Run Unblur with dose-filtering, and then run Summovie without dose-filtering with selection list.

sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' outdir_unblur --summovie_path=~/my_app/summovie --selection_list=selected_micrograph_file --nr_frames=25 --pixel_size=1.19 --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0 --nr_threads=1

Run Unblur without dose-filtering.

sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' outdir_unblur --nr_frames=25 --pixel_size=1.19 --skip_dose_filter --nr_threads=1

Run Unblur without dose-filtering, and save the frames.

sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' outdir_unblur --nr_frames=25 --pixel_size=1.19 --skip_dose_filter --save_frames --nr_threads=1

Run Unblur with dose-filtering, and then run Summovie without dose-filtering with all options.

sxunblur.py ~/my_app/unblur 'movies/micrograph_*_frames.mrc' outdir_unblur --summovie_path=~/my_app/summovie --nr_frames=25 --pixel_size=1.19 --exposure_per_frame=1.0 --voltage=300.0 --pre_exposure=0.0 --save_frames --expert_mode --shift_initial=2.0 --shift_radius=200.0 --b_factor=1500.0 --fourier_vertical=1 --fourier_horizontal=1 --shift_threshold=0.1 --iterations=10 --verbose --nr_threads=1

unblur_path

Unblur executable path: Specify the file path of Unblur executable. (This argument is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default required string)

input_micrograph_pattern

Input movie path pattern: Specify path pattern of input micrograph movies with a wild card (*). Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc). The path pattern must be enclosed by single quotes (') or double quotes (“). (Note: sxgui.py automatically adds single quotes (')). bdb files can not be selected as input micrograph movies. (This argument is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default required string)

output_directory

Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (This argument is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default required string)

--summovie_path

Summovie executable path: Specify the file path of Summovie executable. (This option is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default none)

--selection_list

Movie selection file: Specify a name of micrograph movie selection list text file. The file extension must be '.txt'. If this is not provided, all files matched with the micrograph movie name pattern will be processed. (This option is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default none)

--nr_frames

Number of movie frames: The number of movie frames in each input micrograph. (default 3)

--pixel_size

Pixel size [A]: The pixel size of input micrographs. (default required float)

--voltage

Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. Will be ignored when --skip_dose_filter option is used. (default 300.0)

--exposure_per_frame

Per frame exposure [e/A^2]: The electron dose per frame in e/A^2. Will be ignored when --skip_dose_filter option is used. (default 2.0)

--pre_exposure

Pre-exposure [e/A^2]: The electron does in e/A^2 used for exposure prior to imaging. Will be ignored when --skip_dose_filter option is used. (default 0.0)

--nr_threads

Number of threads: The number of threads Unblur can use. The higher the faster, but it requires larger memory. (default 1)

--save_frames

Save aligned movie frames: Save aligned movie frames. This option slows down the process. (default False)

--skip_dose_filter

Apply dose filter: Indicate if dose filter should be applied or not. With this option, --voltage, --exposure_per_frame, and --pre_exposure will be ignored. By default, apply dose filter. (default False question reversed in GUI)

--expert_mode

Use expert mode: Requires --initial_shift, --shift_radius, --b_factor, --fourier_vertical, --fourier_horizontal, --shift_threshold, --iterations, --dont_restore_noise, and --verbosity options. (default False)

--shift_initial

Minimum shift for initial search [A]: Effective only when --expert_mode option is used. (default 2.0)

--shift_radius

Outer radius shift limit [A]: Effective only when --expert_mode option is used. (default 200.0)

--b_factor

Apply B-factor to images [A^2]: Effective only when --expert_mode option is used. (default 1500.0)

--fourier_vertical

Vertical Fourier central mask size: The half-width of central vertical line of Fourier mask. Effective only when --expert_mode option is used. (default 1)

--fourier_horizontal

Horizontal Fourier central mask size: The half-width of central horizontal line of Fourier mask. Effective only when --expert_mode option is used. (default 1)

--shift_threshold

Termination shift threshold: Effective only when --expert_mode option is used. (default 0.1)

--iterations

Maximum iterations: Effective only when --expert_mode option is used. (default 10)

--dont_restore_noise

Restore noise power: Indicate if noise power should be restored or not. By default, restore noise power. Effective only when --expert_mode option is used. (default False question reversed in GUI)

--verbose

Verbose: Effective only when --expert_mode option is used. (default False)

The program automatically creates the following subdirectories in the specified output directory.

Run without dose-filtering:

• Sum files will be written to the corrsum directory.
• Log files will be written to the logfiles directory.
• Aligned frames will be written to the corrsum directory.
• Shift files will be written to the shift directory.
• FRC files will be written to the frc directory.

Run with dose-filtering (as without dose-filtering plus):

• Dose filtered sum files will be written to the corrsum_dose_filtered directory.
• Log files will be written to the logfiles directory.
• Dose filtered aligned frames will be written to the corrsum_dose_filtered directory.
• Shift files will be written to the shift directory.
• FRC files will be written to the frc directory.

Unblur & Summovie

Markus Stabrin

Category 1:: APPLICATIONS

sparx/bin/sxunblur.py

sxgui_unblur

Beta:: Under evaluation and testing. Please let us know if there are any bugs.

There are no known bugs so far.