Unblur cisTEM: Align frames of micrograph movies with Unblur.

Usage in command line

sp_unblur.py  unblur_path  input_micrograph_pattern  output_directory   --selection_file=SELECTION_FILE  --pixel_size=PIXEL_SIZE   --bin_factor=BIN_FACTOR  --skip_dose_adjustment --additional_dose_unadjusted  --voltage=VOLTAGE  --exposure_per_frame=EXPOSURE  --pre_exposure=EXPOSURE   --min_shift_initial=MIN_SHIFT_INITIAL  --outer_radius=OUTER_RADIUS  --b_factor=B_FACTOR  --half_width_vert=HALF_WIDTH_VERT  --half_width_hor=HALF_WIDTH_HOR  --termination=TERMINATION  --max_iterations=MAX_ITERATIONS  --dont_restore_noise_power  --gain_file=GAIN_FILE  --first_frame=FIRST_FRAME  --last_frame=LAST_FRAME  --distortion_angle=DISTORTION_ANGLE  --major_scale=MAJOR_SCALE  --minor_scale=MINOR_SCALE

sp_unblur exists in both MPI and non-MPI versions (Running MPI version does not require –MPI flag).

Run unblur with dose adjustment

mpirun -np 12 sp_unblur.py path/to/unblur 'Movies/*' unblur_out_dir –pixel_size=1.14 –voltage=300 –exposure_per_frame=1.3

Run unblur with dose adjustment and gain reference file

mpirun -np 12 sp_unblur.py path/to/unblur 'Movies/*' unblur_out_dir –pixel_size=1.14 –voltage=300 –exposure_per_frame=1.3 –gain_file=/path/to/gain.mrc

Run unblur without dose adjustment

mpirun -np 12 sp_unblur.py path/to/unblur 'Movies/*' unblur_out_dir –pixel_size=1.14 –skip_dose_adjustment

Run unblur without dose adjustment and in addition with dose adjustment

mpirun -np 12 sp_unblur.py path/to/unblur 'Movies/*' unblur_out_dir –pixel_size=1.14 –voltage=300 –exposure_per_frame=1.3 –additional_dose_unadjusted

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 (*).. The path pattern must be enclosed by single quotes (') or double quotes (“). (Note: sp_gui.py automatically adds single quotes (')). bdb files cannot 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. It cannot be an existing one. (This argument is specific to SPHIRE, and not directly used by Unblur and Summovie executables.) (default required string)

--selection_file

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)

--pixel_size

Pixel size [A]: The pixel size of input micrographs. (default 1.0)

--bin_factor

Bin factor

Output bin factor. (default 1.0)

--voltage

Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default 300.0)

--skip_dose_adjustment==True

--exposure_per_frame

Per frame exposure [e/A^2]: The electron dose per frame in e/A^2. (default 1.0)

--skip_dose_adjustment==True

--pre_exposure

Pre-exposure [e/A^2]: The electron does in e/A^2 used for exposure prior to imaging. (default 0.0)

--skip_dose_adjustment==True

--additional_dose_unadjusted

Create unadjusted sums in addition: Run unblur twice to also create dose unadjusted sums. (default False)

--skip_dose_adjustment==True

--gain_file

Gain file

Gain file in case of gain uncorrected movies. (default none)

--skip_dose_adjustment

Apply dose filter: Indicate if dose filter should be applied or not. By default, apply dose filter. (default False question reversed in GUI)

--min_shift_initial

Minimum shift for initial search [A]: Minimum shift for initial search [A] (default 2.0)

--outer_radius

Outer radius shift limit [A]: Outer radius shift limit (default 20.0)

--b_factor

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

--half_width_vert

Vertical Fourier central mask size: The half-width of central vertical line of Fourier mask. (default 1)

--half_width_hor

Horizontal Fourier central mask size: The half-width of central horizontal line of Fourier mask. (default 1)

--termination

Termination shift threshold: Termination shift threshold. (default 1)

--max_iterations

Maximum iterations: Maximum iterations. (default 20)

--dont_restore_noise_power

Restore noise power: Indicate if noise power should be restored after dose adjustment or not. By default, restore noise power. (default False question reversed in GUI)

--first_frame

First frame: First frame to use for sum. (default 1)

--last_frame

Last frame: Last frame to use for sum. (default 0)

--distortion_angle

Distortion Angle [deg]: Distortion Angle in degrees. (default 0.0)

--major_scale

Major scale

Major scale. (default 1.0)

--minor_scale

Minor scale: Minor scale. (default 1.0)

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/sp_unblur.py

sp_gui_unblur

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

There are no known bugs so far.