Correct Beam Tilt : Applies beam-tilt correction to particles.

Usage in command line

    sp_beamtilt.py output_directory --input_stack=INPUT_STACK --star_file=STAR_FILE --kv=KV --cs=CS --apix=APIX --tiltx=TILTX --tilty=TILTY --micdir=MICDIR --box_size=BOX_SIZE --coordsdir=COORDSDIR --partdir=PARTDIR --verbosity=verbosity_level --debug

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

The purpose of sp_beamtilt.py is to:

: read beam-tilt information, from a STAR file or from the command line
: corrects images for beam tilt
: applies those corrections to either an input stack or extracts them from particles
: write the correct particle stack to disk

1. Standard usage: Read beam-tilt data from STAR file and particles from stack:

mpirun -np 16 sp_beamtilt.py output_directory --input_stack bdb:Particles#data --star_file particles.star

STAR files from RELION v3.0 and v3.1 have been tested and should work.

2. Provide the beam-tilt parameters directly from the command line:

mpirun -np 16 sp_beamtilt.py output_directory --input_stack bdb:Particles#data --kv=200 --cs=1.4 --apix=0.885 --tiltx=-0.096436 --tilty=0.26850

Beam tilt is to be provided in units of milliradians. Other required parameters are accelerating voltage, spherical aberration constant, and pixel size.

3. Particles are to be extract directly from micrographs

mpirun -np 16 sp_beamtilt.py output_directory --star_file particles.star --micdir=input_micrograph_directory  --box_size=256 --coordsdir=output_coordinates_directory --partdir=output_particles_directry

This option has not been tested thoroughly.

; ; --input_stack : : Input particle stack. (default None) ; ; --star_file : : Input STAR file. (default None)

; ; --kv : : Accelerating voltage, kilovolts. (default None) ; ; --cs : : Spherical aberration constant. (default None) ; ; --apix : : Pixel size, Angstroms. (default None) ; ; --tiltx : : Beam tilt along x, in milliradians. (default None) ; ; --tilty : : Beam tilt along y, in milliradians. (default None) ; ; --micdir : : Input micrograph directory, if extracting particles. (default None) ; ; --box_size : : Box size, in pixels, if extracting particles. (default None) ; ; --coordsdir : : Output coordinates directory, if extracting particles. (default None) ; ; --partdir : : Output particles directory, if extracting particles. (default None) ; ; --verbosity : : Controls how much information will be written to the screen. (default 3) ; ; --debug : : Performs a dry run. (default False)

; ; bdb:all_corrected : : Tilt-corrected particles

Zivanov J., Nakane T., Forsberg B.O., Kimanius D., Hagen W.J.H., Lindahl E, Scheres S.H.W. (2018) “New tools for automated high-resolution cryo-EM structure determination in RELION.” eLife 7: e42166.

Eventually, we want to correct for beam tilt on the fly, and not write the corrected images to disk.

Tapu Shaikh

Category 1:: APPLICATIONS

sphire/bin/sp_beamtilt.py

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