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.

output_directory

Toplevel directory where outputs will be written. (default required string)

--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.