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pipeline:meridien:sp_beamtilt
This version (2021/02/19 16:34) was approved by shaikh.The Previously approved version (2021/02/19 14:19) is available.Diff

sp_beamtilt

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


Usage

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


Typical usage

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

Main Parameters

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)


Advanced Parameters

--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)


Output

bdb:all_corrected
Tilt-corrected particles


Description


Method


Reference

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.

Developer Notes

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


Author / Maintainer

Tapu Shaikh


Keywords

Category 1:: APPLICATIONS


Files

sphire/bin/sp_beamtilt.py


See also


Maturity

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


Bugs


pipeline/meridien/sp_beamtilt.txt · Last modified: 2021/02/19 16:34 by shaikh