Tilt Import : Imports per-particle defocus estimates from gCTF.

Usage in command line:

sp_tilt_import.py input_star_files output_directory --box_size=box_size --apix=pixel_size --verbosity=verbosity

The purpose of sp_tilt_import.py is to:

: merge STAR files created by gCTF
: convert coordinate files to .box format using sp_relion2sphire.py
: extract particles using sp_window.py
: generate SPHIRE particle stack using sp_relion2sphire.py

Standard usage:

sp_tilt_import.py input_star_files output_directory --box_size=box_size

Additional parameters:

sp_tilt_import.py input_star_files output_directory --box_size=box_size --apix=pixel_size --verbosity=verbosity

Pixel size is purely cosmetic, for screen output. Verbosity affects the amount of text written the the screen/log file.

input_star_files

Set of STAR files written by gCTF, one for each micrograph. (default required string)

output_directory

Directory where outputs will be written. (default required string)

--box_size

Particle box size for extraction, in pixels. (default None)

--apix

Angstroms per pixel, purely cosmetic, for screen output. (default 1.0)

--verbosity

Controls how much information is written to screen (default 1)

init_local.star

Merged STAR file from initial conversion from gCTF

sphire_micrographs.txt

List of micrographs

sphire_cter_partres.txt

CTF parameters for each micrograph, in CTER partres format

Coordinates/*.box

Coordinates in box format, one for each micrograph

Rebox/*.rbx

Rebox files, one for each micrograph

Particles/*.mrcs

Particle stacks, one for each micrographs

bdb:sphire_stack

SPHIRE combined particle BDB stack

all_local.star

Merged STAR file following extraction

ctf_params.txt

CTF parameters for each particle

Tapu Shaikh

Category 1:: APPLICATIONS

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

There are no known bugs so far.