pipeline:window:sp_tilt_import []

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

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===== Usage =====

Usage in command line:

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

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.

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===== Input =====
=== Main Parameters ===
  ; 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)
  
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=== Advanced Parameters ===
  ; %%--%%apix : Angstroms per pixel, purely cosmetic, for screen output. (default 1.0)
  ; %%--%%verbosity : Controls how much information is written to screen (default 1)

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===== Output =====
  ; 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

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===== Description =====

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==== Method ====

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==== Reference ====

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==== Developer Notes ====

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==== Author / Maintainer ====
Tapu Shaikh

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==== Keywords ====
Category 1:: APPLICATIONS

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==== Files ====


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==== See also ====

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

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==== Bugs ====
There are no known bugs so far.

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