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pipeline:meridien:sp_beamtilt [2021/02/19 16:19]
shaikh 		pipeline:meridien:sp_beamtilt [2021/02/19 16:34]
shaikh old revision restored (2021/02/19 14:19)
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 Correct Beam Tilt : Applies beam-tilt correction to particles. Correct Beam Tilt : Applies beam-tilt correction to particles.
  
 +\\
 ===== Usage ===== ===== Usage =====
  
 Usage in command line Usage in command line
  
-<code> +  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.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+
  
-</code> 
  
 +\\
 ===== Typical usage ===== ===== Typical usage =====
  
-sp_beamtilt exists in both MPI and non-MPI versions (Running MPI version does not require –MPI flag).+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: The purpose of sp_beamtilt.py is to:
  
-<code> +  : read beam-tilt information, from a STAR file or from the command line 
-: read beam-tilt information, from a STAR file or from the command line +  : corrects images for beam tilt 
-: corrects images for beam tilt +  : applies those corrections to either an input stack or extracts them from particles 
-: applies those corrections to either an input stack or extracts them from particles +  : write the correct particle stack to disk 
-: write the correct particle stack to disk+  
 +\\ __1. Standard usage: Read beam-tilt data from STAR file and particles from stack__:
  
-</code> +  mpirun -np 16 sp_beamtilt.py output_directory --input_stack bdb:Particles#data --star_file particles.star 
- +
- +
-__1. Standard usage: Read beam-tilt data from STAR file and particles from stack__: +
-<code> +
-mpirun -np 16 sp_beamtilt.py output_directory --input_stack bdb:Particles#data --star_file particles.star +
- +
-</code>+
  
 STAR files from RELION v3.0 and v3.1 have been tested and should work. 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__:
-__2. Provide the beam-tilt parameters directly from the command line__: +
-<code> +
-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+
  
-</code>+  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. 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
-__3. Particles are to be extract directly from micrographs__ +
-<code> +
-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 +
- +
-</code>+
  
 This option has not been tested thoroughly. This option has not been tested thoroughly.
 +   
 +\\
 ===== Input ===== ===== Input =====
- 
 === Main Parameters === === Main Parameters ===
- +  ; output_directory : Toplevel directory where outputs will be written. (default required string) 
-; ; <nowiki>--</nowiki>input_stack : : Input particle stack. (default None) ; ; <nowiki>--</nowiki>star_file : : Input STAR file. (default None) +  ; %%--%%input_stack : Input particle stack. (default None) 
 +  ; %%--%%star_file : Input STAR file. (default None) 
 +   
 +\\
 === Advanced Parameters === === Advanced Parameters ===
- +  ; %%--%%kv : Accelerating voltage, kilovolts. (default None) 
-; ; <nowiki>--</nowiki>kv : : Accelerating voltage, kilovolts. (default None) ; ; <nowiki>--</nowiki>cs : : Spherical aberration constant. (default None) ; ; <nowiki>--</nowiki>apix : : Pixel size, Angstroms. (default None) ; ; <nowiki>--</nowiki>tiltx : : Beam tilt along x, in milliradians. (default None) ; ; <nowiki>--</nowiki>tilty : : Beam tilt along y, in milliradians. (default None) ; ; <nowiki>--</nowiki>micdir : : Input micrograph directory, if extracting particles. (default None) ; ; <nowiki>--</nowiki>box_size : : Box size, in pixels, if extracting particles. (default None) ; ; <nowiki>--</nowiki>coordsdir : : Output coordinates directory, if extracting particles. (default None) ; ; <nowiki>--</nowiki>partdir : : Output particles directory, if extracting particles. (default None) ; ; <nowiki>--</nowiki>verbosity : : Controls how much information will be written to the screen. (default 3) ; ; <nowiki>--</nowiki>debug : : Performs a dry run. (default False) +  ; %%--%%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 ===== ===== Output =====
- +  ; bdb:all_corrected : Tilt-corrected particles 
-; ; bdb:all_corrected : : Tilt-corrected particles +  
 +\\
 ===== Description ===== ===== Description =====
  
 +\\
 ==== Method ==== ==== Method ====
  
 +\\
 ==== Reference ==== ==== 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. 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 ==== ==== Developer Notes ====
- 
 Eventually, we want to correct for beam tilt on the fly, and not write the corrected images to disk. Eventually, we want to correct for beam tilt on the fly, and not write the corrected images to disk.
  
 +\\
 ==== Author / Maintainer ==== ==== Author / Maintainer ====
- 
 Tapu Shaikh Tapu Shaikh
  
 +\\
 ==== Keywords ==== ==== Keywords ====
- 
 Category 1:: APPLICATIONS Category 1:: APPLICATIONS
  
 +\\
 ==== Files ==== ==== Files ====
- 
 sphire/bin/sp_beamtilt.py sphire/bin/sp_beamtilt.py
  
 +\\
 ==== See also ==== ==== See also ====
  
 +\\
 ==== Maturity ==== ==== Maturity ====
- 
 Beta:: Under evaluation and testing. Please let us know if there are any bugs. Beta:: Under evaluation and testing. Please let us know if there are any bugs.
  
 +\\
 ==== Bugs ==== ==== Bugs ====
  
 +\\
  
pipeline/meridien/sp_beamtilt.txt · Last modified: 2021/02/19 16:34 by shaikh

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