pipeline:utilities:sp_ctf_refine

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pipeline:utilities:sp_ctf_refine [2019/04/02 11:29] (current)
lusnig created
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 +~~NOTOC~~
 +
 +===== sp_ctf_refine meridien =====
 +CTF refine (Meridien): Refine the defocus per particle
 +
 +
 +\\
 +===== Usage =====
 +
 +Usage in command line
 +
 +  sp_ctf_refine.py meridien path_to_input_stack output_directory refinement_dir ​ --mask=path_to_mask --range=defocus_range --delta=defocus_delta --resolution=nominal_resolution --pixelsize=pixelsize --number_part=NUMBER_PARTICLES
 +
 +\\
 +===== Typical usage =====
 +
 +Before doing defocus refinement, you should have reached ~4 angstrom.
 +sp_ctf_refine.py exists only in non-MPI version.
 +
 +
 +\\
 +===== Input =====
 +=== Main Parameters ===
 +  ; path_to_input_stack : Input stack path  : Path to input stack. (default required)
 +  ; output_directory : Output directory : Folder to output files etc. (default required)
 +  ; refinement_dir : Meridien directory : Path to Merdien directory. ​ (default required)
 +  ; %%--%%mask : Path to mask : Path to mask used. (default none)
 +
 +\\
 +=== Advanced Parameters ===
 +  ; %%--%%range : Defocus search range [mum] : Search range +- around the current defocus value. (default 0.15)
 +  ; %%--%%delta : Defocus search delta [mum] : Finest search delta. (default 0.0025)
 +  ; %%--%%resolution : Nominal resolution [A] : Nominal resolution of the reconstruction. (default None)
 +  ; %%--%%pixelsize : Pixelsize [A] : Pixelsize in Angstrom. (default None) : %%--%%resolution!=None
 +  ; %%--%%number_part : Number of particles : Number of particles to process. Mainly for debugging. (default none)
 +
 +\\
 +===== Output =====
 +It will write a virtual stack with updated defocus information in the header. Furthermore it
 +creates plot for error in the your output directory
 +
 +\\
 +=== List of Output Files ===
 +- A virtual stack with updated header information
 +- particle_results.txt:​ list with PARTICLE_ID,​ERROR,​NEW_DEFOCUS,​SIGNIFICANCE
 +- error_cdf.png:​ Plot of the error distribution
 +- img folder: One image per micrograph containing defocus and error maps
 +
 +
 +\\
 +==== Method ====
 +-
 +
 +\\
 +==== Developer Notes ====
 +=== 2019/02/21 Thorsten Wagner ===
 +  * Initial creation of the document
 +
 +\\
 +==== Reference ====
 +-
 +
 +\\
 +==== Author / Maintainer ====
 +Thorsten Wagner
 +
 +\\
 +==== Keywords ====
 +Category 1:: APPLICATIONS
 +
 +\\
 +==== Files ====
 +sparx/​bin/​sp_ctf_refine.py
  
  • pipeline/utilities/sp_ctf_refine.txt
  • Last modified: 2019/04/02 11:29
  • by lusnig