This version (2019/04/02 11:29) is a draft.
Approvals: 0/1

CTF refine (Meridien): Refine the defocus per particle

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

Before doing defocus refinement, you should have reached ~4 angstrom. sp_ctf_refine.py exists only in non-MPI version.

Main Parameters

Input stack path
Path to input stack. (default required)
Output directory
Folder to output files etc. (default required)
Meridien directory
Path to Merdien directory. (default required)
Path to mask
Path to mask used. (default none)

Advanced Parameters

Defocus search range [mum]
Search range +- around the current defocus value. (default 0.15)
Defocus search delta [mum]
Finest search delta. (default 0.0025)
Nominal resolution [A]
Nominal resolution of the reconstruction. (default None)
Pixelsize [A]
Pixelsize in Angstrom. (default None)
Number of particles
Number of particles to process. Mainly for debugging. (default none)

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


2019/02/21 Thorsten Wagner

  • Initial creation of the document


Thorsten Wagner



  • pipeline/utilities/sp_ctf_refine.txt
  • Last modified: 2019/04/02 11:29
  • by lusnig