sp_ctf_refine manual

CTF refine (Stack): Refine the defocus per particle


Usage

Usage in command line

sp_ctf_refine.py manual path_to_input_stack output_directory volume_path params_file --mask=path_to_mask --range=defocus_range --delta=defocus_delta --resolution=nominal_resolution --pixelsize=pixelsize --number_part=NUMBER_PARTICLES --chunk=PATH_TO_CHUNK_FILE --volume2=PATH_TO_VOLUME


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)
volume_path
Path to volume
Path to volume. (default required)
params_file
Params file: Path to params file (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)
--chunk
Path to chunk file
Path to chunk file (default none)
--volume2
Path to second volume
Path to second half volume. (default none): --chunk!=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