CTF refine (Stack): Refine the defocus per particle

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

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

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)

--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

It will write a virtual stack with updated defocus information in the header. Furthermore it creates plot for error in the your output directory

- 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

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• Initial creation of the document

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Thorsten Wagner

Category 1:: APPLICATIONS

sparx/bin/sp_ctf_refine.py