~~NOTOC~~

===== sp_ctf_refine manual =====
CTF refine (Stack): Refine the defocus per particle


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===== 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 --apix=pixelsize --number_part=NUMBER_PARTICLES --chunk=PATH_TO_CHUNK_FILE --volume2=PATH_TO_VOLUME

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===== Typical usage =====

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


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===== 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)


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=== Advanced Parameters ===
  ; %%--%%range : Defocus search range [um] : Search range +- around the current defocus value. (default 0.15)
  ; %%--%%delta : Defocus search delta [um] : Finest search delta. (default 0.0025)
  ; %%--%%resolution : Nominal resolution [A] : Nominal resolution of the reconstruction. Low-pass Gaussian filter will be applied at this resolution. (default None)
  ; %%--%%apix : Pixel size [A] : Pixel size in Angstroms. (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


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===== 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

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=== 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


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==== Method ====
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==== Developer Notes ====
=== 2019/02/21 Thorsten Wagner ===
  * Initial creation of the document

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==== Reference ====
-

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==== Author / Maintainer ====
Thorsten Wagner

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==== Keywords ====
Category 1:: APPLICATIONS

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==== Files ====
sphire/bin/sp_ctf_refine.py