pipeline:utilities:sp_ctf_refine_stack
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| + | ~~NOTOC~~ | ||
| + | |||
| + | ===== 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. | ||
| + | ; 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: | ||
| + | - error_cdf.png: | ||
| + | - 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/ | ||
pipeline/utilities/sp_ctf_refine_stack.txt ยท Last modified: 2019/04/02 11:31 by lusnig
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