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pipeline:utilities:sxrelion2sphire [2018/02/27 19:06] moriya |
pipeline:utilities:sxrelion2sphire [2019/04/02 10:57] lusnig [Output] |
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~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxrelion2sphire | + | ===== sp_relion2sphire |
- | RELION to SPHIRE Conversion: Create several types of parameter text files and a particle | + | RELION to SPHIRE Conversion: Create several types of parameter text files and per-micrograph virtual stacks of particle |
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Usage in command line | Usage in command line | ||
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===== Typical usage ===== | ===== Typical usage ===== | ||
- | sxrelion2sphire | + | sp_relion2sphire |
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+ | |||
+ | sp_relion2sphire.py | ||
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===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; input_star_file : Input RELION STAR file: Specify a STAR file generated by RELION. The file should contain parameters related to Micrographs, | + | ; input_star_file : Input RELION STAR file: Specify a STAR file generated by RELION. The file should contain parameters related to Micrographs, |
- | ; output_directory : Output directory: All the results will be written in here. This directory will be created automatically and it must not exist previously. (default required string) | + | ; output_directory : Output directory: All the results will be written in here. It cannot |
+ | ; %%--%%relion_project_dir : RELION project directory: Path to RELION project directory associated with the RELION STAR file. By default, the program assume the current directory is the RELION project directory. (default none) | ||
; %%--%%star_section : Section title in STAR file: The section title in the RELION star file where the data should be extracted. (default data_) | ; %%--%%star_section : Section title in STAR file: The section title in the RELION star file where the data should be extracted. (default data_) | ||
- | ; %%--%%box_size : Box size: Box size for particle extraction. | + | |
- | ; %%--%%create_stack : Create particle stack: By default, the program does not generate the stack of particle images because it takes a long time and the file size is large. (default False) | + | |
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=== Advanced Parameters === | === Advanced Parameters === | ||
+ | ; | ||
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=== List of Output Files === | === List of Output Files === | ||
+ | The program copies the subdirectory structure under the RELION project directory based on the information stored in the input RELION STAR file. | ||
+ | For example, if two sets of micrographs are stored in two different subdirectories (e.g. " | ||
+ | Each output subdirectory will contain the files in the table below. | ||
+ | |||
|| **File Name** || **Discription** || | || **File Name** || **Discription** || | ||
- | || sphire_micrographs.txt || Text file containing a list of micrograph names/paths (Micrograph selection file). It can be used as input of [[pipeline: | + | || *_micrographs.txt || Text file containing a list of micrograph names/paths (Micrograph selection file). It can be used as input of [[pipeline: |
- | || sphire_cter_partres.txt || Text file containing a list of CTF parameters in CTER format (CTER partres file). It can be used as an input of [[pipeline: | + | || *_cter_partres.txt || Text file containing a list of CTF parameters in CTER format (CTER partres file). It can be used as an input of [[pipeline: |
- | || sphire_stack_ctf.txt || Text file containing a list of CTF parameters. It can be used as an input of [[pipeline: | + | || Coordinates/ |
- | || Coordinates/ | + | || Rebox/*.rbx || SPHIRE rebox files. One for each micrograph. These files can be used as inputs |
- | || sphire_stack_proj3d.txt || Text file containing a list of 3D projection parameters. It can be used as an input of [[pipeline:utilities:sxheader|sxheader]] %%--%%params=xform.projection. (requires | + | || EMAN2DB/*_stack.bdb || Per-micrograph virtual stacks |
- | || sphire_stack_chunk*.txt || Text file containing a list of particle | + | |
- | || sphire_stack.hdf || Particle image stack (only when %%--%%create_stack option | + | |
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===== Description ===== | ===== Description ===== | ||
- | Run the script to create several types of parameter text files and particle image stack in SPHIRE format from parameters stored in a RELION STAR file. The RELION STAR should contain entries related to Micrographs, | + | Run the script to create several types of parameter text files and particle image stack in SPHIRE format from parameters stored in a RELION STAR file. The RELION STAR should contain entries related to Micrographs, |
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=== Related Header Entries === | === Related Header Entries === | ||
- | The script | + | The script sets the following header entries of EMAN2DB/ |
|| **Header Entry** || **Discription** || | || **Header Entry** || **Discription** || | ||
|| ptcl_source_relion || RELION' | || ptcl_source_relion || RELION' | ||
|| ptcl_source_image || Micrograph path (relative path) where RELION extracted this particle image. || | || ptcl_source_image || Micrograph path (relative path) where RELION extracted this particle image. || | ||
- | || ptcl_source_coord || Coordinates of this particle in the Micrograph in sphire | + | || ptcl_source_coord || Coordinates of this particle in the Micrograph in SPHIRE |
|| ptcl_source_coord_id || Coordinates ID in the original coordinate file RELION used. || | || ptcl_source_coord_id || Coordinates ID in the original coordinate file RELION used. || | ||
+ | || data_path || Relative path to the original particle image location. || | ||
|| data_n || Serial particle image ID. Here, it is same as ptcl_source_coord_id. || | || data_n || Serial particle image ID. Here, it is same as ptcl_source_coord_id. || | ||
|| resample_ratio || Resampling ratio of dimensions or pixel size of extracted particle images relative to micrograph. Here, it is always set to 1.0. || | || resample_ratio || Resampling ratio of dimensions or pixel size of extracted particle images relative to micrograph. Here, it is always set to 1.0. || | ||
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|| ptcl_source_apix || Pixel size of the associated micrograph. || | || ptcl_source_apix || Pixel size of the associated micrograph. || | ||
|| xform.projection || 3D projection parameters. || | || xform.projection || 3D projection parameters. || | ||
+ | || relion_max_prob_dist || Maximum probability distribution value computed by RELION. || | ||
+ | || relion_norm_correct || Normalisation correction value computed by RELION. || | ||
|| chunk_id || Chunk ID (or Subset ID) where this particle belongs. || | || chunk_id || Chunk ID (or Subset ID) where this particle belongs. || | ||
- | NOTE: If you run [[pipeline: | + | NOTE: If you run [[pipeline: |
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==== Reference ==== | ==== Reference ==== | ||
+ | |||
+ | \\ | ||
+ | ==== Developer Notes ==== | ||
+ | === 2018/09/17 Markus Stabrin === | ||
+ | - Remove image stack creation. | ||
+ | - Created stacks only contain meta data. | ||
+ | - Write bdb meta data stacks by default (Change %%--%%create_stack to %%--%%do_not_create_stack). | ||
+ | - Remove %%--%%cs_save_as_hdf option. | ||
+ | |||
+ | === 2018/07/11 Toshio Moriya === | ||
+ | - Change default stack format from HDF to bdb (%%--%%cs_save_as_hdf). | ||
+ | * By default, the script creates a local particle image stack for each micrograph like sp_window.py. | ||
+ | * Likewise, because of synchronisation problem of subprocess execution, user must run particle stack command to create a virtual stack of all particles. | ||
+ | - Accept arbitrary output file name (%%--%%outputs_root). | ||
+ | |||
+ | - Added SPHIRE rebox file output support. The rebox file contains box coordinates, | ||
+ | * This modification solves the problem associated with per-particle defocus estimation. | ||
+ | |||
+ | - Add relion project directory option so that the script can be run from any directory (%%--%%relion_project_dir). | ||
+ | * That is, you don't anymore need to make sure the current directory is the project folder of the RELION (where you run RELION GUI). | ||
+ | * The program appends the path of relion project directory to micrograph path extracted from the star file. | ||
+ | |||
+ | These changes require user not to break the relative path whenever they move or copy the micrographs because sp_relion2sparx.py use full name including the path stored in the input RELION STAR file. | ||
+ | |||
+ | The program does not generate the following output files anymore. | ||
+ | |||
+ | || **File Name** || **Discription** || | ||
+ | || sphire_stack_ctf.txt || Text file containing a list of CTF parameters. It can be used as an input of [[pipeline: | ||
+ | || sphire_stack_proj3d.txt || Text file containing a list of 3D projection parameters. It can be used as an input of [[pipeline: | ||
+ | || sphire_stack_chunk*.txt || Text file containing a list of particle IDs for the subset (#0 and #1). It can be used as an input of [[pipeline: | ||
+ | |||
+ | To create these files, please use [[pipeline: | ||
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==== Author / Maintainer ==== | ==== Author / Maintainer ==== | ||
Toshio Moriya | Toshio Moriya | ||
+ | Markus Stabrin | ||
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==== Files ==== | ==== Files ==== | ||
- | sparx/bin/sxrelion2sphire.py | + | sparx/bin/sp_relion2sphire.py |
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==== See also ==== | ==== See also ==== | ||
- | [[pipeline: | + | [[pipeline: |
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