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pipeline:cter:sxcter [2018/05/14 16:19] 127.0.0.1 external edit |
pipeline:cter:sxcter [2018/08/22 10:35] fmerino |
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\\ __All Micrographs Mode - Process all micrographs in a directory: | \\ __All Micrographs Mode - Process all micrographs in a directory: | ||
- | \\ Specify a list of input micrographs using a wild card (*), called | + | \\ Specify a list of input micrographs using a wild card (*), here called input micrographs path pattern. Running from the command line requires enclosing the string by single quotes (\') or double quotes (\"). sxgui.py will automatically adds single quotes to the string. |
mpirun -np 16 sxcter.py ' | mpirun -np 16 sxcter.py ' | ||
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\\ __Single Micrograph Mode - Process a single micrograph: | \\ __Single Micrograph Mode - Process a single micrograph: | ||
- | \\ In addition to input micrographs path pattern and output directry arguments, | + | \\ One can specify a single micrograph name using --selection_list option. In this mode, only the specified single micrograph will be processed. If this micrograph name does not matches the file name part of the pattern (ignoring the directory paths), the process will exit without processing it. If this micrograph name matches the file name part of the pattern but does not exists in the directory which specified by the micrograph path pattern, again the process will exit without processing it. Use single processor for this mode. |
sxcter.py ' | sxcter.py ' | ||
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===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; input_image_path : Input micrograph path pattern: Specify input micrographs path pattern with a wild card (*) for any of Micrograph Modes. Images | + | ; input_image_path : Input micrograph path pattern: Specify input micrographs path pattern with a wild card (*) for any of Micrograph Modes. Images |
- | ; output_directory : Output directory: The CTF parameters (partres file), rotationally averaged power spectra (rotinf), and micrograph thumbnails (thumb files) will be written here. This directory will be created automatically and it must not exist previously. (default required string) | + | ; output_directory : Output directory: The CTF parameters (partres file), rotationally averaged power spectra (rotinf), and micrograph thumbnails (thumb files) will be written here. It cannot |
; %%--%%selection_list : Micrograph selection file: Specify path of a micrograph selection list text file for Selected Micrographs Mode. The file extension must be ' | ; %%--%%selection_list : Micrograph selection file: Specify path of a micrograph selection list text file for Selected Micrographs Mode. The file extension must be ' | ||
- | ; %%--%%wn : CTF window size [Pixels]: The size should be slightly larger than particle box size. This will be ignored in Stack Mode. (default 512) | + | ; %%--%%wn : CTF window size [Pixels]: The window |
; %%--%%apix : Pixel size [A]: The pixel size of input micrograph(s) or images in input particle stack. (default -1.0) | ; %%--%%apix : Pixel size [A]: The pixel size of input micrograph(s) or images in input particle stack. (default -1.0) | ||
; %%--%%Cs : Microscope spherical aberration (Cs) [mm]: The spherical aberration (Cs) of microscope used for imaging. (default 2.0) | ; %%--%%Cs : Microscope spherical aberration (Cs) [mm]: The spherical aberration (Cs) of microscope used for imaging. (default 2.0) | ||
; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default 300.0) | ; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default 300.0) | ||
- | ; %%--%%ac : Amplitude contrast [%]: The typical | + | ; %%--%%ac : Amplitude contrast [%]: The amplitude contrast is in the range of 7% - 14%. The value depends on the thickness of the ice embedding the particles, among other factors. (default 10.0) |
- | ; %%--%%f_start : Lowest resolution [A]: Lowest resolution | + | ; %%--%%f_start : Lowest resolution [A]: Lowest resolution |
- | ; %%--%%f_stop : Highest resolution [A]: Highest resolution | + | ; %%--%%f_stop : Highest resolution [A]: Highest resolution |
\\ | \\ | ||
=== Advanced Parameters === | === Advanced Parameters === | ||
; %%--%%kboot : Number of CTF estimates per micrograph: Used for error assessment. (default 16) | ; %%--%%kboot : Number of CTF estimates per micrograph: Used for error assessment. (default 16) | ||
- | ; %%--%%overlap_x : X overlap [%]: Overlap between | + | ; %%--%%overlap_x : X overlap [%]: Overlap between |
- | ; %%--%%overlap_y : Y overlap [%]: Overlap between | + | ; %%--%%overlap_y : Y overlap [%]: Overlap between |
- | ; %%--%%edge_x : Edge x [pixels]: | + | ; %%--%%edge_x : Edge x [pixels]: |
- | ; %%--%%edge_y : Edge y [pixels]: | + | ; %%--%%edge_y : Edge y [pixels]: |
; %%--%%check_consistency : Check consistency of inputs: Create a text file containing the list of inconsistent Micrograph ID entries (i.e. inconsist_mic_list_file.txt). (default False) | ; %%--%%check_consistency : Check consistency of inputs: Create a text file containing the list of inconsistent Micrograph ID entries (i.e. inconsist_mic_list_file.txt). (default False) | ||
- | ; %%--%%stack_mode : Use stack mode: Use a stack as the input. Please set the file path of a stack as the first argument and output directory for the second argument. This is advanced option. Not supported by sxgui. (default False) | + | ; %%--%%stack_mode : Use stack mode: Use a stack as the input. Please set the file path of a stack as the first argument and output directory for the second argument. This is an advanced option. Not supported by sxgui. (default False) |
; %%--%%debug_mode : Enable debug mode: Print out debug information. (default False) | ; %%--%%debug_mode : Enable debug mode: Print out debug information. (default False) | ||
- | ; %%--%%vpp : Volta Phase Plate Dataset: UNDER DEVELOPMENT! | + | ; %%--%%vpp : Volta Phase Plate Dataset: UNDER DEVELOPMENT! |
; %%--%%defocus_min : Minimum defocus search [um]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 0.3) | ; %%--%%defocus_min : Minimum defocus search [um]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 0.3) | ||
; %%--%%defocus_max : Maximum defocus search [um]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 9.0) | ; %%--%%defocus_max : Maximum defocus search [um]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 9.0) | ||
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|| 3 || Microscope voltage [kV] || | || 3 || Microscope voltage [kV] || | ||
|| 4 || Pixel size [A] || | || 4 || Pixel size [A] || | ||
- | || 5 || B-factor [A^2] || | + | || 5 || B-factor [A%%^%%2] || |
- | || 6 || Total amplitude | + | || 6 || Amplitude |
|| 7 || Astigmatism amplitude [um] || | || 7 || Astigmatism amplitude [um] || | ||
|| 8 || Astigmatism angle [degrees] || | || 8 || Astigmatism angle [degrees] || | ||
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|| 15 || Frequency at which the signal drops by 50% due to estimated error of defocus alone [1/A] || | || 15 || Frequency at which the signal drops by 50% due to estimated error of defocus alone [1/A] || | ||
|| 16 || Frequency at which the signal drops by 50% due to estimated error of defocus and astigmatism [1/A] || | || 16 || Frequency at which the signal drops by 50% due to estimated error of defocus and astigmatism [1/A] || | ||
- | || 17 || Frequency at which the CTF oscillation can no longer | + | || 17 || Frequency at which the CTF cannot |
|| 18 || NOT IMPLEMENTED YET! Maximum frequency limit (visual-impression-based)[A] || | || 18 || NOT IMPLEMENTED YET! Maximum frequency limit (visual-impression-based)[A] || | ||
|| 19 || NOT IMPLEMENTED YET! Reserved spot for other means of maximum frequency limit or error criterion. Possibly originated from external program || | || 19 || NOT IMPLEMENTED YET! Reserved spot for other means of maximum frequency limit or error criterion. Possibly originated from external program || | ||
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|| 3 || Microscope voltage [kV] || | || 3 || Microscope voltage [kV] || | ||
|| 4 || Pixel size [A] || | || 4 || Pixel size [A] || | ||
- | || 5 || B-factor [A^2] || | + | || 5 || B-factor [A%%^%%2] || |
|| 6 || Amplitude contrast [%] || | || 6 || Amplitude contrast [%] || | ||
|| 7 || Astigmatism amplitude [um] || | || 7 || Astigmatism amplitude [um] || | ||
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\\ | \\ | ||
- |