This shows you the differences between two versions of the page.
Both sides previous revision Previous revision | Next revision Both sides next revision | ||
pipeline:meridien:sxmeridien [2018/06/20 13:12] 127.0.0.1 external edit |
pipeline:meridien:sxmeridien [2018/08/22 11:02] fmerino |
||
---|---|---|---|
Line 2: | Line 2: | ||
===== sxmeridien ===== | ===== sxmeridien ===== | ||
- | 3D Refinement: | + | 3D Refinement: |
\\ | \\ | ||
Line 18: | Line 18: | ||
There are five ways to run the program: | There are five ways to run the program: | ||
- | \\ __1. Standard | + | \\ __1. Standard |
- | \\ The 3D refinement starts from exhaustive searches | + | \\ The standard |
- | mpirun -np 64 sxmeridien.py bdb: | + | mpirun -np 64 --hostfile four_nodes.txt |
- | \\ __2. Standard continuation run:__ | + | \\ __2. Restart |
- | \\ Simple restart where the 3D refinement restarts | + | One can change some parameters |
- | mpirun -np 64 sxmeridien.py | + | mpirun -np 64 --hostfile four_nodes.txt |
- | \\ __3. Local refinement | + | \\ __3. Local refinement: |
- | \\ The restricted search of 3D refinement starts from user-provided orientation parameters | + | \\ |
- | mpirun -np 64 sxmeridien.py --local_refinement bdb: | + | mpirun -np 64 --hostfile four_nodes.txt |
- | \\ __4. Local refinement from meridien iteration: | + | \\ __4. Restart |
- | \\ The restricted search | + | \\ |
- | mpirun -np 64 sxmeridien.py --local_refinement | + | mpirun -np 64 --hostfile four_nodes.txt |
\\ __5. Final reconstruction only:__ | \\ __5. Final reconstruction only:__ | ||
- | \\ Do only final reconstruction using a fully finished iteration of meridien | + | \\ Do only final reconstruction using a fully finished iteration of meridien |
- | mpirun -np 64 sxmeridien.py --do_final=21 | + | mpirun -np 64 sxmeridien.py --do_final=21 |
\\ | \\ | ||
===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; stack : Input image stack: Input image stack. Required | + | ; stack : Input image stack: Input image stack. Required for new runs, not for restarts. (default none) |
- | ; output_directory : Output directory: The results will be written here. This directory will be created automatically if it does not exist. By default, the program | + | ; output_directory : Output directory: The results will be written here. If not given, the program |
- | ; initial_volume : Initial 3D reference: The 3D reference used in the initial iteration of 3D refinement. Required only for standard fresh run. (default none) | + | ; initial_volume : Initial 3D reference: The 3D reference used in the initial iteration of 3D refinement. Required only for new runs. (default none) |
- | ; %%--%%do_final : Do only final reconstruction: | + | ; %%--%%do_final : Do only final reconstruction: |
- | ; %%--%%local_refinement : Perform local refinement: Perform local refinement starting from (1) user-provided orientation parameters stored in the header of input image stack or (2) the last fully finished iteration of meridien fresh run or local refinement run. Specific to local refinement modes. (default False) | + | ; %%--%%local_refinement : Perform local refinement: Perform local refinement starting from user-provided orientation parameters stored in the header of input image stack. (default False) |
- | ; %%--%%radius : Particle radius [Pixels]: Outer radius in pixels | + | ; %%--%%radius : Particle radius [Pixels]: Outer particle |
- | ; %%--%%mask3D : 3D mask file: Soft mask for the volume. If not given, a hard sphere of radius boxsize/2-1 will be used. Ignored in final reconstruction | + | ; %%--%%mask3D : 3D mask file: A mask applied to half-map during iterations of the program. If not given, a hard sphere of radius boxsize/2-1 will be used. Ignored in final reconstruction. (default none) |
- | ; %%--%%symmetry : Point-group symmetry: Point-group symmetry of the refined structure. | + | ; %%--%%symmetry : Point-group symmetry: Point-group symmetry of the refined structure. |
- | ; %%--%%inires : Starting resolution [A]: Resolution of the initial | + | ; %%--%%inires : Starting resolution [A]: Resolution of the initial |
- | ; %%--%%delta : Initial angular sampling step [Degrees]: Initial angular sampling step. Ignored in final reconstruction | + | ; %%--%%delta : Initial angular sampling step [Degrees]: Initial angular sampling step. Ignored in final reconstruction. (default 7.5) |
- | ; %%--%%xr : Search range [Pixels]: Range for translation search in both directions. Search is +/-+xr. It can be fractional. Ignored in final reconstruction | + | ; %%--%%xr : Search range [Pixels]: Range for translation search in both directions. Search is +/-xr. It can be fractional. Ignored in final reconstruction. (default 5.0) |
- | ; %%--%%ts : Search step size [Pixels]: Step size of translation search in both directions. Search is within a circle of radius xr on a grid with steps ts. It can be fractional. Ignored in final reconstruction only. (default 1.0) | + | ; %%--%%ts : Search step size [Pixels]: Step size of translation search in both directions. Search is within a circle of radius xr on a grid with steps ts. It can be fractional. (default 1.0) |
- | ; %%--%%initialshifts : Read shifts from header: Start refinement using orientation | + | ; %%--%%initialshifts : Read shifts from header: Start refinement using translation |
- | ; %%--%%skip_prealignment : Do 2D pre-alignment step: Indicate if pre-alignment should be used or not. Do not use 2D pre-alignment if images are already centered. By default, do 2D pre-alignment. Specific to standard run modes. (default False question reversed in GUI) | + | ; %%--%%skip_prealignment : Skip the 2D pre-alignment step: Indicate if pre-alignment should be omitted. |
; %%--%%memory_per_node : Memory per node [GB]: User provided information about memory per node in GB (NOT per CPU). By default, it uses 2GB * (number of CPUs per node). Used in all modes. (default -1.0) | ; %%--%%memory_per_node : Memory per node [GB]: User provided information about memory per node in GB (NOT per CPU). By default, it uses 2GB * (number of CPUs per node). Used in all modes. (default -1.0) | ||
\\ | \\ | ||
=== Advanced Parameters === | === Advanced Parameters === | ||
- | ; %%--%%an : Angular neighborhood: | + | ; %%--%%an : Angular neighborhood: |
; %%--%%center_method : Centering method: Method for centering averages during initial 2D prealignment of data (0: no centering; -1: average shift method; For 1-7, see center_2D in utilities.py). Specific to standard run modes. (default -1) | ; %%--%%center_method : Centering method: Method for centering averages during initial 2D prealignment of data (0: no centering; -1: average shift method; For 1-7, see center_2D in utilities.py). Specific to standard run modes. (default -1) | ||
; %%--%%target_radius : Target particle radius [Pixels]: For 2D prealignment, | ; %%--%%target_radius : Target particle radius [Pixels]: For 2D prealignment, | ||
- | ; %%--%%shake : Shake: Shake. Ignored in final reconstruction | + | ; %%--%%shake : Shake: Shake randomizes grid searches by a factor of (shake x grid step). Ignored in final reconstruction. (default 0.5) |
- | ; %%--%%small_memory : Keep data in memory: Indicate if data should be kept in memory or not. By default, data will be kept in memory. Ignored in final reconstruction | + | ; %%--%%small_memory : Keep data in memory: Indicate if data should be kept in memory or not. By default, data will be kept in memory. Ignored in final reconstruction. (default False question reversed in GUI) |
- | ; %%--%%ccfpercentage : Correlation peaks to be included [%]: Percentage of correlation peaks to be included. 0.0 corresponds to hard matching. Ignored in final reconstruction | + | ; %%--%%ccfpercentage : Correlation peaks to be included [%]: Percentage of correlation peaks to be included. 0.0 corresponds to hard matching. Ignored in final reconstruction. (default 99.9) |
- | ; %%--%%nonorm : Apply image norm correction: Indicate if image norm correction should be applied or not. By default, apply image norm correction. Ignored in final reconstruction | + | ; %%--%%nonorm : Apply image norm correction: Indicate if image norm correction should be applied or not. By default, apply image norm correction. Ignored in final reconstruction. (default False question reversed in GUI) |
- | ; %%--%%function : Reference preparation function: Specify name of function that program should use to prepare the reference | + | ; %%--%%function : Reference preparation function: Specify name of function that program should use to prepare the reference |
\\ | \\ | ||
Line 103: | Line 104: | ||
\\ | \\ | ||
==== Maturity ==== | ==== Maturity ==== | ||
- | Beta:: Under evaluation and testing. Please let us know if there are any bugs. | + | Alpha:: Fully developed. |
\\ | \\ | ||
==== Bugs ==== | ==== Bugs ==== | ||
- | There are no known bugs so far. | + | Glitches possible. |
\\ | \\ | ||
- |