This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
pipeline:meridien:sxmeridien [2018/08/22 11:02] fmerino |
pipeline:meridien:sxmeridien [2021/02/01 15:16] (current) shaikh |
||
---|---|---|---|
Line 1: | Line 1: | ||
~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxmeridien | + | ===== sp_meridien |
3D Refinement: Performs 3D structure refinement using a quasi-Maximum Likelihood approach. | 3D Refinement: Performs 3D structure refinement using a quasi-Maximum Likelihood approach. | ||
Line 9: | Line 9: | ||
Usage in command line | Usage in command line | ||
- | | + | |
\\ | \\ | ||
===== Typical usage ===== | ===== Typical usage ===== | ||
- | sxmeridien | + | sp_meridien |
There are five ways to run the program: | There are five ways to run the program: | ||
Line 20: | Line 21: | ||
\\ __1. Standard default run:__ | \\ __1. Standard default run:__ | ||
\\ The standard refinement starts from exhaustive searches, uses initial reference structure | \\ The standard refinement starts from exhaustive searches, uses initial reference structure | ||
- | mpirun -np 64 --hostfile four_nodes.txt | + | mpirun -np 64 --hostfile four_nodes.txt |
\\ __2. Restart after the last fully finished iteration: | \\ __2. Restart after the last fully finished iteration: | ||
One can change some parameters (MPI settings have to be the same) | One can change some parameters (MPI settings have to be the same) | ||
- | mpirun -np 64 --hostfile four_nodes.txt | + | mpirun -np 64 --hostfile four_nodes.txt |
\\ __3. Local refinement: | \\ __3. Local refinement: | ||
\\ Local refinement starts from user-provided orientation parameters, delta has to be <= 3.75 | \\ Local refinement starts from user-provided orientation parameters, delta has to be <= 3.75 | ||
- | mpirun -np 64 --hostfile four_nodes.txt | + | mpirun -np 64 --hostfile four_nodes.txt |
\\ __4. Restart of local refinement after the last fully finished iteration.: | \\ __4. Restart of local refinement after the last fully finished iteration.: | ||
\\ One can change some parameters (MPI settings have to be the same) | \\ One can change some parameters (MPI settings have to be the same) | ||
- | mpirun -np 64 --hostfile four_nodes.txt | + | 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 (here number 21). | \\ Do only final reconstruction using a fully finished iteration of meridien (here number 21). | ||
- | mpirun -np 64 sxmeridien.py --do_final=21 | + | mpirun -np 64 sp_meridien.py --do_final=21 |
Line 47: | Line 48: | ||
; %%--%%do_final : Do only final reconstruction: | ; %%--%%do_final : Do only final reconstruction: | ||
+ | ; %%--%%voldir : Output reconstruction directory: Directory in which the output reconstructions will be written. (default None) | ||
; %%--%%local_refinement : Perform local refinement: Perform local refinement starting from user-provided orientation parameters stored in the header of input image stack. (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) | ||
Line 54: | Line 56: | ||
; %%--%%inires : Starting resolution [A]: Resolution of the initial map used to start the refinement. Ignored in final reconstruction. (default 25.0) | ; %%--%%inires : Starting resolution [A]: Resolution of the initial map used to start the refinement. Ignored in final reconstruction. (default 25.0) | ||
; %%--%%delta : Initial angular sampling step [Degrees]: Initial angular sampling step. Ignored in final reconstruction. (default 7.5) | ; %%--%%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. (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. (default 1.0) | ||
; %%--%%initialshifts : Read shifts from header: Start refinement using translation parameters located in the input file header to jumpstart the procedure. Specific to standard run mode. (default False value reversed in GUI) | ; %%--%%initialshifts : Read shifts from header: Start refinement using translation parameters located in the input file header to jumpstart the procedure. Specific to standard run mode. (default False value reversed in GUI) | ||
- | ; %%--%%skip_prealignment : Skip the 2D pre-alignment step: Indicate if pre-alignment should be omitted. | + | ; %%--%%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 === | ||
+ | ; %%--%%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. (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) | ||
; %%--%%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) | ||
Line 70: | Line 73: | ||
; %%--%%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) | ; %%--%%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 structure after each iteration. Ignored in final reconstruction. (default do_volume_mask) | ; %%--%%function : Reference preparation function: Specify name of function that program should use to prepare the reference structure after each iteration. Ignored in final reconstruction. (default do_volume_mask) | ||
+ | ; %%--%%function_ai : Logic function: Specify name of function that the program should use to follow the specified logic. (default ai_spa) | ||
+ | ; %%--%%group_by : Group name for chunks: | ||
+ | ; %%--%%theta_min : Theta min [degree]: | ||
+ | ; %%--%%theta_max : Theta max [degree]: | ||
+ | ; %%--%%even_angle_method : Even anle method: Method to use for even angle creation (S, M, P). (default S) | ||
+ | ; %%--%%group_id : Outlier group ID: Group the particles by the header name for the outlier detection. By default do not do outlier detection. (default None) | ||
+ | ; %%--%%filament_width : Filament width [px]: This is used to normalize the particles in case of filaments. A rectangular mask will be used instead of a circular one. (default None) | ||
+ | ; %%--%%helical_rise : Helical rise [A]: Helical rise used to limit the shift along the helical axis to +-rise/2 (default None) | ||
+ | ; %%--%%a_criterion : Convergence criterion A value: Convergence criterion multiplication for the criterion A. (default 0.75) | ||
+ | ; %%--%%limit_improvement : Limit of improvements: | ||
+ | ; %%--%%plot_ang_dist : Plot angular distribution: | ||
+ | ; %%--%%main000 : Main000 folder: Main000 folder of a previous refinement to presever chunk and group information. By default it will assign new chunks and groups. (default none) | ||
\\ | \\ | ||
Line 88: | Line 103: | ||
\\ | \\ | ||
==== Author / Maintainer ==== | ==== Author / Maintainer ==== | ||
+ | Markus Stabrin | ||
Pawel A. Penczek | Pawel A. Penczek | ||
Line 96: | Line 112: | ||
\\ | \\ | ||
==== Files ==== | ==== Files ==== | ||
- | sparx/bin/sxmeridien.py | + | sparx/bin/sp_meridien.py |
\\ | \\ | ||
Line 111: | Line 127: | ||
\\ | \\ | ||
+ |