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pipeline:sort3d:sxrsort3d [2018/02/16 10:11] 127.0.0.1 external edit |
pipeline:sort3d:sxrsort3d [2018/06/20 13:12] (current) |
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~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxsort3d | + | ===== sxrsort3d |
- | 3D Clustering - SORT3D DEPTH: Sorting heterogeneous | + | 3D Clustering - RSORT3D: Sort out 3D heterogeneity |
\\ | \\ | ||
===== Usage ===== | ===== Usage ===== | ||
- | Usage1 | + | Usage in command line |
- | | + | |
- | + | ||
- | Usage2 in command line | + | |
- | + | ||
- | sxrsort3d_depth.py | + | |
\\ | \\ | ||
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sxrsort3d.py exists only in MPI version. | sxrsort3d.py exists only in MPI version. | ||
- | \\ __Initiate sorting from a SPHIRE/ | + | |
- | | + | |
- | \\ __Initiate sorting from a data stack__: Currently, this mode is not supported by SPHIRE GUI. | + | \\ |
- | mpirun | + | |
- | + | ||
- | \\ __Initiate sorting from a relion refinement__: | + | |
- | mpirun | + | |
- | + | ||
- | \\ NOTE - How to continue sxmeridien refinement using sorting results: Please use --ctrefromsort3d option of sxmeridien, then specify the directory where you wish to continue the refinement to --oldrefdir option and a subset of data to —-subset option. The command will load the refinement information from the directory and continue refinement. Optinally, you can specify the iteration number for continuing refinement using -—ctrefromiter option, which is not necessarily be the same iteration where you used for the 3D sorting. Also, one can modify refinement parameters of the selected iteration through the other options. | + | |
- | mpirun | + | |
- | + | ||
- | \\ | + | |
===== Input ===== | ===== Input ===== | ||
- | === Main Paramaters | + | === Main Parameters |
- | ; refinement_method | + | ; stack : Input images stack: (default |
- | ; refinement_dir | + | ; outdir |
- | ; masterdir | + | ; mask : 3D mask: (default none) |
- | ; niter_for_sorting | + | |
- | ; mask3D | + | ; %%--%%previous_run1 |
- | ; focus : Focus 3D mask: File path of a binary 3D mask for focused clustering. (default none) | + | ; %%--%%previous_run2 |
- | ; radius : Outer radius for rotational correlation [Pixels]: | + | ; %%--%%focus : Focus 3D mask: Mask used for focused clustering (default none) |
- | ; sym : Point-group symmetry: | + | ; %%--%%radius : Outer radius for rotational correlation [Pixels]: |
- | ; number_of_images_per_group : Images per group: | + | ; %%--%%delta : Angular step for projections: |
- | ; smallest_group : Smallest group size: Minimum | + | ; %%--%%CTF : Use CTF: Do a full CTF correction during the alignment. (default False) |
- | ; nxinit | + | ; %%--%%sym : Point-group symmetry: (default c1) |
+ | ; %%--%%number_of_images_per_group : Images per group: | ||
+ | ; %%--%%nxinit : Initial image size for sorting: (default 64) | ||
+ | ; %%--%%smallest_group : Smallest group size: Minimum members for identified group. (default 500) | ||
+ | ; %%--%%chunkdir | ||
\\ | \\ | ||
=== Advanced Parameters === | === Advanced Parameters === | ||
- | ; low_pass_filter | + | ; %%--%%ir |
- | ; Kmeans_lpf | + | ; %%--%%maxit |
- | ; nindependent | + | ; %%--%%rs : Step between rings in rotational correlation: |
- | ; noctf : No CTF correction: Use this option if full CTF correction should not be applied during | + | ; %%--%%xr : X search range [Pixels]: The translational search range in the x direction will take place in a +/xr range. (default |
- | ; PWadjustment : Reference power spectrum | + | ; %%--%%yr : Y search range [Pixels]: The translational search range in the y direction. If omitted it will be set as xr. (default |
- | ; interpolation | + | ; %%--%%ts : Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default |
- | ; comparison_method | + | ; %%--%%an : Local angular search width [Degrees]: This defines the neighbourhood where the local angular search will be performed. (default |
- | ; instack | + | ; %%--%%center : Centering method: 0 - if you do not want the volume to be centered, 1 - center the volume using the center of gravity. (default |
+ | ; %%--%%nassign | ||
+ | ; %%--%%nrefine | ||
+ | ; %%--%%stoprnct : Assignment convergence threshold [%]: Used to asses convergence of the run. It is the minimum percentage of assignment change required to stop the run. (default 3.0) | ||
+ | ; %%--%%function | ||
+ | ; %%--%%independent : Number of independent runs: Number of independent equal-Kmeans(default 3) | ||
+ | ; %%--%%low_pass_filter : Low-pass filter frequency [1/Pixel]: Low-pass filter used for the 3D sorting on the original image size. (default | ||
+ | ; %%--%%unaccounted : Reconstruct unaccounted images: (default False) | ||
+ | ; %%--%%seed : Random seed: Seed used for the initial random assignment for EQ Kmeans. The program | ||
+ | ; %%--%%group_size_for_unaccounted : Unaccounted particles group size: (default 500) | ||
+ | ; %%--%%sausage : Use sausage filter: | ||
+ | ; %%--%%PWadjustment : Power spectrum | ||
+ | ; %%--%%protein_shape | ||
+ | ; %%--%%upscale | ||
+ | ; %%--%%wn | ||
+ | ; %%--%%interpolation : 3D interpolation method: Method interpolation in 3D. Options are tr1 or 4nn. (default | ||
\\ | \\ | ||
===== Output ===== | ===== Output ===== | ||
- | Please use --masterdir option to specify the output directory. The results will be written here. This directory will be created automatically if it does not exist Here, you can find a log.txt that describes the sequences of computations in the program. | ||
\\ | \\ | ||
===== Description ===== | ===== Description ===== | ||
- | sxrsort3d finds out stable members by carrying out two-way comparison of two independent sxsort3d runs. | + | sxrsort3d.py finds out stable members by carrying out two-way comparison of two independent sxsort3d.py runs. |
For small tested datasets (real and simulated ribosome data around 10K particles), it gives 70%-90% reproducibility. However, this rate also depends on the choice of number of images per group and number of particles in the smallest group. | For small tested datasets (real and simulated ribosome data around 10K particles), it gives 70%-90% reproducibility. However, this rate also depends on the choice of number of images per group and number of particles in the smallest group. | ||
+ | |||
+ | \\ | ||
+ | === Time and Memory === | ||
+ | On lonestar cluster of TACC, using 264 cpus, it takes about 2 hours and 23 minutes to accomplish 95953 128x128 images for one sxsort3d.py independent run, 2 hours 24 minutes to accomplish one independent sxrsort3d.py run with number_of_images_per_group set as 30000. | ||
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==== Reference ==== | ==== Reference ==== | ||
Not published yet. | Not published yet. | ||
+ | |||
+ | \\ | ||
+ | ==== Developer Notes ==== | ||
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==== Files ==== | ==== Files ==== | ||
- | sxrsort3d.py | + | sparx/bin/sxrsort3d.py |
\\ | \\ | ||
==== See also ==== | ==== See also ==== | ||
- | [[sxsort3d|sxsort3d.py]] | + | [[pipeline: |
\\ | \\ | ||
==== Maturity ==== | ==== Maturity ==== | ||
- | beta:: Under development. It has been tested, The test cases/ | + | Alpha:: Under development. |
\\ | \\ | ||
- | ==== Known Bugs ==== | + | ==== Bugs ==== |
- | None so far. | + | There are no known bugs so far. |
\\ | \\ | ||