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pipeline:sort3d:sxsort3d [2018/02/16 10:11] 127.0.0.1 external edit |
pipeline:sort3d:sxsort3d [2018/02/23 16:59] moriya |
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Usage in command line | Usage in command line | ||
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sxsort3d exists only in MPI version. | sxsort3d exists only in MPI version. | ||
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=== Main Parameters === | === Main Parameters === | ||
; stack : Input images stack: (default required string) | ; stack : Input images stack: (default required string) | ||
- | ; mask : 3D mask: (default none) | + | |
- | ; focus : Focus 3D mask: Mask used for focused clustering (default none) | + | |
- | ; radius : Outer radius | + | |
- | ; delta : Angular step for projections: | + | ; focus : Binary |
- | ; CTF : Use CTF: Do a full CTF correction during the alignment. (default False) | + | ; radius : Particle |
- | ; sym : Point-group symmetry: (default c1) | + | ; delta : Angular step for projections |
- | ; number_of_images_per_group : Images per group: Critical | + | ; CTF : Use CTF: Do a full CTF correction during the alignment. (default False) |
- | ; nxinit : Initial image size for sorting: (default 64) | + | ; sym : Point-group symmetry: |
+ | ; number_of_images_per_group : Images per group: Critical | ||
+ | ; nxinit : Initial image size for sorting: | ||
; smallest_group : Smallest group size: Minimum members for identified group. (default 500) | ; smallest_group : Smallest group size: Minimum members for identified group. (default 500) | ||
- | ; chunk0 : Chunk file name for 1st subset: Name of chunk file containing particle IDs of 1st subset | + | ; chunk0 : Chunk file name for 1st halfset: Name of chunk file containing particle IDs of 1st halfset |
- | ; chunk1 : Chunk file name for 2nd subset: Name of chunk file containing particle IDs of 2nd subset | + | ; chunk1 : Chunk file name for 2nd halfset: Name of chunk file containing particle IDs of 2nd halfset |
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=== Advanced Parameters === | === Advanced Parameters === | ||
; ir : Inner radius for rotational correlation [Pixels]: Must be bigger than 1. (default 1) | ; ir : Inner radius for rotational correlation [Pixels]: Must be bigger than 1. (default 1) | ||
- | ; maxit : Maximum iterations: (default 25) | + | ; maxit : Maximum iterations: |
; rs : Step between rings in rotational correlation: | ; rs : Step between rings in rotational correlation: | ||
- | ; xr : X search range [Pixels]: The translational search range in the x direction will take place in a +/xr range. (default 1) | + | ; xr : X search range [Pixels]: The translational search range in the x direction will take place in -xr to +xr range. (default |
- | ; yr : Y search range [Pixels]: The translational search range in the y direction. If omitted it will be set as xr. (default -1) | + | ; yr : Y search range [Pixels]: The translational search range in the y direction |
- | ; ts : Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default 0.25) | + | ; ts : Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default |
; an : Local angular search width [Degrees]: This defines the neighbourhood where the local angular search will be performed. (default ' | ; an : Local angular search width [Degrees]: This defines the neighbourhood where the local angular search will be performed. (default ' | ||
; center : Centering method: 0 - if you do not want the volume to be centered, 1 - center the volume using the center of gravity. (default 0) | ; center : Centering method: 0 - if you do not want the volume to be centered, 1 - center the volume using the center of gravity. (default 0) | ||
; nassign : Number of reassignment iterations: Performed for each angular step. (default 1) | ; nassign : Number of reassignment iterations: Performed for each angular step. (default 1) | ||
; nrefine : Number of alignment iterations: Performed for each angular step. (default 0) | ; nrefine : Number of alignment iterations: Performed for each angular step. (default 0) | ||
- | ; 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) | + | ; 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 : Reference preparation function: | + | ; function : Reference preparation function: |
- | ; independent : Number of independent runs: Number of independent equal-Kmeans(default 3) | + | ; 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 -1.0) | + | ; low_pass_filter : Low-pass filter frequency [1/Pixels]: Low-pass filter used for the 3D sorting on the original image size. Specify with absolute frequency. (default -1.0) |
- | ; unaccounted : Reconstruct unaccounted images: (default False) | + | ; unaccounted : Reconstruct unaccounted images: |
- | ; seed : Seed: Seed used for the initial random assignment for EQ Kmeans. The program generates a random integer by default. (default -1) | + | ; seed : Random seed: Seed used for the initial random assignment for EQ Kmeans. The program generates a random integer by default. (default -1) |
- | ; sausage : Use sausage filter: (default False) | + | ; sausage : Use sausage filter: |
- | ; PWadjustment : Power spectrum reference: Text file containing a 1D reference power spectrum. (default none) | + | ; PWadjustment : Power spectrum reference: Text file containing a 1D reference power spectrum |
; protein_shape : Protein Shape: It defines protein preferred orientation angles. " | ; protein_shape : Protein Shape: It defines protein preferred orientation angles. " | ||
- | ; upscale : Power spectrum adjustment strength: This parameters adjusts how strongly the power spectrum of the volume should be modified to match the reference. A value of 1 brings the volume' | + | ; upscale : Power spectrum adjustment strength: This parameters adjusts how strongly the power spectrum of the volume should be modified to match the reference. A value of 1 brings the volume' |
- | ; wn : Target image size [Pixels]: If different than 0, then the images will be rescaled to fit this size. (default 0) | + | ; wn : Target image size [Pixels]: |
; interpolation : 3D interpolation method: Method interpolation in 3D. Options are tr1 or 4nn. (default ' | ; interpolation : 3D interpolation method: Method interpolation in 3D. Options are tr1 or 4nn. (default ' | ||
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===== Output ===== | ===== Output ===== | ||
- | ; outdir : Output directory: There is a log.txt that describes the sequences of computations in the program. (default required string) | ||
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===== Description ===== | ===== Description ===== | ||
- | + | The clustering algorithm in the program combines a couple of computational techniques, equal-Kmeans clustering, K-means clustering, and reproducibility of clustering such that it not only has a strong ability but also a high efficiency to sort out heterogeneity of cryo-EM images. The command sxsort3d.py is the protocol I (P1). In this protocol, the user defines the group size and thus defines the number of group K. Then the total data is randomly assigned into K group and an equal-size K-means (size restricted K-means) is carried out. N independent equal-Kmeans runs would give N partition of the K groups assignment. Then, two-way comparison of these partitions gives the reproducible number of particles. | |
- | The clustering algorithm in the program combines a couple of computational techniques, equal-Kmeans clustering, K-means clustering, and reproducibility of clustering such that it not only has a strong ability but also a high efficiency to sort out heterogeneity of cryo-EM images. The command sxsort3d.py is the protocol I {P1). In this protocol, the user defines the group size and thus defines the number of group K. Then the total data is randomly assigned into K group and an equal-size K-means (size restricted K-means) is carried out. N independent equal-Kmeans runs would give N partition of the K groups assignment. Then two-way comparison of these partitions gives the reproducible number of particles. | + | |
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==== Reference ==== | ==== Reference ==== | ||
- | Described by A.Einstein in his first paper on spectrum of radiation | + | Described by A.Einstein in his first paper on spectrum of radiation from a house heater kept at room temperature. Journal of Irreproducible Results, 12, 1905, 12-1127. |
- | from a house heater kept at room temperature. Journal of Irreproducible | + | |
- | Results, 12, 1905, 12-1127. | + | \\ |
+ | ==== Developer Notes ==== | ||
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==== Author / Maintainer ==== | ==== Author / Maintainer ==== | ||
Zhong Huang | Zhong Huang | ||
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==== Files ==== | ==== Files ==== | ||
- | applications.py | + | sparx/ |
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==== See also ==== | ==== See also ==== | ||
- | [[sxrsort3d|sxrsort3d.py]] | + | [[pipeline: |
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==== Maturity ==== | ==== Maturity ==== | ||
- | stable while under development:: Two programs (P1,P2) have been tested on both simulated and experimental ribosome data. For experimental ribosome data, P2 has a reproducible ratio-70-90%. P2 can 100%separate two conformations from the simulated ribosome data that contains 5 conformations. | + | Alpha:: Under development. |
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- | ==== Known Bugs ==== | + | ==== Bugs ==== |
- | None. | + | There are no known bugs so far. |
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