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pipeline:sort3d:sxrsort3d [2018/02/23 16:55] moriya |
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- | ~~NOTOC~~ | ||
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- | ===== sxsort3d ===== | ||
- | 3D Clustering - SORT3D: Sort 3D heterogeneity based on the reproducible members of K-means and Equal K-means classification. It runs after 3D refinement where the alignment parameters are determined. | ||
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- | ===== Usage ===== | ||
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- | Usage in command line | ||
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- | sxsort3d.py | ||
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- | ===== Typical usage ===== | ||
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- | sxsort3d exists only in MPI version. | ||
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- | mpirun -np 192 sxsort3d.py bdb:data sort3d_outdir1 mask.hdf --focus=ribosome_focus.hdf --chunkdir=/ | ||
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- | ===== Input ===== | ||
- | === Main Parameters === | ||
- | ; stack : Input images stack: (default required string) | ||
- | ; outdir : Output directory: There is a log.txt that describes the sequences of computations in the program. (default required string) | ||
- | ; mask : 3D mask: File path of the global 3D mask for clustering. (default none) | ||
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- | ; focus : Binary Focus 3D mask: Binary 3D mask used for focused clustering. (default none) | ||
- | ; radius : Particle radius [Pixels]: Used as outer radius for rotational correlation. | ||
- | ; delta : Angular step for projections [Degrees]: Angular step of reference projections. (default ' | ||
- | ; CTF : Use CTF: Do a full CTF correction during the alignment. (default False) | ||
- | ; sym : Point-group symmetry: Point-group symmetry of the target structure. (default c1) | ||
- | ; number_of_images_per_group : Images per group: Critical value defined by user. It suggests program the number of groups. (default 1000) | ||
- | ; nxinit : Initial image size for sorting: Initial image size for sorting. (default 64) | ||
- | ; smallest_group : Smallest group size: Minimum members for identified group. (default 500) | ||
- | ; chunk0 : Chunk file name for 1st halfset: Name of chunk file containing particle IDs of 1st halfset (chunk0) for computing margin of error. (default none) | ||
- | ; chunk1 : Chunk file name for 2nd halfset: Name of chunk file containing particle IDs of 2nd halfset (chunk1) for computing margin of error. (default none) | ||
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- | === Advanced Parameters === | ||
- | ; ir : Inner radius for rotational correlation [Pixels]: Must be bigger than 1. (default 1) | ||
- | ; maxit : Maximum iterations: Maximum number of iteration. (default 25) | ||
- | ; rs : Step between rings in rotational correlation: | ||
- | ; 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 will take place in -yr to +yr range.. If omitted, it will be set as xr. (default ' | ||
- | ; 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 ' | ||
- | ; 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) | ||
- | ; 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) | ||
- | ; function : Reference preparation function: Specify name of function used to prepare the reference volume. (default do_volume_mrk05) | ||
- | ; independent : Number of independent runs: Number of independent equal-Kmeans. (default 3) | ||
- | ; 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: Reconstruct unaccounted images. (default False) | ||
- | ; 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: A way of filtering volume. (default False) | ||
- | ; PWadjustment : Power spectrum reference: Text file containing a 1D reference power spectrum used for EM density map power spectrum correction. Typically, compute 1D power spectrum from PDB file. (default none) | ||
- | ; 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' | ||
- | ; wn : Target image size [Pixels]: Specify optimal window size for data processing. If different than 0, then the images will be rescaled to fit this size. (default 0) | ||
- | ; interpolation : 3D interpolation method: Method interpolation in 3D. Options are tr1 or 4nn. (default ' | ||
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- | ===== Output ===== | ||
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- | ===== 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. | ||
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- | ==== Method ==== | ||
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- | ==== Reference ==== | ||
- | 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. | ||
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- | ==== Developer Notes ==== | ||
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- | ==== Author / Maintainer ==== | ||
- | Zhong Huang | ||
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- | ==== Keywords ==== | ||
- | Category 1:: APPLICATIONS | ||
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- | ==== Files ==== | ||
- | sparx/ | ||
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- | ==== See also ==== | ||
- | [[pipeline: | ||
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- | ==== Maturity ==== | ||
- | Alpha:: 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. | ||
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- | ==== Bugs ==== | ||
- | There are no known bugs so far. | ||
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