~~NOTOC~~ ===== 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. \\ ===== Usage ===== Usage in command line sxsort3d.py stack outdir mask --focus=3Dmask --ir=inner_radius --radius=outer_radius --maxit=max_iter --rs=ring_step --xr=xr --yr=yr --ts=ts --delta=angular_step --an=angular_neighborhood --center=centring_method --nassign=nassign --nrefine=nrefine --CTF --stoprnct=stop_percent --sym=c1 --function=user_function --independent=indenpendent_runs --number_of_images_per_group=number_of_images_per_group --low_pass_filter=low_pass_filter --nxinit=nxinit --unaccounted --seed=random_seed --smallest_group=smallest_group --sausage --chunk0=CHUNK0_FILE_NAME --chunk1=CHUNK1_FILE_NAME --PWadjustment=PWadjustment --protein_shape=protein_shape --upscale=upscale --wn=wn --interpolation=method \\ ===== Typical usage ===== sxsort3d exists only in MPI version. mpirun -np 176 --host n1,n5,n6,n8,n9,n10,n0,n4,n3,n7 sxsort3d.py bdb:data sort3d_outdir1 mask.hdf --focus=ribosome_focus.hdf --chunkdir=/data/n10/pawel/ribosome_frank/ri3/main013 --radius=52 --CTF --number_of_images_per_group=2000 --low_pass_filter=.125 --stoprnct=5 \\ ===== Input ===== === Main Parameters === ; 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 for rotational correlation [Pixels]: Must be smaller than half the box size. Please set to the radius of the particle. (default -1) ; delta : Angular step for projections: (default '2') ; CTF : Use CTF: Do a full CTF correction during the alignment. (default False) ; sym : Point-group symmetry: (default c1) ; number_of_images_per_group : Images per group: Critical number of images per group, defined by user. (default 1000) ; nxinit : 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 subset: Name of chunk file containing particle IDs of 1st subset (chunk0) for computing margin of error. (default none) ; chunk1 : Chunk file name for 2nd subset: Name of chunk file containing particle IDs of 2nd subset (chunk0) for computing margin of error. (default none) \\ === Advanced Parameters === ; ir : Inner radius for rotational correlation [Pixels]: Must be bigger than 1. (default 1) ; maxit : Maximum iterations: (default 25) ; rs : Step between rings in rotational correlation: Must be bigger than 0. (default 1) ; xr : X search range [Pixels]: The translational search range in the x direction will take place in a +/xr range. (default 1) ; yr : Y search range [Pixels]: The translational search range in the y direction. If omitted it will be set as xr. (default -1) ; ts : Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default 0.25) ; an : Local angular search width [Degrees]: This defines the neighbourhood where the local angular search will be performed. (default '-1') ; 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: Function used to prepare the reference volume. (default do_volume_mrk02) ; 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) ; unaccounted : Reconstruct unaccounted images: (default False) ; seed : 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) ; PWadjustment : Power spectrum reference: Text file containing a 1D reference power spectrum. (default none) ; protein_shape : Protein Shape: It defines protein preferred orientation angles. "g" is for globular proteins and "f" is for filament proteins. (default 'g') ; 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's power spectrum completely to the reference, while a value of 0 means no modification. (default 0.5) ; wn : Target image size [Pixels]: 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 '4nn') \\ ===== Output ===== ; outdir : Output directory: There is a log.txt that describes the sequences of computations in the program. (default required string) \\ ===== 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. \\ ==== Method ==== \\ ==== Reference ==== \\ ==== Author / Maintainer ==== Zhong Huang \\ ==== Keywords ==== Category 1:: APPLICATIONS \\ ==== Files ==== applications.py \\ ==== See also ==== [[http://sparx-em.org/sparxwiki/sxrsort3d|sxrsort3d]] \\ ==== 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. \\ ==== Known Bugs ==== None. \\