sxresolution72020-09-15 14:37:28penczek62020-06-23 16:40:34penczek52020-06-19 20:22:14penczek42020-05-13 01:19:07penczek32020-05-12 05:08:56penczek22020-05-12 05:07:45penczek12020-05-12 05:04:00penczekNamesxresolution - FSCM resolution measures: Compute overall and local resolution measures using a pair of half-maps. UsageUsage in command lines: sxresolution.py firstvolume secondvolume maskfile outputdir --wn=window_size --step=shell_step_size --cutoff=res_cutoff --res_overall=overall_resolution --radius=radius --fsc=output_file_name --MPI Typical usage sxresolution.py refinementdir/main002/vol0.hdf refinementdir/main002/vol2.hdf outputdir --radius=28 InputfirstvolumeFirst half-volume: (default required string) secondvolumeSecond half-volume: (default required string) maskfile3D mask: Defines the region within which FSCM will be computed. (default none) outputdirOutput directory: results will be written to this directory. If it does not exist it will be created. wnFSCM box size: Defines the size of a 3D box within which local FSCM values will be computed. (default 15) stepFourier shell step size [Pixels]: (default 1.0) lfiLFI: Low Fourier index to begin calculations from (default 1) hfiHFI: High Fourier index to end calculations on (default nx//2-2) significanceSIGNIFICANCE: Significance level for the Upper Confidence Interval. (default 0.99, which corresponds to 1%) sigmagSIGMAG: sigma of the Fourier space Gaussian window in pixels (default 1.0) ndf_reduceNDF_REDUCE: Reduction of ndf due to point group symmetry, for example for D3 set to 6 (default 1.0) cutoffResolution cut-off [1/Pixel]: Cut-off for the Local FSCM CI. (default 0.143) radiusMask radius [Pixels]: If there is no maskfile, sphere with r=radius will be used. (default -1) local_fscLOCAL_FSC: Set to 1 to compute local resolution volume (default 0). nthreadsNTHREADS: Number of threads (mainly for 3D FFT) (default 4) Outputoutputdirresults will be written to this directory Output volume: Each voxel contains the resolution for this area in absolute frequency units. (default required string) DescriptionLocal resolution values are computed within small windowed areas (size wn^15). Due to small sample size the values are inaccurate and outcome tends to be noisy. It is thus suggested to use broader Gaussian window when local resolution is computed, say sigmag=3.0. Author / MaintainerPawel Penczek Keywordscategory 1APPLICATIONS Maturitystableworks for most people, has been tested; test cases/examples available.