PyTom is a software package for the analysis of volumetric data obtained by cryo electron tomography (cryo-ET). It covers a complete pipeline of processing steps for tomogram reconstruction, localization of macromolecular complexes in tomograms, fine alignment of subtomograms extracted at these locations, and their classification.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive [user@cn4199 ~]$ module load PyTom [+] Loading PyTom 1.0 ...Running tests:
[user@cn4199 ~]$ wget https://github.com/FridoF/PyTom/archive/refs/tags/v1.0.tar.gz [user@cn4199 ~]$ tar -zxf v1.0.tar.gz && rm -f v1.0.tar.gz [user@cn4199 ~]$ cd PyTom-1.0/tests [user@cn4199 ~]$ pytom -m unittest discover ... This license affects the software package PyTom and all the herein distributed source / data files. Authors: Marten Chaillet Gijs van der Schot Ilja Gubins Mihajlo Vanevic Thomas Hrabe Yuxiang Chen Friedrich Foerster Copyright (c) 2021 Utrecht University http://www.pytom.org This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. The complete license can be obtained from http://www.gnu.org/licenses/gpl-2.0.html. RMSD = 0.72 ....................We adjusted msdz to 5.000 nm to make it an integer multiple of pixel size. Number of slices for multislice: 12 Determining DQE for K2SUMMIT chi-square value for fitting sinc function is 0.0005657000438432647 Determining MTF for K2SUMMIT chi-square value for fitting sinc function is 1.0941206081582777e-05 Projecting the model with 1 processes [Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers. Transforming sample for tilt/frame 0 Reduced rotation height for relevant specimens: 300 Simulating projection with multislice method for frame/tilt 0 Number of electrons per pixel (before oversampling and sample absorption): 100.00 [Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 8.2s remaining: 0.0s [Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 8.2s finished ... .variance for spline interpolation with numba: 3.850465873256326e-06 .before parallel: 24 after setting for parallel: 4 execution numba 4 threads: 0.1669407606124878 variance for spline interpolation with numba parallel: 3.816609478235478e-06 .variance for pt linear interpolation: 3.833221927715919e-06 variance for pt cubic interpolation: 3.817091292496215e-06 variance for pt spline interpolation: 3.816610180137391e-06 .variance for vt linear interpolation on cpu: 3.8332236727001145e-06 variance for vt bspline interpolation on cpu: 3.826985903288005e-06 variance for vt bspline_simple interpolation on cpu: 3.826985903288005e-06 variance for vt filt_bspline interpolation on cpu: 3.910493887815392e-06 variance for vt filt_bspline_simple interpolation on cpu: 3.910493887815392e-06 .variance for vt linear interpolation on gpu: 3.846456e-06 variance for vt bspline interpolation on gpu: 3.8316716e-06 variance for vt bspline_simple interpolation on gpu: 3.8315306e-06 variance for vt filt_bspline interpolation on gpu: 3.879772e-06 variance for vt filt_bspline_simple interpolation on gpu: 3.87833e-06 ... ---------------------------------------------------------------------- Ran 55 tests in 72.486s OK [user@cn4199 ~]$ exit salloc.exe: Relinquishing job allocation 59748321 [user@biowulf ~]$