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  • Description

    unifies standard tomogram processing steps in a single python-based toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies.

  • Usage

    To list all executables provided by PyTOM, run: $ sbgrid-list pytom Copy to clipboard
  • Usage Notes

    PyTom uses an older OpenMPI, version 1.6.3. To run PyTOM with this older MPI, the full path to mpirun can be used.

    For example :

    $ /programs/x86_64-linux/openmpi/1.6.3/bin/mpirun -c 4 /programs/x86_64-linux/pytom/0.971/pytom/bin/pytom <your python script>

    The 'mpirun' executable can be called with the full path as above, or alternatively a version override for OpenMPI can be used. To override OpenMPI to 1.6.3, add this line in your ~/.sbgrid.conf.


    Then open a new terminal ( or source the /programs/sbgrid.(c)shrc ) . More information on version overrides can be found here :

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install pytom Copy to clipboard Available operating systems: Linux 64, OS X INTEL
  • Primary Citation*

    T. Hrabe, Y. Chen, S. Pfeffer, L. K. Cuellar, A. V. Mangold, and F. Foerster. 2012. PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. Journal of Structural Biology. 178(2): 177-188.

    • *Full citation information available through

  • Keywords

    Python Module, Tomography

  • Default Versions

    Linux 64:  1.0a (6.3 GB)
    OS X INTEL:  0.971 (58.0 MB)

  • Other Versions

      Linux 64:

      0.971 (123.0 MB)
    • OS X INTEL:

  • Developers

    Friedrich Foerster