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SBGridTV

Supported Applications

PyTOM

  • 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 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.

    OPENMPI_X=1.6.3
    



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

  • 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:  0.971
    OS X INTEL:  0.971

  • Developers

    Friedrich Foerster
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