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.
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 : https://sbgrid.org/wiki/usage/versions
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.
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