Supported Applications

PyTOM

Description

a tool that 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
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
Installation
Use the following command to install this title with the CLI client: $ sbgrid-cli install pytom 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: 1.1 (4.6 GB)
OS X INTEL: 0.971 (58.0 MB)
Other Versions
- OS X INTEL:
Developers

Friedrich Foerster, Stefan Pfeffer, Ann-Victoria Mangold, Thomas Hrabe, Yuxiang Chen, Luis Kuuhn Cuellar