PyChimera

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Use UCSF Chimera packages in any Python 2.7 interpreter

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With PyChimera you can…

• Run scripts depending on chimera from CLI with pychimera script.py.
• Enable import chimera in interactive coding sessions outside UCSF Chimera, including IPython and Jupyter Notebooks.
• Launch a standard UCSF Chimera instance, with the benefit of importing all your conda or virtualenv packages with pychimera --gui.

I hope it’s useful! Feedback is appreciated!

Documentation

The updated documentation is always available at readthedocs_.

Acknowledgments

Largely based on ideas by Greg Couch at chimera-users_.

.. _UCSF Chimera: https://www.cgl.ucsf.edu/chimera/ .. _latest UCSF Chimera: http://www.cgl.ucsf.edu/chimera/download.html .. _Greg Couch at chimera-users: http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html .. _readthedocs: http://pychimera.readthedocs.io

Citation

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PyChimera is scientific software, funded by public research grants (Spanish MINECO's project CTQ2014-54071-P, Generalitat de Catalunya's project 2014SGR989 and research grant 2017FI_B2_00168, COST Action CM1306). If you make use of PyChimera in scientific publications, please cite it. It will help measure the impact of our research and secure future funding!

.. code-block:: latex

@article{pychimera2018, author = {Rodríguez-Guerra Pedregal, Jaime and Maréchal, Jean-Didier}, title = {PyChimera: use UCSF Chimera modules in any Python 2.7 project}, journal = {Bioinformatics}, volume = {34}, number = {10}, pages = {1784-1785}, year = {2018}, doi = {10.1093/bioinformatics/bty021}, URL = {http://dx.doi.org/10.1093/bioinformatics/bty021}, eprint = {/oup/backfile/content_public/journal/bioinformatics/34/10/10.1093_bioinformatics_bty021/1/bty021.pdf} }