PyChimera

Use UCSF Chimera packages in any Python 2.7 interpreter

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.

Projects using PyChimera

• GaudiMM
• InsiliChem Tangram
• @jrjhealey’s chimera scripts & bioinfo-tools

User Guide

• Quickstart
  • Why?
  • Usage
  • Multiplatform compatibility
• Installation
  • Recommended steps
  • Alternative procedure
  • Extra packages
• FAQ & Known issues
  • Numpy problems
  • PyChimera GUI has ugly fonts
  • Setuptools problems
  • Chimera reports problems with libgfxinfo.so and pcrecpp
  • dateutil version
• For developers
  • Quick API
  • Alternative methods
  • How does it work?

Indices and tables

• Index
• Module Index
• Search Page

Acknowledgments

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

Citation

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!

@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}
}