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Ammolite logo

Ammolite - From Biotite to PyMOL and back again

This package enables the transfer of structure related objects from Biotite to PyMOL for visualization, via PyMOL's Python API:

  • Import AtomArray and AtomArrayStack objects into PyMOL - without intermediate structure files.
  • Convert PyMOL objects into AtomArray and AtomArrayStack instances.
  • Use Biotite's boolean masks for atom selection in PyMOL.
  • Display images rendered with PyMOL in Jupyter notebooks.

Have a look at this example:


ammolite demo


PyMOL is a trademark of Schrodinger, LLC.