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.