PyMOL Schrödinger

Advanced Scripting Workshop

Part 8: Anaconda Cloud with PyMOL 2.0

PyMOL 2.0 distributions include Anaconda Python and the conda package manager. This allows to install popular 3rd party software (e.g. rdkit or biopython) into the same environment with PyMOL.

Examples of PyMOL extensions which require 3rd party components:

Install "pymol-psico" into PyMOL 2.0 bundle

  1. Download bundle from (On Windows, use the .zip bundle, not the .exe installer)
  2. You'll find conda here:
    • On Windows: PyMOL/Scripts/conda.exe
      Pro-tip: run PyMOLWin.exe and type into the command line: system cmd
    • On Linux: pymol/bin/conda
    • On MacOS:
  3. Install "pymol-psico" with:
    conda install -c schrodinger pymol-psico
  4. Use a psico feature in PyMOL, e.g. rmsf2b:
    fetch 1nmr, async=0
    import psico.editing
    cartoon putty

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