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This page describes how to use the Computational Crystallography Toolbox (cctbx) with open-source PyMOL on Fedora 32 which has python3 only installed.

CCTBX and PyMOL need to be compiled with the same Python distribution, otherwise they won't be compatible.

Confirmed procedure to get this working on Linux Fedora 32 with PyQt5 and CCTBX build dev-2130, which is based on conda:

1. Download cctbx from

2. Install cctbx:

./install --prefix=/usr/local

3. Install latest Miniconda3 in /usr/local from

4. Install pymol dependencies with conda into the cctbx environment:

 /usr/local/miniconda3/bin/conda install -p /usr/local/cctbx-dev-2130/conda_base -c conda-forge glew freeglut libpng freetype libxml2 msgpack-c pyqt qt glm qt catch2 libnetcdf

5. Download mmtf-cpp from and copy the content of the include subdirectory to /usr/local/cctbx-dev-2130/conda_base/include

6. Activate cctbx:

source /usr/local/cctbx-dev-2130/cctbx_env.csh

7. Compile PyMOL with:

cctbx.python install

8. Install Pmw from with:

cctbx.python install

9. Run PyMOL with:

cctbx.python -m pymol