PyChimera is a wrapper around UCSF Chimera, so it makes sense that you have to install it beforehand. Additionally, to reduce compatibility problems, PyChimera is best used within a conda environment.

Alternative procedure

If you don’t want (or can’t) use conda, you can also install PyChimera with pip:

pip install pychimera

or directly from source:

# With git
git clone
cd pychimera
python install

# With wget
unzip pychimera*.zip
cd pychimera-master
python install

While this should work in an ideal environment, it would probably have some rough edges due to the libraries installed in your system being different than the ones provided by UCSF Chimera. The pychimera conda package has been finetuned to work with the correct versions so, if possible use that. Otherwise, refer to the conda recipe to identify the correct versions.

Extra packages

So far, you have a barebones pychimera installation. If you want to make use of all the Jupyter compatibility features, you will need to install some extra packages. Namely:

  • IPython support: ipython (in Windows, qtconsole is also required).
  • Notebook support: jupyter, notebook.
  • Interactive molecule depiction: nglview.

This is easily installed with conda:

## First, activate your environment if necessary
# source activate pychimera
## In Windows, it would be:
# activate pychimera
conda install ipython jupyter notebook
## In Windows, you will also need:
conda install qtconsole
## For interactive visualization in the notebook:
conda install -c bioconda nglview
## might need:
# jupyter-nbextension enable nglview --py --sys-prefix