Installation#

There are two main ways of interacting with FRETraj:

  1. as a PyMOL plugin with a GUI

  2. as a Python module in a Jupyter notebook

1. PyMOL plugin#

Depending on your operating system and preference there are multiple options to install PyMOL

1.1 Install PyMOL and FRETraj#

  • Get PyMOL from Schrödinger or follow the instructions here.

  • Search for Anaconda/Miniforge prompt in the Windows start menu and run the following command to install FRETraj

    conda install fretraj -c conda-forge
    
  • Locate the installation directory by running

    fretraj --path
    
  • Get PyMOL either from Schrödinger or from your package manager (e.g. on Ubuntu apt-get install pymol). Alternatively, you can compile PyMOL yourself from the source code on Github.

  • Install FRETraj

    Install from PyPI

    pip install fretraj
    

    Install from the conda-forge channel on Anaconda.org

    conda install fretraj -c conda-forge
    

    Install the latest development version from Github with Poetry

    curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
    git clone https://github.com/RNA-FRETools/fretraj.git
    cd fretraj/
    poetry install
    
  • Locate the installation directory by running

    fretraj --path
    

1.2 Register the Plugin#

  • Start PyMOL and install the FRETraj GUI with PyMOL’s Plugin manager: PluginPlugin managerInstall New PluginChoose file... and select the fretraj_gui.py file located in the directory that was issued by fretraj --path. In the popup window select where you would like to install the plugin (default: <PyMOL_path>/site-packages/pmg_tk/startup/). Confirm with OK.

../_images/pymol_plugin_manager.png

Fig. 2 PyMOL’s plugin manager on Windows.#

Tip

For faster computation of the accessible-contact volumes you may additionally consider installing the C++ library LabelLib with either pip or conda. However, this is not required since FRETraj features a built-in Python implementation of the ACV algorithm.

pip install labellib
conda install labellib -c tpeulen

1.3 Install with Docker#

As an alternative to the native installation outlined above, you may also use a Docker image with PyMOL and FRETraj preinstalled. Make sure you have Docker and an X11 server installed (e.g. VcXsrv for Windows, configured with Wgl="False" and DisableAC="True"). Then pull and run the image from DockerHub (replace hostdir with a directory on your host system that you would like to mount into the image)

docker pull fdsteffen/fretraj-pymol:latest
docker run -e DISPLAY=host.docker.internal:0 -v hostdir:/mnt fdsteffen/fretraj-pymol

Incentive or open-source PyMOL

PyMOL was developed by Warren DeLano [1] and is currently maintained by Schrödinger. Binaries for Windows, Linux and macOS are distributed by Schrödinger under academic and commercial licensing options. The source-code is available on Github. The cross-platform, open-source PyMOL can be installed with conda

conda install conda-forge::pymol-open-source

2. Juypter notebook#

If you prefer a programmatic approach to calculating accessible-contact volumes and predicting FRET efficiencies you may interact with FRETraj in a Jupyter [2] notebook and use NGLview [3] instead of PyMOL for visualization. A demo notebook can be found here.

pip install fretraj   # Linux / macOS
or
conda install fretraj -c conda-forge   # Linux / macOS / Windows