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

• install PyMOL and add FRETraj as a Plugin manually → Install PyMOL and FRETraj

• install a Docker image with PyMOL and FRETraj preconfigured (see Docker image) → Install with Docker

1.1 Install PyMOL and FRETraj

For Windows

• 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
  

For Linux

• 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

  pip

  Install from PyPI

  pip install fretraj
  

  conda

  Install from the conda-forge channel on Anaconda.org

  conda install fretraj -c conda-forge
  

  from source

  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: Plugin → Plugin manager → Install New Plugin → Choose 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.

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

pip install labellib

conda

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