Installation#
There are two main ways of interacting with FRETraj:
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#
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
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 thefretraj_gui.py
file located in the directory that was issued byfretraj --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.
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