Installation

Installation#

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

1.1 Install PyMOL and FRETlabel#

  • Get PyMOL from Schrödinger or install the open-source version, e.g. via conda-forge conda install conda-forge::pymol-open-source.

  • Open the PyMOL via the Anaconda/Miniforge shell

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

  • Install FRETlabel by running the following commands

    pip install fretlabel

  • Locate the installation directory by running

    fretlabel --path

1.2 Register the Plugin#

  • Start PyMOL and install the FRETlabel GUI with PyMOL’s Plugin manager: Plugin → Plugin manager → Install New Plugin → Choose file... and select the fretlabel_gui.py file located in the directory that was issued by fretlabel --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.

1.3 Install with Docker#

As an alternative to the native installation outlined above, you may also use a Docker image with PyMOL and FRETlabel 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/fretlabel-pymol:latest
docker run -e DISPLAY=host.docker.internal:0 -v hostdir:/mnt fdsteffen/fretlabel-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.

Tip

To generate your own fragments you further need:

  • the preprocessing toolbox Antechamber packaged with Ambertools

    conda install -c conda-forge ambertools=20

  • the AnteChamber PYthon Parser interfacE Acpype

    conda install -c conda-forge acpype

  • A quantum chemistry package such as Gaussian or GAMESS

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