RING-PyMOL

RING-PyMOL is a plugin for PyMOL providing a set of analysis tools for structural ensembles and molecular dynamic (MD) simulations. RING-PyMOL combines residue interaction networks, as provided by the RING software (RING source, RING webserver), with structural clustering to enhance the analysis and visualization of the conformational complexity. RING software has been improved extensively. It is ten times faster, can process mmCIF files and it identifies typed interactions also for nucleic acids.

Go to the Wiki for the full documentation and usage examples.

RING-PyMOL features

• Precise calculation of non-covalent interactions
• Identifies and highlights correlating contacts and interaction patterns that can explain structural allostery, active sites and structural heterogeneity connected with molecular function
• Easy to use and extremely fast, processing and rendering hundreds of models and long trajectories in seconds
• Generates a number of interactive plots and output files for use with external tools

References

• RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics. Del Conte A, Monzon AM, Clementel D, Camagni GF, Minervini G, Tosatto SCE, Piovesan D. (2023) Bioinformatics [https://doi.org/10.1093/bioinformatics/btad260]
• RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles. Clementel D, Del Conte A, Monzon AM, Camagni GF, Minervini G, Piovesan D and Tosatto SCE. (2022) Nucleic Acids Research [https://doi.org/10.1093/nar/gkac365]

Install

In order to work, Ring-PyMOL requires PyMOL and some Python packages.

If you don't want to go through all the commands or you have problems with your PyMOL/Python version you can use a pre-built Singularity container, instructions are provided at the end of this document here.

Manual install

Dependencies

We provide three diffent solutions to insatll PyMOL and RING-PyMOL dependecies. The first two use Conda and gives the same result. The isntallation with APT works only for Linux users and might give different results depending on the version and distribution of your operating system.

NOTE Please make sure you install Python pakages for the correct PyMOL executable. In Linux you can type which pymol and which python to see the path of the PyMOL and Python executables. If installed with Conda, the command should return something like /opt/miniconda3/envs/myenv/bin/pymol and /opt/miniconda3/envs/myenv/bin/python

Conda YAML (RECOMMENDED)

• Install conda or miniconda
• Download the environment.yml YAML file from this repository
• Create the environment conda env create -f environment.yml
• Activate the environment conda activate ring-pymol-plugin

Conda

Same as before but with all commands issued explicitly

• Install conda or miniconda
• Create a new environment and activate it
  • conda create -n myenv
  • conda activate myenv
• Install PyMOL
  • conda install -c conda-forge -c schrodinger pymol-bundle (shrodinger version)
  • conda install -c conda-forge pymol-open-source (open-source version)
• Install Python dependencies
  • conda install networkx numpy scipy seaborn pandas requests biopython
  • pip install qt-material (install qt-material in the conda environment)

APT (Linux only)

This will use system environment. The version of PyMOL and Python packages depend on the version and distribution of your operating system (OS). RING-PyMOL might not work with an obsolete OS.

• sudo apt install pymol python3-pip python3-tk
• pip install pmw networkx numpy~=1.20 scipy seaborn pandas qt-material biopython requests

RING-PyMOL plugin

Once you have installed PyMOL and all the RING-PyMOL dependencies you have to install the RING-PyMOL plugin.

• Open PyMOL and go to Plugin > Plugin Manager > Install New Plugin > Install from Repository > Add..
• Add https://old.ring.biocomputingup.it/plugin/
• Click on ring-plugin.zip in the right panel and then click Install
• Set the installation directory
• The plugin should now appear on the Plugin menu of PyMOL

If you need to update the plugin with a newer version, just remove and reinstall.

Singularity container

Another option for installing the RING-PyMOL is to use a Singularity container. We provide the definition file that yuou can use to build the corresponding image.

To create the image file you can follow these steps:

• Install Singularity
• sudo singularity build -F ring-pymol-plugin.sif singularity.def (create the image file)
• singularity shell --cleanenv --writable-tmpfs -B ~/.Xauthority ring-pymol-plugin.sif (open a shell in the container). Note that the -B option is needed to allow the container to access the X server of the host machine for displaying the GUI.
• Start PyMOL with pymol
• Add a new directory where to find new plugins
  • Plugin > Plugin Manager > Settings > Add new directory...
  • Add /opt
• Restart PyMOL
• The plugin should now appear on the Plugin menu of PyMOL

Usage

Go to the Wiki for the full documentation.