fingernat-pymol-plugin

• fingernat-pymol-plugin
• About
• Installation
  • Prerequisities
  • Plugin installation in PyMOL
• Compatibility and tests
• Usage
• Screenshots
• Contributors

About

This PyMOL plugin visualizes interactions detected by the fingeRNAt progam. This means that you need to run it first and generate data to be visualized in this plugin. But don't worry, it's quite simple :)

This plugin works best with PyMOL >= 2.2.3 and Python 3.

To cite: Szulc, N. A., Mackiewicz, Z., Bujnicki, J. M., & Stefaniak, F. (2022). fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions. PLOS Computational Biology, 18(6), e1009783. https://doi.org/10.1371/journal.pcbi.1009783

This repo DOI:

Installation

Prerequisities

The plugin works under the Python 3 and makes use of the pandas module. To install it:

# using pip
python3 -m pip install pandas

# or conda
conda install pandas

# or in debian/ubuntu using apt:
apt install python3-pandas

# or install the full conda environment of pymol and pandas, ready to install this plugin
conda create -y --name pymol-pandas -c conda-forge  python">=3.5" pandas pymol-open-source

Plugin installation in PyMOL

1. In PyMOL window go to top menu - Plugin -> Plugin manager -> Install new plugin
2. In the URL field paste one of the following links:

• the latest release: https://github.com/filipsPL/fingernat-pymol-plugin/archive/refs/tags/0-4-2-8.zip,
• or the latest code archive: https://github.com/filipsPL/fingernat-pymol-plugin/archive/refs/heads/main.zip

click Fetch, confirm the installation and the path.

3. The fingeRNAt plugin is available from the Plugin menu:

Compatibility and tests

This PyMOL plugin was tested in the following setups:

PyMOL version	Linux	MacOS	Windows
2.2.3	✅
2.3.2	✅
2.4.0	✅	✅
2.5.0	✅
2.6.0a	✅

Usage

1. Load into PyMOL nucleic acid and ligand structures you had used to detect interactions with the fingeRNAt.

2. Open the fingeRNAt plugin, click Browse and point to the DETAIL_... tsv file which was generated by fingeRNAt.

3. Click Proceed!

4. A bunch of new groups and objects are created:

• Interactions: objects holding detected interactions. The exact number depends of the detected inteactions types.
• Receptor preferences: objects showing preferences of the receptor for forming/accomodating the given type of interaction.
• Ligand preferences: objects showing preferences of the ligand binding pocket for forming/accomodating the given type of interaction.
• Neighbours: fragment of the receptor containing residues which form interactions with ligand

Each group and object can be hidden/shown separately.

5. Each ligand's model (state) contains interactions detected for this particular model. The last model (state) contains the visual legend of the detected interactions:

Additionally, the color codes are printed in the console.

---------- Colors legend: -----------
  Hydrogen bond (HB) is presented in marine
  Cation-anion (CA) is presented in red
  Halogen bond (HAL) is presented in purple
  Lipophilic (Lipophilic) is presented in silver
  Pi-stacking (Pi_Stacking) is presented in orange
  Pi-cation (Pi_Cation) is presented in green
  Pi-anion (Pi_Anion) is presented in hotpink
  Water-mediated (Water-mediated) is presented in blue
  Ion-mediated (Ion-mediated) is presented in salmon
  any_contact (any_contact) is presented in teal

The exact number of interactions depends on the input data.

Screenshots

pymol	description
	Overview of the formed interactions
	Receptor preferences
	Ligand preferences in the ligand binding site
	Preferred positions of Pi-involving interactions and cation anion-interactions
	As above, but for the receptor
	User defined interactions; some bonds are heading to implicit hydrogens

Contributors

	github	contact
Filip Stefaniak	@filipsPL
Natalia Szulc	@n-szulc