Background

ARNy Plotter 🪄

This webserver allows you to create plots of useful metrics from RNA molecular dynamics simulations and view them in real-time alongside the trajectory.

Upload Files

Topology File: (Input here the Native state to be used in analysis)

Trajectory File: (Max 400 MB, please use a format supported by MDAnalysis and MDtraj)

Atom Selection

No modification Remove waters Remove all heterogens Custom selection

Uses MDAnalysis selection syntax.

Topology PDB File:

Frame Settings:

Select Plots:

Structural Deviation Analysis

RMSD
ERMSD
Radius of Gyration
End-to-End Distance (5' to 3')

Secondary Structure Analysis

SEC_STRUCTURE
DOTBRACKET
ARC
Base Pairing 2D Plot

Conformational Analysis

CONTACT_MAPS
TORSION

Torsion Mode:

Single Residue Multiple Residues All Residues

Residue:

Select Residues:

Upload topology file to see available residues

Select Torsion Angles:

Alpha Beta Gamma Delta Epsilon Zeta Chi

Dimensionality Reduction

PCA (Principal Component Analysis)
UMAP (Uniform Manifold Approximation)
t-SNE (t-Distributed Stochastic Neighbor Embedding)

Conformational Landscape

LANDSCAPE

First Dimension:

Second Dimension:

Processing...

Copy link to retrieve results later

Example

Click the buttons below to view precomputed results.

Documentation

If you want to learn more about how this webserver, click on this button to access the documentation

Trajectory Tools

Command-line scripts for playing, selecting parts of, and re-encoding your MD trajectories.

View Trajectory Tools

Retrieve Previous Results

Input in here the session id given at the top of the results page of your previous calculation, it allow you to retrieve this page without the need to recalculate everything

Old Session ID:

Recent Sessions

Your last 6 analysis sessions. Click on any session to retrieve its results.

Plot Settings

Please Cite Our Work

If you use ARNy Plotter in your research, please cite our paper:

Thank you for supporting our research!