Logo
ScienceStack
Table of Contents
Fetching ...
Sign In

VTX: Real-time high-performance molecular structure and dynamics visualization software

Maxime Maria, Simon Guionnière, Nicolas Dacquay, Cyprien Plateau-Holleville, Valentin Guillaume, Vincent Larroque, Jean Lardé, Yassine Naimi, Jean-Philip Piquemal, Guillaume Levieux, Nathalie Lagarde, Stéphane Mérillou, Matthieu Montes

TL;DR

The paper addresses the need for scalable, real-time visualization of massive molecular structures and trajectories beyond existing tools. It introduces VTX, a meshless high-performance rendering engine with a minimal GUI, open-source under non-commercial terms, and broad format support via chemfiles, enabling real-time viewing of systems up to hundreds of millions of atoms on consumer hardware. The approach combines impostor-based rendering, ray-casting, and a deferred shading pipeline with adaptive cartoon and SES representations, achieving high-quality visuals and 8K image export, validated against large benchmarking datasets. The work has practical impact for research and education by enabling interactive analysis of large-scale molecular data and providing a flexible, extensible platform with future plans for SES analytics, ambient occlusion, and Python-like bindings.

Abstract

Summary: VTX is a molecular visualization software capable to handle most molecular structures and dynamics trajectories file formats. It features a real-time high-performance molecular graphics engine, based on modern OpenGL, optimized for the visualization of massive molecular systems and molecular dynamics trajectories. VTX includes multiple interactive camera and user interaction features, notably free-fly navigation and a fully modular graphical user interface designed for increased usability. It allows the production of high-resolution images for presentations and posters with custom background. VTX design is focused on performance and usability for research, teaching and educative purposes. Availability and implementation: VTX is open source and free for non commercial use. Builds for Windows and Ubuntu Linux are available at http://vtx.drugdesign.fr. The source code is available at https://github.com/VTX-Molecular-Visualization . Supplementary Information: A video displaying free-fly navigation in a whole-cell model is available

VTX: Real-time high-performance molecular structure and dynamics visualization software

TL;DR

The paper addresses the need for scalable, real-time visualization of massive molecular structures and trajectories beyond existing tools. It introduces VTX, a meshless high-performance rendering engine with a minimal GUI, open-source under non-commercial terms, and broad format support via chemfiles, enabling real-time viewing of systems up to hundreds of millions of atoms on consumer hardware. The approach combines impostor-based rendering, ray-casting, and a deferred shading pipeline with adaptive cartoon and SES representations, achieving high-quality visuals and 8K image export, validated against large benchmarking datasets. The work has practical impact for research and education by enabling interactive analysis of large-scale molecular data and providing a flexible, extensible platform with future plans for SES analytics, ambient occlusion, and Python-like bindings.

Abstract

Summary: VTX is a molecular visualization software capable to handle most molecular structures and dynamics trajectories file formats. It features a real-time high-performance molecular graphics engine, based on modern OpenGL, optimized for the visualization of massive molecular systems and molecular dynamics trajectories. VTX includes multiple interactive camera and user interaction features, notably free-fly navigation and a fully modular graphical user interface designed for increased usability. It allows the production of high-resolution images for presentations and posters with custom background. VTX design is focused on performance and usability for research, teaching and educative purposes. Availability and implementation: VTX is open source and free for non commercial use. Builds for Windows and Ubuntu Linux are available at http://vtx.drugdesign.fr. The source code is available at https://github.com/VTX-Molecular-Visualization . Supplementary Information: A video displaying free-fly navigation in a whole-cell model is available
Paper Structure (5 sections, 1 figure, 1 table)

This paper contains 5 sections, 1 figure, 1 table.

Table of Contents

  1. Introduction
  2. Methods
  3. Competing interests
  4. Author contributions statement
  5. Acknowledgments

Figures (1)

  • Figure 1: A. Illustration of the VTX GUI organized with different dockable panels. The Scene Tree panel contains and allows the selection of all the objects present in the scene, such as molecules, labels and viewpoints. The Sequence panel displays and allows the selection of the sequence of each biomolecule , while the Visualization Panel allows the selection, observation, and manipulation of their 3D structure. Frequently used options for manipulation and rendering are directly accessible in the visualization panel through the use of button overlays. When an object is selected in the scene, detailed information about the loaded object, additionally loaded trajectories and chosen representations are available in the Inspector panel. The Console panel displays all logs. B. Different molecular representations available in VTX (Saccharomyces Cerevisiae BCP1, PDB id : 7C4H) Cartoon (upper left), Van der Waals (upper right), balls and sticks (bottom left), Solvent Excluded Surface (bottom right) C. Illustration of the coarse-grained whole mycoplasma cell model from marrink23 with (left) and without (right) clipping. Martini beads are displayed as surface and flat color (membrane lipids in green, membrane proteins in blue, ribosomes in yellow, chromosome in light blue, cytoplasmic proteins in dark blue).