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arXiv · 2503.07181

Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model

Maxime Maria·Valentin Guillaume·Simon Guionniere·Nicolas Dacquay·Cyprien Plateau Holleville·Vincent Larroque·Jean Larde·Yassine Naimi·Jean Philip Piquemal·Guillaume Levieux·Nathalie Lagarde·Stephane Merillou·Matthieu Montes
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Abstract

VTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software when handling massive molecular datasets. VTX employs a meshless molecular graphics engine utilizing impostor-based techniques and adaptive level-of-detail (LOD) rendering. This approach significantly reduces memory usage and enables real-time visualization and manipulation of large molecular systems. Performance benchmarks against VMD, PyMOL, and ChimeraX using a 114-million-bead Martini minimal whole-cell model demonstrate VTX's efficiency, maintaining consistent frame rates even under interactive manipulation on standard computer hardware. VTX incorporates features such as screen-space ambient occlusion (SSAO) for enhanced depth perception and free-fly navigation for intuitive exploration of large molecular systems. VTX is open-source and free for non commercial use. Binaries for Windows and Ubuntu Linux are available at http://vtx.drugdesign.fr. VTX source code is available at https://github.com/VTX-Molecular-Visualization.

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Maxime Maria, Valentin Guillaume, Simon Guionniere, Nicolas Dacquay, Cyprien Plateau Holleville, Vincent Larroque, Jean Larde, Yassine Naimi, Jean Philip Piquemal, Guillaume Levieux, Nathalie Lagarde, Stephane Merillou, Matthieu Montes. 2025-03-10. Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model. https://doi.org/10.3389/fbinf.2025.1588661

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