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

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.

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 (Stevens et al. 2023) 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).