Molecular Visualisation Suite
Browser-based 3D rendering of all simulation outputs from the foundation's programs. Inspect trajectories, map electron density surfaces, analyse binding modes, and export publication-quality images — directly in the browser, with no external software required.
The Molecular Visualisation Suite is the visual layer of the Jorgensen Foundation platform. Every output from BOSS, MCPRO, BOMB, FEP, and the OPLS parameter engine feeds directly into the suite without format conversion or file download. The renderer is built on WebGL, delivering hardware-accelerated 3D graphics in any modern browser. Protein-ligand complexes, Monte Carlo trajectories, free energy convergence plots, and electron density maps all open within seconds of a simulation completing — turning computational results into insight that can be shared immediately with collaborators.
3D Molecular Rendering
Hardware-accelerated WebGL rendering of molecular structures in ball-and-stick, space-fill, ribbon, and surface representations. Switch display modes interactively. Supports systems from single small molecules to full protein-ligand complexes with explicit solvent.
Trajectory Playback
Frame-by-frame or continuous playback of Monte Carlo and MD trajectories. Adjustable playback speed, looping, and frame-stepping. Overlay multiple frames to visualise conformational sampling. Export selected frames as PDB snapshots.
Electron Density Surfaces
Isosurface rendering of electron density and electrostatic potential maps from semi-empirical QM calculations in BOSS. Adjustable isovalue with colour-mapped ESP overlay. Identifies electrophilic and nucleophilic regions to guide ligand design.
Binding Mode Analysis
Overlay of docked or simulated ligand poses within the protein active site. Hydrogen bond detection and display. Residue-by-residue interaction energy heatmap from MCPRO decomposition analysis, colour-mapped onto the protein surface.
Free Energy Plots
Interactive plots of FEP convergence, per-window ΔG contributions, overlap matrices, and cumulative free energy as a function of simulation length. Zoom, pan, and export as SVG or PNG for papers and presentations.
Export and Sharing
Export rendered scenes as high-resolution PNG or publication-quality SVG. Generate shareable links to visualisation states for collaborators with platform access. Download underlying data (PDB, CSV) directly from within the viewer.
WebGL Renderer
The suite's rendering engine uses WebGL 2.0 for hardware-accelerated 3D graphics with no plugin or installation requirement. Molecular geometry is passed as vertex buffers to the GPU; surface meshes are generated client-side using marching-cubes for electron density isosurfaces. Supports systems up to ~100,000 atoms at interactive frame rates on modern hardware. Falls back gracefully to WebGL 1.0 where 2.0 is unavailable.
Trajectory Streaming
Trajectory files from BOSS and MCPRO simulations are streamed progressively from cloud storage rather than downloaded in full before playback. The first frame renders immediately; subsequent frames load in the background. Supports trajectories of arbitrary length. Frame interpolation provides smooth playback between coarsely-spaced coordinate snapshots. Playback state is preserved when switching between browser tabs.
Electron Density Isosurfaces
Electron density grids from BOSS semi-empirical QM calculations are stored as volumetric data in a compact binary format. The suite renders adjustable-isovalue surfaces using a GPU-accelerated marching-cubes implementation. Electrostatic potential mapped onto the density surface is colour-coded from red (negative) to blue (positive), with adjustable colour scale limits. Grid resolution is typically 0.5 Å for BOSS output.
Interaction Energy Heatmap
Per-residue interaction energies from MCPRO decomposition analysis are mapped onto the protein surface as a colour gradient. Residues with strong favourable interactions (hotspots) are coloured distinctly from neutral and unfavourable contacts. Clicking a residue in the 3D view highlights it in the accompanying data table and displays the LJ and electrostatic components separately. Useful for identifying key binding contacts and guiding SAR hypotheses.
Hydrogen Bond Detection
Geometric hydrogen bond detection across trajectory frames: donor-acceptor distance ≤ 3.5 Å and D-H···A angle ≥ 120°. H-bond occupancy (fraction of frames with a given contact) displayed as a label on the 3D view and listed in a sortable table. Threshold values are user-adjustable. Solute-solute (ligand-protein) and solute-solvent bonds detected independently.
Image and Data Export
Rendered scenes exported as PNG at user-specified resolution (up to 4096 × 4096 px) or as SVG for vector graphics workflows. The underlying molecular coordinates of any displayed frame can be downloaded as PDB. Numerical data displayed in plots — ΔG values, RDFs, convergence curves — are downloadable as CSV. Shareable links encode the full viewer state including camera angle, display mode, and active analysis overlay.
What the Suite reads
Structure and trajectory files (.pdb)
Single-frame structures or multi-model PDB trajectory files from BOSS, MCPRO, BOMB, and FEP. Loaded directly from the platform's output storage or uploaded from local disk.
Electron density grids (.cube)
Gaussian cube-format volumetric electron density and electrostatic potential grids from BOSS QM calculations. Supports both density and potential on the same grid for ESP-mapped surface rendering.
Numerical results (.csv)
Free energy values, per-residue decompositions, RDF data, and convergence statistics from simulation log files. Parsed automatically to generate interactive plots within the viewer.
Small-molecule structures (.mol2 / .sdf)
Direct upload of ligand structures for standalone visualisation or overlay with protein binding site structures outside of a full simulation workflow.
What the Suite returns
Rendered images (.png)
High-resolution raster exports of the 3D view at any camera angle. Configurable resolution up to 4096 × 4096 px with transparent background option for figure preparation.
Vector plots (.svg)
Scalable vector exports of all 2D data plots — FEP convergence, overlap matrices, RDFs, decomposition bar charts. Suitable for direct inclusion in manuscripts without quality loss.
Frame snapshots (.pdb)
Coordinate download of any trajectory frame displayed in the viewer. Used to extract representative binding mode structures for further analysis or reporting.
Shareable view links
Encoded URLs capturing the full viewer state — loaded files, camera orientation, display mode, and active overlays. Share with collaborators who have platform access for instant reproduction of the view.
Sign in to open the Molecular Visualisation Suite — all simulation outputs rendered interactively in the browser, no installation required.