> ## Documentation Index
> Fetch the complete documentation index at: https://docs.revilico.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# 3D Visualization

> Interactive 3D Molecular and Structural Visualization with Mol* for Proteins, Ligands, Densities, and Trajectories

## Why Use 3D Visualization?

3D Visualization is Revilico's interactive structure viewer, built on Mol\*, for exploring protein structures, protein-ligand complexes, molecular dynamics trajectories, and electron density maps directly in the browser. It is the primary tool for visual inspection of computational results from RevTarget, RevBind, and RevDynamics engines, enabling researchers to examine binding poses, assess structural quality, and communicate structural findings without requiring a local molecular graphics installation.

<Frame>
  <img src="https://mintlify.s3.us-west-1.amazonaws.com/revilicoinc/images/rev3dvizworkflow.png" alt="3D Visualization Interface" />
</Frame>

## Background

Mol\* (pronounced "molstar") is a modern, high-performance molecular visualization framework developed by the RCSB PDB and PDBe teams. It renders large molecular assemblies efficiently in the browser using WebGL, supports a wide range of structure and data formats, and provides a comprehensive set of representation and analysis tools. RevTarget integrates Mol\* as the primary visualization layer for all structural outputs across the platform.

## Interface Panels

**Left panel (data and options):**

The Home tab provides structure loading tools. Structures can be loaded from PDB by entering a PDB ID with download source selection (PDB or PDB IDs), or downloaded as PDB files. Additional options include:

* **Download Density:** Fetch electron density maps for deposited structures
* **Download File:** Open local structure files
* **Open Files:** Access files from the Data Engineering environment
* **Load Trajectory:** Load MD trajectory files for dynamic visualization
* **Load Genome 3D (G3D):** Load genome 3D structure data
* **Download Tunnels:** Overlay channel and tunnel calculations
* **Zenodo Import:** Import structures and data from Zenodo repositories
* **Remote States:** Access saved visualization states

**Main canvas:**
The central 3D canvas renders the molecular structure with full rotation (drag), zoom (scroll), and translation (right-drag) controls. The canvas supports simultaneous display of multiple structure components, density maps as isosurface meshes, and trajectory playback.

**Right panel (Structure Tools):**

The Structure panel provides representation and analysis controls:

**Measurements:**
Add distance, angle, dihedral, and orientation measurements directly on the 3D structure by clicking atoms. Measurements persist and can be toggled or deleted.

**Quick Styles:**
Apply pre-configured representation presets with a single click:

* **Default:** Standard cartoon backbone with ball-and-stick ligand
* **Cartoon:** Cartoon secondary structure representation with colored helices, sheets, and loops
* **Spacefill:** Van der Waals sphere representation for each atom
* **Surface:** Molecular surface (solvent-accessible or solvent-excluded)

**Apply Style:**

* **Default:** Standard atom coloring by element and chain
* **Illustrative:** Cel-shading style for publication-quality renders with flat colors and visible outlines

**Apply Wiggle (Animation):**
Simulate thermal motion by applying positional displacement to atoms. Dynamics and uncertainty controls adjust the amplitude and visual feedback of the wiggle animation.

**Components:**
Fine-grained control over individual structural components. Each component (polymer chain, ligand, water, ions) can be shown or hidden, and its representation and color scheme can be independently configured using the add and delete controls.

**Export:**

* **Export Models:** Download the currently loaded structure as a PDB or mmCIF file
* **Export Animation:** Render and download a trajectory animation as a video file
* **Export Geometry:** Export the rendered 3D geometry for external visualization tools

## Running the Engine

### Inputs

| Input           | Description                                                |
| --------------- | ---------------------------------------------------------- |
| PDB ID          | Fetch directly from RCSB or PDBe by 4-character identifier |
| Structure file  | PDB, mmCIF, BCIF, SDF, MOL, XYZ, GRO formats               |
| Trajectory file | DCD, XTC, TRR, PDBQT formats from MD simulations           |
| Density map     | CCP4, MAP, MRC, DSN6 electron density formats              |
| Topology file   | PSF, TOP, ITP, PRMTOP for trajectory context               |

### Outputs

* **Interactive 3D view:** Rotatable, zoomable molecular visualization with all loaded components
* **Measurements:** Annotated distance, angle, and dihedral values on the structure
* **Exported structure:** PDB or mmCIF file of the current state
* **Exported animation:** Video file of trajectory playback
* **Exported geometry:** 3D mesh for external rendering