Color Modes

Viso supports several coloring schemes for backbones, sidechains, and nucleic acids. Colors are computed during background scene processing and baked into vertex data for zero-cost rendering.

Backbone Color Modes

Set via DisplayOptions::backbone_color_mode:

#![allow(unused)]
fn main() {
pub enum BackboneColorMode {
    Score,              // Per-residue energy score (blue-white-red)
    ScoreRelative,      // Relative scoring within the structure
    SecondaryStructure, // Helix/sheet/coil coloring
    Chain,              // Each chain gets a distinct color (default)
}
}

Chain (Default)

Each chain gets a distinct color interpolated from blue to red across the chain count. Single-chain proteins use a gradient along the chain. This is the most common mode for general visualization.

Secondary Structure

Colors residues by their computed secondary structure type:

• Alpha helix – distinct helix color
• Beta sheet – distinct sheet color
• Coil/Loop – neutral color

Secondary structure is computed from backbone geometry using dihedral angle analysis.

Score

Colors residues by per-residue energy scores from Rosetta. Uses a blue-white-red gradient:

• Blue – favorable (low) energy
• White – neutral
• Red – unfavorable (high) energy

Scores are cached on each EntityGroup via set_per_residue_scores(). The background processor converts scores to RGB colors during mesh generation.

Score Relative

Similar to Score mode but normalizes within the structure, highlighting relative differences rather than absolute energy values.

Sidechain Color Modes

Set via DisplayOptions::sidechain_color_mode:

#![allow(unused)]
fn main() {
pub enum SidechainColorMode {
    Hydrophobicity,  // Default -- hydrophobic vs hydrophilic
}
}

Hydrophobicity (Default)

Sidechain atoms are colored by hydrophobicity:

• Hydrophobic – blue (default: [0.3, 0.5, 0.9])
• Hydrophilic – orange (default: [0.95, 0.6, 0.2])

These colors are configurable in ColorOptions.

Nucleic Acid Color Modes

Set via DisplayOptions::na_color_mode:

#![allow(unused)]
fn main() {
pub enum NaColorMode {
    Uniform,  // Default -- single color for all nucleic acid backbone
}
}

Uniform (Default)

All nucleic acid backbone uses a single color (default: light blue-violet [0.45, 0.55, 0.85]), configurable via ColorOptions::nucleic_acid.

Non-Protein Coloring

Ligands, ions, and waters use element-based CPK coloring in the ball-and-stick renderer:

• Standard CPK colors for common elements (C, N, O, S, P, etc.)
• Lipid carbons use a special warm beige/tan tint (configurable via ColorOptions::lipid_carbon_tint)
• Cofactors can have per-residue-name tints via ColorOptions::cofactor_tints

Color Transitions During Animation

When backbone colors change between poses (e.g., score coloring updates after minimization), the background processor caches per-residue colors in the PreparedScene. During animation, the tube and ribbon renderers interpolate between start and target colors using the same easing function as the backbone position interpolation.

This means color changes are smooth – residues don’t suddenly flash to new colors but transition over the animation duration.

How Colors Flow Through the Pipeline

1. Scene sync – DisplayOptions and ColorOptions are sent to the background processor as part of SceneRequest::FullRebuild
2. Background thread – during mesh generation, colors are computed per-vertex based on the active color mode and baked into vertex data
3. GPU upload – vertex buffers with embedded colors are uploaded to the GPU
4. Rendering – shaders read per-vertex colors directly, with selection highlighting applied as an overlay in the fragment shader via the SelectionBuffer bit-array