Function apply_mvs_colors 

pub fn apply_mvs_colors(
    mesh: &mut Mesh,
    color_nodes: &[(ComponentSelector, ColorT)],
    model: &AtomCollection,
    vertex_map: &[usize],
    map_kind: VertexMapKind,
)

Paint vertex colors on mesh by applying MVS color nodes in order.

initial is the per-vertex base color (e.g. from initial_colors_from_theme). Each (ComponentSelector, ColorT) pair selects atoms and overrides their color. Later nodes override earlier nodes on overlapping vertices.

vertex_map[vertex_idx] holds the atom index (for VertexMapKind::AtomMap) or the amino-acid residue iteration index (for VertexMapKind::ResidueMap) that produced that vertex.