Visual Pipeline Editor

megane's pipeline editor lets you build visualization workflows by wiring nodes — no code required. Open the pipeline panel from the sidebar to start building.

Pipelines can also be built programmatically in Python, TypeScript, or written directly as JSON.

For real-world examples, see the Gallery.

Concept

A pipeline is a directed graph of nodes connected by edges. Data flows from source nodes (like Load Structure) through processing nodes (like Filter or Modify) and into a Viewport node for rendering.

Each edge carries a specific data type — particle, bond, cell, label, mesh, trajectory, or vector — and only matching types can connect.

When a node encounters an error — for example, a parse failure in LoadStructure — an error icon appears on the node with a tooltip showing the details.

AI Pipeline Generator

Describe the visualization you want in natural language, and megane builds the node graph for you. Open the AI chat panel from the pipeline editor toolbar and type a prompt like:

Load protein.pdb with bonds and make water translucent

The generator creates the appropriate LoadStructure, AddBond, Filter, Modify, and Viewport nodes, wires them together, and places them in the editor. You can then adjust parameters or add more nodes manually.

VSCode Extension Auto-Setup

When you open a supported molecular file (.pdb, .gro, .xyz, .mol, .sdf, .cif) in the megane VSCode extension, it automatically creates a default pipeline consisting of LoadStructure → AddBond → Viewport. This gives you an immediate 3D view of the structure with bonds, without needing to build a pipeline manually. You can then modify the auto-generated pipeline in the editor as needed.

Getting Started

The simplest pipeline loads a structure and displays it:

LoadStructure → Viewport

To add bonds inferred from atomic distances:

LoadStructure → AddBond → Viewport
                       ↘
              LoadStructure → Viewport (particle + cell)

Use the Templates dropdown to load pre-built pipelines:

• Molecule — Caffeine (caffeine_water.pdb) with structure-based bonds and a vibration trajectory (caffeine_water_vibration.xtc). Nodes: LoadStructure → AddBond → Viewport, LoadTrajectory → Viewport.
• Solid — Perovskite SrTiO₃ 3×3×3 supercell with distance-based bonds and TiO₆ coordination polyhedra. Nodes: LoadStructure → AddBond → Viewport, PolyhedronGenerator → Viewport. Center = Ti (22), Ligand = O (8), max distance = 2.5 Å.

Node Reference

Data Loading

Node	Description	Inputs	Outputs
Load Structure	Load a molecular structure file (PDB, GRO, XYZ, MOL/SDF, CIF, LAMMPS data)	—	particle, trajectory, cell
Load Trajectory	Load an XTC or ASE .traj trajectory file	particle	trajectory
Streaming	WebSocket-based real-time data delivery	—	particle, bond, trajectory, cell
Load Vector	Load per-atom vector data from a file	—	vector

Processing

Node	Description	Inputs	Outputs
Filter	Select atoms using a query expression	particle (in)	particle (out)
Modify	Override scale and opacity for a group of atoms	particle (in)	particle (out)

Overlay

Node	Description	Inputs	Outputs
Add Bond	Detect bonds from structure or by distance	particle	bond
Label Generator	Generate text labels at atom positions	particle	label
Polyhedron Generator	Render coordination polyhedra (convex hulls)	particle	mesh
Vector Overlay	Configure per-atom vector visualization (e.g. forces)	vector	vector

Output

Node	Description	Inputs	Outputs
Viewport	3D rendering output	particle, bond, cell, trajectory, label, mesh, vector	—

Node Parameters

Load Structure

Parameter	Type	Description
File path	string	Path to molecular structure file. Supported: .pdb, .gro, .xyz, .mol, .sdf, .cif, .data, .lammps

Load Trajectory

Parameter	Type	Description
xtc	string	Path to XTC trajectory file
traj	string	Path to ASE .traj trajectory file

Requires a connection from a LoadStructure node. Frames are loaded lazily when frame_index changes.

Load Vector

Parameter	Type	Description
File path	string	Path to vector data file (JSON with per-atom 3D vectors)

Add Bond

Parameter	Values	Default	Description
Bond source	structure	—	Read bonds from the structure file (CONECT records in PDB, etc.)
	distance	✓	Infer bonds from van der Waals radii

Filter

Parameter	Type	Default	Description
Query	string	"" (all)	Atom selection query expression (see Filter DSL)
Bond query	string	"" (all)	Bond selection query expression (see Bond Selection DSL)

Both input fields validate your query in real time — invalid syntax is highlighted in red.

The Query field filters which atoms pass through when the Filter node is connected to a particle stream (particle input/output). The Bond query field filters which bonds are selected when the Filter node is connected to a bond stream; this selection is used by downstream nodes (for example, Modify) to apply per-bond opacity overrides — it does not remove bonds from the scene. Because a Filter node has a single generic in → out port and only one data type flows through it at a time, using both atom and bond queries in the same workflow typically means adding two Filter nodes: one on the particle edge and one on the bond edge.

Modify

Parameter	Range	Default	Description
Scale	0.1 – 2.0	1.0	Atom sphere radius multiplier
Opacity	0 – 1.0	1.0	Transparency (0 = invisible, 1 = opaque)

Label Generator

Parameter	Values	Default	Description
Source	element	✓	Chemical element symbol (C, O, Fe, ...)
	resname	—	Residue name (ALA, HOH, ...)
	index	—	Atom index (0, 1, 2, ...)

Polyhedron Generator

Parameter	Type	Default	Description
Center elements	number[]	—	Atomic numbers of center atoms (e.g., Ti=22, Si=14)
Ligand elements	number[]	O (8)	Atomic numbers of ligand atoms
Max distance	number	2.5 Å	Maximum center–ligand distance
Opacity	number	0.5	Face transparency (0–1)
Show edges	boolean	off	Display wireframe edges
Edge color	string	#dddddd	Wireframe edge color (hex)
Edge width	number	3.0	Wireframe edge width (px)

Vector Overlay

Parameter	Type	Default	Description
Scale	number	1.0	Vector arrow length multiplier

Viewport

Parameter	Default	Description
Perspective	off	Toggle perspective / orthographic projection
Cell axes visible	on	Show simulation cell axes with labels
Pivot marker visible	on	Show the rotation pivot marker at the camera target

A Render Export button is available in the pipeline editor toolbar. Click it to export the current viewport as a PNG image (or other formats such as EPS, GIF, and MP4 via the render modal).

Data Types

Seven typed data channels flow through color-coded edges:

Type	Color	Description
particle	Blue	Atom positions, elements, and optional indices/overrides
bond	Amber	Bond pairs and orders
cell	Emerald	Simulation cell (3×3 matrix)
label	Violet	Text labels positioned at atoms
mesh	Gray	Triangle mesh for polyhedra rendering
trajectory	Pink	Multi-frame coordinate data
vector	Teal	Per-atom 3D vector data (forces, velocities, etc.)

Filter DSL

The Filter node accepts Python-like query expressions to select atoms.

Available Fields

Field	Type	Description
element	string	Element symbol (e.g., "C", "O", "Fe")
index	number	Atom index (0-based)
x, y, z	number	Cartesian coordinates
resname	string	Residue name (e.g., "ALA", "HOH")
mass	number	Atomic mass

Operators

==, !=, >, <, >=, <=

Logical Operators

and, or, not, parentheses ()

Special Keywords

all — select all atoms, none — select no atoms

Examples

element == "C"                         # All carbon atoms
index > 10 and index < 20             # Atoms 10–19
resname == "HOH"                       # Water molecules
not element == "H"                     # Non-hydrogen atoms
element == "O" or element == "N"       # Oxygen or nitrogen
(x > 0 and x < 10) and element == "C" # Carbons in x range
mass > 32                              # Atoms heavier than sulfur

Bond Selection DSL

The Bond query field in the Filter node accepts expressions to select bonds.

Available Fields

Field	Type	Description
bond_index	number	0-based sequential bond index
atom_index	number	Atom endpoint index
element	string	Element symbol of an atom endpoint (e.g., "C", "O")

Operators

==, !=, >, <, >=, <=

Logical Operators

and, or, not, parentheses ()

Special Keywords

• all — select all bonds (default when query is empty)
• none — select no bonds
• both — prefix on a comparison involving atom_index or element to require both atoms of the bond to satisfy the condition (default: either atom, OR semantics). Has no effect on bond_index comparisons.

Examples

element == "C"                         # Bonds where either atom is carbon
both element != "H"                    # Bonds where neither atom is hydrogen
atom_index >= 24                       # Bonds involving atom 24 or higher
bond_index < 10                        # First 10 bonds only
both atom_index >= 0 and bond_index < 50  # First 50 bonds (all-atom filter)

The bond query selects which bonds a downstream Modify node applies opacity overrides to. This lets you selectively fade specific bonds without removing them from the scene.

Editor Examples

TiO₆ Octahedra in SrTiO₃

1. Load a perovskite structure (LoadStructure)
2. Add a PolyhedronGenerator node
3. Set center = Ti (22), ligand = O (8), max distance = 2.5 Å
4. Connect LoadStructure.particle → PolyhedronGenerator.particle
5. Connect PolyhedronGenerator.mesh → Viewport.mesh

Or use the Solid template which sets this up automatically.

Make Solvent Translucent

Use Filter + Modify nodes to fade out water molecules while keeping the protein fully visible.

1. Add a LoadStructure node and load your PDB file
2. Add a Filter node with query: resname == "HOH"
3. Add a Modify node and set opacity to 0.2, scale to 0.5
4. Connect: LoadStructure.particle → Filter.in → Modify.in → Viewport.particle
5. Connect the original LoadStructure.particle → Viewport.particle as well (for the protein)

The viewport renders both streams — the protein at full opacity, and the water as translucent small spheres.

Multiple Structure Layers

You can load multiple structure files simultaneously, with each file rendered as a separate layer in the viewport. Each LoadStructure node connected to a Viewport creates an independent rendering layer, allowing you to combine different molecules in a single view.

For example, to display a protein and a ligand loaded from separate files:

LoadStructure (protein.pdb) → AddBond → Viewport
LoadStructure (ligand.mol)  → AddBond ↗

Each layer is processed independently through its own chain of Filter, Modify, and overlay nodes before reaching the Viewport.

---

For more examples with code, see the Gallery.