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aseview

Interactive molecular visualization for ASE (Atomic Simulation Environment)

DeepWiki

aseview is a powerful, browser-based molecular viewer that integrates seamlessly with ASE. It provides interactive 3D visualization for molecules, crystals, and trajectories with support for normal mode animations.

Features

  • Multiple Viewer Types: Standard molecular viewer, overlay comparison, normal mode visualization, and interactive fragment selector
  • Rich Styling: Multiple visual styles including Cartoon, Neon, Glossy, Metallic, Cinematic, Bubble, Grey, and 2D (Styles)
  • Themes: Swap the entire look and feel with dark, spring, glass, darkgreen, simple, or custom themes (Theming guide)
  • Display Controls: Hide hydrogens without deleting data, add render blur for saved images, and tune radius contrast
  • Trajectory Support: Animate trajectories with synchronized energy and max-force plots
  • Normal Modes: Visualize vibrational modes from ASE vibrations, ORCA Hessian files, or VASP OUTCAR files
  • Cell and Constraints: Display periodic cells and highlight fixed atoms from FixAtoms
  • Radius Contrast: Adjust element-radius differences from uniform radii to full element radii
  • Polyhedron: Render coordination polyhedra for solid-state structures (CN ≥ 4)
  • Ring Highlight: Fill aromatic and aliphatic rings with semi-transparent color
  • Fragment Selector: Synchronized 2D/3D atom picker — select fragments visually, copy indices to clipboard
  • CLI & Python API: Use from command line or Jupyter notebooks
  • Export: Save as PNG, GIF, standalone HTML, or copy structures as xyz, extxyz, cif, and POSCAR

Quick Example

from ase.io import read
from aseview import MolecularViewer

atoms = read("molecule.xyz")
viewer = MolecularViewer(atoms)
viewer.show()  # In Jupyter notebook

aseview molecule.xyz

Viewer Types

Viewer Description Use Case
MolecularViewer Standard 3D molecular viewer with animation Single structures, trajectories
OverlayViewer Overlay multiple structures for comparison Comparing conformers, reaction paths
NormalViewer Vibrational mode visualization Frequency analysis, IR/Raman
FragSelector Synchronized 2D/3D interactive atom selector Fragment picking, QM/MM region assignment

Installation

pip install aseview

Or install from source:

git clone https://github.com/kangmg/aseview.git
cd aseview
pip install -e .