Amira Molecular Option

Molecular visualization and analysis tool

This option combines Amira's strong capabilities for 3D data visualization, such as hardware-accelerated volume rendering, with specific tools for molecular visualization and analysis, such as molecular surfaces, sequence alignment, configuration density computation and molecule trajectory animation. Due to Amira's innovative user interface, using the features of the Molecular Option is easy. The Amira Molecular Option comes with self-running demos and step-by-step tutorials for the most common molecular visualization tasks.


Windows 32-bit, Windows 64-bit, Mac OS, Linux

Visualize and Model Molecules

The Molecular Option offers state-of-the-art molecular visualization and
several advanced tools for molecular simulation combined with the
high-end Amira features.

  • Secondary structure extraction and visualization
  • Molecular trajectory computation and visualization
  • Potential field computation
  • Pseudo-electron density computation
  • Molecule labeling
  • Molecule surface computation
  • Intermolecular alignment
  • Pareto-optimal set computation
  • H-bond computation and visualization
  • Ribbon, tube, cartoon chain visualization
  • Dynamic visualization
  • Configuration density computation
  • Mean-molecule computation
Amira Molecular File Formats

AMBER Assisted Model Building with Energy Refinement format

AMF Amira Molecule Format 

DX APBS DX electrostatic field file

GROMACS Groningen Machine for Chemical Simulations format

MDL MDL file format saving chemical structures

PDB protein data base file format

PHI Congen PHI Electrostatic field file 

PSF/DCD (CHARMM) file format used by CHARMM 

Tripos file format used to save Tripos Sybyl mol2 molecules

UniChem file format used by the UniChem molecular software

ZIB Molecular format developed as molecular exchange