Molecular Option

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.

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

Features


Visualize and Model Moleculesmolecular

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

 

 

 

 

File Formats

Extension Read/Write

AMBER Assisted Model Building with Energy Refinement format

top/crd/vel

r

AMF Amira Molecule Format

amf

rw

DX APBS DX electrostatic field file

dx/apbs

r

GROMACS Groningen Machine for Chemical Simulations format

gro/top/trr

rw

MDL MDL file format saving chemical structures

sdf

r

PDB protein data base file format

pdb

rw

PHI Congen PHI Electrostatic field file

phi

r

PSF/DCD (CHARMM) file format used by CHARMM

psf/dcd

r

Tripos file format used to save Tripos Sybyl mol2 molecules

mol2

rw

UniChem file format used by the UniChem molecular software

uni

rw

ZIB Molecular format developed as molecular exchange

zmf

rw