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Chemis3D, Molecular Viewer Applet

Chemis3D is a Java Applet which renders virtual 3D molecular models within a Web document. It is specially designed for open interactive molecular visualization on the Internet or via an intranet. Molecular structures can be manipulated in real-time and rendered in various styles and appearances.

Chemis3D is a small applet (~30Ko) running well on any Java-enabled browser and requiring no specialized plug-in nor professional applications.

Main Features  

  • Real-time manipulation and fast 3D rendering.

  • Wide variety of molecular representations including special styles and color coding schemes for proteins and nucleic acids .

  • Enhanced interface using popumenu and key shortcuts .

  • Multi-models display and molecular animation capabilities.

  • Measuring and analysing tools.

  • Support of the most popular molecular data formats :
    • Brookhaven Protein DataBank (*.pdb).
    • MSC XMol files (*.xyz).
    • MDL molfiles (*.mol).

  • Zip and GZIP chemical datafiles support.

  • Simple integration and easy customization in a web page.

  • Javascript-Java and inter-Applet communication support.

No Java 2 SDK, Standard Edition v 1.4 support for APPLET!!

Select a molecule >>

Quick Start

With Mouse, Popup Menu or Key Shortcuts,

  • the model can be viewed as balls, sticks, ball&stick, wireframe, and backbone (proteins and nucleics).

  • the model can be colorized according to atoms nature (CPK Element), appartenance (residue, shapely, chain) and position (group, temperature).

  • the model can be rotated in 3D, rotated in plane, translated or zoomed.

  • the model can be autorotated or animated (multi-models file).

  • atoms or groups can be identified, labeled and highlighted.

  • distances, angles and torsions can be easily measured.

Website which use the Chemis3D applet - Amino acids guide.

Command List

Manipulation Mouse Action Key
Rotate in 3D Left click and Drag  (hold down mouse left button while moving the pointer) [R]
Zoom [Shift] and Left click and Drag   [Z]
Translate [Ctrl]   and Left click and Drag   [T]
Rotate in plane X^Y  [Alt]    and Left click and Drag   [X]
Popup Menu Right click [M]
Menu Option Action Key
Edit Data Edit Molecular Data [D]
Clear Clear Molecular Display  
Reset Initial size and position [O]
Rotation Model auto-rotation [I]
Animation Multi-models molecular animation [J]
Display Wireframe Multi-bonds wireframe representation [W]
Stick Cylinder bonds representation [S]
Ball & Stick Atoms and bonds representation [K]
Ball Spherical atoms representation (Van der Walls radii) [B]
Backbone Backbone alpha carbons representation for Proteins (Ca-Ca) and oxygen phosphoester for Nucleic acids (O3'-O3')  
Color CPK Atom CPK color coding scheme according to atom (element) type [A]
Residues Amino Acids or Nucleotides color coding scheme  
Shapely Residues colour scheme derived from Rasmol (Bob Flettericks' "Shapely Models") .
Group Spectral colour scheme based on residues position in protein/nucleotide sequence
(blue = amino / 5' to red = carboxy / 3')
Chain Chains (or models) color scheme [C]
Temperature Spectral colour scheme based on protein anisotropic temperature (B factor)
(blue = cold to red = hot')
Structure Color scheme based on protein secondary structure
(pink = alpha helix; gold = beta sheet; blue = beta turn)
User User defined plain colour (32 supported colours, see Colour Table) .  
Options Display Hydrogens View/Mask Hydrogen Atoms [H]
Display HeteroAtoms View/Mask Hetero Atoms (in PDB files)
Labels Atoms labeling [L]
Fastmove Wireframe style on move
Lighting Ambient lighting (over/under expose model and background)  
Select Identity Identify pointed atom or group
Distance Interatomic distance measure
Angle Bonds angle measure
Torsion Dihedral angle measure
Highlight Highlight preselected atoms or molecule regions [G]
Mouse Rotate in 3D Rotate Model [R]
Zoom Resize Model [Z]
Translate Translate Model [T]
Rotate in X^Y Rotate Model in screen plane [X]
About Chemis3D Informations, Version and Copyright [3]
Quick Help This help (if present in the applet's directory) [Q]
Full Help ? Chemis3D Web Site [?]

Chemis3D v 2.89- Copyright © 2000-2013 www.mol3d.com, All Rights Reserved.