Chemis3D, Molecular Viewer Applet

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. 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!!

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.

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	[?]