GLmol - Molecular Viewer on WebGL/Javascript

About GLmol

GLmol is a 3D molecular viewer based on WebGL and Javascript. You can embed molecular models in Web pages without using Java or plugins. GLmol is open-source software licensed under LGPL3.

There is also Android version; ESmol and NDKmol.

Features

Currently GLmol has following features. More is coming...

• Read PDB file
• Read SDF/MOL file
• Load local files (File API is used; Safari is not supported)
• Load PDB files directly from RCSB PDB server
• Rotate/Translate/Zoom model with mouse (touchpanel support is under development)
• Fog & Slab
• Representations
  • Line (depiction of double/triple bonds is supported for SDF/MOL file)
  • Stick
  • Sphere (van der Waals radius or fixed radius)
  • Star
  • Alpha carbon trace
  • Strand
  • Ribbon
  • Thick ribbon
  • Cylinder & Plate
  • Tube with radius reflecting B factor
  • Combination of above
• Smoothing of Beta sheets
• Special representations for Nucleic acid bases
  • Stick
  • Ladder
  • Line
• Surface calculation and visualization (in development; available in special version)
  • van der Waals surface
  • Molecular surface
  • Solvent accessible surface
  • Solvent excluded surface
• Coloring
  • By chain
  • By secondary structure (when defined in SHEET/HELIX records)
  • By Elements
  • Gradation (chainbow)
  • Polar/Nonpolar
  • B factor
  • Custom
• Crystallography
  • Display unit cell
  • Show crystal packing (when defined in REMARK section)
• Display biological assembly (when defined in REMARK section)
• Perspective or Orthographic projection
• Take screenshot

System requirements

GLmol runs on newer versions of Firefox, Chrome, Safari or Opera. Safari users have to enable WebGL manually. Internet Explorer is not supported because IE doesn't implement WebGL. Some old video cards are blacklisted by browsers due to insufficient compatibility. You can still force enable WebGL as shown below, but GLmol might not work.

GLmol runs on Sony Ericsson's Android devices which support WebGL. Support for Firefox Mobile is currently underway. Reportedly, GLmol also runs on WebGL enabled safari in iOS (see this video by Dr. Quinn)

If you see only black screen and you are using

• Internet Explorer: sorry. IE doesn't support WebGL.
• Firefox (version 4 or later): try force enable WebGL.
• Chrome: try force enable WebGL.
• Safari: enable WebGL.

Demo

You can try GLmol below.

• Demo -- initial model is porin (try 'show biological assemblies').
  You might also enjoy looking at beta-2 adrenergic receptor in complex with G protein (try 'color by chain', 'B factor tube', 'color by B factor'), isoleucine-tRNA synthase (try various nucleic acid representations). You can open big molecular machines like GroEL-ES complex or even 50S ribosome!
• Example of embedding
• The bookmarklet "Open with GLmol" gets PDB ID from your current selection and open it with GLmol. Please bookmark it or add to the toolbar for use.
• There is an exporter for Pymol. You can export a scene in Pymol to GLmol.

The previous version of GLmol (0.35) is also available.

Download

You can download GLmol from the following link.

Changelog

• 0.40(20120428) - Bug fix in SDF parser and nucleotide representation, Migrated to Three.js r49 and compacted it (350KB to 200KB), Improved lighting, Improved performance of symmetry operation, Improved performance of cylinder rendering, Reversed spectrum color, Implemented of "cylinder&plate", Implemented of ribbon with thickness, Implemented beta sheet smoothing, C-alpha trace will no be smoothened now. Unfortunately, some old video cards such as Intel GMA950 cannot run this version.
• 0.35(20111214) - Bug fix. Supported Xperia phones (Android).
• 0.34(20111211) - Added 'strand' representation, Supported zooming by mouse wheel, Fixed a bug with textarea in Chrome, Changed codes for touchpanel support (experimental)
• 0.33(20111210) - Added 'star' representation and 'small sphere' representation for non-bonded atoms, Added getNonbonded and UI for it, Added setBackground, Added 'take screenshot' button, Refactored onResize handler, Supported antialiasing (enabled in Chrome but disabled in Firefox), Minor fix in loading message, Attached mouse event handler to renderer, Refactored lighting (doubleSided issues), Improved slab/fog/zoom adjustments, Fixed ribbon width, Supported dotted line
• 0.30(20111130) - Fixed a bug in PDB parser (CONNECT), Fixed a bug in SDF parser (ignore non-SDF file), Supported viewport size change, Changed to Tab-based userinterface, Added mouse mode switch for single-button mouse and touchpanel users, Read PDB file specified in URL, Removed GLmol.protein.chainname (which was not used at all and interfered with protein.a/b/c), Supported nucleic acid representations(ribbon, ladder, stick, line), Improved Zoom, Supported Fog and Slab, Supported drawing helix as cylinder, Enhanced PDB parser to reads TITLE and HEADER, Added GLmol.setView and GLmol.getView, Improved color by chain and color by spectrum to support nucleic acids, Separated parser and buildScene (WARNING: API changed!), Added GLmol.zoomInto (EXPERIMENTAL: must be improved), Added color by B factor, Added tube representation (similar to 'B factor putty/ in Pymol), Supported drawing double/triple bonds in line representation (SDF File ONLY), Improved detection of bonds involving deuterium, Supported reading local files (needs File API)
• 0.25(20111120) - ribbon for nucleic acids, color by chain for nucleic acids, color by polar/nonpolar, SDF/MOL format support, upgrade to Three.js r45, bug fix in subdivide, improvement of detection of bonds involving sulfer or hydrogen atoms, ignoring alternative locations (ad hoc fix)
• 0.23 - first release

Document

Design principles and Architecture of GLmol describes details of implementation and current limitations.

To learn how to embed GLmol into your page, please examine source code of Example of embedding.

Contacts

Comments and suggestions are welcome. Please mail to biochem_fan at users.sourceforge.jp or write in the forum.