The Jmol viewer for 3D structures
Jmol: an open-source Java viewer for chemical structures in 3D, with features for chemicals, crystals, materials and biomolecules.
3D models
- interactive
- different styles: ball and stick, sticks, spheres (spacefill), ribbons, etc.
- programmable
- recognizes the underlying (bio)chemical information: proteins, DNA, RNA, ligands, solvent, alpha, beta, polar, nonpolar...
Use
- as a regular program ("Jmol application")
- as a component in web pages ("Jmol applet")
- as a component or module within other programs
Features
- multiplatform (Java runs on Windows, Mac, Linux... —not on iPad et al. - however... JSmol is now available for these)
- translated to many languages (yours and mine too!)
Reference addresses:
- the official website www.jmol.org — General information, downloads
- the official wiki wiki.jmol.org — Useful information for users
- the complete manual — advanced and detailed
Jmol Scripting Documentation — access via the website
- sites with help, tutorials, examples... — by users; there is a list in the wiki
- Mouse Manual (how to manipulate Jmol models with the mouse and keyboard)
- my book ;-)
- the email distribution lists, for users and for developers — see the website for details
The application
Download it:
- www.jmol.org and follow the links up to:
- Jmol-14.0.x-binary.zip (for anyone in general)
- or Jmol-14.0.x-binary.tar.gz (only if you know what is tar.gz)
- but not Jmol-14.0.x-full.tar.gz (for programmers)
- It is a compressed package. Depending on the use you are after, you will have to extract (unpack, unzip) the needed files.
Instalation?
- it is not installed, it is just copied; you can put it in any folder
- from the downloaded file (zip or gz), you must extract Jmol.jar and then you use it by executing it (double-click normally)
Use
- Top bar menu
- Context or pop-up menu (right-click or Ctrl+click, or click on the Jmol logo at bottom right)
- Pop-up menu > Language
- Command or script console
- Commands from "scripts" in files or web pages
