Jmol

From FaHWiki

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

• The JmolApplet is a web browser applet that can be integrated into web pages.
• The Jmol application is a standalone Java application that runs on the desktop.
• The JmolViewer is a development tool kit that can be integrated into other Java applications.

Since version 10.00.05, Jmol can read current.xyz files produced by Folding@Home in the work folder.

Since version 10.7.1, Jmol can read wudata_xx.top and wudata_xx.trj files produced by the Amber core in the work folder to create animations. This files are most interesting when the WU is almost finished (98% or 99%), to have more frames in the resulting animation.

Both the applet and the application are concerned.

Some specific parts have been developed for Folding@Home:

• A webpage where you can look in 3D at (almost) each project. Several parameters can be given to the webpage to customize it. The parameters can be combined by separating them with a &. Currently available parameters are:
  • project: opens a specific project in the applet (.../fah/?project=1112).
  • showList: displays the projects list in a dropbox (.../fah/?showList=dropbox), a array of buttons (.../fah/?showList=button), or a combination of both (.../fah/?showList=both).
  • appletSize: changes the size of the applet (.../fah/?appletSize=500).
  • appletWidth: changes the width of the applet, can be used to display rectangular applet (.../fah/?appletSize=300&appletWidth=500).
  • stereo: enables stereographic visualization in cross-eyed viewing (.../fah/?stereo=5), in wall-eyed viewing (.../fah/?stereo=-5), for red/cyan glasses (.../fah/?stereo=redcyan), for red/blue glasses (.../fah/?stereo=redblue), for red/green glasses (.../fah/?stereo=redgreen).
  • detailLocation: changes the position of the detailed information to the left (.../fah/?detailLocation=left), to the right (.../fah/?detailLocation=right), to the top (.../fah/?detailLocation=top) or to the bottom (.../fah/?detailLocation=bottom).

• The Jmol MediaWiki Extension to use the Jmol applet in this Wiki.

You can contribute to the webpage by sending current.xyz, wudata_xx.top and wudata_xx.trj files for the missing projects at nicove@users.sourceforge.net, or by joining the Jmol developers team.

Other third party tools can be used to help complete this list:

• EM III: you can configure it to save current.xyz file for each project (check "Save XYZ File" in the "HTML Stats" tab of the Options window).
• FahMon:
  • you can configure it to save current.xyz file for each project (check "Collect .xyz files" in the "General" tab of the Preferences window).
  • by pressing F3, the Jmol webpage is opened to display the current project. I have to modify my webpage to ask for the current.xyz file if the project is missing.
• fahinfo.org: when you submit a score there, you will be told that the current.xyz file is missing and you will be able to send it directly.
• A dedicated tool that check for useful files and send them by mail.

I am also looking for translators for Jmol (see here for explanations). The following parts can be translated :

• the Jmol webpage for FoldingAtHome
• the rest of Jmol website
• the Jmol application
• the Jmol applet
• the Jmol documentation

Even partial translations will be appreciated.