Jmol

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.

• Cross-platform, running on Windows, 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.

New:

• Set nboCharges (default true)
• Connect NBO
• Label %[nbo];
• Quintuple and sextuple bonds.
• Viewer.runScriptCautiously(String) replacement name for older Viewer.runScript(String)
• Plugin main menu item.
• Startup options -U nbo or --plugin nbo
• NBO n BETA - for GenNBOReader nth beta orbital; could be expanded

Bug Fixes:

• SHOW CHEMICAL JME (from NCI CIR) does not properly return formal charges
• JSpecView, when open in application, does not allow ZAP
• draw POINTGROUP crashes Jmol if model is not first model
• DRAW circle rendering broken (load $2-butene ; draw pointGroup)
• NBO/ISOSURFACE command - Displaying BETA orbitals for NBO types (NHO, PNBO, etc.) that are from a file other than the current file causes read failure and no orbital display.
• Viewer.runScript(String) now uses evaluateExpression(T[])
• Lesson learned: Never mix viewer.runScript() and viewer.runScriptQueued() calls.
• *.CA should pick up calcium in a PDB file
• cfi format (for NBOPro) writing broken
• La and Ac should be in transitionmetal
• GenNBO reader not recognizing FILTER "BETA"
• code: NBO options extended using the NBO VIEW or NBO OPTIONS "..." command options
• noting previously undocumented: set fontscaling true; font label 10 arial plain 0.020