Jmol 11.7.45 – Molecule viewer for students/educators/researchers.

June 29, 2009

Jmol 11.7.45

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

WHAT’S NEW
Version 11.7.45:

  • bug fix: load trajectory XXX.cif not applying fractional coordinates.
  • bug fix: load trajectory {0 -1 1} not loading any models if first model has 0 atoms (as in certain cif files)
  • bug fix: dipole offsetside not working for molecular dipole (EVER!)
  • code: refactored scriptEvaluator and Jmol.java. Now it is much simpler to create a truly “headless” Jmol application, where Jmol is being used for the investigation of the structure instead of visualization.
  • new application: JmolFrameless.jar: This application completely disallows any display — it is totally formless. There are no Java Swing JFrames involved, no dialogs, no popup menus, no display of any kind.
  • script editor behaving properly except for a nasty SWING bug that will require recasting this in AWT instead of SWING. See http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4353673
  • new feature: gamessUS reader now reads dipoles and partial charges.
  • TODO script editor — search? argh… I knew this would be a can of worms… script editor — undo/redo works (CTRL-Z, then SHIFT-CTRL-Z or CTRL-Y)
  • new feature: drag/drop and file menu-open scripts directly into editor, from where they can be checked or tested.
  • code: refactored readers, allowing for more obvious initialization/finalization methods
  • new feature: App and applet consoles now have “editor” buttons that load scripts into a “script editor” and allow stepping through scripts (and changing values during the pauses) – preliminary only opens a rough draft ScriptEditor
  • new feature: Gamess file reader now translates internal basis set and calculation methods representations into roughly literature standard for Pople & Dunning basis sets as well as perturbation, CI and CC calculation methods. This is dumped to calculationType.
  • new feature: application console buttons: PAUSE, ?, STEP
  • new feature: SHOW TRACE — reports stack trace
  • bug fix: functions with names starting with _ were local instead of global
  • bug fix: 2 pixels off in y for labels. Don’t know why I thought that was necessary in Text.java::setBoxXY.
  • new feature: SHOW VARIABLES now gives variable trace through function stack
  • new feature: [Oh, VERY COOL!] You can now pause the app anywhere in a script, do anything you want — even within functions — change variables, set parameters, anything — and then resume with RESUME. Some of us have dreamt of having this with JavaScript. Very very useful!
  • bug fix: problems with PAUSE/RESUME within App
  • bug fix: “set ?” nonfunctional
  • bug fix: unmatched { in quotes in @{ } not properly treated: echo @{” testing}”}
  • new feature: strings may start with ‘ or “, like JavaScript
  • new feature: print getProperty(“PDBInfo”,”REMARK300″)

REQUIREMENTS
Mac OS X 10.3 or later.

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