The Edit menu

Select All

Selects all atoms in the view screen.

Deselect All

Deselects all atoms in the view screen.

Make Crystal...

Opens a dialog that permits to build a new crystal starting from the present file.

This dialog is only active if the file does not contain information about the crystal structure. Once the crystal has been created, the Make Crystal item is disabled but the crystal structure information can be accessed through the Crystal Properties dialog in the Extra menu.

The Make Crystal dialog in the Edit menu and the Crystal Properties dialog in the Extra menu are actually the same but their behavior is slightly different depending from where there are called. Their description is given in the section called “Crystal Properties...” later on in this manual.

Atom Properties...

This menu opens a dialog in which atomic properties can be added to a large number of atom types. These properties include the colors used to depict atoms.

Preferences...

This menu opens a dialog to change settings and make user customized preferences. These settings are saved from one session to the next

Display Tab

In these frame a few display settings can be changed. By default anti-aliasing is turned off. Turning it on improves the images considerably but will also reduce performance.

Note: The 1.3.1 JVM which ships with Macintosh OS X and OS X 10.2 (Jaguar) has crash bugs with some pixel interpolation and anti-aliasing operations. Therefore, you may need to disable the use of Java Graphics2D on this platform.

Note: The 1.4.1 JVM which has been released by Apple seems to have fixed a few problems for jmol ... but created a *lot* more :(

Colors Tab

In these frame some general display colors can be changed. Like the background color, and the color used to highlight selected atoms.