AtomSetChooser

The AtomSetChooser is a new JFrame, available under the Tools... menu in the Jmol application.

The elements of the AtomSetChooser dialog are as follows:

Atom Set Collection

• Tree: The hierarchical representation of the collection of all the atom sets that were read in a hierarchical tree format. Currently only two readers (the ones for NWChem and Gaussian) provide the necessary information for the AtomSetChooser to allow a more complex than just a flat hierarchy to be built.
  When selecting a node in the tree:
  • the first structure under that tree is the one that will become visible.
  • one 'selects' all the structures under that node as the active set of structure on which the other controllers work.
    Note when one selects a different structure using any of the other controllers, the tree view will not track this. This is done deliberately since the selection of the atom sets should not change when a different one in the list is shown...
• Properties: This text area shows the properties associated with the structure shown.

Collection

• Info : Displays the name of the current atom set shown.
• Select : A slider to pick/show which atom set in the list is shown.
• Controller: A VCR type set of buttons to go to the first/previous/next/last structure in the selected structures, and to start or stop the automatic increment of the shown structure within the list of atom sets.
  • Repeat: A check box to allow for wrap during playing through the collection.
• FPS: a slider to change the frame rate for playing through the list of atoms.

Vector

Contains controllers for the vector information that may be associated with an atom set. These controls are enabled whether or not vector information is associated with the current structure or with the selected set of structures. So if nothing happens when using these controls, no vector information is present.

• Radius: The radius of the vector
• Scale: The scale (length multiplication) of the vector
• Amplitude: The amplitude of the animation of the vibration
• Period: The period of the animation of the vibration
• Controller: A VCR type set of buttons to go to the first/previous/next/last vibration in the set and to start or stop the animation of the vibration.

Contributors

NicolasVervelle, Rkanters