The Atom Context Menu

Select

Makes this atom the current selection.

Select Molecule

Makes the molecule the atom is in the current selection.

Cut

Removes the atom and all of its bonds from the molecule and puts it into the clipboard for later paste actions.

Cut Selected

Removes the selected part from the model.

Change Element...

Changes the element symbol of the atom to the selected symbol.

Change Isotope...

Changes the isotope of the atom to the selected option.

Convert to radical...

TODO when does this work?.

Hydrogens

Add Implicit Hydrogens

JCP can run in two different modes with respect to implicit hydrogens. You can switch between them here. The two modes are:

Note that: The following menu options allow manipulations of the implicit Hs.

Make Hydrogens Explicit

This will transform implicit hydrogens to separate atoms connected by a single bond. This will only have an effect if you are in implicit mode (see "Add Implicit Hydrogens")

Make Hydrogens Implicit

This will delete bonds to hydrogens and add hydrogens directly to their parent atoms as implicit hydrogens.

Update Implicit Hydrogen Count

This will set the implicit hydrogens on all atoms to satisfy valency. This can be called in both modes. If tracking of implicit Hs is off, this will only have a one-off effect.

Reaction

Here you can make the molecule in which the atom is part of either a new reaction or an existing one as either reactant or product.

Reset Bond Orders

Sets the order of all bonds to single.

Run validate

Runs a validation on this atom. See Report menu help for details.

Properties

Here you can directly set symbol, charge and hydrogen count.

Molecule Properties

Here you can directly set properties (title) of the molecule the atom is in.