When you are debugging Jython script, you can set line breakpoints. Breakpoints are saved upon termination of a debug session.
When the workbench is running the script and encounters a breakpoint, the script temporarily stops running. Execution suspends at the breakpoint before the script is executed, at which point you can check the contents of variables. You can then step over (execute) and see what effect the statement has on the script.
With the debugger, setting breakpoints is easily accomplished by way of pop-up menus in the editor. Once set, you can disable breakpoints so they do not suspend execution and then, later, enable them again.