information in a curve's `info` dictionary (e.g. `flat filter peaks`).
You can, if necessary, adjust the names of input and output columns
and `info` values to combine the available commands in new and useful
-ways.
+ways.::
hooke> zero_surface_contact_point --block retract
hooke> flat_filter_peaks --block retract --min_points 1
See each command's `Help`_ for details.
-.. todo:: Discuss command stacks and polymer model fitting.
+Command stacks
+~~~~~~~~~~~~~~
+
+Since you are likely to apply similar analysis to several curves,
+Hooke provides :mod:`command stacks <hooke.command_stack>` for
+bundling groups of commands.::
+
+ hooke> start_command_capture
+ hooke> zero_surface_contact_point --block retract
+ hooke> flat_filter_peaks --block retract --min_points 1
+ ...
+ hooke> stop_command_capture
+
+You can check the state of the command stack with
+``get_command_stack`` and the state of capture with
+``get_command_capture_state``. If you make mistakes, you can pop
+commands from the stack with ``pop_command_from_stack``. If you stop
+capturing a command stack (e.g. to test a complicated command before
+continuing), you can continue adding to the same stack with
+``restart_command_capture.``
+
+You can also save command stacks to disk (and reload them later,
+potentially in a different Hooke session).
+
+ hooke> save_command_stack --output my_stack
+ hooke> load_command_stack --input my_stack
Multiple curve fitting and measuring
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~