hannahbaumann · Nov 9, 2026 · Nov 6, 2026 · Nov 6, 2026
diff --git a/docs/guide/execution/index.rst b/docs/guide/execution/index.rst
@@ -25,10 +25,10 @@ Both can be used from the command line or from Python.
 
 .. admonition:: Related How-To Guides
 
-   * :doc:`/cookbook/dumping_transformation`
-   * :doc:`/cookbook/run_quickrun`
-   * :doc:`/cookbook/resume_quickrun`
-   * :doc:`/cookbook/run_on_slurm`
-   * :doc:`/cookbook/run_repeats_in_parallel`
-   * :doc:`/cookbook/run_with_mps`
-   * :doc:`/cookbook/run_task_based`
+   * :doc:`/how_to_guides/dumping_transformation`
+   * :doc:`/how_to_guides/run_quickrun`
+   * :doc:`/how_to_guides/resume_quickrun`
+   * :doc:`/how_to_guides/run_on_slurm`
+   * :doc:`/how_to_guides/run_repeats_in_parallel`
+   * :doc:`/how_to_guides/run_with_mps`
+   * :doc:`/how_to_guides/run_task_based`
diff --git a/docs/guide/execution/quickrun_execution.rst b/docs/guide/execution/quickrun_execution.rst
@@ -28,16 +28,16 @@ and writes the free energy estimate and its uncertainty to the results file.
 
 quickrun keeps track of which tasks have finished, so an interrupted run can be resumed with ``--resume``.
 Finished tasks are skipped, and an interrupted simulation continues from its last checkpoint
-(see :doc:`/cookbook/resume_quickrun`).
+(see :doc:`/how_to_guides/resume_quickrun`).
 
 Organizing a campaign
 ---------------------
 
 You decide where and when each Transformation runs, for example by
-:doc:`submitting one job per Transformation to a cluster </cookbook/run_on_slurm>`.
+:doc:`submitting one job per Transformation to a cluster </how_to_guides/run_on_slurm>`.
 You can run multiple simulations in parallel by running several quickrun calls at the same time,
-for example one per Transformation, :doc:`one per repeat </cookbook/run_repeats_in_parallel>`,
-or :doc:`several on the same GPU </cookbook/run_with_mps>`.
+for example one per Transformation, :doc:`one per repeat </how_to_guides/run_repeats_in_parallel>`,
+or :doc:`several on the same GPU </how_to_guides/run_with_mps>`.
 The results files are then collected with :ref:`openfe gather <cli_gather>`.
 
 .. TODO: link the "Gather free energy results" how-to instead of the CLI reference once it exists.
@@ -47,11 +47,11 @@ see :ref:`userguide_task_based_execution`.
 
 .. admonition:: How-to guides
 
-   * :doc:`/cookbook/run_quickrun`
-   * :doc:`/cookbook/resume_quickrun`
-   * :doc:`/cookbook/run_on_slurm`
-   * :doc:`/cookbook/run_repeats_in_parallel`
-   * :doc:`/cookbook/run_with_mps`
+   * :doc:`/how_to_guides/run_quickrun`
+   * :doc:`/how_to_guides/resume_quickrun`
+   * :doc:`/how_to_guides/run_on_slurm`
+   * :doc:`/how_to_guides/run_repeats_in_parallel`
+   * :doc:`/how_to_guides/run_with_mps`
 
 See Also
 --------

diff --git a/docs/guide/protocols/absolutebinding.rst b/docs/guide/protocols/absolutebinding.rst
@@ -132,7 +132,7 @@ the `Boresch restraint analysis tutorial
 The multistate trajectory (``simulation.nc``) and its topology
 (``alchemical_system.pdb``) can be analysed further using `openfe_analysis`_.
 
-.. TODO: Link to the trajectory visualisation cookbook when published.
+.. TODO: Link to the trajectory visualisation how_to_guide when published.
 
 See Also
 --------
@@ -154,7 +154,7 @@ See Also
 
 **How-to guides**
 
-:ref:`How-to guides <cookbooks>`
+:ref:`How-to guides <how_to_guides>`
 
 **API Documentation**
 

diff --git a/docs/guide/protocols/absolutesolvation.rst b/docs/guide/protocols/absolutesolvation.rst
@@ -115,7 +115,7 @@ the structural analysis is skipped. The multistate trajectories
 (``solvent.nc`` and ``vacuum.nc``) can be analysed further using
 `openfe_analysis`_.
 
-.. TODO: Link to the trajectory visualisation cookbook when published.
+.. TODO: Link to the trajectory visualisation how_to_guide when published.
 
 
 See Also
@@ -135,7 +135,7 @@ See Also
 
 **How-to guides**
 
-:ref:`How-to guides <cookbooks>`
+:ref:`How-to guides <how_to_guides>`
 
 **API Documentation**
 

diff --git a/docs/guide/protocols/index.rst b/docs/guide/protocols/index.rst
@@ -243,7 +243,7 @@ These limitations apply to all binding free energy protocols.
 See also
 --------
 
-* :doc:`Choose and configure a protocol </cookbook/choose_protocol>`
+* :doc:`Choose and configure a protocol </how_to_guides/choose_protocol>`
 * :ref:`Assessing simulation health <userguide_simulation_health>`
 * :doc:`Troubleshooting simulations </guide/troubleshooting>`
 

diff --git a/docs/guide/protocols/relativehybridtopology.rst b/docs/guide/protocols/relativehybridtopology.rst
@@ -201,7 +201,7 @@ evidence of ligand displacement.
 The multistate trajectory (``simulation.nc``) and the hybrid topology
 (``hybrid_system.pdb``) can be analysed further using `openfe_analysis`_.
 
-.. TODO: Link to the trajectory visualisation cookbook when published.
+.. TODO: Link to the trajectory visualisation how_to_guide when published.
 
 
 See Also
@@ -219,7 +219,7 @@ See Also
 
 **How-to guides**
 
-:ref:`How-to guides <cookbooks>`
+:ref:`How-to guides <how_to_guides>`
 
 **API Documentation**
 

diff --git a/docs/guide/protocols/septop.rst b/docs/guide/protocols/septop.rst
@@ -144,7 +144,7 @@ the `Boresch restraint analysis tutorial
 The multistate trajectory (``simulation.nc``) and its topology
 (``alchemical_system.pdb``) can be analysed further using `openfe_analysis`_.
 
-.. TODO: Link to the trajectory visualisation cookbook when published.
+.. TODO: Link to the trajectory visualisation how_to_guide when published.
 
 See Also
 --------
@@ -165,7 +165,7 @@ See Also
 
 **How-to guides**
 
-:ref:`How-to guides <cookbooks>`
+:ref:`How-to guides <how_to_guides>`
 
 **API Documentation**
 

diff --git a/docs/guide/results/index.rst b/docs/guide/results/index.rst
@@ -14,7 +14,7 @@ and entire networks of results analysed.
 
 .. admonition:: How-to guides
 
-   * :doc:`/cookbook/dumping_transformation`
-   * :doc:`/cookbook/jq_inspection`
+   * :doc:`/how_to_guides/dumping_transformation`
+   * :doc:`/how_to_guides/jq_inspection`
 
 .. TODO: add the gather, load results, cinnabar and openfe_analysis how-tos.
diff --git a/docs/guide/results/simulation_health.rst b/docs/guide/results/simulation_health.rst
@@ -454,7 +454,7 @@ Some problems only show up across a network. Relative free energies around a
 cycle should sum to zero within their uncertainties, and each edge should
 agree with the value implied by the rest of the network. Large deviations
 point to unreliable edges worth checking with the diagnostics above. These checks need a network with redundant edges
-(see :doc:`Generate ligand networks </cookbook/generate_ligand_network>`).
+(see :doc:`Generate ligand networks </how_to_guides/generate_ligand_network>`).
 To calculate cycle closure errors, see the `cinnabar cycle closure tutorial
 <https://cinnabar.openfree.energy/en/latest/tutorials/cycle-closure.html>`_.
 

diff --git a/docs/guide/setup/alchemical_network_model.rst b/docs/guide/setup/alchemical_network_model.rst
@@ -43,14 +43,14 @@ is often done through a :class:`.LigandNetwork`.
 
 You can manually create a :class:`.AlchemicalNetwork` by creating a list
 of :class:`.Transformation` objects. For examples using the Python API,
-see :ref:`cookbook on creating alchemical networks <cookbook/create_alchemical_network.nblink>`.
+see :ref:`How-to guide on creating alchemical networks <how_to_guides/create_alchemical_network.nblink>`.
 
 2. Python ``NetworkPlanner`` Convenience Classes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 OpenFE also provides the convenience classes :class:`.RBFEAlchemicalNetworkPlanner` and :class:`.RHFEAlchemicalNetworkPlanner`,
 which use the :class:`.RelativeHybridTopologyProtocol` for creating :class:`.AlchemicalNetwork`\s.
-For example usage of these convenience classes, see :ref:`Relative Alchemical Network Planners cookbook <cookbook/rfe_alchemical_planners.nblink>`.
+For example usage of these convenience classes, see :ref:`Relative Alchemical Network Planners How-to guide <how_to_guides/rfe_alchemical_planners.nblink>`.
 
 .. note::
    The Network Planners are provided for user convenience. While they cover

diff --git a/docs/guide/setup/creating_ligand_networks.rst b/docs/guide/setup/creating_ligand_networks.rst
@@ -44,7 +44,7 @@ Generating Ligand Networks
    # plan the ligand network
    ligand_network = network_planner(ligands=mols, mappers=[mapper], scorer=scorer)
 
-Practical information on generating ligand networks can be found in our :ref:`cookbook for ligand network generation <cookbook/generate_ligand_network.nblink>`.
+Practical information on generating ligand networks can be found in our :ref:`How-to guide for ligand network generation <how_to_guides/generate_ligand_network.nblink>`.
 
 .. note::
    Like the Component objects, a ``LigandNetwork`` object is immutable once created!
diff --git a/docs/guide/setup/index.rst b/docs/guide/setup/index.rst
@@ -47,22 +47,22 @@ See :ref:`dumping transformations <dumping_transformations>` for more details.
 
    **Setup**
 
-   * :doc:`/cookbook/loading_molecules`
-   * :doc:`/cookbook/user_charges`
-   * :doc:`/cookbook/bespoke_parameters`
+   * :doc:`/how_to_guides/loading_molecules`
+   * :doc:`/how_to_guides/user_charges`
+   * :doc:`/how_to_guides/bespoke_parameters`
 
    **Planning: Ligand networks**
 
-   * :doc:`/cookbook/generate_ligand_network`
-   * :doc:`/cookbook/hand_write_ligand_network`
-   * :doc:`/cookbook/network_from_orion_fepp`
-   * :doc:`/cookbook/ligandnetwork_vis`
-   * :doc:`/cookbook/repairing_broken_networks`
+   * :doc:`/how_to_guides/generate_ligand_network`
+   * :doc:`/how_to_guides/hand_write_ligand_network`
+   * :doc:`/how_to_guides/network_from_orion_fepp`
+   * :doc:`/how_to_guides/ligandnetwork_vis`
+   * :doc:`/how_to_guides/repairing_broken_networks`
 
    **Planning: Protocols and alchemical networks**
 
-   * :doc:`/cookbook/choose_protocol`
-   * :doc:`/cookbook/rfe_alchemical_planners`
-   * :doc:`/cookbook/create_alchemical_network`
+   * :doc:`/how_to_guides/choose_protocol`
+   * :doc:`/how_to_guides/rfe_alchemical_planners`
+   * :doc:`/how_to_guides/create_alchemical_network`
 
 .. TODO: add the new Setup and Planning how-tos to this box as they are added.
diff --git a/docs/guide/setup/input_preparation.rst b/docs/guide/setup/input_preparation.rst
@@ -82,7 +82,7 @@ The inputs are loaded as follows:
       * **Pre-solvated systems:** ``SolvatedPDBComponent.from_pdb_file`` or
         ``ProteinMembraneComponent.from_pdb_file``.
 
-      See :doc:`Loading Molecules and Chemical Systems </cookbook/loading_molecules>` for examples.
+      See :doc:`Loading Molecules and Chemical Systems </how_to_guides/loading_molecules>` for examples.
 
 .. _prep_protein:
 
@@ -180,7 +180,7 @@ results.
 
 Partial charges are assigned during protocol setup but can also
 be assigned in advance for reproducibility and to avoid repeated calculations.
-See :doc:`Assigning partial charges </cookbook/user_charges>` (Python API) or
+See :doc:`Assigning partial charges </how_to_guides/user_charges>` (Python API) or
 :doc:`Generating Partial Charges with the OpenFE CLI </tutorials/charge_molecules_cli_tutorial>`.
 
 .. rubric:: Binding poses
@@ -225,7 +225,7 @@ Checklist for preparing input ``Components``
 See also
 --------
 
-* :doc:`Loading Molecules and Chemical Systems </cookbook/loading_molecules>`
+* :doc:`Loading Molecules and Chemical Systems </how_to_guides/loading_molecules>`
 * :doc:`Components, Chemical Systems and Thermodynamic Cycles <chemical_systems_and_thermodynamic_cycles>`
 * :doc:`Membrane RBFE tutorial </tutorials/rbfe_membrane_protein>`
 * :ref:`Protocols and domain of applicability <userguide_protocols>`
diff --git a/docs/cookbook/bespoke_parameters.nblink → docs/how_to_guides/bespoke_parameters.nblink b/docs/cookbook/bespoke_parameters.nblink → docs/how_to_guides/bespoke_parameters.nblink
diff --git a/docs/cookbook/choose_protocol.nblink → docs/how_to_guides/choose_protocol.nblink b/docs/cookbook/choose_protocol.nblink → docs/how_to_guides/choose_protocol.nblink
diff --git a/...cookbook/create_alchemical_network.nblink → ...o_guides/create_alchemical_network.nblink b/...cookbook/create_alchemical_network.nblink → ...o_guides/create_alchemical_network.nblink
diff --git a/docs/cookbook/dumping_transformation.rst → .../how_to_guides/dumping_transformation.rst b/docs/cookbook/dumping_transformation.rst → .../how_to_guides/dumping_transformation.rst
diff --git a/docs/cookbook/generate_ligand_network.nblink → ..._to_guides/generate_ligand_network.nblink b/docs/cookbook/generate_ligand_network.nblink → ..._to_guides/generate_ligand_network.nblink
diff --git a/...cookbook/hand_write_ligand_network.nblink → ...o_guides/hand_write_ligand_network.nblink b/...cookbook/hand_write_ligand_network.nblink → ...o_guides/hand_write_ligand_network.nblink
diff --git a/docs/cookbook/index.rst → docs/how_to_guides/index.rst b/docs/cookbook/index.rst → docs/how_to_guides/index.rst
@@ -1,4 +1,4 @@
-.. _cookbooks:
+.. _how_to_guides:
 
 How-To Guides
 =============

diff --git a/docs/cookbook/jq_inspection.rst → docs/how_to_guides/jq_inspection.rst b/docs/cookbook/jq_inspection.rst → docs/how_to_guides/jq_inspection.rst
diff --git a/docs/cookbook/ligandnetwork_vis.nblink → docs/how_to_guides/ligandnetwork_vis.nblink b/docs/cookbook/ligandnetwork_vis.nblink → docs/how_to_guides/ligandnetwork_vis.nblink
diff --git a/docs/cookbook/loading_molecules.nblink → docs/how_to_guides/loading_molecules.nblink b/docs/cookbook/loading_molecules.nblink → docs/how_to_guides/loading_molecules.nblink
diff --git a/docs/cookbook/network_from_orion_fepp.nblink → ..._to_guides/network_from_orion_fepp.nblink b/docs/cookbook/network_from_orion_fepp.nblink → ..._to_guides/network_from_orion_fepp.nblink
diff --git a/docs/cookbook/packmol_memgen_setup.nblink → ...how_to_guides/packmol_memgen_setup.nblink b/docs/cookbook/packmol_memgen_setup.nblink → ...how_to_guides/packmol_memgen_setup.nblink
diff --git a/...cookbook/repairing_broken_networks.nblink → ...o_guides/repairing_broken_networks.nblink b/...cookbook/repairing_broken_networks.nblink → ...o_guides/repairing_broken_networks.nblink
diff --git a/docs/cookbook/resume_quickrun.rst → docs/how_to_guides/resume_quickrun.rst b/docs/cookbook/resume_quickrun.rst → docs/how_to_guides/resume_quickrun.rst
diff --git a/docs/cookbook/rfe_alchemical_planners.nblink → ..._to_guides/rfe_alchemical_planners.nblink b/docs/cookbook/rfe_alchemical_planners.nblink → ..._to_guides/rfe_alchemical_planners.nblink
diff --git a/docs/cookbook/run_on_slurm.rst → docs/how_to_guides/run_on_slurm.rst b/docs/cookbook/run_on_slurm.rst → docs/how_to_guides/run_on_slurm.rst
diff --git a/docs/cookbook/run_quickrun.rst → docs/how_to_guides/run_quickrun.rst b/docs/cookbook/run_quickrun.rst → docs/how_to_guides/run_quickrun.rst
diff --git a/docs/cookbook/run_repeats_in_parallel.rst → ...how_to_guides/run_repeats_in_parallel.rst b/docs/cookbook/run_repeats_in_parallel.rst → ...how_to_guides/run_repeats_in_parallel.rst
diff --git a/docs/cookbook/run_task_based.rst → docs/how_to_guides/run_task_based.rst b/docs/cookbook/run_task_based.rst → docs/how_to_guides/run_task_based.rst
diff --git a/docs/cookbook/run_with_mps.rst → docs/how_to_guides/run_with_mps.rst b/docs/cookbook/run_with_mps.rst → docs/how_to_guides/run_with_mps.rst
diff --git a/docs/cookbook/user_charges.nblink → docs/how_to_guides/user_charges.nblink b/docs/cookbook/user_charges.nblink → docs/how_to_guides/user_charges.nblink
diff --git a/docs/index.rst b/docs/index.rst
@@ -39,7 +39,7 @@ The **OpenFE** ecosystem is a free and open-source framework for planning, runni
    installation
    guide/index
    tutorials/index
-   cookbook/index
+   how_to_guides/index
    reference/index
    CHANGELOG
 

diff --git a/docs/tutorials/index.rst b/docs/tutorials/index.rst
@@ -46,7 +46,7 @@ Post-Simulation Analysis
 Generating Partial Charges
 --------------------------
 
-.. todo: this should be in cookbook
+.. todo: this should be in how_to_guides
 
 -  :ref:`Generating Partial Charges CLI tutorial <charge_molecules_cli_tutorial>`: how to use the CLI to assign and store partial charges for mall molecules which can be used throughout the OpenFE ecosystem.