# SAMSON Documentation Center

> The Documentation Center contains information about using SAMSON and SAMSON extensions. It integrates the SAMSON User Guide that helps users install SAMSON, learn the interface, work with molecular structures, visualize and present results, simulate and analyze systems, collaborate, automate workflows, and find reference material. It also contains intro guides about developing with SAMSON in Python or C++.

## Home

- [Home](https://documentation.samson-connect.net/index.md)

## Documentation Map

- [Documentation map](https://documentation.samson-connect.net/documentation-map/index.md)

## User Guide

- [Welcome to the SAMSON User Guide](https://documentation.samson-connect.net/users/latest/index.md)

## User Guide - Start here

- [Start here](https://documentation.samson-connect.net/users/latest/start/index.md)
- [Getting Started](https://documentation.samson-connect.net/users/latest/getting-started/index.md)
- [Requirements and Platforms](https://documentation.samson-connect.net/users/latest/requirements-and-platforms/index.md)
- [Install SAMSON](https://documentation.samson-connect.net/users/latest/installation/index.md)
- [First look: the interface](https://documentation.samson-connect.net/users/latest/first-look/index.md)
- [Moving around](https://documentation.samson-connect.net/users/latest/moving-around/index.md)
- [Loading molecules](https://documentation.samson-connect.net/users/latest/loading-molecules/index.md)
- [Interactive tutorials](https://documentation.samson-connect.net/users/latest/interactive-tutorials/index.md)
- [SAMSON AI](https://documentation.samson-connect.net/users/latest/samson-ai/index.md)
- [SAMSON Connect](https://documentation.samson-connect.net/users/latest/samson-connect/index.md)
- [Webinars](https://documentation.samson-connect.net/users/latest/webinars/index.md)

## User Guide - Work with structures

- [Work with structures](https://documentation.samson-connect.net/users/latest/work-with-structures/index.md)
- [Selecting](https://documentation.samson-connect.net/users/latest/selecting/index.md)
- [Inspecting](https://documentation.samson-connect.net/users/latest/inspecting/index.md)
- [Measuring](https://documentation.samson-connect.net/users/latest/measuring/index.md)
- [History: Undo and redo](https://documentation.samson-connect.net/users/latest/history/index.md)

## User Guide - Build and edit

- [Build and edit](https://documentation.samson-connect.net/users/latest/build-and-edit/index.md)
- [Moving objects](https://documentation.samson-connect.net/users/latest/moving-objects/index.md)
- [Building molecules](https://documentation.samson-connect.net/users/latest/building-molecules/index.md)
- [Creating patterns](https://documentation.samson-connect.net/users/latest/creating-patterns/index.md)
- [Minimizing](https://documentation.samson-connect.net/users/latest/minimizing/index.md)

## User Guide - Visualize and present

- [Visualize and present](https://documentation.samson-connect.net/users/latest/visualize-and-present/index.md)
- [Visualizing](https://documentation.samson-connect.net/users/latest/visualizing/index.md)
- [Colorizing](https://documentation.samson-connect.net/users/latest/colorizing/index.md)
- [Labeling](https://documentation.samson-connect.net/users/latest/labeling/index.md)
- [Rendering effects](https://documentation.samson-connect.net/users/latest/rendering-effects/index.md)
- [Rendering using Cycles](https://documentation.samson-connect.net/users/latest/rendering/index.md)
- [Presenting and animating](https://documentation.samson-connect.net/users/latest/presenting/index.md)

## User Guide - Simulate and analyze

- [Simulate and analyze](https://documentation.samson-connect.net/users/latest/simulate-and-analyze/index.md)
- [Modeling and Simulation](https://documentation.samson-connect.net/users/latest/modeling-and-simulation/index.md)
- [Path Analyzer](https://documentation.samson-connect.net/users/latest/path-analyzer/index.md)
- [Interaction designer](https://documentation.samson-connect.net/users/latest/interaction-designer/index.md)
- [Cloud computations](https://documentation.samson-connect.net/users/latest/cloud/index.md)

## User Guide - Share and collaborate

- [Share and collaborate](https://documentation.samson-connect.net/users/latest/share-and-collaborate/index.md)
- [Share documents](https://documentation.samson-connect.net/users/latest/share-documents/index.md)
- [Collaboration](https://documentation.samson-connect.net/users/latest/collaboration/index.md)

## User Guide - Automate and extend

- [Automate and extend](https://documentation.samson-connect.net/users/latest/automate-and-extend/index.md)
- [Scripting](https://documentation.samson-connect.net/users/latest/scripting/index.md)
- [Extending SAMSON](https://documentation.samson-connect.net/users/latest/extending-samson/index.md)

## User Guide - Reference and help

- [Reference and help](https://documentation.samson-connect.net/users/latest/reference-and-help/index.md)
- [FAQ](https://documentation.samson-connect.net/users/latest/faq/index.md)
- [Troubleshooting](https://documentation.samson-connect.net/users/latest/troubleshooting/index.md)

## User Guide - References

- [References](https://documentation.samson-connect.net/users/latest/references/index.md)
- [Apps](https://documentation.samson-connect.net/users/latest/apps/index.md)
- [Camera](https://documentation.samson-connect.net/users/latest/camera/index.md)
- [Default color palettes](https://documentation.samson-connect.net/users/latest/color-palettes/index.md)
- [Documents](https://documentation.samson-connect.net/users/latest/documents/index.md)
- [Editors](https://documentation.samson-connect.net/users/latest/editors/index.md)
- [Exporters](https://documentation.samson-connect.net/users/latest/exporters/index.md)
- [Importers](https://documentation.samson-connect.net/users/latest/importers/index.md)
- [SAMSON Interface](https://documentation.samson-connect.net/users/latest/interface/index.md)
- [Models](https://documentation.samson-connect.net/users/latest/models/index.md)
- [Node types](https://documentation.samson-connect.net/users/latest/node-types/index.md)
- [Preferences](https://documentation.samson-connect.net/users/latest/preferences/index.md)
- [Sequence view](https://documentation.samson-connect.net/users/latest/sequence-view/index.md)
- [Supported formats](https://documentation.samson-connect.net/users/latest/supported-formats/index.md)
- [Versioning](https://documentation.samson-connect.net/users/latest/versioning/index.md)
- [Visual presets](https://documentation.samson-connect.net/users/latest/visual-presets/index.md)

## User Guide - Animations

- [Animations](https://documentation.samson-connect.net/users/latest/animations/index.md)
- [Appear](https://documentation.samson-connect.net/users/latest/animations/appear/index.md)
- [Assemble](https://documentation.samson-connect.net/users/latest/animations/assemble/index.md)
- [Conceal atoms](https://documentation.samson-connect.net/users/latest/animations/conceal-atoms/index.md)
- [Disappear](https://documentation.samson-connect.net/users/latest/animations/disappear/index.md)
- [Disassemble](https://documentation.samson-connect.net/users/latest/animations/disassemble/index.md)
- [Dock](https://documentation.samson-connect.net/users/latest/animations/dock/index.md)
- [Dolly camera](https://documentation.samson-connect.net/users/latest/animations/dolly-camera/index.md)
- [Flash](https://documentation.samson-connect.net/users/latest/animations/flash/index.md)
- [Follow atoms](https://documentation.samson-connect.net/users/latest/animations/follow-atoms/index.md)
- [Hidden](https://documentation.samson-connect.net/users/latest/animations/hidden/index.md)
- [Hide](https://documentation.samson-connect.net/users/latest/animations/hide/index.md)
- [Hold atoms](https://documentation.samson-connect.net/users/latest/animations/hold-atoms/index.md)
- [Hold camera](https://documentation.samson-connect.net/users/latest/animations/hold-camera/index.md)
- [Look at atoms](https://documentation.samson-connect.net/users/latest/animations/look-at-atoms/index.md)
- [Move atoms](https://documentation.samson-connect.net/users/latest/animations/move-atoms/index.md)
- [Move camera](https://documentation.samson-connect.net/users/latest/animations/move-camera/index.md)
- [Orbit camera](https://documentation.samson-connect.net/users/latest/animations/orbit-camera/index.md)
- [Pause](https://documentation.samson-connect.net/users/latest/animations/pause/index.md)
- [Pedestal camera](https://documentation.samson-connect.net/users/latest/animations/pedestal-camera/index.md)
- [Play path](https://documentation.samson-connect.net/users/latest/animations/play-path/index.md)
- [Play reverse path](https://documentation.samson-connect.net/users/latest/animations/play-reverse-path/index.md)
- [Pulse](https://documentation.samson-connect.net/users/latest/animations/pulse/index.md)
- [Record path](https://documentation.samson-connect.net/users/latest/animations/record-path/index.md)
- [Reveal atoms](https://documentation.samson-connect.net/users/latest/animations/reveal-atoms/index.md)
- [Rock](https://documentation.samson-connect.net/users/latest/animations/rock/index.md)
- [Rotate](https://documentation.samson-connect.net/users/latest/animations/rotate/index.md)
- [Set background](https://documentation.samson-connect.net/users/latest/animations/set-background/index.md)
- [Show](https://documentation.samson-connect.net/users/latest/animations/show/index.md)
- [Shown](https://documentation.samson-connect.net/users/latest/animations/shown/index.md)
- [Simulate](https://documentation.samson-connect.net/users/latest/animations/simulate/index.md)
- [Stop](https://documentation.samson-connect.net/users/latest/animations/stop/index.md)
- [Truck camera](https://documentation.samson-connect.net/users/latest/animations/truck-camera/index.md)
- [Undock](https://documentation.samson-connect.net/users/latest/animations/undock/index.md)
- [Zoom camera](https://documentation.samson-connect.net/users/latest/animations/zoom-camera/index.md)

## User Guide - Node Specification Language

- [Node Specification Language](https://documentation.samson-connect.net/users/latest/nsl/index.md)
- [Animation attributes](https://documentation.samson-connect.net/users/latest/nsl/animation/index.md)
- [Atom attributes](https://documentation.samson-connect.net/users/latest/nsl/atom/index.md)
- [Backbone attributes](https://documentation.samson-connect.net/users/latest/nsl/backbone/index.md)
- [Bond attributes](https://documentation.samson-connect.net/users/latest/nsl/bond/index.md)
- [Camera attributes](https://documentation.samson-connect.net/users/latest/nsl/camera/index.md)
- [Chain attributes](https://documentation.samson-connect.net/users/latest/nsl/chain/index.md)
- [Conformation attributes](https://documentation.samson-connect.net/users/latest/nsl/conformation/index.md)
- [NSL examples](https://documentation.samson-connect.net/users/latest/nsl/examples/index.md)
- [File attributes](https://documentation.samson-connect.net/users/latest/nsl/file/index.md)
- [Folder attributes](https://documentation.samson-connect.net/users/latest/nsl/folder/index.md)
- [Label attributes](https://documentation.samson-connect.net/users/latest/nsl/label/index.md)
- [Light attributes](https://documentation.samson-connect.net/users/latest/nsl/light/index.md)
- [Mesh attributes](https://documentation.samson-connect.net/users/latest/nsl/mesh/index.md)
- [Molecule attributes](https://documentation.samson-connect.net/users/latest/nsl/molecule/index.md)
- [Node attributes](https://documentation.samson-connect.net/users/latest/nsl/node/index.md)
- [Node group attributes](https://documentation.samson-connect.net/users/latest/nsl/nodeGroup/index.md)
- [Note attributes](https://documentation.samson-connect.net/users/latest/nsl/note/index.md)
- [Path attributes](https://documentation.samson-connect.net/users/latest/nsl/path/index.md)
- [Presentation attributes](https://documentation.samson-connect.net/users/latest/nsl/presentation/index.md)
- [Property model attributes](https://documentation.samson-connect.net/users/latest/nsl/propertyModel/index.md)
- [Render preset attributes](https://documentation.samson-connect.net/users/latest/nsl/renderPreset/index.md)
- [Residue attributes](https://documentation.samson-connect.net/users/latest/nsl/residue/index.md)
- [Segment attributes](https://documentation.samson-connect.net/users/latest/nsl/segment/index.md)
- [Side chain attributes](https://documentation.samson-connect.net/users/latest/nsl/sideChain/index.md)
- [Structural group attributes](https://documentation.samson-connect.net/users/latest/nsl/structuralGroup/index.md)
- [Structural model attributes](https://documentation.samson-connect.net/users/latest/nsl/structuralModel/index.md)
- [Visual model attributes](https://documentation.samson-connect.net/users/latest/nsl/visualModel/index.md)

## User Guide - Path Analyzer References

- [Path Analyzer Reference](https://documentation.samson-connect.net/users/latest/references/path-analyzer/index.md)
- [Angle](https://documentation.samson-connect.net/users/latest/references/path-analyzer/angle/index.md)
- [Asphericity](https://documentation.samson-connect.net/users/latest/references/path-analyzer/asphericity/index.md)
- [Average Force](https://documentation.samson-connect.net/users/latest/references/path-analyzer/average-force/index.md)
- [Average Velocity](https://documentation.samson-connect.net/users/latest/references/path-analyzer/average-velocity/index.md)
- [Contact Persistence](https://documentation.samson-connect.net/users/latest/references/path-analyzer/contact-persistence/index.md)
- [Contacts](https://documentation.samson-connect.net/users/latest/references/path-analyzer/contacts/index.md)
- [Custom Scatter](https://documentation.samson-connect.net/users/latest/references/path-analyzer/custom-scatter/index.md)
- [Density Curve](https://documentation.samson-connect.net/users/latest/references/path-analyzer/density-curve/index.md)
- [2D Density Map](https://documentation.samson-connect.net/users/latest/references/path-analyzer/density-map-2d/index.md)
- [Dihedral](https://documentation.samson-connect.net/users/latest/references/path-analyzer/dihedral/index.md)
- [Distance](https://documentation.samson-connect.net/users/latest/references/path-analyzer/distance/index.md)
- [Energy Landscape](https://documentation.samson-connect.net/users/latest/references/path-analyzer/energy-landscape/index.md)
- [Energy](https://documentation.samson-connect.net/users/latest/references/path-analyzer/energy/index.md)
- [Radius of Gyration](https://documentation.samson-connect.net/users/latest/references/path-analyzer/radius-of-gyration/index.md)
- [Ramachandran](https://documentation.samson-connect.net/users/latest/references/path-analyzer/ramachandran/index.md)
- [RDF](https://documentation.samson-connect.net/users/latest/references/path-analyzer/rdf/index.md)
- [RMSD (pairwise)](https://documentation.samson-connect.net/users/latest/references/path-analyzer/rmsd-pairwise/index.md)
- [RMSD](https://documentation.samson-connect.net/users/latest/references/path-analyzer/rmsd/index.md)
- [RMSF](https://documentation.samson-connect.net/users/latest/references/path-analyzer/rmsf/index.md)
- [SASA](https://documentation.samson-connect.net/users/latest/references/path-analyzer/sasa/index.md)
- [Secondary Structure Content](https://documentation.samson-connect.net/users/latest/references/path-analyzer/secondary-structure-content/index.md)
- [Shape Parameter](https://documentation.samson-connect.net/users/latest/references/path-analyzer/shape-parameter/index.md)

## Updates

- [Updates and Release Notes](https://documentation.samson-connect.net/updates/index.md)

## January 2025

- [January 2026](https://documentation.samson-connect.net/updates/2026-01/index.md)

## December 2025

- [December 2025 - 2025 Wrap-Up](https://documentation.samson-connect.net/updates/2025-12/index.md)

## November 2025

- [November 2025](https://documentation.samson-connect.net/updates/2025-11/index.md)

## October 2025

- [October 2025](https://documentation.samson-connect.net/updates/2025-10/index.md)

## September 2025

- [September 2025](https://documentation.samson-connect.net/updates/2025-09/index.md)

## August 2025

- [August 2025](https://documentation.samson-connect.net/updates/2025-08/index.md)

## July 2025

- [July 2025](https://documentation.samson-connect.net/updates/2025-07/index.md)

## June 2025

- [June 2025](https://documentation.samson-connect.net/updates/2025-06/index.md)

## May 2025

- [May 2025](https://documentation.samson-connect.net/updates/2025-05/index.md)

## Release Notes

- [SAMSON Release Notes](https://documentation.samson-connect.net/samson-release-notes/index.md)

## SAMSON 2026 R1 Release Notes

- [SAMSON 2026 R1](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2026-r1/index.md)

## SAMSON 2025 R3 Release Notes

- [SAMSON 2025 R3](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2025-r3/index.md)

## SAMSON 2025 R2 Release Notes

- [SAMSON 2025 R2](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2025-r2/index.md)

## SAMSON 2025 R1 Release Notes

- [SAMSON 2025 R1](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2025-r1/index.md)

## SAMSON 2024 Release Notes

- [SAMSON 2024](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2024/index.md)
- [Coding](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2024/coding/index.md)
- [Collaboration](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2024/collaboration/index.md)
- [Core updates](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2024/core-updates/index.md)
- [Modeling](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2024/modeling/index.md)
- [Visualization and animation](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2024/visualization-and-animation/index.md)

## SAMSON 2023 R1 Release Notes

- [SAMSON 2023 R1](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2023-r1/index.md)
- [Integrated Python Development Environment](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2023-r1/integrated-python-development-environment/index.md)
- [Interface redesign, and so much more!](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2023-r1/interface-redesign-and-so-much-more/index.md)
- [Molecular Cycles](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2023-r1/molecular-cycles/index.md)
- [New Pricing Structure](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2023-r1/new-pricing-structure/index.md)
- [SAMSON AI](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2023-r1/samson-ai/index.md)

## SAMSON 2022 R2 Release Notes

- [SAMSON 2022 R2](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2022-r2/index.md)

## SAMSON 2022 R1 Release Notes

- [SAMSON 2022 R1](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2022-r1/index.md)

## SAMSON 2021 Release Notes

- [SAMSON 2021](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2021/index.md)

## SAMSON 2020 R3 Release Notes

- [SAMSON 2020 R3](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2020-r3/index.md)

## SAMSON 2020 R2 Release Notes

- [SAMSON 2020 R2](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2020-r2/index.md)

## SAMSON 2020 R1 Release Notes

- [SAMSON 2020 R1](https://documentation.samson-connect.net/samson-release-notes/whats-new-in-samson-2020-r1/index.md)

## Extensions Tutorials

- [SAMSON Extensions Tutorials](https://documentation.samson-connect.net/tutorials/index.md)
- [Adenita](https://documentation.samson-connect.net/tutorials/adenita/adenita/index.md)
- [Dock Ligands with AutoDock Vina Extended in SAMSON](https://documentation.samson-connect.net/tutorials/adve/docking-libraries-of-ligands-with-autodock-vina-extended/index.md)
- [Generate Transition Paths with ARAP Interpolation](https://documentation.samson-connect.net/tutorials/arap/arap-interpolation-for-protein-structures/index.md)
- [Predict Biomolecular Structures in SAMSON](https://documentation.samson-connect.net/tutorials/bsp/bsp/index.md)
- [Generate Crystal Models with Crystal Creator](https://documentation.samson-connect.net/tutorials/crystal-creator/generating-crystal-models/index.md)
- [Export Atom Trajectories Along Paths in SAMSON](https://documentation.samson-connect.net/tutorials/export-along-path/export-atoms-trajectories-along-paths/index.md)
- [Optimize Molecular Geometry with the FIRE Minimizer](https://documentation.samson-connect.net/tutorials/fire/ready-set-fire/index.md)
- [Dock Protein-Ligand Complexes with the FITTED Suite](https://documentation.samson-connect.net/tutorials/fitted/fitted-suite/index.md)
- [GROMACS Wizard Tutorials](https://documentation.samson-connect.net/tutorials/gromacs-wizard/index.md)
- [Add Custom Index Groups in GROMACS Wizard](https://documentation.samson-connect.net/tutorials/gromacs-wizard/adding-custom-index-groups/index.md)
- [Applying custom parameters](https://documentation.samson-connect.net/tutorials/gromacs-wizard/applying-custom-parameters/index.md)
- [Batch computations](https://documentation.samson-connect.net/tutorials/gromacs-wizard/batch-computations/index.md)
- [Run GROMACS Wizard Jobs in the Cloud](https://documentation.samson-connect.net/tutorials/gromacs-wizard/cloud/index.md)
- [Coarse-grained systems](https://documentation.samson-connect.net/tutorials/gromacs-wizard/coarse-grained-systems/index.md)
- [COM Pulling](https://documentation.samson-connect.net/tutorials/gromacs-wizard/com-pulling/index.md)
- [Step 2: Energy Minimization](https://documentation.samson-connect.net/tutorials/gromacs-wizard/energy-minimization/index.md)
- [Step 4: NPT Equilibration](https://documentation.samson-connect.net/tutorials/gromacs-wizard/npt-equilibration/index.md)
- [Step 3: NVT Equilibration](https://documentation.samson-connect.net/tutorials/gromacs-wizard/nvt-equilibration/index.md)
- [Periodic Boundary Conditions in GROMACS Wizard](https://documentation.samson-connect.net/tutorials/gromacs-wizard/periodic-boundary-conditions/index.md)
- [PMF Analysis](https://documentation.samson-connect.net/tutorials/gromacs-wizard/pmf-analysis/index.md)
- [Step 1: Prepare](https://documentation.samson-connect.net/tutorials/gromacs-wizard/preparation/index.md)
- [Pre-processing of the system](https://documentation.samson-connect.net/tutorials/gromacs-wizard/preprocess/index.md)
- [Step 5: Production Molecular Dynamics Simulation](https://documentation.samson-connect.net/tutorials/gromacs-wizard/production-md/index.md)
- [Prepare Protein-Ligand Systems with GROMACS Wizard](https://documentation.samson-connect.net/tutorials/gromacs-wizard/protein-ligand-systems/index.md)
- [Configure Custom GROMACS Versions and Performance Settings](https://documentation.samson-connect.net/tutorials/gromacs-wizard/settings/index.md)
- [Umbrella Sampling](https://documentation.samson-connect.net/tutorials/gromacs-wizard/umbrella-sampling/index.md)
- [Run Protein-Protein Docking with Hex in SAMSON](https://documentation.samson-connect.net/tutorials/hex/protein-docking-with-hex/index.md)
- [Compute Ligand Unbinding Paths with Ligand Path Finder](https://documentation.samson-connect.net/tutorials/ligand-path-finder/ligand-path-finder/index.md)
- [Create MARTINI Coarse-Grained Models with Martinize2](https://documentation.samson-connect.net/tutorials/martinize2/martinize2/index.md)
- [Create Molecular Boxes with Molecular Box Builder](https://documentation.samson-connect.net/tutorials/molecular-box-builder/molecular-box-builder/index.md)
- [Refine NMR-Derived Structures with Molecular Restrainer](https://documentation.samson-connect.net/tutorials/molecular-restrainer/molecular-restrainer/index.md)
- [Build Carbon Nanotube Models in SAMSON](https://documentation.samson-connect.net/tutorials/nanotubes/building-nanotubes-models/index.md)
- [Compute Binding-Site Opening Motions with Normal Modes Advanced](https://documentation.samson-connect.net/tutorials/nma/calculating-non-linear-normal-modes/index.md)
- [Predict Protein-Ligand Complexes with NMR2](https://documentation.samson-connect.net/tutorials/nmr2/predicting-protein-ligand-complexes-using-nmr2/index.md)
- [Visualize Center-of-Mass Motion with Pathlines](https://documentation.samson-connect.net/tutorials/pathlines/pathlines/index.md)
- [Optimize Transition Paths with Parallel Nudged Elastic Band](https://documentation.samson-connect.net/tutorials/pneb/optimize-transition-paths-with-parallel-nudged-elastic-band/index.md)
- [Build Custom Polymers with Polymer Builder](https://documentation.samson-connect.net/tutorials/polymer-builder/polymer-builder/index.md)
- [Protein Preparation and Validation in SAMSON](https://documentation.samson-connect.net/tutorials/prepare-protein/prepare-protein/index.md)
- [Align Protein Sequences and Structures in SAMSON](https://documentation.samson-connect.net/tutorials/protein-aligner/protein-aligner/index.md)
- [Compute Protein Transition Paths with Protein Path Finder](https://documentation.samson-connect.net/tutorials/protein-path-finder/protein-path-finder/index.md)
- [Inspect Protein Backbone Angles with the Ramachandran Plot](https://documentation.samson-connect.net/tutorials/ramachandran/ramachandran-plot/index.md)
- [Explore the SARS-CoV-2 Spike Opening Motion](https://documentation.samson-connect.net/tutorials/sars-cov-2/coronavirus-computing-the-opening-motion-of-the-sars-cov-2-spike/index.md)
- [Make Nano-Batarangs with Simple Script](https://documentation.samson-connect.net/tutorials/simple-script/making-nano-batarangs-and-more/index.md)
- [Generate Analogue Series with Positional Analogue Scanning](https://documentation.samson-connect.net/tutorials/smiles-manager/perform-positional-analogue-scanning-using-the-smiles-manager-element/index.md)
- [Manage and Transform SMILES Data in SAMSON](https://documentation.samson-connect.net/tutorials/smiles-manager/using-the-rdkit-smiles-manager/index.md)
- [Explore Ligand Strain with Strain Explorer in SAMSON](https://documentation.samson-connect.net/tutorials/strain-explorer/strain-explorer/index.md)
- [Detect Symmetry in Biological Assemblies](https://documentation.samson-connect.net/tutorials/symmetry/computing-axes-of-symmetry-of-biological-assemblies/index.md)
- [Generate Symmetry Mates for Proteins](https://documentation.samson-connect.net/tutorials/symmetry/generating-symmetry-mates/index.md)
- [Use IM-UFF for Interactive Molecular Modeling](https://documentation.samson-connect.net/tutorials/uff/im-uff/index.md)
- [Use the Universal Force Field in SAMSON](https://documentation.samson-connect.net/tutorials/uff/uff/index.md)
- [Use the UMA Force Field in SAMSON](https://documentation.samson-connect.net/tutorials/uma-force-field/uma-force-field/index.md)

## Developing extensions

- [Developing SAMSON Extensions](https://documentation.samson-connect.net/developing-samson-extensions/index.md)

## Python

- [Accessing SAMSON functionality via Python](https://documentation.samson-connect.net/python/index.md)