Getting started with SAMSON
First steps
How-to guides
- Changing the view – learn how to orient the viewport and use cameras.
- Selecting objects – learn how to select various objects (nodes) in documents, in the viewport using selection filters, editors, and the Node Specification Language.
- Moving objects – learn how to rotate and translate nodes using move editors.
- Inspecting objects – learn how to inspect nodes and change their parameters using the Inspector.
- Building molecules – learn how to build systems from atoms and fragments.
- Creating images – learn how to apply visualizations and make high-quality images.
- Making presentations and animations – learn how to create presentations and various animations of your systems.
- See the User guide for more guides and tips.
Releases
- SAMSON 2023 R1
- SAMSON 2022 R2
- SAMSON 2022 R1
- SAMSON 2021
- SAMSON 2020 R3
- SAMSON 2020 R2
- SAMSON 2020 R1
References
Extensions guides
Drug discovery and structural biology
- Aligning proteins
- Computing axes of symmetry of biological assemblies
- Computing non-linear normal modes
- Computing normal modes that open a binding site
- Coronavirus: computing the opening motion of the SARS-CoV-2 spike
- Covalent and non-covalent protein-ligand docking with the Fitted Suite by Molecular Forecaster
- Docking ligands and ligand libraries with AutoDock Vina Extended
- Generating a path between protein structures
- Generating symmetry mates
- Interactive Ramachandran Plot
- Ligand Path Finder
- Perform Positional Analogue Scanning using the SMILES Manager
- Prepare, minimize, equilibrate and simulate using GROMACS Wizard
- Protein docking with Hex
- Protein Path Finder
- Running simulations in the cloud
- Using the RDKit – SMILES Manager
Materials science
DNA origami
Multi-domain extensions
- Create molecular boxes with Molecular Box Builder
- Export atoms trajectories along paths
- Fast geometry optimization with the FIRE minimizer
- Interactive Modeling Universal Force Field (IM-UFF)
- Making nano-batarangs (and more)
- Optimize transition paths with P-NEB
- Pathlines: show a path of the center of mass of an atomic system
- Universal Force Field
Developing SAMSON Extensions
Getting started
- Installing the SAMSON SDK
- Generating a SAMSON Extension
- Building a SAMSON Extension on Windows
- Building a SAMSON Extension on MacOS
- Building a SAMSON Extension on Linux
- Distributing a SAMSON Extension on SAMSON Connect
Tutorials
- Programming new apps
- Handling units and dimensional analysis
- Importing data
- Exporting data
- Creating novel visualizations
- Programming new force fields
- Programming new state updaters: Steepest descent
- Programming new state updaters: Monte Carlo
- Cite your research in SAMSON Extensions
- Programming a path generator
- Integrating external programs