Interaction designer#
The Interaction Designer in SAMSON makes it possible to visualize molecular interactions in 2D – such as protein-ligand interactions – in 2D, and design molecules directly in 2D. This functionality is seamlessly integrated with the 3D viewport, providing a tightly coupled 2D–3D environment for intuitive molecular exploration and design.
The Interaction Designer has two main modes:
- Creating interaction diagrams: use the Home > Diagram command to automatically create an interaction diagram based on the current selection, or the whole document if nothing is selected.
- Creating new molecules in 2D: use the Edit > Design command to start a new molecule.
The Interaction Designer keeps the 2D documents synchronized with the 3D viewport: selecting, adding, and removing atoms and fragments is performed in both 2D and 3D.
Acknowledgments
The Interaction Designer uses functionality from RDKit.
Create interaction diagrams#
Use the Home > Diagram command to automatically create an interaction diagram based on the current selection, or the whole document if nothing is selected.
The Interaction Designer provides the following features when creating interaction diagrams:
- Tight integration with the 3D viewport: select structures, atoms, and zoom on them. Click on an atom or structure to select it, double-click to zoom on it.
- Show the binding pocket for protein-ligand interactions.
- Show solvent accessibility of ligand atoms.
- Show interacting residues and structural groups. See the list of supported interactions.
-
Editable 2D diagram:
- You can move all labels and interaction symbols to control the diagram layout, as well as the caption/legend.
- You can hide and show interactions by clicking on their name or icon in the caption/legend.
- You can change the interaction colors by double-clicking on their name or icon in the caption/legend. You can restore the colors in the Interaction Designer settings that you can access via its window title bar.
Tip
Use the bottom menu of the Interaction Designer to update the view and align the 2D and 3D views.
You can zoom in/out by holding Ctrl/Cmd and using the scroll button of the mouse.
To translate the diagram, hold either middle mouse button and right mouse button and move the mouse.
Video tutorial#
You can learn how to create and edit 2D and 3D protein-ligand interaction diagrams from the following extract of the SAMSON 2025 webinar:
Supported interactions#
The Interaction Designer aims to support the same types of interatomic contacts as the arpeggio tool by the PBDe team and is validated against results from arpeggio and other tools.
Atom-atom interactions#
| Interaction | Description |
|---|---|
| Clash | The atom is involved in a steric clash. |
| Covalent | The atom appears to be covalently bonded. |
| van den Waals (VdW) | The van der Waals radius of the the atom is interacting with one or more other atoms. |
| VdW Clash | The van der Waals radius of the atom is clashing with one or more other atoms. |
| Proximal | The atom is > the VdW interaction distance, but within 5 Angstroms of other atom(s). |
| Hydrogen Bond | The atom forms a hydrogen bond. |
| Weak Hydrogen Bond | The atom forms a weak hydrogen bond. |
| Halogen Bond | The atom forms a halogen bond. |
| Ionic | The atom may interact via charges. |
| Metal Complex | The atom is part of a metal complex. |
| Aromatic | An aromatic ring atom interacting with another aromatic ring atom. |
| Hydrophobic | Hydrophobic interaction. |
| Carbonyl | A carbonyl-carbon:carbonyl-carbon interaction. |
| Polar | Less strict hydrogen bonding (without angle terms). |
| Weak Polar | Less strict weak hydrogen bonding (without angle terms). |
Atom-plane interactions#
| Interaction | Description |
|---|---|
| Carbon-\(\pi\) | Weakly electropositive carbon atom - \(\pi\) interactions [ref] |
| Cation-\(\pi\) | Positively charged group - \(\pi\) (aromatic ring) interactions [ref] |
| Donor-\(\pi\) | Hydrogen Bond donor - \(\pi\) (aromatic ring) interactions [ref] |
| Halogen-\(\pi\) | Halogen Bond donor - \(\pi\) (aromatic ring) interactions [ref] |
| Sulfur-\(\pi\) | Methionine sulfur - \(\pi\) (aromatic ring) interactions [ref] |
Plane-plane interactions#
Group-group/plane interactions#
| Interaction | Description |
|---|---|
| \(\pi\)-\(\pi\) | Direct interactions between two \(\pi\)-systems (aromatic rings) |
| Amide-amide | Interactions between two amide groups |
| Amide-\(\pi\) | Interactions between amides and aromatic rings [ref] |
Create new molecules in 2D#
Use the Edit > Design command to start drawing a new molecule in 2D.
Note
The Interaction Designer keeps the 2D documents synchronized with the 3D viewport: selecting, adding, and removing atoms and fragments is performed in both 2D and 3D.
Tip
To learn more about other ways to build molecules in SAMSON, especially in 3D, please refer to the Building molecules section.
You can start building a molecule:
- from scratch,
- starting from a molecule in the active document,
- starting from the current selection.
In the left panel of the Interaction designer, click on 
Add - this will switch it into the building mode with the Carbon atom set as the default atom for building.
Click anywhere in the designer window to add an atom. To add another atom, click on the atom to which you would like to connect it.
Tip
You can switch off the display of solvent accessibility by clicking on it in the legend.
Tip
Use the bottom menu of the Interaction Designer to update the view and align the 2D and 3D views.
You can zoom in/out by holding Ctrl/Cmd and using the scroll button of the mouse.
To translate the diagram, hold either middle mouse button and right mouse button and move the mouse.
You can use any atom element or any fragment to build molecules in 2D. You can change to a different atom element or a fragment using the Asset Browser (1).
- The Asset Browser provides access to the assets (molecule fragments, etc.) included by default in SAMSON together with the assets you can obtain from SAMSON Connect.
To open it use: Interface > Assets, , : Ctrl+4, : Cmd+4
Build with atoms#
You can change to another atom element via the Assets Browser in two ways.
For H, C, N, O atoms, you can use one of the buttons at the bottom of the Asset Browser.
For other atomic elements, open the Periodic table 
(1) and click on the desired element.
- Asset Browser > Periodic Table or Interface > Periodic Table,
, : Ctrl+5,
: Cmd+5
Note
Clicking in the designer on an atom while having a different atom element chosen as the atom for building will modify the clicked atom type.
Build with fragments#
To use a fragment for building, choose it from the Assets Browser.
You can change the pivot atom in the fragment used for building. For that hold Ctrl/Cmd and choose the desired pivot atom.
Erase atoms#
To erase atoms, click on 
Erase in the left panel of the Interaction Designer and then click on the atoms you want to delete.
Export interaction diagrams and 2D sketched#
You can save your interaction diagrams and 2D drawings of molecules in various image formats, including png, jpg, jpeg, bmp, and svg. For that, click on 
Save in the bottom panel of the Interaction Designer.