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What’s new in SAMSON 2025 R1#

We're excited to introduce SAMSON 2025 R1, a major release that brings a ton of new features and improvements throughout SAMSON.

Webinar: Introducing SAMSON 2025 R1#

Coming soon! Register on SAMSON Connect or follow us on social media to get notified about the upcoming webinars and other updates.

Interaction Designer#

SAMSON 2025 R1 introduces the Interaction Designer to visualize and design molecules and interactions.

You can use this extension to understand interactions between ligands and other molecules, including proteins, water, chemical groups, etc., as well as create and edit molecules in 2D.

Interaction Designer

Create interaction diagrams and molecules#

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.

Everything is editable#

Everything in the 2D diagram is editable:

  • You can move all labels and interaction symbols to control the diagram layout, as well as the caption.
  • You can hide and show interactions by clicking on their name in the caption.
  • You can change the interaction colors by double-clicking on their name in the caption.

Easily export interaction diagrams#

You can save your interaction diagrams in various image formats, including png, jpg, jpeg, bmp, and svg.

Interactions#

The Interaction Designer determines ligand pockets and various atom-atom, atom-plane, plane-plane, and group-group/plane interactions. See User Guide: Interaction Designer for more information.

New functionality for building#

The arsenal of tools to build molecular systems in SAMSON has become even larger making it now possible to easily create complex patterns, align and distribute structures, and thanks to quick groups quickly memorize selections to easily switch between selections and perform complex operations on them.

Pattern creation#

SAMSON 2025 R1 introduces pattern building editors to rapidly build advanced patterns.

You can find the three pattern builders in the editors toolbar on the left side of the viewport or via the Find everything... on top of SAMSON:

  • Create circular pattern editor (shortcut: W)
  • Create curved pattern editor (shortcut: Q)
  • Create linear pattern editor (shortcut: L)

These editors makes it possible to rapidly create advanced patterns from selections:

  1. Select the structures you want to replicate. This can be any number of atoms and bonds.
  2. Use the widgets to translate and rotate the copies. You can press the Ctrl / Cmd key and click on a widget to enter a precise value for a translation or rotation. You can also use snap displacements to chosen lengths and angles.
  3. Control the number of copies by clicking on the main UI widget. You can use the mouse wheel to increase and decrease this number. You can also press the Ctrl / Cmd key while using the wheel to increase and decrease the number of copies faster.
  4. Press accept () to complete the model.

In the main Preferences, you can go to Edit > Create circular/curved/linear pattern to choose:

  • whether copies are automatically merged when they are nearby,
  • whether hydrogen atoms are automatically adjusted,
  • whether copies create new structures or are combined with existing ones.

Align and distribute structures#

SAMSON 2025 R1 introduces new commands to align and distribute atomic structures, meshes, and lights. You can find them in Edit > Align and Edit > Distribute.

Commands for aligning

Commands for distributing

You can also align with axes and planes using the compass actions - simply right-click on a compass widget to access the related commands for alignement.

Align using Compass

Quick groups#

SAMSON 2025 R1 introduces Quick groups to store selections and perform operations on them. They can be easily accessed from the Document view or via numberic shortcuts (1, 2, ...) and allow you to quickly select associated nodes and perform complex selections.

Quick groups

Updates in the Interface#

The main Preferences window now integrates the search making it easier for you to find the settings you are looking for.

Now, directly in the main Preferences, you can access the settings for apps, editors, importers, exporters, that expose them. For apps that expose such settings, you can also quickly access them via their window toolbar - simply click on the gear icon (⚙).

Preferences for editors

Updates in visualizations#

  • New color schemes (you can find them in Visualization > Color):

    • per structural model,
    • per structural model (illustrative),
    • CPK with constant carbons per structural model.

  • Improved performance: parallel implementation of Solvent Excluded Surface (S.E.S.) and Solvent Accessible Surface (S.A.S.) visual models.

  • The changes of default visual model properties are now undoable.
  • New color palette - pLDDT - for colorization of confidence of structures predicted with AlphaFold, etc.
  • Optimizations in rendering.
  • Fixes in the Stereo mode.

Revised Protein Aligner#

SAMSON 2025 R1 comes with an updated Protein Aligner that lets you align multiple sequences and structures of proteins. You can find it in Home > Align.

Protein Aligner

Other updates#

Added support for CALVADOS coarse grained models for protein and RNA systems.

Imported structures, trajectories, conformations, and meshes now refer to the original, source, files, so you can better keep track of your work.

Updated values for fundamental physical constants to the latest 2022 CODATA.

For developers#

The SAMSON API has been upgraded to expose the new functionalities of this release and let developers create extensions that they can distribute on SAMSON Connect. See the Developer Guide: Changelog.

Get SAMSON#

This is an overview, and SAMSON 2025 R1 also provides a variety of new features and fixes of reported issues. SAMSON 2025 R1 also incorporates updates in default extensions released after the previous release.

If you have any feedback or suggestions feel free to reach out via the Forum, via e-mail, by using the Feedback button in SAMSON, or by directly discussing with us.

If you already have SAMSON, just restart it and you will be offered to update: follow the steps and your installation will be upgraded to the latest SAMSON.

If not, create your free account and download SAMSON! You'll be all set and ready to go within a few minutes.