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What’s new in SAMSON 2024 - Visualization and animation#

This is Part II of What’s new in SAMSON 2024, the release notes for SAMSON 2024.

Visual Presets#

In SAMSON, Visual Presets are a powerful way to create complex visualizations in a few clicks. In SAMSON 2024, Visual Presets have been redesigned and made even more flexible and powerful.

Each Visual Preset consists of a series of steps, and each step is composed of four choices:

  • A selection of nodes to which the step applies (e.g., "Heavy atoms and polar atoms in ligands")
  • An optional set of actions applied to the selection (e.g., "Hide", "Label atoms", "Zoom to", etc.)
  • An optional visual model applied to the selection (e.g., "Van der Waals", "Licorice", etc.)
  • An optional color scheme applied to the selection or the visual model (if added) (e.g., "Per chain", "Per occupancy", etc.)

Visual Presets can be easily customized or created from scratch, with any number of steps, using the Visual Preset Editor:

Visual Preset Editor

Given the importance of Visual Presets, they were made accessible from both the Visualization menu and the Home menu:

Visual Preset Command

Here is how the Protein-ligand preset looks like on PDB code 1AA1:

Protein-ligand preset example

Colorization#

SAMSON 2024 introduces new color schemes. For example, the Per element (custom carbons) color scheme lets you choose a custom color for carbon atoms, but uses the default colors for all other atoms:

Per element (custom carbons) colorization

SAMSON 2024 also introduces discrete palettes:

List of discrete palettes

as well as a Color Vision Deficiency Emulator visible whenever you choose a color palette:

Color Vision Deficiency Emulator

New rendering defaults#

The default rendering settings have been updated to increase the shininess of objects:

New rendering defaults: increased shininess of objects

As before, go to Preferences > Rendering > Lighting to edit settings:

New rendering defaults: new light preferences

Combining animation and simulation for physically-based design#

SAMSON's Animator might be the most advanced dedicated tool to create molecular animations, with the possibility to animate molecules, cameras, shapes, etc. by combining animation tracks and controlling their keyframes.

SAMSON 2024 introduces two new animation tracks to perform simulations during animation. Precisely, a new Simulate track performs a number of simulation steps (with a custom force field) at each frame of an animation. Combined with the possibility of precisely controlling atom paths, this makes it possible to analyze ligand paths, prepare trajectories for umbrella sampling simulations, or even design nanosystems in a physically-based way, by easily testing design hypotheses:

A new Record path track also makes it possible to "bake" animated motions (resulting from other animation tracks, including the Simulate one) and avoid recomputing trajectories.

Viewport updates#

The Viewport Toolbar has an increased number of options to quickly control the visibility of nodes:

Viewport Toolbar: visibility of nodes

There is also a new Rock command to rock the viewport:

Viewport Toolbar: Rock

Finally, it is now possible to zoom into something by double-clicking on it (all other methods continue to exist: Shift + left-click, toolbar commands, etc.).

Next#

Go to Part III about Modeling.