Moving around

The Viewport displays visualization of structural models, visual models, some other nodes, editors and apps, and you can move around in it using a mouse, a keyboard, or the Compass in the bottom-left corner of the viewport.

The key element of visualization in SAMSON is a camera, it provides a 3D view of visualizable objects, and can be easily controlled to point to a specific location, zoom in or out, translate, rotate, etc. Basically, you may consider your screen as a camera pointing into the screen and yourself as an operator seeing through the camera.

A camera is a part of a SAMSON document, and each document has at least one camera, and you can add multiple cameras into a document to easily switch between different views. Cameras (with all their properties) are saved and loaded together with a document. A camera has three modes: rotation, translation, and zoom.

Default editors

When you start SAMSON for the first time, you are promted to select your default editor from the following ones:

• View Editor
• Point Selection Editor
• Rectangle Selection Editor

The first two editors are especially helpful for users who are familiar with other traditional molecular visualization tools and have specific preferences for how to explore, select, or build molecular structures. Together with the Rectangle Selection Editor and other editors, they give you the flexibility to tailor the interface to your workflow — whether you're visualizing, selecting, or designing molecular systems.

View and selection editors and when to use them

Editor	Shortcut	Best for
View Editor	V	Visualizing structures (recommended for users familiar with standard visualization software)
Point Selection Editor	P	Combining visualization and design (e.g. bio-structural editing, residue or atom selections)
Rectangle Selection Editor	R	Detailed structural design and construction (e.g. nanostructures)

Switching editors

You can switch editors anytime:

• Via the editor icons in the Editors toolbar on the left side of the viewport.

  Editor toolbar

  The Editor Toolbar on the left side of the viewport includes all available editors, including those installed via extensions.

• By pressing the appropriate keyboard shortcut.

• Or by pressing Esc to return to your default editor.

Setting default editor

You can change the default editor anytime in the Preferences > Editors > Default.

How to navigate with the View Editor

The View editor (V) provides intuitive navigation for exploring molecular systems.

Action	How to perform
Rotate	- Click and drag with the left or right mouse button (or single-finger drag on a trackpad) - Use keyboard arrows: Up, Down, Left, Right
Pan	Use the middle mouse button, or Shift + Ctrl/Cmd + drag on a trackpad
Zoom	Scroll wheel or pinch gesture on a trackpad

Tip

SAMSON includes tooltips and UI hints to guide navigation based on your hardware (mouse or trackpad). Hover over tools to view shortcuts and usage tips.

Note

The rotation behavior slightly changes depending on whether the grid is on or off:

• When the grid is on, consider it as a table on which you rotate a system.
• When the grid is off, consider that you rotate a system that is floating free.

How to navigate with the Point Selection Editor

The Point selection editor (P) has the same navigation commands as the View editor with an addition of selecting objects on click.

How to navigate with the Rectangle Selection Editor

Using a mouse

• Click on the right mouse button to rotate the view.
• Press the mouse wheel to translate the view.
• Scroll the mouse wheel to zoom in/out.
• Double-click on the middle button/mouse wheel to center the view. Ctrl/Cmd + right mouse button replaces the middle button.

Using a keyboard

• Up, Down, Left, Right - rotate the view around horizontal or vertical axis.
• Alt and Left, Right - rotate the view in the viewport plane around its center.
• Ctrl and Up, Down, Left, Right - translates the view horizontally or vertically.
• Ctrl++ - zoom in.
• Ctrl+- - zoom out.
• Shift+Space - center the camera on the selection or on the full view if nothing is selected.

Note

The rotation behavior slightly changes depending on whether the grid is on or off:

• When the grid is on, consider it as a table on which you rotate a system.
• When the grid is off, consider that you rotate a system that is floating free.

Rotation mode

To switch the camera into a rotation mode, press and hold the right mouse button. There are two rotation modes: close to the borders of the viewport and a trackball rotation mode (the view point is rotating around the center) in the middle part of the viewport.

Translation mode

To switch the camera into a translation mode, press and hold the mouse wheel. Try to move your mouse and you will see that the molecule follows it.

Zoom mode

To switch the camera into a zoom mode, scroll the mouse wheel: turn the wheel and the camera will zoom in and zoom out depending on the wheel scrolling direction.

Centering

Double-click on the mouse wheel to center the view.

The Shift+Space shortcut changes the camera focus. Select an atom and press Shift+Space, this centers the camera on the selected part (so that the selection will be in focus). If nothing is selected, then the camera is centered on the full view of the molecular system (the whole molecular system in the active document).

Tip

If you loose your molecular system, press Shift+Space and the camera will be re-positioned.

Tip

If the camera is centered on an atom and you rotate the view, the rotation will be centered around the atom.

Compass

The compass is a dedicated camera controller, which is situated in the bottom-left corner of the viewport and can be shown/hidden using the menu in the bottom part of the viewport by clicking on the corresponding icon. The compass allows you to easily align the camera and rotate it around different axis.

Camera functions

You can access some of the camera's functionality through its context menu. Right-click on a camera in the Document view to apply some of its actions:

• center the camera on the selection or on the whole document
• activate the camera inertia which will allow for a movement with inertia
• activate the camera orthographic projection which is useful e.g. for viewing crystals
• set the camera as the active one
• move the camera

Try switching the camera inertia on and move or rotate the molecule.

Try switching on and off the orthographic projection mode.

Multiple cameras

You can have multiple cameras in one document but only one camera can be active at a time. Having multiple cameras might be useful if you want to switch fast between different views (e.g., positions, projections, close-up views, and a full view) in the same document. To switch between cameras, double-click on one or right-click on one in the Document view and in its context menu click Set as active camera.

To add a new camera, click Visualization > Camera (1). A newly added camera will have a default starting position.

1. , : Ctrl+Shift+C, : Cmd+Shift+C

Clipping structures

Progressive clipping is a new visualization feature in SAMSON, introduced in SAMSON 2025 R2 it significantly improves the previous clipping implementation. It enhances how molecular structures are visually explored. Unlike traditional clipping, which creates an abrupt cutoff in the view, progressive clipping offers a gradual transition and it incorporates the previously separate fog rendering option. This helps intuitively understand which parts of the structure are being clipped based on their distance from the camera.

This feature is especially useful when inspecting dense molecular structures (e.g., proteins) or creating visualizations with depth clarity for presentations, publications, or interactive analysis.

The progressive clipping is activated by default. To see how you can control the way clipping (before the camera target) and fog (after the camera target) work, see the description below.

Video tutorial

You can learn how to use progressive clipping from the following extract of the SAMSON 2025 webinar:

How to use progressive clipping

1. Load a structure

To try out progressive clipping, load any structure. For example, use Home > Fetch to load a protein of your choice.

2. Activate and control progressive clipping

Progressive clipping is activated by default. It gradually fades parts of the structure depending on their distance from the camera, providing a more informative and realistic depth perception.

Controls

• Mouse + Keyboard shortcuts:

  • To change the clipping distance: press Ctrl (on Windows/Linux) or Cmd (on macOS) and scroll or slide on the trackpad.
  • To change the thickness of the visible region ("viewing slab" governed by clipping and fog): hold Shift + Ctrl (Windows/Linux) or Shift + Cmd (macOS) while scrolling.

• Viewport toolbar:

  • Use the clipping and fog control icon at the bottom of the SAMSON viewport to open the clipping control panel.

  

Clipping control panel

The control panel shows:

• Camera Eye - your current viewing position.
• Camera Target - what you're looking at.
• Background - infinite depth.

You can:

• Adjust clipping distance (on the left): Defines how close structures begin to be clipped.
• Adjust fog distance (on the right): Hides parts further in the background.
• Access the clipping preferences.

3. Customize the appearance

You can tailor the clipping style to suit your needs: click the Settings icon near the clipping panel, or go to Interface > Preferences > Rendering > Clipping. The options include:

• Presets: Choose from the predefined clipping styles for common visualization needs. For example, choose between progressive and traditional (sharp cut) clipping.
• Border size: Change the thickness of the clipping edge border to highlight what is being clipped.

4. Enhance your view

Combine progressive clipping with other visualization and rendering tools:

• Change background color.
• Enable silhouettes.
• Apply visual presets and colorization.
• Select nearby residues (e.g., binding site residues) via Select > Biology > Binding sites.
• Label selections for clarity.

All of this remains dynamically visible as you rotate and zoom, thanks to the smooth clipping transitions.

When to use clipping

Progressive clipping is especially helpful when:

• Exploring internal binding sites or ligand environments.
• Generating images or animations where depth clarity is critical.
• Teaching or demonstrating 3D molecular features interactively.