When working with complex molecular structures, clarity and visual control can make a huge difference. Molecular modelers often encounter a common pain: they spend more time than necessary navigating their workspace and managing visibility of molecular components instead of actually analyzing structures. You can have the most powerful algorithms, but if your interface is cluttered or unintuitive, productivity drops.
The Viewport in SAMSON is more than just a 3D display area. It’s packed with interactive menus and shortcuts that reduce friction between you and your data, allowing you to focus on science rather than software. In this blog post, we’ll explore the interface elements integrated directly into the viewport that help you manage selections, rendering, and favorite tools with minimal mouse travel.
Quick Access Where You Need It 📌
SAMSON’s viewport interface features menus in all four corners of the 3D view, each offering a specific set of tools:
- Top-right corner: Selection tools, including filtering types of selectable nodes (e.g., only atoms or only residues) and quick-select buttons like Select all and Deselect all.
- Bottom menu bar: View and rendering options, such as toggling effects or switching camera modes.
- Left side: Access to all editors installed in your SAMSON—Add, Move, Selection, Erase, Measure, and more.
- Right side: Quick launch area for your favorite apps. Less time digging through menus, more time modeling.
Editor Shortcuts That Feel Natural ⚡
Each editor is bound to easy-to-remember keyboard shortcuts. For example:
V: View editor – default navigation toolA: Add editor – add atoms or fragmentsM: Local move – move parts of the structure in local coordinatesE: Eraser – rapidly remove selected atoms or structures
Using these keys along with mouse gestures lets you perform complex manipulations very quickly. The menu even contains visual cues and tooltips, so you don’t have to memorize everything up front.
Find the Right Tool Instantly
SAMSON includes a convenient Find Everything search box in the top-right of the interface. Use it to search for commands, apps, or editors by name, shortcut, or tooltip. It’s helpful when you have dozens of extensions and need to locate a function without hunting through menus.
Reduce Clutter and Maintain Focus
Advanced selection tools available directly from the viewport allow you to maintain focus with fewer distractions. For example, selecting only water molecules, or only ligands, can be done quickly using filter-based options, making it easier to isolate relevant molecular features.
Similarly, you can arrange your favorite tools and frequently used editors for even faster access, minimizing interruptions to your workflow.
Try It in Action
The viewport system is especially valuable when modeling large biomolecular assemblies, such as protein-ligand systems or nucleic acids. Viewport menus allow you to zoom in on interactions, measure distances, label key components, and adjust rendering effects in real-time—right from where your eyes already are.
By mastering these tools, you can improve your day-to-day efficiency as a modeler and reduce fatigue from repetitive interface interactions.
You can explore more about SAMSON’s interface in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.