SAMSON Blog – Page 208

Precise Atom Selection Made Easy: Exploring NSL’s Symbol and Element Attributes

When working on molecular models, whether you’re preparing structures for simulation, visualizing proteins, or analyzing large molecular systems, being able to select specific atoms quickly is essential. For SAMSON users, the Node Specification Language (NSL) provides a powerful and flexible…

Why You Don’t Need to Reinvent the Wheel in Molecular Modeling

OneAngstrom

Molecular modeling is an exciting but challenging field, especially when it comes to integrating different tools into a cohesive workflow. Many researchers spend a significant amount of time connecting existing software, writing wrappers, or just manually transferring data between tools.…

Opening molecular files in SAMSON: What you need to know

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One common challenge for molecular modelers is handling the wide array of data formats used in structural biology, materials science, and chemistry. Whether it’s PDB, MOL, CIF, or dozens of others, molecular data often comes in different shapes and storage…

How to Quickly Access Editors in SAMSON Without Getting Lost

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When working on complex molecular systems, every second spent navigating software is a second not spent modeling. If you’re using SAMSON for integrative molecular design, you might find yourself wondering: where do I find the tools I need to build,…

Synchronizing Multiple Molecular Paths in SAMSON Animations

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Visualizing molecular dynamics or conformational transitions often involves analyzing and comparing several trajectory paths. Whether you are inspecting a ligand binding pathway, protein folding steps, or exploring alternative conformations, understanding how molecules move over time is key. But how can…

Managing Molecular Visibility and Selection in NSL

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When working with complex molecular systems, keeping your visualizations clean and relevant is crucial. Whether you’re navigating a large biomolecular complex or focusing on a specific small molecule in a crowded environment, performing visibility and selection queries quickly and precisely…

Filtering Molecular Structures Using Selection Attributes in SAMSON

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When working with complex molecular systems, molecular modelers often need to quickly identify and interact with specific subsets of structures—those visible in the viewport, carrying specific material properties, or comprising a targeted number of atoms. Doing this manually for large…

What is the Difference Between ‘visible’ and ‘visibilityFlag’ in SAMSON?

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When working with large molecular systems in SAMSON, staying organized is essential. One common challenge for molecular modelers—especially those refining complex visualizations for publications, teaching, or simulations—is making sense of what is currently displayed and what is not. This is…

How to Create Smooth Horizontal Camera Movements in Molecular Animations

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When you’re presenting a molecular model or visualizing a simulation result, smooth camera motion plays a key role in capturing your audience’s focus. Whether you’re demonstrating an active site interaction, exploring a supramolecular complex, or producing an educational video, simple…

Smooth Transitions Between Molecular Presentation Slides

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When creating molecular presentations, clarity and visual appeal are key. Molecular modelers often need to explain complex mechanisms, compare conformational states, or guide an audience through molecular interactions. But managing visual transitions between slides or images in a molecular visualization…