SAMSON Blog – Page 31

When ‘Visible’ Isn’t Enough: Understanding Structural Model Visibility in SAMSON

When molecular modelers build or import complex systems in SAMSON, they often need to programmatically filter or organize their structures. One common challenge is determining whether a structural component is actually shown in the viewport—and it’s not as straightforward as…

Controlling Visibility and Selection of Notes in SAMSON

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When dealing with complex molecular models, it can be useful to add annotations to guide collaborators, highlight relevant parts of a structure, or track modeling workflows. In SAMSON, these annotations can be represented as note nodes. While note nodes may…

Avoiding Static Molecules: Illustrating Flexibility with the Rock Animation in SAMSON

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In molecular modeling, communicating structure is only part of the story. Dynamic behavior—like vibrations, flexibility, and motion—often plays a central role in understanding biological function, drug binding mechanisms, or material properties. However, unless you build your animations carefully, your structures…

Avoiding Atom-Bond Confusion: A Quick Guide to Bond Types in NSL

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When working on molecular models, distinguishing between different bond types is more than just a detail—it’s critical. Misclassifying a bond could result in incorrect simulations or incorrect property predictions, potentially skewing results and leading to confusion down the road. Fortunately,…

Making Your Molecular Labels Work for You: Smarter Visibility in SAMSON

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When building complex molecular models, labels are essential for tracking atoms, residues, measurements, or annotations. But as models grow in size and complexity, overloading your Viewport with labels can make things harder to interpret, not easier. Fortunately, SAMSON offers several…

Making Atoms Disappear in Sequence: A Useful Trick for Molecular Animations

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When creating molecular presentations or videos, showing everything at once can overwhelm the viewer. Sometimes, revealing or concealing parts of the structure at specific moments helps focus attention and communicate more clearly. But how do you make atoms disappear gradually…

How to Quickly Select Paths by Atom Count in SAMSON

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When working with complex molecular systems, it’s common to deal with thousands of atoms and multiple conformations. If you’re trying to isolate only those paths that include a specific number of atoms—say, for comparing structural motifs or focusing simulations—you might…

Choosing the Right Color Palette for Molecular Visualizations in SAMSON

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When working with complex molecular systems, effective visualization isn’t just about generating eye-catching graphics — it’s about clarity, interpretation, and communication. A common challenge many molecular modelers face is choosing color schemes that not only highlight specific properties of a…

Making Molecular Models Rotate Between Keyframes in SAMSON

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When presenting molecular structures to colleagues, students, or for outreach purposes, it’s often helpful to add movement to focus attention or communicate structural symmetry. One simple visual tool that can significantly enhance your presentation is a rotation animation. Imagine you’ve…

Quickly Find Molecular Paths with >100 Atoms in SAMSON

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When working with complex molecular systems, it’s easy to feel overwhelmed by the sheer number of paths, residues, or chains in a structure. Whether you’re studying protein folding or evaluating ligand binding, pinpointing relevant fragments fast is key to staying…