OneAngstrom – Page 14

One structure, many symmetries: how to choose the right one in molecular modeling

Molecular assemblies often exhibit a variety of symmetric patterns — but selecting the one that best suits your modeling objective isn’t always straightforward. If you’re dealing with large protein complexes or viral capsids, you may run into a common scenario:…

Hiding Molecular Elements During Animations in SAMSON

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When preparing a molecular animation, clarity is often just as important as accuracy. Whether you’re presenting a targeted conformation change or emphasizing a binding pocket, excess molecular clutter can become a visual distraction. Molecular modelers often face the issue of…

Creating Vertical Flythroughs in Molecular Models with the Pedestal Camera

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When presenting complex molecular systems, clarity is essential. One visually effective yet often underused technique is the vertical viewpoint shift — moving the camera up or down while keeping the orientation consistent. This is where SAMSON’s Pedestal camera animation becomes…

Quickly Filter Hidden and Visible Elements in SAMSON Using NSL

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Visual clutter is a common challenge for molecular modelers, especially when working with large and complex systems. Whether you’re assembling multiscale models, debugging simulations, or preparing clean visuals for publication, knowing exactly which parts of your model are visible or…

Making Notes Disappear in SAMSON: A Quick Guide to the ‘visible’ and ‘hidden’ Attributes

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When molecular modeling projects grow in complexity, collapsing visual clutter becomes essential. One of the simplest yet most useful tricks is managing the visibility of annotations and notes added during your exploration. SAMSON, the integrative molecular design platform, allows researchers…

Quickly Find the Right Chains Using Attributes in SAMSON

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When working with complex molecular systems, one of the recurring frustrations for molecular modelers is navigating large structures with dozens (or hundreds) of chains. Whether you’re prepping for simulations, visual analysis, or editing molecular systems, trying to find specific chains…

Making Sense of Molecular Models: How to Filter Backbones by Atom Counts in SAMSON

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When working on complex molecular systems, clarity and focus are essential. One challenge molecular modelers often face is the ability to isolate specific structural elements—like protein backbones—based on detailed chemical composition. For example, what if you only want to work…

Interactive φ/ψ Editing: A Faster Way to Tweak Protein Backbone Conformations

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Protein structure modeling often involves spotting and correcting outlier conformations in the backbone. These problematic residues can affect simulation stability, energy minimization, or interpretation of function. Fixing them typically means switching between raw coordinate editing or laborious script-based correction. But…

Avoiding common selection mistakes with presentation nodes in SAMSON

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In molecular modeling, selecting the right things – atoms, groups, visual representations – is part of almost every workflow. But when working in complex models in SAMSON, especially with presentation nodes, it’s easy to think you’ve selected something when you…

Filtering Side Chains by Atomic Composition in SAMSON

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When dealing with large biomolecular systems, keeping track of the structural components—especially side chains—can be overwhelming. If you’ve ever needed to pinpoint side chains based on the number of atoms or specific elements they contain, then you know how time-consuming…