SAMSON Blog – Page 380

Quickly Find Molecules by Size or Composition in SAMSON Using NSL

For anyone working with complex molecular systems, a common challenge is quickly filtering and selecting molecules based on specific characteristics—like the number of atoms, chains, or even the number of specific elements (e.g., carbon, oxygen, sulfur). If you’ve ever panned…

Making Molecular Elements Appear Seamlessly in Animations

OneAngstrom

When creating molecular animations to highlight specific steps in a mechanism, processes in a simulation, or structural features of a complex system, precise control over visibility can make or break the effectiveness of your presentation. One common challenge that many…

Quickly Filter Molecular Folders by Atom Counts in SAMSON

OneAngstrom

Filtering and analyzing large molecular datasets can quickly become overwhelming, especially when you’re looking for structures with specific characteristics like atom counts, element compositions, or number of chains. For researchers and molecular modelers dealing with large projects inside SAMSON, locating…

Structuring Scientific Animations: Using ‘Stop’ to Create Slide-Like Transitions in SAMSON

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Designing molecular presentations that clearly guide an audience through complex simulations or structural changes can be challenging. Often, molecular modelers want to highlight specific moments during an animation, explain transitions with voiceovers, or simply manage timing better during a live…

Select with Words: Natural Language Queries in SAMSON AI

OneAngstrom

For molecular modelers, one recurring challenge is precise atom or residue selection—especially in large or complex systems. Traditionally, users rely on syntax-heavy search commands, filters, or visual inspection, which can slow down workflows and introduce errors. However, there’s a more…

How to Find Motions That Open a Binding Pocket in Seconds (Without Manual Tinkering)

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One of the persistent challenges in computational structural biology is predicting how to open or close a binding pocket in a macromolecule like a protein. Whether you’re studying allosteric effects, conformational gating, or simply trying to dock a ligand into…

Tracking Atomic Motion: A Practical Guide to Recording Paths in Molecular Animations

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Molecular modelers and educators often face a common challenge: how to visually trace and document the atomic motion resulting from complex simulations or animations when presenting molecular mechanisms. Whether you’re simulating molecular docking, assembling a protein complex, or showcasing a…

Manually Controlling Atom Types and Bond Orders in Your UFF Simulation

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When working with molecular systems, the accuracy of simulations often depends on proper atom typization and bond order assignment. Most molecular modelers rely on automated perception to handle this, especially when using force fields like the Universal Force Field (UFF).…

How to Find Large Molecular Conformations with NSL

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When studying large molecular systems, modelers often need to isolate specific conformations based on size—such as filtering out all conformations with fewer than 100 atoms. Manually scanning through complex molecular systems can be time-consuming and error-prone. Fortunately, the Node Specification…

Making Molecular Models Easier to Read with Shadows

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When visualizing molecular systems, researchers often struggle with a surprisingly common challenge: understanding how different parts of a structure relate to each other in space. Despite complex 3D views, depth and spatial separation can remain ambiguous—especially in crowded systems. That’s…