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Tweaking the Universal Force Field: Customizing Typization in SAMSON

Molecular modelers often encounter situations where automated force field parameters don’t perfectly match their specific chemical systems. Default atom types or bond orders might not reflect the intended structure, especially in complex or unusual molecules. In SAMSON, this is addressed…

Model Fade In, Fade Out: Animating Molecular Structures with Pulse

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One of the challenges in molecular modeling and presentation is directing the attention of your viewers. Whether you’re teaching a class, giving a talk, or recording a video, clearly visualizing molecular processes—especially the dynamic ones—can be difficult. Enter the Pulse…

Effortlessly Navigate Molecular Design Changes with Undo and Redo

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One of the most common frustrations in molecular modeling arises from accidental changes, experimental edits that don’t pan out, or simply wanting to compare different model states. For molecular modelers working on complex structures, reverting changes isn’t just a nice-to-have—it…

Quickly Find and Hide Labels in SAMSON Using NSL

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When working on complex molecular models in SAMSON, the visualization can quickly become cluttered—especially when labels pile up. Whether you’re labeling specific atoms, groups, or molecular fragments, having too many visible labels can detract from what you’re actually trying to…

Tired of Static Molecular Presentations? Here’s a Simple Way to Add Motion

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When trying to communicate molecular structures and processes effectively, nothing conveys spatial relationships and dynamics better than motion. Yet, many molecular modelers still present their work using static snapshots, missing the opportunity to make insights more intuitive and memorable. Fortunately,…

Quickly Spot the Right Molecular Chain with NSL’s Chain Attribute Filters

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When exploring or refining large biomolecular systems, molecular modelers often face the frustrating challenge of navigating through numerous chains trying to isolate just the ones relevant to their study. Whether you’re interested only in chains with a high number of…

Lock the View Without Disruptions in Your Molecular Animation Workflow

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When creating molecular animations in SAMSON, one common challenge that modelers face is keeping the camera viewpoint consistent throughout specific segments of the animation. This is particularly frustrating when you’re trying to highlight subtle conformational changes or focus attention on…

Steepest Descent Got You Stuck? Try FIRE Instead

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If you’ve ever optimized molecular geometries using traditional methods like steepest descent, you’ve probably found yourself frustrated by slow convergence—especially when working with complex systems involving large-scale atomic motions. The Fast Inertial Relaxation Engine (FIRE) minimizer in SAMSON offers a…

Why You Might Not Want to Delete All Waters in Your Molecular System

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When preparing a protein structure for simulation, one frequently encounters the question: should I delete all the water molecules from the structure? Many molecular modelers default to removing all crystal water molecules at the preprocessing stage, but in some cases,…

Struggling to Share Molecular Models? Here’s How to Export Them from SAMSON

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Sharing molecular models and visualizations across different tools is a common part of the molecular modeling workflow. But if you’ve ever been stuck trying to convert your work from one format to another — maybe to submit a structure to…