SAMSON Blog – Page 91

Struggling to Showcase Your Molecular Designs? Try Orbit Camera Animation in SAMSON

Molecular modelers often know what they want to show, but not how to show it. When presenting complex molecular assemblies or dynamic motions, a static image or even a simple rotation often doesn’t do justice to the structure’s spatial features.…

Building Lipid Bilayers Around Proteins with Molecular Box Builder

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Modeling membrane proteins realistically often hinges on embedding them within a lipid bilayer. But placing lipids manually around a protein system can be time-consuming, potentially error-prone, and quite repetitive for simulations involving different lipid types or membrane compositions. Fortunately, Molecular…

Making Molecular Structures Easier to Understand with Visual Models in SAMSON

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One of the common challenges in molecular modeling — whether you’re analyzing proteins, designing nanosystems, or preparing presentations — is clearly communicating what you’re seeing. At the atomic and molecular scale, raw geometry and topology data can quickly become hard…

Making Light Nodes Work for You: A Guide to Visibility and Selection in SAMSON

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In molecular modeling projects, visualization is not just an aesthetic choice—it’s a critical part of understanding, analyzing, and communicating your results. Whether you’re fine-tuning the lighting of a molecular scene for publication, or preparing complex renderings for a presentation, managing…

A Simple Way to Visualize Protein Conformational Transitions in Seconds

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When exploring large-scale conformational changes in proteins, molecular modelers often face the same bottlenecks: visualizing smooth transition paths is time-consuming, and most available tools either require heavy computation or offer limited interactivity. This can slow down studies related to conformational…

Avoid Topology Errors in Molecular Dynamics: Renumbering Chains and Residues for Martinize2

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One of the most common but often underestimated sources of errors when preparing molecular systems for coarse-grained simulations is improper residue and chain numbering. This becomes especially important when working with multiple copies (or replicas) of a protein in a…

Cleaning Up Dozens of Protein Structures in One Go

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If you’ve ever worked with large sets of protein structures—from databases like the PDB or in-house experimental data—you already know how time-consuming the preparation step can be. Downloading structures, checking for missing atoms, stripping unnecessary molecules, adding hydrogens… doing it…

Avoid Common Pitfalls in Protein Docking: Setting Up Your System in SAMSON

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One of the most common pain points for molecular modelers starting with protein docking is the setup of the system. Performing docking without carefully preparing your molecular models can lead to wasted computing time and misleading results. If you’ve ever…

Quickly Filter Your Molecular Render Presets in SAMSON with These NSL Attributes

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Rendering molecular systems often involves combining clarity and aesthetic precision. In SAMSON, a powerful molecular design platform, users can assign different render presets to define how components are visually represented—whether it’s ribbons, surfaces, or atom spheres. But sorting or filtering…

Easily Animate Molecular Transformations Using Keyframes in SAMSON

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Creating animations of molecular behavior can be essential for illustrating dynamics, conformational changes, or transformations in chemical systems. However, many molecular modelers find this process time-consuming or difficult to control precisely. If you’re looking for a straightforward way to animate…