OneAngstrom – Page 251

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

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

OneAngstrom

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…

Keeping Focus While Molecules Move: A Simple Camera Trick for Better Trajectory Animations

OneAngstrom

When visualizing molecular dynamics, static snapshots don’t always capture the full story. Animations help, but they introduce a common problem: as atoms move along a trajectory, it’s easy to lose sight of the specific region or molecule you’re interested in.…

How to Simulate Defects in Diamond Structures Using SAMSON

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Defects play a major role in the properties of crystalline materials: they can influence conductivity, hardness, optical behavior, and more. Yet, modeling them can be time-consuming if you’re not equipped with the right tools. If you’re exploring how imperfections affect…

Why Your SAMSON Extension Might Not Load—and How to Fix It

OneAngstrom

When working on complex molecular models, nothing is more frustrating than launching your simulation platform only to find out that a crucial extension just won’t load. If you’ve ever experienced this problem while using SAMSON, the integrative platform for molecular…

How to find atoms near residues using NSL in SAMSON

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One of the most repetitive (and error-prone) tasks in molecular modeling is selecting atoms or groups of atoms located close to a residue, a ligand, or a functional group. Whether you’re preparing a simulation, inspecting an interaction site, or filtering…

Creating smooth molecular presentations with SAMSON’s Animator panel

OneAngstrom

Sharing scientific discoveries effectively often means going beyond static visuals. Molecular modelers today are increasingly asked to create engaging and clear presentations, whether for publications, teaching, or collaboration. One recurring challenge is: how to animate molecular scenes smoothly, without spending…