OneAngstrom – Page 226

Quickly Find the Right Molecule Folders Based on Atoms, Charges, and More

If you’ve ever worked on complex molecular systems, you’ve probably run into this problem: hundreds or thousands of folders in a project, each one containing various structural models and atom groups. Locating the exact subset of structures you want to…

Fine-tuning Molecular Visuals in SAMSON: A Deep Dive into Rendering Preferences

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Visual clarity is crucial when studying molecular structures. Whether you’re presenting a molecular mechanism or investigating the details of a ligand-binding site, your visual output must aid — not hinder — understanding. Fortunately, SAMSON offers an extensive set of rendering…

Why Protein-Ligand Docking Fails: A Simple Check That Can Save You Hours

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Have you ever run a protein-ligand docking simulation, only to find that the ligand doesn’t bind correctly—or worse, doesn’t bind at all? 🤯 Before diving into docking parameters or refining your scoring function, consider this: the problem might lie in…

Easier Multi-Walled Carbon Nanotube Models in Minutes

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Creating accurate molecular models is essential in nanoscience, especially when working with complex carbon-based structures like carbon nanotubes (CNTs). Yet, constructing customized multi-walled nanotube models can be surprisingly time-consuming in many modeling platforms. If you’ve ever wished for a more…

Wrapping Proteins with Lipid Layers Using Molecular Box Builder

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Building realistic lipid environments around membrane proteins can be challenging and time-consuming. Ensuring proper orientation of the molecule, avoiding atom overlaps, adding buffer space… these steps often involve a patchwork of tools and manual adjustments that take hours—even before you…

Keeping Track of Molecular Distances: A Simple Labeling Tip That Saves Time

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When working with complex molecular systems, it is often necessary to repeatedly check specific distances, angles or torsion angles between atoms. However, a common frustration among molecular modelers is the need to re-measure these values after every view change or…

Keeping Everything in One Place: Embedding Files Inside Your Molecular Design Projects

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If you’re a molecular modeler juggling multiple tools, supplementary data, scripts, or even presentation figures, you’ve likely experienced the frustration of losing track of crucial files. Whether you’re preparing a publication, sharing a molecular model with collaborators, or switching between…

Easily Select Helices, Strands, and Loops in Molecular Models

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A common pain point for molecular modelers is the need to quickly select and manipulate secondary structure elements—like alpha helices, beta sheets, and loops—in large biomolecular systems. Whether you’re preparing a visualization, performing a simulation setup, or designing mutations, manually…

How note attributes help streamline molecular documentation

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For molecular modelers working with complex systems, keeping track of annotations within a project can be just as crucial as modeling structures and reactions. Whether you’re leaving comments for collaborators or marking specific components for further analysis, notes in SAMSON…

Making Atoms Appear Step-by-Step in Your Molecular Animations

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When presenting molecular designs or creating educational content, timing and visibility can make a big difference. Instead of overwhelming viewers with full molecular structures displayed at once, imagine revealing atoms and bonds gradually—highlighting the assembly or focus of a system…