OneAngstrom – Page 206

Focusing on Function: How to Align Specific Protein Regions for Better Structural Insight

When comparing protein structures, most tools default to full-chain alignment. But what if you’re only interested in specific regions, like active sites, functional motifs, or conserved helices? Aligning entire proteins can dilute meaningful structural comparisons in such cases. This is…

Speed Up Molecular Modeling with Attribute-Based Backbone Filters

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When building or analyzing complex molecular systems, molecular modelers often face a recurring challenge: identifying specific fragments such as backbones with particular properties—like charge, composition, visibility, and more—across vast datasets or large molecular assemblies. Manually browsing through molecular groups wastes…

Adding New Molecular Modeling Capabilities to SAMSON with Apps

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Molecular modelers often face a recurring challenge: integrating various tools and external workflows into a single streamlined environment. Whether it’s docking, simulation, or data analysis, moving between multiple software tools can slow down research and increase complexity. This is where…

Managing Note Visibility in SAMSON: How to Hide or Show Annotations Efficiently

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If you’ve ever worked on a complex molecular model in SAMSON, you know how important annotations—such as notes—can be. Notes are extremely helpful for adding context, reminders, or visual explanations for you and your collaborators. However, when the number of…

A Seamless Way to Add Backgrounds to Molecular Presentations

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When creating scientific presentations with molecular animations, one common challenge faced by molecular modelers is how to integrate context — such as presentation slides or background visuals — directly into the animation. Switching between external slide decks and SAMSON can…

A Visual Way to Show Molecular Disassembly for Presentations and Learning

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When preparing presentations or educational material with molecular models, one common challenge is: How do you clearly show the internal organization of a complex molecular structure? Whether you’re teaching protein assembly, preparing research visuals for a talk, or simply trying…

A Clearer View of Protein-Ligand Interactions: 2D Meets 3D

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When analyzing protein-ligand complexes, understanding non-covalent interactions—like hydrogen bonds, van der Waals contacts, and pi-stacking—can feel overwhelming in 3D alone. That’s where 2D interaction diagrams make a difference: they simplify complexity and help researchers interpret molecular details more clearly. Interaction…

When Less Is More: Concealing Atoms to Clarify Molecular Animations

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One common challenge in molecular modeling is how to clearly communicate structural changes or dynamic behaviors, especially when dealing with crowded molecular scenes. Important insights can be hidden in a cluster of atoms or overwhelmed by visual complexity. The Conceal…

How to Easily Customize Metallic, Transparent, and Emissive Materials in Molecular Models

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Creating molecular visuals that are both accurate and visually engaging is a common challenge among molecular modelers. While generating molecular structures can be straightforward, rendering them with materials that are scientifically meaningful—or simply aesthetically pleasing—can become time-consuming without the right…

Creating Lipid Bilayers Around Proteins in Minutes

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Preparing realistic molecular environments around membrane proteins can be a time-consuming task. Building lipid bilayers manually, aligning structures, avoiding bad contacts — this setup work often becomes the bottleneck before simulation even begins. If you’re using SAMSON, there’s a dedicated…