OneAngstrom – Page 292

Avoid This Common Pitfall When Generating Protein Transition Paths

When generating interpolated paths between protein structures, it’s easy to forget one crucial step—structure preparation. If your structures contain water molecules, ligands, or disconnected fragments, the As-Rigid-As-Possible (ARAP) interpolation tool in SAMSON may fail with the error: “Cannot proceed because…

Mapping Confidence in Predicted Protein Structures with AlphaFold-2 in SAMSON

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Predicting the three-dimensional structure of proteins is a common challenge in molecular modeling. Even with recent AI-based methods like AlphaFold-2, understanding the quality of predictions across a structure remains critical for interpreting results or deciding which regions of a protein…

Understanding Color Palettes in Molecular Visualization with SAMSON

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If you’ve ever struggled to interpret or share molecular models effectively due to unclear or inconsistent coloring, you’re not alone. Color plays a critical role in structure analysis—whether you’re trying to identify hydrophobic versus hydrophilic residues, distinguish chains, or highlight…

Creating Lipid Bilayers Around Proteins Without the Guesswork

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Building realistic molecular systems, such as protein–membrane complexes, is often a time-consuming and meticulous task in molecular modeling workflows. While several tools and techniques exist for assembling lipid bilayers, many require manual file editing or scripting, and often lack integration…

Struggling with Molecular Modeling Tools? Try This Built-In Guide in SAMSON

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Anyone who has ever worked on molecular modeling—whether you’re designing new drugs, simulating biomolecular systems, or analyzing protein-ligand interactions—knows that mastering a powerful platform like SAMSON can be a time investment. Even when surrounded by documentation and videos, it’s easy…

From Docked to Undocked: Visualizing Molecular Detachment with Ease

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If you’ve ever tried to explain or visualize how a ligand detaches from a receptor—or how components of a molecular system move apart during a simulation—you’ve probably encountered this common challenge: how do you create a clear, visually engaging animation…

Quickly Identifying Molecular Folders With Specific Structures in SAMSON

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Modeling complex molecular systems often involves navigating through large, layered hierarchies of folders in your design environment. If you’ve ever found yourself digging through countless folders in SAMSON trying to locate a structure with precisely 100 to 200 atoms or…

A Better Way to Animate Atoms: Avoid Rebuilding Scenes Frame by Frame

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If you’re working on molecular animations and tired of manually rebuilding scenes for every step, you’re not alone. Many molecular modelers struggle with creating smooth, reproducible animations that clearly communicate structural transformations or molecular motions over time. One recurring pain:…

A Simple Way to Select Atoms with Mathematical Precision

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Selecting specific atoms in large molecular systems can be time-consuming and error-prone—especially when working with complex structures like proteins, nucleic acids, or crystalline materials. If you’re a molecular modeler frustrated with manual selection tools or the limited filtering options in…

Protein folding in minutes: AlphaFold-2 predictions in SAMSON

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Predicting protein structures has long been a time-consuming challenge. Even with the advent of deep learning models like AlphaFold-2, integrating such powerful algorithms into your workflow can feel daunting. But what if you could launch an AlphaFold-2 structure prediction directly…