OneAngstrom – Page 199

Tracking Molecular Measurements Permanently with Labels in SAMSON

When modeling molecular systems, a recurring frustration among researchers is having to remeasure distances, angles, or torsions each time the system changes or is reopened. Whether you’re analyzing bond lengths after a minimization or monitoring torsion angles in a conformational…

A More Intuitive Way to Fix Outliers in Protein Models

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Refining protein structures can be inefficient when outlier residues fall outside allowed conformations in a Ramachandran plot. If you’ve ever opened a homology model or experimental structure only to see white dots far from the safe yellow zones, you know…

Tracking Ligand Motion with Center-of-Mass Pathlines

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Understanding how ligands move within and around proteins is essential for interpreting molecular dynamics simulations and gaining insights into unbinding mechanisms. However, with the large number of atoms and data points in simulations, the movement of the ligand as a…

Feeling Lost in Structure Prediction? Try AlphaFold-2 in SAMSON

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If you’re a molecular modeler working with proteins and struggling to generate accurate 3D structures from FASTA sequences, you’re not alone. Waiting for software installations, configuring environments, and handling compatibility issues can be a huge time sink. Fortunately, SAMSON offers…

Can’t See Your Labels? Understanding Label Visibility in SAMSON

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Have you ever added labels to atoms, residues, or molecules in SAMSON and suddenly found they weren’t visible any longer? This is a common situation, especially when zooming in and out or working with complex structures containing multiple hierarchical node…

Tidy Up Molecular Models with Chain Visibility Flags

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When working on complex biomolecular systems in SAMSON, clarity is key. Whether you’re visualizing protein-ligand interactions, preparing presentation materials, or just cleaning up a display for focused analysis, showing only specific chains in your molecular model can save time and…

Filtering Bonds by Length: A Practical Guide in SAMSON’s NSL

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When analyzing complex molecular systems, identifying bonds of specific lengths can be vital. Whether you’re refining a molecular structure, studying strain in a bond, or just verifying model integrity, being able to query and filter bonds by length saves time…

Keeping Atoms Still in Molecular Animations

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When crafting molecular animations, researchers often want to highlight movement in one part of a system while keeping another part still for clarity or comparison. For example, during a protein-ligand docking animation, you might want the protein to remain static…

Using Python Scripts in SAMSON: A Simple Way to Automate Molecular Modeling

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For many molecular modelers, one recurring challenge is the lack of flexible scripting capabilities in their software tools. Whether the goal is to extract custom properties, automate repetitive tasks, or prototype an analysis workflow, scripting support can often make the…

Visualizing Ligand Unbinding Paths with Energy Curves in SAMSON

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Understanding how a ligand dissociates from a protein binding pocket is a key question in many areas of molecular modeling and drug design. Once you’ve found potential unbinding paths, the next practical challenge is making sense of them—where does the…