SAMSON Blog – Page 236

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

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…

A Closer Look at the Sequence View in SAMSON: Why It Can Save You Time

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For structural biologists and molecular modelers, the frustration of navigating complex macromolecular systems is all too familiar. You often know the residue or chain you need to focus on—but shifting through a crowded 3D visualization can be tedious and inefficient.…

Write and Run Molecular Scripts Directly in SAMSON’s Code Editor

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When working on complex molecular modeling tasks, Python scripting can save hours of repetitive work. However, switching between external editors, terminals, and visualization platforms often breaks your workflow and makes it harder to test and debug scripts on the fly.…

Easily Managing What You See (and Don’t See) in Property Model Nodes

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One of the common challenges molecular modelers face is managing complex scenes filled with numerous nodes — atoms, molecules, property models, and materials. A cluttered viewport can slow down analysis, impact rendering performance, and simply make it harder to focus.…

Avoid setup mistakes: how GROMACS Wizard auto-assigns the MARTINI force field

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When preparing coarse-grained (CG) molecular dynamics simulations with the MARTINI force field, many modelers spend time double-checking whether they’ve configured the correct parameters and files. One small but frequent pitfall is using a CG topology—often from Martinize2—but forgetting to assign…