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Quickly Modify Molecular Properties Using the SAMSON Inspector

When exploring molecular systems, molecular modelers often reach a turning point: they need to go beyond viewing and start editing atomistic properties. Whether for preparing simulations, constructing variants of a molecule, or cleaning up input data, changing a molecule’s internal…

Quick Presence, Quick Exit: Flash Animations for Molecular Storytelling

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When you’re designing molecular presentations, timing is everything. Whether you’re teaching, presenting to colleagues, or preparing a video abstract for a publication, manually toggling the visibility of molecular nodes can be time-consuming—and often results in jarring, unnatural transitions. This is…

One Motion, Many Snapshots: Saving Conformations Effectively in SAMSON

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When exploring molecular motions, one common challenge for modelers is how to effectively capture and reuse intermediate or final conformations. Whether you’re inspecting how a ligand access channel opens, or evaluating different configurations of a flexible loop, you often find…

Creating Custom Atom Selection Groups in GROMACS Using SAMSON

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When setting up a molecular system for simulation in GROMACS, atom group selections—known as index groups—play an important role in defining regions for restraints, analysis, and advanced sampling techniques like umbrella sampling. While GROMACS automatically generates standard index groups (e.g.,…

Improving Molecular Presentations with Background Transitions in SAMSON

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Crafting clear, visual molecular presentations often requires more than just beautiful molecules — context is important. If you’ve ever found yourself wishing your molecular animations could flow more smoothly between informational slides or contextual backgrounds, SAMSON’s Set background animation can…

Getting Structures into Place: Using Assemble Animation in Molecular Presentations

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When preparing molecular presentations, one frequent challenge is communicating spatial relationships without overwhelming the viewer with motion or detail. If a complex appears out of nowhere or its components aren’t clearly transitioning into place, the educational value can be diminished.…

When ChatGPT Writes Your Python Scripts for Molecular Modeling

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One of the most time-consuming and repetitive tasks in molecular modeling is scripting. Whether you want to automate structure manipulation, calculate properties, or build custom GUIs, scripting remains essential—but not always straightforward. For many users, the hurdles range from not…

Avoid Simulation Bugs: Know Which Nodes Are Actually Visible

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When building or analyzing molecular systems in SAMSON, it’s common to face unexpected behaviors: some atoms or structures might not be appearing in the workspace, or your scripts seem to be skipping parts of your model. Often, this is because…

Stop Manually Clicking: A Cleaner Way to Select Files in SAMSON with NSL

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Have you ever found yourself manually clicking through molecular models, trying to locate and select the right file nodes? If you’re spending too much time doing this, especially on large projects, there’s a better way. The Node Specification Language (NSL)…

No More Waiting: How to Run Molecular Simulations in the Cloud Without Overloading Your Computer

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Running molecular simulations can be incredibly resource-intensive. If you’re working with large systems, you might have faced the frustrating reality: your local machine simply can’t handle it. Or worse, trying to run the simulation slows your entire workflow down. 😓…