SAMSON Blog – Page 35

Fine-tuning Molecules in SAMSON: How to Quickly Edit and Customize Analogs

When working on lead optimization or virtual screening in molecular design, it’s common to generate multiple analogs of a candidate molecule. But once you’ve created these potential variants, how do you efficiently refine, edit, or investigate them without leaving your…

Quickly Select and Control Chain Visibility in Molecular Models

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When working with complex biomolecular systems, it’s common to navigate and manipulate multiple chains alongside other structural groups. Whether you’re preparing publication-quality visuals, analyzing specific interactions, or just trying to declutter your scene, being able to selectively show or hide…

A Clearer Story: Gradually Revealing Atoms in Molecular Animations

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When illustrating complex molecular systems, the way you present your data can make a big difference. Whether you’re explaining interactions within a protein or visualizing assembly processes in a material, clarity matters. One common problem modelers face is how to…

Take Full Control of Molecular Presentations by Stopping at Key Frames

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When you’re preparing a molecular animation to explain your research, showcase a protein-ligand interaction, or present a simulation workflow, timing is everything. A smooth animation is great—but what if you want to pause and provide more context, discuss a mechanism,…

Why Saving Molecular Structures Isn’t Just ‘Save As’

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When working on molecular simulations, structural predictions, or drug design pipelines, you often find yourself needing to export your molecular models for use in other tools. Whether it’s to share your structure with colleagues, analyze it with a different software,…

Spotting the Right Render Preset in SAMSON Using NSL

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When working with complex molecular models, keeping track of how elements are displayed can become challenging. Whether highlighting active sites, customizing visual styles for presentations, or debugging display issues, efficiently selecting and manipulating render presets is key to productivity when…

Struggling to Export Your Molecular Models? Here’s What You Can Do

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If you’re a molecular modeler working with multiple tools and file formats, you’ve probably bumped into this common issue: exporting your models in the right format for a collaborator, a publication, or a specific simulation package. Whether you need .pdb…

Solvation Tips for Coarse-Grained Systems: Avoiding Pitfalls with Martini Water

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One of the trickiest steps when setting up a coarse-grained (CG) system for molecular dynamics (MD) simulations is solvation — especially when using popular CG force fields like Martini. A common frustration among researchers is finding out, only after running…

Making Your Molecular Projects Portable: Embedding Files and Folders in SAMSON

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One constant challenge in molecular modeling is project portability. Whether you’re collaborating with colleagues, moving projects across machines, or preparing simulations for publication, keeping everything together can be frustrating. Files often get separated, paths break, or dependencies go missing. Fortunately,…

Visualizing Molecular Motion in Reverse Can Clarify Hidden Transitions

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When analyzing molecular simulations or transitions between conformations, understanding the complete trajectory—including its reverse—can offer essential insights. While most users typically examine forward motions, playing animations in reverse can reveal details such as intermediate conformations, relaxation events, or path symmetries…