OneAngstrom – Page 283

Avoid Abrupt Cuts: Add Natural Pauses to Molecular Animations

Creating compelling molecular animations often means more than just stringing frames together. For many molecular modelers, one recurring challenge is how to effectively control the tempo of a presentation. Rapid transitions can overwhelm the viewer, especially when introducing complex conformations…

Split Your Molecular Animations Into Slides: A Simple Tip That Saves Time

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Creating presentations with molecular animations often involves showing complex processes in a clear, structured way. However, without control over the flow, animations can feel like watch-and-hope events. One common challenge molecular modelers face is how to build multi-part animations that…

Freezing Atoms to Minimize Just Part of a Molecule in SAMSON

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When modeling complex molecular systems, it’s common to want to optimize only a specific part of the system—say, a ligand binding site or a reactive region—without altering the rest of the molecule. Re-minimizing the entire structure each time can not…

Setting Up Umbrella Sampling Projects in GROMACS Wizard Without the Hassle

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Running umbrella sampling simulations in molecular modeling can be complex, especially when dealing with dozens of starting conformations and ensuring consistency across multiple simulations. One challenge that many molecular modelers face is setting up those initial conformations and defining simulation…

Cleaning Hundreds of Protein Structures in One Go: A Look at SAMSON’s Batch Protein Prepare Extension

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If you’ve ever worked with protein simulation pipelines, you know that preparing a clean structure is foundational—but incredibly repetitive when dealing with large datasets. Whether it’s removing water molecules, adding hydrogens, or fixing alternate locations, these tasks consume time that…

Quickly Select Molecular Backbones with Custom Attributes

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When working with large molecular systems, biological macromolecules, or custom-designed coarse-grained models, quickly identifying specific structural components based on their chemical and structural properties can be a challenge. Whether you’re preparing simulations, visualizing data, or extracting substructures, manually selecting regions…

Tired of Manually Styling Molecular Models? Try Visual Presets in SAMSON

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If you’re a molecular modeler, chances are you’ve spent a lot of time adjusting representations and color schemes just to get your visualizations to look right. From ribbons to atoms, VDW surfaces to chain coloring — great visuals often take…

Improving Clarity in Molecular Models: Managing Label Visibility in SAMSON

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When working with complex molecular systems, clarity is everything. Having the right labels—on atoms, residues, or entire molecules—can guide understanding and communication. But when you’re visualizing thousands of atoms, labels can quickly become overwhelming. Fortunately, SAMSON helps molecular modelers manage…

When to Make Molecules Disappear: Using the Hide Animation in SAMSON

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Sometimes, less is more—especially when creating animations to communicate complex molecular systems. If you’re working in SAMSON to design a molecular presentation or video, you might want certain molecules or nodes to vanish at key moments to maintain focus or…

Need to Revert? Here’s How to Install an Older Version of SAMSON

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As a molecular modeler, you might have experienced this situation: an update rolls out for your favorite modeling platform, and suddenly a plugin or workflow you depend on no longer works as expected. Or perhaps a collaborator is using a…