OneAngstrom – Page 89

Tired of Writing Custom Parsers? How Importers Can Save You Hours

If you’re a molecular modeler, you’re probably no stranger to file format frustrations. Whether it’s a legacy format from a colleague, or a PDB file with just enough quirks to make standard tools fail, turning file data into usable molecular…

Quickly Find Molecular Subsets in SAMSON with Folder Attribute Filters

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When working with complex molecular systems in SAMSON, structure organization often becomes a challenge. Projects can contain thousands of atoms, dozens of molecules or chains, and rich hierarchical folders. If you’ve ever found yourself toggling through folders trying to isolate…

From Chaos to Structure: Easily Animate Molecular Assembly

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When creating molecular animations, showing how parts come together can be just as important as showing structure or function. Whether you’re preparing educational content, a presentation, or a research video, it’s often useful to illustrate how a complex molecular system…

Animating Molecular Pulses: A Simple Way to Clarify Transient Structures

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In molecular modeling, one persistent challenge is effectively conveying how structures transiently appear and disappear during processes like docking, folding, or dynamic transformations. Researchers often want to emphasize certain regions of a molecular system momentarily — perhaps to draw attention…

Quickly Select the Right Molecules: Using Attribute Filters in SAMSON

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When dealing with large molecular systems in SAMSON, selecting just the right subset of molecules for analysis or simulation can quickly become overwhelming. Suppose you’re working with a structural model containing hundreds of molecules and you only want to isolate…

When Molecules Fade In: Creating Smooth Appearance with the Appear Animation in SAMSON

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Molecular modelers often create presentations to convey the structure and function of molecules. But when complex systems are revealed all at once, audiences can easily become overwhelmed and miss key details. That’s where animation – specifically, progressive visibility – can…

Writing Smart Atom Selection Scripts for Molecular Modeling

OneAngstrom

Working at the atomic scale often means navigating through an overwhelming number of atoms, chains, and residues within complex structures. A recurring pain for molecular modelers is selecting the right subset of atoms from larger structures — for analysis, editing,…

Adding Pauses That Matter in Scientific Animations

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When communicating the results of molecular modeling workflows, animations play a key role. They help convey complex transitions, mechanisms, and structural changes in a clear and engaging way. However, one simple but often overlooked issue is control over timing: how…

Controlling the Camera: A Practical Guide to Dolly Effects in Molecular Animations

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One of the challenges molecular modelers often encounter is clearly communicating spatial relationships and subtle structural changes in their simulations. Whether you’re preparing a research presentation or an educational video, getting the camera movements just right can significantly impact the…

Planning Your Simulation Space: How to Define the Periodic Box for COM Pulling in GROMACS Wizard

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When setting up molecular dynamics simulations involving pulling—like center-of-mass (COM) pulling—it’s easy to overlook a crucial step: properly defining the simulation box. Yet, neglecting this may lead to artifacts caused by interactions with periodic images of the pulled molecule. If…