OneAngstrom – Page 150

Find Atoms That Matter: Filtering with Atom Attributes in NSL

If you’ve ever worked on a large molecular system, you likely faced this: you want to isolate atoms based on specific chemical or structural properties, but manual selection is tedious and error-prone. Whether you’re preparing a simulation or analyzing hydrogen…

Tired of flat-looking molecules? Material presets in SAMSON make a difference

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Creating visually clear and publication-ready molecular images can be a time-consuming process. Many molecular modelers struggle to find a balance between scientific accuracy and aesthetic quality. Flat-looking models can obscure important structural details or make figures harder to interpret, especially…

Finding Segments with Just the Right Composition

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When working with molecular models that include thousands of nodes, efficiently filtering and selecting parts of your system is essential. One recurring challenge for modelers is identifying molecular segments with specific atomic compositions—say, segments with high oxygen content, a fixed…

Making Molecular Animations Easier to Manage with Visibility Flags

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When working with complex molecular scenes in SAMSON, things can get cluttered fast. Molecules, annotations, trajectories, and even animations can pile up in a hurry—especially when you’re diving into systems with dozens or even hundreds of components. One common challenge…

Simplifying View Adjustments with the Pedestal Camera in SAMSON

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When working with molecular structures, especially in dense environments like biological macromolecular assemblies or complex materials, slight adjustments to the camera angle often make a significant difference in understanding spatial relationships. For example, viewing a protein complex from slightly higher…

Running Molecular Dynamics Simulations in the Cloud with GROMACS Wizard

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Running molecular dynamics (MD) simulations can be time-consuming and resource-intensive. Many researchers find themselves waiting on local machines for hours — if not days — for simulations to finish. Upgrading local hardware is not always an option, and institutional clusters…

Avoiding Topology Conflicts When Modeling Protein Replicas

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When setting up coarse-grained molecular dynamics (MD) simulations, many researchers seek to model systems with multiple identical proteins—often for crowding effects, comparative studies, or simulations of assemblies. A common challenge that arises during this workflow is how to correctly prepare…

Quickly Finding Conformations with Many Atoms in SAMSON

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One common task in molecular modeling—especially when working with large molecular datasets or complex simulations—is identifying which conformations meet certain structural criteria. For example, maybe you’re only interested in conformations that contain a large number of atoms. Manually searching through…

Making Sense of Animation Visibility in Molecular Models

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When working on molecular modeling projects involving animations—whether for simulations, presentations, or collaborations with colleagues—clarity and control over what you see and what you don’t are critical. But how do you programmatically control visibility, selection, and naming of animation nodes…

Installing Python Packages in SAMSON Without Leaving the Interface

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For many molecular modelers, scripting in Python has become a core part of their workflow. Whether you’re automating analyses, performing simulations, or applying data science tools, access to Python packages is essential. But managing packages—especially across different environments—can be frustrating.…