OneAngstrom – Page 69

Can’t open your molecular file? Here’s what to do

Molecular modelers often encounter a familiar frustration: you download a dataset from a database, receive a file from a collaborator, or export something new from your lab’s instrument software… only to find that your modeling platform can’t open the file.…

Easily Find Atoms, Residues, and More with NSL in the Document View

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Molecular modelers often work with complex structures containing thousands of atoms, residues, ligands, and other node types. Selecting the right subset of these nodes precisely and efficiently can be a challenge, especially during structure analysis, preparing simulations, or performing molecular…

Using Your Own GROMACS Installation in SAMSON: Why and How

OneAngstrom

Many molecular modelers rely on GROMACS to simulate molecular dynamics because of its flexibility, performance, and open-source nature. While integrative platforms like SAMSON offer out-of-the-box integration with GROMACS, a common need arises: what if your project requires a specific version…

Quickly Find Segments with Specific Molecular Properties in SAMSON

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When designing or analyzing biological macromolecules, one of the most time-consuming tasks is filtering or locating specific parts of your molecular model. For example, you might need to: Find all protein segments with more than 100 residues Identify RNA segments…

A Simpler Way to Show Molecular Disassembly

OneAngstrom

When presenting complex molecular mechanisms or structural transitions, molecular modelers often encounter a recurring problem: how to clearly communicate spatial changes without overwhelming their audience. Whether your goal is to demonstrate a protein’s binding interface or visually highlight subunit relationships,…

Quickly Filter Side Chains by Elemental Composition with NSL

OneAngstrom

When working with complex biomolecular structures, identifying specific subgroups—like side chains with a particular number of atoms or elements—can be time-consuming. Whether you’re analyzing reactive sites, searching for hydrophobic residues, or customizing visual representations, targeted selection is essential for efficient…

Quickly Find and Edit Render Presets Using NSL Filters in SAMSON

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When working with complex molecular systems, visual clarity is essential. Render presets in SAMSON—the integrative molecular design platform—help users control how molecular objects are displayed. Whether you’re comparing different visual styles or identifying specific render setups in a large workspace,…

Keeping Track of Molecular Geometry with Measurement Labels in SAMSON

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One challenge molecular modelers face regularly is documenting and tracking geometrical parameters—bond lengths, angles, and torsion angles—during interactive modeling sessions. Whether you’re refining structures manually, running minimizations, or preparing presentations, keeping these measurements visible and editable can be essential. In…

Making Molecular Models Fade In Gradually

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Scientific visualizations are essential to communicating complex molecular structures clearly. But for molecular modelers, a common challenge appears when presenting structures: how to smoothly make elements appear in a scene to emphasize specific spatial or temporal relationships? Sudden pop-ins can…

A Simple Way to Show Molecular Motion: Rotating Atom Groups Around Their Center

OneAngstrom

One of the most common needs in molecular modeling is to convey motion. Whether you’re presenting a molecular mechanism, visually inspecting orientation-dependent properties, or simply building educational or outreach material, showing the movement of molecular structures often works better than…