OneAngstrom – Page 114

Struggling with molecular file formats? Here’s how SAMSON handles them.

One of the first technical hurdles many molecular modelers face when working with new tools is simply getting their data into the platform. This pain is universal: a structure from the Protein Data Bank, electron microscopy results, quantum simulation outputs…

Filtering molecules by composition with NSL: A guide to atom count attributes

OneAngstrom

Molecular modelers often work with large datasets of molecules, ranging from small organic compounds to complex proteins. In such workflows, it’s common to filter molecules based on their composition: whether they contain a certain number of carbon atoms, nitrogen groups,…

Stop Copy-Pasting Scripts: Embed Python Apps Directly Into Your Molecular Models

OneAngstrom

Have you ever shared a molecular model with a colleague or a student, only to realize later that the associated analytical Python code or visualization script didn’t make it across? Or maybe your research notes, simulation workflow, and data were…

Making Sense of Molecular Visibility in SAMSON’s NSL

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When working with complex molecular assemblies, clarity is key. Visual clutter can quickly become overwhelming when your workspace contains hundreds—or even thousands—of molecular structures, segments, or chains. If you’ve ever wished you could filter or selectively focus on visible molecules…

What if your molecule looked back at you?

OneAngstrom

One of the most common challenges in molecular modeling is presenting complex structures in a clear and engaging way. Whether you’re preparing a presentation, teaching a concept, or just trying to show the result of your work, the ability to…

Quickly Find Charged Structural Groups in SAMSON Using NSL

OneAngstrom

When modeling complex molecular systems, knowing which parts of your structure carry a net charge is essential. Charged regions can determine interactions with solvents, ligands, and other biomolecules, and they often play a central role in binding and reactivity. But…

Quickly Visualize Protein-Ligand Interactions After Docking in SAMSON

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Understanding how a ligand interacts with a receptor at the molecular level is vital in structure-based drug design. After running docking simulations, it’s often difficult to visualize results effectively, especially in complex molecular systems with multiple atoms and chains. If…

Ways to Select Paths by Atom Count in SAMSON

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When working with complex molecular systems, it’s often necessary to focus on specific entities depending on their characteristics—for instance, filtering out molecular paths that meet a certain level of structural detail. If you’re using SAMSON and dealing with large conformational…

When and Why to Use Your Own GROMACS Version in SAMSON

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If you’re a molecular modeler using GROMACS for simulations, you probably know how important reproducibility and computational optimization can be. While SAMSON’s GROMACS Wizard comes bundled with a recent GROMACS version ready for cloud and local jobs, there are cases…

Managing Custom Monomers in SAMSON’s Polymer Builder: A Practical Guide

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Designing polymers with specific properties often requires assembling them from custom monomers rather than relying on predefined sets. Whether you’re exploring new biopolymers, studying conjugated systems, or building molecular scaffolds for simulation, the ability to define and reuse your own…