OneAngstrom – Page 115

Visualizing Molecular Transitions: Concealing Atoms Over Time

Presenting molecular transitions in a visual and understandable way is one of the common challenges molecular modelers face, especially during presentations or when generating animations for educational and research purposes. Complex structures often clutter the screen, making it hard to…

Easily Control What You See: Using the ‘visible’ Attribute in SAMSON NSL

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When working on complex molecular models, visual clarity is essential. Whether you’re trying to isolate a ligand, examine interactions, or prepare a clean visual for publication, quickly showing or hiding parts of a scene is a common need. SAMSON’s Node…

Why your molecular models lack depth (and how to fix it with ambient occlusion)

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When visualizing complex molecular systems in 3D, capturing depth and spatial relationships clearly is often a challenge. Have you ever looked at your protein or material structure and felt it looked flat or lacked realistic depth perception? If so, you’re…

Collaborating on Molecular Models with Shared Documents in SAMSON

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Working on molecular models often involves teams of researchers, spread across institutions and time zones. Sharing progress, simulations, and models efficiently — without versioning headaches or manual file exchanges — can be a challenge. This is where Shared Documents on…

Struggling to Load Your Molecular Data? Here’s How SAMSON Handles It.

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Whether you’re visualizing a protein-ligand complex or analyzing cryo-EM data, loading external molecular data is often the very first—and sometimes frustrating—step of your workflow. Inconsistent file formats, unsupported extensions, or partial loading of structures can make this simple task surprisingly…

Running Multiple Molecular Simulations at Once with GROMACS Wizard

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Setting up molecular dynamics (MD) simulations is often time-consuming, especially when you need to run many initial conformations of the same molecular system. For example, you might want to test different ligand poses, protein conformations, or results from docking, normal…

What’s Really Visible in Your Molecular Model? A Close Look at the `visible` Attribute

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When working on large and complex molecular systems, one common frustration for molecular modelers is managing visual clarity. Whether designing a nanosystem or analyzing simulation results, ensuring that only the relevant parts of the model are visible can dramatically impact…

Missed a Tool in SAMSON? Here’s How to Make Sure GROMACS Wizard Is Installed

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For molecular modelers who rely on powerful tools like GROMACS to perform simulations efficiently, it can be frustrating to realize that a crucial extension isn’t installed—or worse, to not even know it’s missing. If you’re using the SAMSON platform, ensuring…

How to Find Atoms Inside a Spatial Region in SAMSON

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When analyzing or simulating molecular systems, it’s often helpful to focus on a specific part of the structure. Whether you are calculating partial charges, analyzing solvent distribution, or preparing a local environment for docking or QM calculations, selecting atoms in…

Running Python Scripts Inside SAMSON: What You Need to Know

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If you’re working with molecular modeling and already using SAMSON, you might often find yourself juggling different tools just to run or tweak a Python script. But did you know SAMSON has native support for Python scripting? Whether you’re analyzing…