OneAngstrom – Page 325

Quickly Find Structural Groups by Atom Count in Your Models

When building or analyzing large molecular systems, it can be a challenge to identify specific structural groups of interest — especially when dealing with hundreds or even thousands of groups. What if you want to isolate only those groups with…

Running GROMACS in the Background: How to Monitor Local Simulations with Ease

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When running molecular dynamics (MD) simulations, especially those that take time to compute, a common frustration among molecular modelers is not being able to track progress easily without interrupting their workflow. Whether you’re testing new force field parameters, prepping simulations…

Easily Select Visual Representations in SAMSON Using NSL

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A common task in molecular modeling involves managing the many visual representations of structures—especially when the scene includes numerous models like ball-and-stick, ribbon, or surface renderings. Being able to quickly isolate, hide, or modify these visual elements is essential for…

Working Late? Make Molecular Modeling Easier on Your Eyes with Dark Mode

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Many molecular modelers spend hours working with intricate structures, adjusting render settings, and preparing visuals for publications or presentations. If you’re someone who often finds yourself working in dim lighting or during evening hours, you’ve likely experienced some discomfort from…

Why Your Molecular Labels Look Off — And How to Fix It

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Labels are a critical part of molecular visualization — they help identify atoms, residues, molecules, and key spatial measurements. But if you’re a molecular modeler working in SAMSON and your Viewport looks cluttered or unclear, misaligned labels might be the…

Avoid This Common Mistake When Setting Up Protein Transitions

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One of the most frequent issues faced when interpolating between protein conformations is something many don’t anticipate: disconnected molecular structures. If you’ve ever encountered the error message “Cannot proceed because the structure does not make one connected component” while using…

Navigating Molecular Space: A Practical Guide to SAMSON Move Editors

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Precise control over molecular geometries is a core part of any modeling or simulation workflow. Whether you’re adjusting a ligand orientation, fine-tuning a molecular assembly, or preparing a structure for simulation, moving atoms and molecular fragments accurately is essential. This…

Quickly Identify Large Molecular Paths with NSL

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If you’ve ever worked with complex molecular systems, you probably know the frustration of having to search through large collections of molecular paths looking for the relevant ones. Whether you’re modeling conformations, analyzing structural dynamics, or filtering outputs, being able…

Quickly Explore Protein-Ligand Interactions in 2D and 3D with SAMSON

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Understanding how molecules interact at the atomic level can make or break a drug discovery or molecular design project. Yet, identifying and interpreting specific interactions—hydrogen bonds, steric clashes, aromatic stacking—can be tricky, especially when working solely in 3D. This is…

Quickly Hide or Find Notes in Complex Molecular Projects

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When working on complex molecular models, visual clutter can quickly become a problem. Notes are a convenient way to annotate models — whether to highlight important residues, describe reactions, or mark areas for collaboration. But as projects grow, managing these…