OneAngstrom – Page 10

When Less is More: Concealing Atoms to Clarify Molecular Mechanisms

Complex molecular structures often overwhelm audiences when presenting biochemical mechanisms or molecular simulations. Showing every atom and bond might be accurate, but it quickly becomes counterproductive if the viewer can’t follow what’s happening. This is a challenge many molecular modelers…

Avoiding Input Errors in GROMACS Equilibration: A Quick Guide to Selecting Structures

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If you’ve ever run into issues at the start of an equilibration step in GROMACS, you know how frustrating it can be to realize that the problem was simply an incorrect input file path or format. This is particularly common…

Making Fragments Fit: A Closer Look at Orienting Molecular Fragments in SAMSON

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When building complex molecular models, one of the recurring challenges is aligning functional groups or fragments precisely and efficiently. Incorrect orientation can result in steric clashes, unrealistic geometries, or simply more work adjusting everything afterwards. If you’ve ever tried rotating…

Tweaking the Universal Force Field: Customizing Typization in SAMSON

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Molecular modelers often encounter situations where automated force field parameters don’t perfectly match their specific chemical systems. Default atom types or bond orders might not reflect the intended structure, especially in complex or unusual molecules. In SAMSON, this is addressed…

Model Fade In, Fade Out: Animating Molecular Structures with Pulse

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One of the challenges in molecular modeling and presentation is directing the attention of your viewers. Whether you’re teaching a class, giving a talk, or recording a video, clearly visualizing molecular processes—especially the dynamic ones—can be difficult. Enter the Pulse…

Effortlessly Navigate Molecular Design Changes with Undo and Redo

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One of the most common frustrations in molecular modeling arises from accidental changes, experimental edits that don’t pan out, or simply wanting to compare different model states. For molecular modelers working on complex structures, reverting changes isn’t just a nice-to-have—it…

Quickly Find and Hide Labels in SAMSON Using NSL

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When working on complex molecular models in SAMSON, the visualization can quickly become cluttered—especially when labels pile up. Whether you’re labeling specific atoms, groups, or molecular fragments, having too many visible labels can detract from what you’re actually trying to…

Tired of Static Molecular Presentations? Here’s a Simple Way to Add Motion

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When trying to communicate molecular structures and processes effectively, nothing conveys spatial relationships and dynamics better than motion. Yet, many molecular modelers still present their work using static snapshots, missing the opportunity to make insights more intuitive and memorable. Fortunately,…

Quickly Spot the Right Molecular Chain with NSL’s Chain Attribute Filters

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When exploring or refining large biomolecular systems, molecular modelers often face the frustrating challenge of navigating through numerous chains trying to isolate just the ones relevant to their study. Whether you’re interested only in chains with a high number of…

Lock the View Without Disruptions in Your Molecular Animation Workflow

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When creating molecular animations in SAMSON, one common challenge that modelers face is keeping the camera viewpoint consistent throughout specific segments of the animation. This is particularly frustrating when you’re trying to highlight subtle conformational changes or focus attention on…