OneAngstrom – Page 115

Struggling to Export Your Molecular Models? Here’s What You Might Be Missing

One common task in molecular modeling workflows is exporting structures or visualizations for use in other tools, sharing with collaborators, or inclusion in publications. Unfortunately, many users run into the same frustrating problem: they can’t find the export format they…

Keeping It Visible: Understanding Animation Visibility in SAMSON

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When working with complex molecular simulations in SAMSON, keeping track of what is visible — and when — is absolutely essential. Whether presenting your work, preparing visualizations for publications, or designing molecular sequences, clarity matters. This is where animation visibility…

Quickly Find Charged Groups in Your Molecular Model

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When modeling complex molecular systems, it’s often crucial to identify specific structural groups that carry a formal charge. Whether you’re studying ion-binding mechanisms, charge distributions, or preparing your system for electrostatics calculations, filtering for charged entities quickly can save you…

Quickly Toggle Label Visibility in SAMSON Using NSL

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When working with complex molecular systems in SAMSON, labels can become both essential and overwhelming. Whether you’re trying to annotate specific atoms, highlight interactions, or trace functional groups, label visibility plays a key role in clearly communicating your molecular model.…

Quickly Find Large Molecular Segments in SAMSON with NSL

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Identifying large biomolecular segments quickly can save time and reduce errors, especially during molecular editing, visualization, or simulation prep. Whether you’re selecting protein domains, isolating specific chains, or filtering data before analysis, there’s a faster way with SAMSON’s Node Specification…

Visualizing the SARS-CoV-2 Spike Protein in Motion: A Resource for Molecular Modelers

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One of the frustrating challenges in molecular modeling is understanding and simulating large conformational changes in biomolecular complexes. For researchers working on viral mechanisms or drug discovery, visualizing the conformational transition of key viral components—such as the spike glycoprotein on…

Getting Polymer Sequences Right: A Practical Guide for Molecular Designers

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Designing complex polymers from scratch can be a rewarding yet error-prone task. A common challenge faced by molecular designers is managing repeat units (monomers) and their connections, especially when diverse bond types and large polymer chains are involved. If you’ve…

Instant Structure Refinement: Edit Dihedral Angles Directly with the Interactive Ramachandran Plot

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Refining protein structures can be a subtle and time-consuming process. One of the common challenges molecular modelers face is fixing residues with unfavorable conformations before running simulations. A residue that slightly deviates from a stable region in Ramachandran space can…

Quickly Reveal and Hide Atoms in Your Molecular Animations with Flash

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Creating molecular animations often involves showing or hiding specific atoms, residues, or molecular structures across time. But if you’re changing visibility in a manual, step-by-step process, it can quickly become tedious—especially if you’re trying to time these changes precisely in…

Keeping Track of Your Cloud Simulations with SAMSON’s Job Manager

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Running molecular simulations in the cloud can be an efficient way to access high-performance computing resources, but staying organized and in control of your calculations is another matter entirely. If you’ve ever struggled to manage multiple job states, find your…