OneAngstrom – Page 121

Turning Molecular Animations into Slide-Like Presentations with the Stop Animation

For many molecular modelers and scientific presenters, creating impactful animations of molecular mechanisms or simulation results is a crucial part of communicating their work. But there is often a key element missing: control. In traditional presentations, slides let you decide…

Quickly Control What You See: Managing Animation Visibility in SAMSON

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If you’ve ever worked on complex molecular systems where multiple animations coexist—conformations, simulations, or visual transitions—you’ve probably encountered an all-too-familiar dilemma: how do I quickly hide or show specific animation elements without manually toggling through a long list of nodes?…

How to Speed Up Protein-Ligand Structure Predictions with Assigned Methyls

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When working with complex protein-ligand systems in solution, one of the biggest bottlenecks in using Nuclear Magnetic Resonance (NMR) data—especially for integrative modeling—is the time it can take for structure prediction tools to evaluate all possible methyl group combinations. If…

How to Improve Depth Perception in Molecular Models Without Additional Software

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Visual clarity is a recurring challenge in molecular modeling. When working with complex structures—particularly in 3D—being able to intuitively grasp spatial relationships between atoms and molecules can significantly improve understanding and communication. Whether you’re preparing publications, creating teaching materials, or…

Selective Water Removal Before Simulations: Avoiding the Common Pitfall

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When preparing a biomolecular system for simulations in GROMACS, one common step is to remove water molecules from the structure. However, indiscriminately deleting all water can lead to the removal of functionally important or tightly bound waters, especially those located…

Breaking and Creating Bonds in Real Time During Molecular Modeling

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One persistent challenge for molecular modelers is the need to rebuild molecular topologies every time structural changes occur. Whether you’re exploring reaction pathways, molecular docking, or simply correcting a bond type, switching between building mode and simulation mode can disrupt…

Quickly Select Protein Chains by Size with NSL

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When working with large biomolecular structures, one common challenge for molecular modelers is quickly identifying and selecting specific protein chains based on their attributes — for example, their number of residues. Whether you’re preparing a system for simulation, simplifying a…

Making Your Molecular Workflows Portable with Embedded Python Scripts in SAMSON

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Sharing reproducible, working molecular models with others—students, colleagues, or collaborators—can be a challenge when your workflow depends on multiple scripts, data files, or third-party tools. How often have you sent a Python script over email or GitHub, only to have…

How to Select Nearby Atoms and Residues in SAMSON Using Proximity Operators

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When working with molecular models, it’s often crucial to examine which atoms or residues are near a specific site of interest. Whether you’re studying binding pockets, analyzing molecular interactions, or inspecting local environments, being able to precisely select nearby nodes…

Focusing on the Right Spot: How to Zoom Without Losing Your Target in Molecular Animations

OneAngstrom

When presenting molecular systems, especially in animations, clarity of focus can make all the difference. Whether you’re creating a visual explanation for a complex biomolecular interaction or preparing insightful imagery for publication or teaching, the ability to zoom smoothly into…