OneAngstrom – Page 66

Working Smarter with Visual Model Visibility Flags in SAMSON

If you’ve ever opened a molecular model in SAMSON and found yourself overwhelmed by a cluttered workspace, you’re not alone. When dealing with complex assemblies, visual noise can slow down your analysis and make focusing on specific components more difficult.…

Quickly Identify Specific Files in SAMSON Using NSL

OneAngstrom

In large molecular modeling projects, keeping track of different data files can quickly become overwhelming. When you’re dealing with networks containing hundreds or thousands of files and nodes, being able to rapidly locate, filter, or select specific types of files…

Reducing Eye Strain While Modeling Molecules in SAMSON

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Long hours spent working on molecular structures can be visually demanding, especially when navigating intricate 3D models and data-rich interfaces. If you’re a molecular modeler using SAMSON, you might have experienced eye fatigue, particularly in low-light environments or during evening…

Making Molecules Fade Away: When and How to Use the Disappear Animation in SAMSON

OneAngstrom

Controlling the visibility of molecular structures during animated presentations is useful — and sometimes essential — in molecular modeling and communication. One common challenge modelers face is creating a smooth visual transition to hide parts of a complex system without…

Residue Outliers in Protein Models? Here’s a Fast Way to Detect and Fix Them

OneAngstrom

When building or refining protein structures—whether from experimental data, homology modeling, or simulations—one common challenge is spotting conformational outliers that may introduce artifacts in downstream analyses. A residue that strays too far from allowed dihedral angles can destabilize simulations, distort…

Easier Structure Alignment in Molecular Modeling: A Visual, Click-Based Approach

OneAngstrom

Repositioning molecules is one of those routine tasks that can quickly become a bottleneck in molecular modeling workflows. Whether you’re preparing a simulation system, organizing figures for a presentation, or simply exploring molecular interactions, aligning structures precisely and efficiently is…

From Closed to Open: Animating the SARS-CoV-2 Spike with SAMSON

OneAngstrom

When modeling protein structures, especially those involved in viral entry mechanisms, capturing their motion from one functional state to another is often challenging. For molecular modelers investigating SARS-CoV-2 or designing therapeutics targeting protein conformations, having access to a visual and…

Tracking Molecular Motion: A Simple Way to Keep Your Focus on Atoms

OneAngstrom

When working with molecular dynamics simulations, one of the common challenges is maintaining a clear view of specific parts of a system as they evolve over time. Whether you’re following a ligand binding to a receptor, monitoring a conformational change,…

Avoid GRO File Confusion: Smarter Input Management with GROMACS Wizard

OneAngstrom

Preparing input files for molecular dynamics (MD) simulations can often feel more complicated than the simulations themselves. If you’ve ever found yourself re-tracing project folders to locate the right .gro file after energy minimization, you’re not alone. This post focuses…

Quickly Filter Molecular Animation Nodes by Visibility in SAMSON

OneAngstrom

When working with large molecular systems and complex animations in SAMSON, clarity and focus are key. A common challenge for molecular modelers lies in quickly identifying which animation nodes are visible and which are hidden, especially when juggling multiple animation…