SAMSON Blog – Page 4

A practical look at selecting node groups in SAMSON

In molecular modeling projects, it’s common to group elements—such as atoms, residues, or entire molecular domains—for better control and visualization. With larger molecular models, efficiently selecting and working with these groups can become cumbersome, especially if you need to apply…

Avoid This Common Pitfall When Preparing Proteins for Conformational Analysis

OneAngstrom

Before modeling transitions between protein structures or generating conformational pathways, there’s a crucial preparatory step that often causes trouble for even experienced users: ensuring your input systems are clean and connected. In SAMSON, failing to clean up your protein structures…

A quick way to find a color scheme that works for your molecular models

OneAngstrom

Choosing the right color palette is essential when building or analyzing molecular models, especially when attempting to convey complex information clearly. Whether you’re preparing figures for a scientific publication, explaining results during a presentation, or exploring molecular systems visually during…

Keeping Your Eye on the Action: Dynamic Focus with ‘Look at Atoms’ in SAMSON

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When simulating molecular systems, it’s easy to lose sight of the atoms you care most about. Molecules twist and turn, and regions of interest may drift out of view just when interactions start to get interesting. That’s where the Look…

Avoiding Errors in NPT Equilibration: How to Use the Right Input in GROMACS Wizard

OneAngstrom

Molecular dynamics (MD) simulations often involve long workflows composed of successive stages: minimization, temperature equilibration (NVT), pressure equilibration (NPT), production runs, and post-analysis. Each step builds on the previous one. However, a frequent frustration among modelers—especially those new to MD…

Why Can’t I Just Export to PDB? Tips for Managing File Formats in Molecular Modeling

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One of the small but surprisingly frustrating challenges in molecular modeling is moving files between different tools. Whether you’re preparing results for publication, sharing models with collaborators, or using a tool that only supports specific formats, you’ve probably found yourself…

When Pressure Matters: Stabilizing System Density with NPT Equilibration in SAMSON

OneAngstrom

One common challenge molecular modelers face lies in achieving a stable simulation environment after initial energy minimization and temperature equilibration. Even with a minimized system at the right temperature, unstable density can still derail longer molecular dynamics (MD) simulations. Fortunately,…

Speed Up Your Molecular Modeling: Filter Cameras in SAMSON with Precision

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When working on complex molecular scenes in SAMSON, it’s easy to accumulate multiple camera nodes—each representing different viewpoints, lighting setups, or visual documentation stages. But managing them efficiently can become challenging, especially when quickly switching perspectives or automating workflows. That’s…

From PDB to Motion: Visualizing Spike Protein Transitions in SAMSON

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Generating biologically meaningful motion pathways between molecular conformations—especially for large biomolecules—is a common challenge in structural biology and molecular modeling. When the structures differ in atom count or residue indexing, things can get especially tricky. If you’ve ever attempted to…

Tired of File Format Headaches in Molecular Modeling?

OneAngstrom

One of the most common frustrations scientists face when working with molecular modeling software is file compatibility. You find the perfect dataset online, but when you try to load it into your molecular modeling environment, you’re met with cryptic error…