SAMSON Blog – Page 73

Quickly Explore Molecular Variants by Replacing Functional Groups

One of the most common challenges in molecular modeling today is exploring how small, strategic changes in chemical structures can affect properties like binding affinity or biological activity. If you’ve ever wanted a fast and visual way to generate and…

Precise Molecular Arrangements: Making the Most of Snapping in SAMSON

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When working with molecular models, precision matters. Whether you’re aligning atoms for structural comparison, assembling molecules symmetrically around a core, or preparing a visualization for publication, even slight errors in position and orientation can impact your results significantly. One common…

More Than Hide: A Smoother Way to Make Molecules Disappear in SAMSON

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When you’re preparing molecular animations for presentations, publications, or educational purposes, the goal is often to guide attention without overwhelming your audience. A common frustration for molecular modelers is the crude nature of traditional atom or structure removal — objects…

A practical look at selecting node groups in SAMSON

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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

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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

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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

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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

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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,…