SAMSON Blog – Page 193

How to Select Terminal Residues in SAMSON with NSL

When analyzing biomolecular structures, it’s often essential to identify and isolate terminal residues—those at the ends of polymer chains, such as the N-terminal or C-terminal amino acids in proteins. Whether you’re preparing a system for simulation, cleaning up a model,…

Why Your Ligand Path Sampling May Be Failing (and How to Fix It)

OneAngstrom

Finding plausible ligand unbinding pathways in complex protein environments is a critical step in molecular modeling—but it can also be frustrating. Even with sophisticated tools, the system may return incomplete or biologically implausible results. One frequent pain point? The sampling…

Easier Than You Think: Adding and Removing SAMSON Extensions

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Many molecular modelers appreciate having specialized tools for specific simulations, from free energy estimation to advanced visualization techniques. But customizing your environment without wasting time or disrupting your scientific workflow can be a challenge. That’s where SAMSON Connect’s Extension Marketplace…

Facing Multiple Symmetries? Here’s How to Choose the Right One

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When working with large biological assemblies in molecular modeling, symmetry can unlock valuable speed-ups and insights. But with size comes ambiguity: large protein complexes often exhibit multiple plausible symmetry groups. If you’ve ever asked yourself “Which symmetry should I use?”,…

Why Can’t I See My Molecule? Understanding Hidden and Visible Nodes in SAMSON

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“Where did my structure go?” If you’ve ever worked on a molecular system in SAMSON and suddenly found that parts of your molecule seem to disappear or won’t respond to selection, you’re not alone. Visibility issues are a common source…

From Trajectory to Insight: Preparing Initial Conformations for Umbrella Sampling in SAMSON

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For molecular modelers seeking accurate free energy landscapes, Umbrella Sampling remains an essential technique. But before you can compute the Potential of Mean Force (PMF), the often overlooked bottleneck lies in one critical step: selecting meaningful initial conformations from your…

How to Limit the Search Space for Faster Protein Docking in SAMSON Hex

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One common challenge in molecular modeling is reducing protein docking times without compromising the quality of results. When you already have an idea of the binding site location, unconstrained searches can become unnecessary and slow. This blog post introduces a…

Avoid Email Chaos: A Better Way to Share Molecular Models and Results

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Collaborating on molecular modeling projects often involves exchanging simulation results, models, and notes with multiple colleagues. Unfortunately, sending files over email or juggling several cloud drives can quickly become chaotic: inconsistent versions, lost files, unclear permissions, and confusion over who…

Modeling Protein Replicas Faster with SAMSON’s Martinize2 Extension

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Creating coarse-grained models of large molecular systems often requires not one, but many replicas of the same protein. This is a common setup when studying aggregation, protein crowding, or behavior in complex environments. But preparing these systems—ensuring residue IDs don’t…

Quickly Select Molecules by Properties in SAMSON Using NSL

OneAngstrom

If you’ve ever managed large molecular systems, you know how time-consuming it can be to manually identify and select specific molecules based on their features. Whether you’re isolating potential drug candidates, preparing a molecular visualization, or analyzing a biomolecular complex,…