SAMSON Blog – Page 148

Smoothly Shift Your Point of View with the Pedestal Camera in SAMSON

In molecular modeling and design, visually exploring your system from different perspectives is often essential. Whether you’re preparing high-quality animations to showcase a particular biological phenomenon, or simply wish to inspect the vertical structure of a complex nanomaterial, moving the…

Filtering Molecular Models by Size and Composition with NSL in SAMSON

OneAngstrom

When working with complex molecular systems, one of the recurring challenges for modelers is quickly identifying molecules based on their size or composition. Whether you’re managing assemblies of proteins, ligands, small organic compounds, or even coarse-grained structures, manually selecting or…

Locked Views, Better Movies: Freezing the Camera in Molecular Animations

OneAngstrom

When creating animations in molecular modeling, one common frustration is unintended shifts in camera perspective. You carefully orient your structure, press play, and suddenly the molecule jumps or drifts—especially if you’ve been editing frames or adding content. This happens because…

Managing Cloud Jobs in SAMSON: A Practical Guide to the Job Manager

OneAngstrom

If you’ve ever run long molecular simulations or relied on machine learning models for structure prediction, you know that managing computational jobs—especially remotely—isn’t just a convenience, it’s a necessity. Whether you’re using AlphaFold, NVIDIA BioNeMo models, or GROMACS simulations through…

Why Geometry Optimization Matters: A Closer Look at FIRE Minimization in SAMSON

OneAngstrom

One of the subtle but recurring challenges in molecular modeling is achieving a structure that is not only plausible but also energetically stable. Whether you’re preparing a system for a simulation, refining a molecular model from experimental data, or prototyping…

Building Your Own Simulation Tools in SAMSON Without Starting from Scratch

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Molecular researchers and simulation specialists often hit a wall: they need a specific modeling or simulation tool, but it simply doesn’t exist yet – or at least not in the form they need it. What if you could build exactly…

Selecting Amino Acids by Polarity and Charge in SAMSON

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When working with protein structures, molecular modelers often need to quickly select specific types of residues. For example, you might want to highlight all acidic residues in a protein to study interactions with a positively charged ligand, or perhaps isolate…

Practical Tips for Filtering Chains by Residues and Segments in SAMSON

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Working with complex biomolecular structures can quickly become challenging when you’re dealing with large systems: proteins with multiple chains, cofactors, solvents, and more. One frequent need among molecular modelers is the ability to quickly isolate relevant parts of a structure.…

Easily Export Ligand Trajectories From Binding Paths

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When studying molecular interactions like ligand binding and unbinding, tracking the movement of specific atoms over time is often essential. Whether you’re preparing a reaction coordinate for free energy calculations or simply analyzing how a ligand navigates through a protein…

Make Molecular Structures Gently Appear in SAMSON Animations

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When creating molecular presentations or videos, one recurring challenge is helping viewers understand the step-by-step buildup of complex molecular structures. Rather than showing everything all at once—which can be overwhelming—it can be much more effective and pedagogical to have components…