SAMSON Blog – Page 388

How to Tweak Just Part of a Molecule in SAMSON

When working with complex molecular systems, it’s not always necessary (or desirable) to optimize the whole structure. Whether you’re fine-tuning a ligand inside a binding pocket or just adjusting a fragment of a large biomolecule, minimizing only a specific region…

Avoiding Restraint Errors in NMR Minimization: How Molecular Restrainer Deals with Pseudoatoms

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Working with NMR-derived molecular structures often means handling NOE distance restraints that involve pseudoatoms—averaged positions typically used to represent equivalent hydrogen atoms. While helpful from an experimental perspective, pseudoatoms can become a bottleneck during structure refinement, especially when your modeling…

A Simple Way to Animate Molecular Trajectories in SAMSON

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Visualizing molecular dynamics or conformational changes often means working with complex trajectories. While such motion can reveal critical biological or chemical insights, turning a trajectory into a clear, smooth animation can become a time-consuming task. That’s where SAMSON’s Play path…

Running GROMACS in the Cloud: A Step-by-Step Workflow for Molecular Simulations

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Launching molecular dynamics simulations can be time-consuming and demanding on local machines, especially when working with large systems or when you want to stay productive while simulations run. Fortunately, if you’re using SAMSON, there’s a streamlined way to run GROMACS…

Quickly Find the Right Molecular Folders Using NSL Filters in SAMSON

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When working with complex molecular systems, SAMSON users often deal with large collections of structures organized into folders. These folders contain atoms, molecules, chains, and other entities that together define the models. As projects grow, identifying the right folders based…

Making Molecules Fade into View: A Simple Way to Enhance Molecular Presentations

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When presenting molecular systems, clarity and focus are everything. But when everything appears on screen at once, it often becomes hard to direct attention where needed. This is especially important in educational videos, presentations, or when preparing materials for grant…

Easily Target Camera Nodes Using NSL in SAMSON

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When working on complex molecular scenes in SAMSON, clarity is key. Whether you’re preparing a presentation, setting up multiple viewpoints, or scripting analyses, you often need to isolate and interact with camera nodes specifically. Unlike atoms or molecules, cameras have…

Stop Wasting Time on Broken Protein Structures: A Simple Guide to Preparing Protein Models in SAMSON

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If you’re working with experimental protein data, chances are your structure files come with imperfections: alternate locations, missing atoms, ligands you don’t need, or solvent cluttering your simulation. For molecular modelers, preparing the system properly is not just optional—it’s the…

Choosing the Right Symmetry Group in Large Molecular Assemblies

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When working with complex biological assemblies—like viral capsids or symmetrical protein complexes—one of the recurring challenges in molecular modeling involves identifying and exploiting symmetry. Symmetry helps reduce computational costs, validate structure quality, and guide the design of biomolecular nanostructures. But…

Why Running GROMACS on the Cloud Can Save You Time and Headaches

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If you’ve ever tried to simulate a large molecular system using GROMACS, you’ve probably run into limitations on your local machine. RAM usage, simulation time, or even GPU availability can quickly become bottlenecks. Fortunately, the GROMACS Wizard extension in SAMSON…