SAMSON Blog – Page 197

How to Handle Bond Changes Interactively Without Breaking Your Model

When building or modifying molecular structures, one of the most frequent roadblocks in molecular modeling is the difficulty of adapting molecular topologies on the fly. Typically, breaking bonds or introducing new connections means re-running perception algorithms or manually adjusting atom…

Fully Removing SAMSON from Your System: A Step-by-Step Guide for Every OS

OneAngstrom

Whether you’re reinstalling, switching systems, or simply cleaning up your workspace, fully uninstalling specialized software like SAMSON can sometimes be more than a simple drag-and-drop. Many users in molecular modeling mention lingering files or confusion regarding leftover directories, settings, or…

Walking Backward Through Molecular Trajectories in SAMSON

OneAngstrom

Molecular modeling often involves exploring how molecules transition from one conformation to another. These trajectories can contain vital insights about the stability and behavior of biological systems, materials, or reactions. But what happens when you want to focus not only…

Quickly Review Molecular Simulations in Reverse Using SAMSON

OneAngstrom

When working with molecular simulations, understanding a system’s behavior often requires going back and forth between different conformations or timepoints. Whether you’re reviewing docking animations, conformational transitions, or reaction paths, having precise control over the direction of playback can make…

Quickly Filter Conformations by Atom Count in SAMSON

OneAngstrom

When working with molecular systems in SAMSON, researchers often deal with complex models containing numerous conformations. A common challenge during analysis is identifying conformations based on specific structural features—such as the number of atoms. For instance, in simulations involving conformational…

Keeping Track of Cloud Simulations in Molecular Modeling

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Running molecular simulations in the cloud can save time and computational resources, especially when using tools like AlphaFold or GROMACS directly from SAMSON. But once you’ve launched your jobs, how do you stay organized? How do you check the progress,…

Working with Visibility Flags for Lights in SAMSON

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Managing complex molecular scenes in SAMSON can quickly become challenging when multiple lights are added for visualization. Lighting plays a crucial role in highlighting structural details, but keeping track of what’s visible — especially when debugging rendering settings — can…

A Quick Way to Build Protein Transition Paths Without Simulations

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Researchers often need to visualize or quantify conformational transitions in proteins. Whether you’re modeling domain movements, setting up umbrella sampling, or preparing steered dynamics, having a continuous path between two experimentally determined structures can save you time—and avoid launching time-consuming…

Struggling to Open Molecular Files? A Quick Guide on Adding Importers in SAMSON

OneAngstrom

Anyone who’s worked in molecular modeling knows the moment: you’ve found the perfect structure file online — maybe a .pdb, .mmtf, or a cube file — but your software doesn’t recognize the format. It’s frustrating, especially when you’re focused on…

Running GROMACS Simulations in the Cloud, Without the Headaches

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Setting up and running molecular dynamics (MD) simulations can be time-consuming and computationally expensive, especially for large systems or long simulations. Many modelers face hardware limitations on their local machines and end up spending hours managing dependencies or queue systems…