OneAngstrom – Page 182

Selecting Atoms with Mathematical Precision in SAMSON

If you’ve ever tried to isolate a specific subset of atoms in a complex molecular structure for visualization, simulation, or manipulation, you know how time-consuming and frustrating it can be. Manual selection becomes inefficient very quickly. Whether you’re targeting a…

Keeping Your Focus: How to Animate the Camera to Follow Selected Atoms Without Moving the Viewpoint

OneAngstrom

When analyzing molecular simulations, it’s often crucial to focus on a specific part of your system — a binding site, an interface, or a reactive center — as atoms move through time. But there’s a common frustration: if you want…

What Happens After You Click ‘Simulate in the Cloud’?

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Running molecular dynamics (MD) simulations can be time-consuming and compute-intensive — especially on large biomolecular systems. Molecular modelers frequently face the challenge of limited local computational resources. And while high-performance computing facilities are an option, they often involve complex setup…

Tired of endless clicking? Select molecules in SAMSON with precision using attributes

OneAngstrom

Anyone who’s worked with large molecular systems in SAMSON knows that identifying and selecting specific molecules based on their properties can quickly become tedious. If you’ve ever found yourself manually seeking out molecules with a certain number of residues, or…

Rewinding Molecular Paths: A Practical Guide to Reverse Trajectory Playback in SAMSON

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Analyzing molecular simulations often means reviewing complex motions over many frames of a trajectory. For modelers studying folding patterns, automated docking, or multistep reactions, reviewing these paths backward can reveal behavior that is missed in typical forward playback. If you’ve…

Easily Find Molecular Conformations with a Specific Number of Atoms

OneAngstrom

When working with large molecular datasets, especially during simulations or conformational analyses, it often becomes crucial to filter and identify specific conformations based on simple yet decisive properties like the number of atoms. If you’re building workflows in SAMSON, the…

How to Build a Lipid Layer Around a Protein in SAMSON

OneAngstrom

When setting up molecular dynamics simulations, embedding a protein within a lipid membrane can be time-consuming and error-prone. Whether you’re studying membrane proteins, simulating transmembrane transport, or modeling realistic biological environments, creating these lipid environments from scratch often requires multiple…

Visualizing Crystal Defects in Diamond: A Straightforward Guide

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If you’re working in materials science, computational chemistry, or crystallography, you’ve probably run into the challenge of understanding how atomic defects influence crystal properties. Whether you’re studying mechanical strength, thermal conductivity, or electronic behavior, point defects—like vacancies or substitutional impurities—can…

Why You Might Be Missing Key Interactions by Not Filtering with Bond Types in NSL

OneAngstrom

When analyzing molecular structures, it’s easy to get lost in atoms and forget that the bonds connecting them are just as critical. Bond types strongly influence molecular behavior, from conformations to reaction mechanisms. Yet, many modelers ignore this during search…

Organizing Complex Molecular Projects with SAMSON’s Document View

OneAngstrom

Working on complex molecular systems often means managing numerous components: multiple protein structures, ligands, solvents, ions, and various annotations or scripts. This complexity can quickly become overwhelming, especially when switching between tasks or sharing projects across teams. This is where…