SAMSON Blog – Page 536

Gearing Up for Protein Transition Pathways: Setting Up Start and Goal Conformations in SAMSON

When studying large-scale protein motions or conformational changes, especially in enzymes or signaling proteins, it often becomes critical to trace plausible transition pathways between two experimentally observed or predicted conformations. But before you begin applying multiscale planning algorithms like ART-RRT,…

Filtering Render Presets Based on Name and Selection in SAMSON

OneAngstrom

When working on complex molecular scenes in SAMSON, efficiently managing rendering styles can make a big difference. Whether you’re switching between molecular representations, preparing figures, or comparing visualizations for various states of a molecular system, render presets help you save…

Controlling Access to Molecular Design Projects with SAMSON Connect

OneAngstrom

If you work in molecular modeling, you’re probably familiar with the challenge of sharing simulation data, structural models, or research documents securely and efficiently—especially when projects involve collaborators across different institutions or disciplines. SAMSON Connect provides a way to manage…

Making Molecular Structures Rock to Highlight Conformational Changes

OneAngstrom

When preparing molecular presentations or tutorials, it’s often important to draw focus to subtle structural changes in molecular assemblies. However, small conformational shifts can be difficult to notice—especially in large biomolecular systems. A simple technique that can make these changes…

How to Apply Pocket and Contact Restraints for Structure Prediction with Chai-1

OneAngstrom

When predicting biomolecular structures of complex assemblies, one common challenge is incorporating prior knowledge—such as known binding sites or residue interactions—into structure models. Without these constraints, automated prediction methods may miss critical interactions, especially in flexible systems. This is where…

Introducing Defects into Diamond Structures: A Simple CIF File Trick

OneAngstrom

When exploring the fascinating world of materials modeling, understanding how defects in a crystal impact its properties is a crucial step. Defects can significantly alter a material’s electrical, optical, or mechanical behavior, and modeling them accurately is central to many…

A Quick Way to Highlight Key Molecular Regions in Animations

OneAngstrom

When creating molecular animations, one common challenge is directing the viewer’s attention to a specific part of the system—like the binding pocket of a protein or an active site in a large molecular complex. Static shots often fail to convey…

How to export trajectories of specific atoms along protein transition paths in SAMSON

OneAngstrom

Working with protein conformational transitions often leads to a fundamental question after the paths are computed: How do I get the motion of specific atoms along a transition path? Whether you’re interested in backbone atoms, catalytic residues, or specific side…

Why Your Molecular Animation Keeps Shifting—and How to Fix It

OneAngstrom

If you’ve ever created a molecular animation and noticed that the camera seems to mysteriously drift between frames—even when you haven’t explicitly animated it—you’re not alone. This is a common issue molecular modelers face in visualization workflows, particularly when using…

Using the Ramachandran Plot to Spot and Fix Strained Residues Before Simulation

OneAngstrom

One common challenge in molecular modeling is verifying that a protein structure is ready for simulation. Even with high-quality data or carefully built homology models, strained residues can sometimes go unnoticed. These outliers can result in unstable simulations and inaccurate…