SAMSON Blog – Page 69

Exporting Protein Conformational Paths as 3D Trajectories in SAMSON

Understanding how a protein transitions between conformations is a key goal in structural biology. While computational tools for finding these paths exist, researchers frequently struggle with an important practical question: how can we export and visualize these conformational transitions in…

How to Turn Molecules into Monomers in SAMSON’s Polymer Builder

OneAngstrom

One of the most common challenges in molecular modeling lies in **polymer customization**. You might have specific monomer units you want to connect or test, but lack a visual, structured, and flexible way to define them before building full polymer…

How to Quickly Filter Cameras in Large Molecular Projects

OneAngstrom

When working with complex molecular scenes in SAMSON, it’s easy to lose track of your camera nodes. Especially in projects where multiple team members are defining views, capturing specific angles, or setting up animations, camera nodes can accumulate—and selecting or…

Avoid Topology Errors in MARTINI Coarse-Grained Models of Protein Replicas

OneAngstrom

When setting up coarse-grained (CG) molecular dynamics simulations using the MARTINI force field, one recurring roadblock for molecular modelers is handling multiple replicas of the same protein. Whether you’re modeling crowded cellular environments or testing multimeric assemblies, creating multiple instances…

Selecting Atoms and Residues in SAMSON with Natural Language

OneAngstrom

For molecular modelers working with complex biomolecular systems, selecting specific atoms, residues, chains, or regions in a structure can be tedious and time-consuming—especially when working with large systems. Traditional selection often requires navigating a tree of molecular nodes or writing…

Move an Atom. Watch the Simulation React in Real Time.

OneAngstrom

When working on molecular modeling, seeing immediate feedback from your simulation can make all the difference. Whether you’re adjusting geometries or exploring structural responses, waiting for batch simulations can slow down discovery and reduce intuition. This is where interactive simulation…

Selecting Initial Conformations for Umbrella Sampling Without Guesswork

OneAngstrom

Choosing the right initial conformations is a crucial step when preparing an umbrella sampling simulation with GROMACS. But what if there was a way to automate this process, visualize it in real time, and avoid manual frame selection from a…

When Your Molecules Move, Capture the Path

OneAngstrom

In molecular modeling presentations, showing how atoms move from one place to another can be just as important as the final result. Whether you’re simulating docking, rearranging atoms manually, or animating structural changes, being able to capture these transitions can…

Hidden or Just Invisible? Clarifying Molecular Presentation in SAMSON

OneAngstrom

When working on complex molecular systems, keeping your modeling environment organized and understandable is essential. As a molecular modeler, you’ve probably faced situations where your scene becomes cluttered with numerous elements, making it harder to focus on specific parts of…

Getting Unstuck: Faster Molecular Relaxation with FIRE

OneAngstrom

If you’ve ever found yourself watching a molecule slowly crawl towards equilibrium during a simulation, you’re not alone. Many molecular modelers start with raw or predicted structures and need to refine them before simulation. Geometry optimization is essential to remove…