Filtering Structures by Atom Count in SAMSON’s NSL

When working with complex molecular assemblies, one of the key challenges for computational chemists and molecular modelers is filtering out irrelevant parts of a structure to focus only on regions of interest. You might be looking at thousands of components…

Switching Selections Fast When Modeling Molecules

When working with complex molecular systems, switching between different parts of a model—like a ligand, a protein pocket, or solvent shell—can quickly become tedious. Imagine selecting a group of atoms, navigating to another component, and then needing to go back…

From Conformations to Clearer Pathways: A Quick Optimization Strategy

When modeling molecular systems, capturing the transition between two known structures—say, a ligand binding or unbinding event—often involves generating intermediate conformations. Although these conformations may be linearly interpolated or derived using dedicated algorithms like the Ligand Path Finder, they rarely…

Building Lipid Layers Around Proteins Without the Headache

Setting up simulations of membrane proteins often starts with a significant bottleneck: building a reliable lipid layer around a protein. This step is critical for many molecular modeling projects, from studying membrane protein dynamics to simulating lipid-mediated interactions. Yet, the…

A clearer way to filter node groups with NSL in SAMSON

In structural modeling projects, distinguishing specific parts of complex systems can often be labor-intensive. Molecular modelers frequently need to filter or classify different parts of their system—such as ligands, water molecules, or fragments—based on attributes or naming conventions. SAMSON’s Node…