OneAngstrom – Page 57

Quickly Hide or Show Nodes in SAMSON Using NSL

Managing complex molecular scenes in SAMSON can be challenging, especially when dealing with large biomolecular assemblies or hierarchical structures. Often, molecular modelers want a quick way to hide some elements (e.g., water molecules, ligands, labels) or show only the parts…

From Clashing Atoms to Clean Docks: A Quick Way to Present Molecular Interactions

OneAngstrom

Anyone who’s built molecular presentations knows the challenge: how do you illustrate atoms or molecular groups smoothly docking into their target without manually keyframing every move? This is where the Dock animation in SAMSON becomes particularly useful. It provides a…

Keeping Molecular Projects Fully Portable with Embedded Files in SAMSON

OneAngstrom

One common concern among molecular modelers is project portability. Sharing project files with colleagues, collaborating across institutions, or simply switching workstations often brings up the familiar headache: missing dependencies, broken links, Python files misplaced, or data sets that didn’t make…

Avoiding Solvent Clashes in Coarse-Grained Simulations with GROMACS Wizard

OneAngstrom

When preparing a coarse-grained (CG) molecular system for simulations, a common frustration is the appearance of solvent clashes that can cause a simulation to fail. These clashes often originate during the solvation stage, especially for CG models using the MARTINI…

Easily Filter Molecular Structures by Formal or Partial Charge in SAMSON

OneAngstrom

One common task in molecular modeling is to quickly identify and filter structures based on their electrostatic characteristics—namely, formal and partial charges. Whether you’re working with charged ligands, simulating ionized states, or preparing systems for docking and dynamics, locating structures…

Let the Camera Do the Tracking While You Explore Molecular Motion

OneAngstrom

When studying molecular simulations, it can be frustrating to lose track of a molecule or region of interest as it moves during an animation. Maybe you’ve spent time perfectly positioning the viewpoint, only to have the target drift off screen…

A Simple Trick to Make Your Molecular Animations Feel More Natural

OneAngstrom

Creating clear and compelling molecular animations can be challenging, especially when you’re trying to smoothly follow a system across frames. One common issue molecular modelers face is making camera movements that feel natural and professional, especially when visualizing structural changes…

Get to the Point: Filtering Atom Attributes in SAMSON’s Inspector

OneAngstrom

When working with molecular structures, efficiency matters. Whether you’re adjusting positions or reviewing properties of atoms in bulk, you’re likely dealing with a flood of information. SAMSON’s Inspector is designed to help—but if you’re not filtering attributes, you might not…

Simplifying Molecular Animations: Controlling Keyframes in SAMSON

OneAngstrom

If you’ve ever tried to illustrate a molecular motion — a protein conformational change, a nanotube twist, or a docking transition — chances are you’ve faced the challenge of producing a smooth, realistic animation. You may have asked yourself: how…

Export Atomic Coordinates Along a Ligand Pathway: A Simple Way to Prepare Reaction Coordinate Files

OneAngstrom

Tracking the motion of molecules in a system can be crucial for understanding mechanisms like ligand binding and unbinding, conformational changes, or for generating reaction coordinate files in free energy methods. If you’ve been manually extracting coordinates along a path,…