SAMSON Blog – Page 304

Quickly Define Custom Atom Groups for GROMACS Simulations in SAMSON

When setting up a simulation involving custom pulling forces in GROMACS, one of the first roadblocks many molecular modelers face is the creation of appropriate index groups. These groups are essential to define regions of interest in biomolecular simulations—whether you’re…

Quick ways to filter hidden and visible nodes in SAMSON with NSL

OneAngstrom

When working on complex molecular systems in SAMSON, we often deal with a multitude of objects: atoms, groups, models, data nodes, and more. Among these, property models define additional data on molecular systems, such as electrostatic potentials, surface properties, or…

A Simple Way to Visualize Molecular Rotation in Your Animations

OneAngstrom

Adding motion to molecular simulations can help communicate structural dynamics and emphasize specific interactions. One common need in molecular modeling is showcasing how a group of atoms or residues rotates in 3D space—whether for presenting conformational changes or emphasizing the…

Switching Views Without Losing Your Spot: Using Multiple Cameras in SAMSON

OneAngstrom

When working on complex molecular systems, modelers often need to switch between different spatial views—zoomed-in interactions, overall structure, or specific orientations. However, changing perspective often means losing track of a previously tuned camera view, and manually restoring it can be…

Taming Scenes: How to Identify and Work with Render Presets in SAMSON

OneAngstrom

When working on complex molecular models in SAMSON, visual clarity can quickly become a challenge. Whether you’re preparing a scene for publication, for collaboration, or simply managing multiple layers of molecular systems, you may find yourself needing to precisely control…

Quickly Share Molecular Models with Colleagues or Students Using SAMSON Documents

OneAngstrom

If you’re working in molecular modeling, you’ve probably been through the painstaking task of sharing files and simulations with collaborators: emailing attachments, using third-party storage platforms, managing access rights manually… not to mention syncing updates across multiple versions of the…

Stop Clicking, Start Searching: Selecting Molecular Structures with NSL

OneAngstrom

One of the most common points of friction for molecular modelers is efficiently selecting structures—like ligands, residues, or atoms—from large and complex molecular systems. If you’ve ever spent more time than you’d like manually clicking through molecules to highlight regions…

Quickly Filter Structural Models by Atom Counts in SAMSON

OneAngstrom

Molecular modelers often work with large, complex systems made up of multiple chains, molecules, and atoms. When managing dense structural data, it can become overwhelming to manually search, select, and manage folders that contain specific types or quantities of atoms.…

Why You Should Care About visibilityFlag When Animating Molecular Models

OneAngstrom

When working with complex molecular animations, one frequent challenge molecular modelers encounter is tracking which components of a structure are visible during different steps of the animation. Whether you’re creating educational visuals or exploring conformational changes, ensuring clarity in what’s…

Sketching Molecules in 2D with Full 3D Integration

OneAngstrom

When starting a molecular modeling project, it’s often easier to sketch a molecule quickly in 2D before diving into more complex 3D manipulations. But what if your 2D work could be instantly synchronized with a 3D viewport, allowing you to…