SAMSON Blog – Page 189

How to Define Reactive Sites for Analogue Generation Using SMARTS Patterns

When designing new molecular analogues, chemists often wonder: Which part of the molecule should I modify to explore new activity profiles? In early-stage drug design, this is one of the most frequent roadblocks. If you’re interested in systematic molecular modification,…

Quickly Identify Complex Paths in Large Molecular Models Using NSL

OneAngstrom

When working with large molecular systems, it’s often necessary to filter out simpler conformations and focus on more complex molecular substructures. For example, in DNA-protein complexes, signaling pathways, or molecular machines, paths containing a high number of atoms can represent…

Controlling Label Visibility in Molecular Models with NSL

OneAngstrom

When working with complex molecular models, clarity is key. Whether you’re preparing figures for publication, sharing a model with collaborators, or simply trying to declutter your workspace, the ability to selectively show or hide label nodes can make a significant…

Stabilizing Your View in Molecular Simulations: The ‘Look at Atoms’ Feature in SAMSON

OneAngstrom

When working with complex molecular trajectories, a common challenge is keeping your focus on a specific region of interest. Atoms may move, conformations may shift, and before you know it, your camera has lost track of the very part of…

Make Your Molecules Breathe: Highlighting Dynamics with the Pulse Animation in SAMSON

OneAngstrom

A common challenge in molecular modeling is effectively communicating complex 3D structures and dynamic behaviors to both colleagues and broader audiences. Whether for presentations, publications, or teaching, clarity and visual engagement are key – and this is where animations shine.…

A Clearer Way to Design Polymer Sequences: Fewer Errors, Better Control

OneAngstrom

If you build custom polymers for molecular modeling, you’ve probably dealt with challenges when specifying complex monomer sequences. How do you know your defined sequence is valid? Have you correctly designated bond types between monomers? Are your naming conventions traceable?…

Design Photorealistic Molecular Models with Materials in SAMSON

OneAngstrom

When it comes to creating molecular models that are both scientifically accurate and visually compelling, the choice of materials can make a massive difference. Whether you’re customizing metallic proteins, simulating glassy channels, or adding a glowing ligand for effect, the…

Working with visibility and selection flags in SAMSON label nodes

OneAngstrom

When working on complex molecular models in SAMSON, it’s common to use annotations or graphical labels to highlight specific regions, monitor simulation data, or organize your workspace. These label nodes are versatile, but as your models grow in size and…

Quickly Filter Molecular Backbones by Visibility, Name, and More in SAMSON

OneAngstrom

When modeling complex molecular systems, isolating specific components—like molecular backbones based on their attributes—can save a considerable amount of time and help reduce visual clutter. If you’ve ever asked yourself, “How do I hide all backbones that are not selected?”…

Mistake in Your Molecular Model? Here’s How to Safely Undo It in SAMSON

OneAngstrom

Whether you’re tweaking geometries, testing force field parameters, or building complex biomolecular assemblies, making changes efficiently and confidently is key. But with complexity comes a familiar concern among molecular modelers: what if you make a mistake and can’t go back?…