SAMSON Blog – Page 32

Quickly Find Molecular Paths with >100 Atoms in SAMSON

When working with complex molecular systems, it’s easy to feel overwhelmed by the sheer number of paths, residues, or chains in a structure. Whether you’re studying protein folding or evaluating ligand binding, pinpointing relevant fragments fast is key to staying…

Quickly Generate Molecule Libraries by Replacing Fragments with SMILES Manager

OneAngstrom

Many molecular modelers face the repetitive task of exploring small chemical modifications to a lead compound. It’s increasingly common in early-stage drug discovery to generate large libraries of analogues by substituting small fragments, in order to evaluate changes in properties,…

Stop Rewriting Tools: Add the Functionality You Need from SAMSON’s Extension Marketplace

OneAngstrom

If you’re a molecular modeler or working in computational chemistry, you’ve probably encountered this scenario: your software offers 80% of what you need, but you’re stuck writing wrappers, scripts, or even your own tools to fill in the remainder. While…

Visualizing the SARS-CoV-2 Spike in Motion: A Molecular Animation Pipeline

OneAngstrom

One of the most common difficulties faced by molecular modelers is how to generate meaningful animations of conformational transitions between known protein states—especially when those states do not perfectly match in residue count or structure. Such animations are invaluable for…

Stop Wasting Time on Invisible Molecular Data: Use visibility flags the smart way

OneAngstrom

When working with large and complex molecular systems, it’s common to hide parts of the model to reduce visual clutter or focus on a specific region. But if you’ve ever found it confusing to manage visibility in SAMSON, especially when…

How to Precisely Select Structures with NSL in SAMSON

OneAngstrom

Selecting specific molecular components can often feel overwhelming when working on large macromolecular complexes. You might be looking to isolate only atoms in ligands, or visualize hydrogens within water molecules. Knowing how to express those search criteria accurately can save…

A Faster Way to Build Carbon Nanotubes Visually

OneAngstrom

Creating carbon nanotube (CNT) models can be time-consuming if you’re constrained by parameter entry forms and repetitive manipulation steps. Molecular modelers often need to generate and iterate through multiple CNT geometries before locking one down for simulations. But what if…

A Simple Way to Query File Nodes in Your Molecular Models

OneAngstrom

When working with complex molecular systems in SAMSON, it’s common to handle multiple datasets, simulations, or structural variations, each encapsulated in distinct file nodes. Whether you’re juggling docking runs or importing external molecular files, a recurring need arises: how do…

Defining Custom Monomers for Smarter Polymer Design

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Designing complex polymers with specific properties often starts with the simplest building block: the monomer. But if you’ve ever needed to go beyond standard monomer libraries to define your own, you know how tedious that process can be in many…

Easily Select Negatively Charged Residues (And Other Filters) in SAMSON with NSL

OneAngstrom

When working with macromolecular structures, a common challenge for molecular modelers is to efficiently identify and manipulate residues that meet specific biochemical or structural criteria. Whether you’re preparing a protein for simulation, adjusting protonation states, or studying interactions near active…