SAMSON Blog – Page 13

From Atoms to Lattices: Easily Create Custom Crystals in SAMSON

Many molecular modelers know how to import molecules, dock ligands, or simulate dynamics. But when it comes to designing materials from the inside out—like building custom crystal structures—things often get more complicated. Whether you’re trying to study a novel inorganic…

Minimizing Only Part of a Molecule in SAMSON Without Affecting the Rest

OneAngstrom

One common challenge in molecular modeling is selectively optimizing only certain parts of a molecular structure while leaving the rest untouched. This becomes particularly relevant when working on large biomolecules, designing ligands, or when assessing localized conformational changes. Minimizing an…

Quickly Setting Up Protein Docking in SAMSON with Hex

OneAngstrom

Manually configuring a protein docking setup can be tedious and error-prone, especially when dealing with complex biomolecular structures. One common difficulty for molecular modelers is quickly and accurately preparing a system for docking simulations while minimizing preprocessing time. Fortunately, SAMSON…

Tired of Writing Custom Parsers? How Importers Can Save You Hours

OneAngstrom

If you’re a molecular modeler, you’re probably no stranger to file format frustrations. Whether it’s a legacy format from a colleague, or a PDB file with just enough quirks to make standard tools fail, turning file data into usable molecular…

Quickly Find Molecular Subsets in SAMSON with Folder Attribute Filters

OneAngstrom

When working with complex molecular systems in SAMSON, structure organization often becomes a challenge. Projects can contain thousands of atoms, dozens of molecules or chains, and rich hierarchical folders. If you’ve ever found yourself toggling through folders trying to isolate…

From Chaos to Structure: Easily Animate Molecular Assembly

OneAngstrom

When creating molecular animations, showing how parts come together can be just as important as showing structure or function. Whether you’re preparing educational content, a presentation, or a research video, it’s often useful to illustrate how a complex molecular system…

Animating Molecular Pulses: A Simple Way to Clarify Transient Structures

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In molecular modeling, one persistent challenge is effectively conveying how structures transiently appear and disappear during processes like docking, folding, or dynamic transformations. Researchers often want to emphasize certain regions of a molecular system momentarily — perhaps to draw attention…

Quickly Select the Right Molecules: Using Attribute Filters in SAMSON

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When dealing with large molecular systems in SAMSON, selecting just the right subset of molecules for analysis or simulation can quickly become overwhelming. Suppose you’re working with a structural model containing hundreds of molecules and you only want to isolate…

When Molecules Fade In: Creating Smooth Appearance with the Appear Animation in SAMSON

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Molecular modelers often create presentations to convey the structure and function of molecules. But when complex systems are revealed all at once, audiences can easily become overwhelmed and miss key details. That’s where animation – specifically, progressive visibility – can…

Writing Smart Atom Selection Scripts for Molecular Modeling

OneAngstrom

Working at the atomic scale often means navigating through an overwhelming number of atoms, chains, and residues within complex structures. A recurring pain for molecular modelers is selecting the right subset of atoms from larger structures — for analysis, editing,…