SAMSON Blog – Page 302

Filtering Molecular Structures by Atom Counts in SAMSON

If you’ve ever worked with large molecular datasets, you know how valuable it is to filter and select structures based on their composition. Whether you’re modeling organic molecules, studying reaction mechanisms, or analyzing biomolecular systems, identifying specific groups based on…

Dragging Atoms, Watching Molecules Respond: A Closer Look at Interactive Simulation in SAMSON

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Simulating molecular movement is a core task for many researchers, but getting immediate feedback from changes made in a visual editor is often time-consuming or unavailable altogether in some tools. One common pain point in molecular modeling is not being…

Visualizing Atomic Defects in Diamond Structures with SAMSON

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Crystals may seem perfect in textbooks, but in the real world, they’re far from flawless. Atomic defects—tiny irregularities in the structure—can have dramatic effects on material properties like conductivity, strength, and color. For molecular modelers and materials scientists, simulating and…

Filtering Molecules by Functional Groups: Substructure Search with the SMILES Manager

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When working with molecular libraries, identifying subsets of molecules that contain specific functional groups can be both repetitive and error-prone. Whether you’re hunting for fluorinated compounds, analogs with nitrogen-containing backbones, or custom motifs for SAR analysis, manual filtering isn’t scalable.…

Why Your Molecular Modeling Plugin Won’t Load (And How to Fix It)

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If you’re developing or using custom extensions in SAMSON for your molecular modeling projects, you may have run into this: a SAMSON Extension won’t load at startup, even though it worked perfectly fine before. No error message is immediately helpful,…

Creating Custom Index Groups for GROMACS Pulling Simulations in SAMSON

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When performing molecular dynamics simulations with GROMACS, creating custom index groups is often a source of friction—especially for those performing pulling simulations. Manually generating index files (.ndx) using the GROMACS command line can be tedious and error-prone, particularly for users…

Making Molecular Animations Simpler with the ‘Show’ Effect

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One of the challenges faced by many molecular modelers when preparing visualizations is controlling the timing and visibility of molecular components in animations. Whether you’re building an educational video, a research presentation, or simply exploring dynamic behavior, it can be…

A Simpler Way to Add, Try, or Remove a SAMSON Extension

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As molecular modelers, we often need specific tools for our research—whether it’s visualization tweaks, structure preparation helpers, or access to advanced simulation algorithms. But installing and managing plug-ins or modules across platforms can be frustrating and time-consuming, especially when you…

Following the Center of Mass: A Simple Way to Visualize Molecular Pathways

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When studying molecular systems—especially large biomolecules—understanding how ligands move, how proteins shift domains, or how groups of atoms migrate through a structure is often central to your investigation. Yet, translating this dynamic behavior from raw trajectories into visually meaningful representations…

Effortlessly Switch Between Views in SAMSON with Multiple Cameras

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Molecular modeling often involves inspecting structures from many angles: a close-up of an active site, a top-down view of a cavity, or a wide view of the entire system. Constantly tweaking the camera position to get these views back and…