OneAngstrom – Page 178

How to Superimpose Two Hemoglobins Without a Script

Superimposing protein structures to compare their folds or map conserved regions is a common task in computational biology. But doing it manually—whether with PyMOL scripts or rigid RMSD calculations—can be repetitive and error-prone. If you’re spending time writing custom scripts…

Quickly Find and Filter Property Model Attributes in SAMSON with NSL

OneAngstrom

When working with complex molecular systems in SAMSON, it can quickly become challenging to identify and filter specific components, especially when models grow in size. Whether you’re preparing a dataset for analysis, working on visualizations, or trying to isolate a…

Before You Interpolate: Cleaning Up PDB Structures in SAMSON

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Generating realistic transition paths between protein conformations is valuable for structural analysis, molecular dynamics, and free energy calculations. However, a common, often frustrating hurdle in these workflows is preparing protein structures: missing atoms, extra chains, water molecules, and ligands can…

Avoid Email Chaos: Send Your Molecular Models the Right Way

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Many molecular modelers find themselves endlessly emailing large project files back and forth with colleagues. With multiple versions circulating and storage tools that aren’t tailored for research data, things can get convoluted quickly. Who has the latest version? Where did…

Finding Specific Molecular Paths with NSL: Filtering by Atom Count and State

OneAngstrom

When working with large and complex molecular systems, modelers often face the challenge of isolating meaningful subsets of data within a structure. Whether it’s identifying loops in protein backbones or analyzing particular conformational changes, precise selection is essential. Thankfully, SAMSON’s…

From Glass to Gold: Fine-Tuning Materials in Molecular Renderings

OneAngstrom

High-quality molecular renderings are more than just accurate representations; they’re also an important tool for communication, teaching, and research. A common challenge? Making molecules look realistic or stylized enough to effectively tell the story behind your data, while avoiding the…

From Conformations to Continuous Pathways: Choosing the Right NEB Strategy

OneAngstrom

When studying transitions between molecular states, a common challenge in computational chemistry is building a reliable minimum energy path connecting two conformations. This is essential for exploring reaction mechanisms, ligand unbinding, or protein conformational changes. But what’s the most efficient…

Understanding Relative Positioning in SAMSON’s Inspector

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For many molecular modelers, adjusting the position of multiple atoms simultaneously is a common need — whether you’re setting up a complex structure, refining a model, or exploring conformational changes. But moving multiple nodes in 3D space without breaking the…

Avoiding Topology Errors When Creating CG Models of Protein Replicas

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When working with coarse-grained (CG) molecular dynamics simulations, one common scenario is modeling systems that contain multiple copies—or replicas—of the same protein. This is typical in studies involving protein aggregation, crowding effects, or multi-component assemblies using approaches like the MARTINI…

Finding Exactly the Atoms You Want: Using Atom Attributes in NSL

OneAngstrom

When working with large molecular systems, identifying specific atoms with precision can be time-consuming and frustrating. Whether you’re cleaning up a model, extracting meaningful subsets, or analyzing specific substructures, selecting atoms by hand becomes inefficient and error-prone very quickly. This…