SAMSON Blog – Page 138

Easier Molecular Flythroughs with ‘Move Camera’ in SAMSON

Creating compelling visualizations in molecular modeling is often critical—whether to explain a docking mechanism, present a complex structure at a conference, or simply share your work with collaborators. But one challenge that holds many modelers back from producing dynamic molecular…

Exporting Protein Conformation Paths and Energies with SAMSON

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When studying protein conformational changes, modeling how a protein transitions from one conformation to another is just the beginning. Molecular modelers often need to analyze and share results: extract key conformations, view transition energies, or export trajectories for visualization and…

Loading and Preparing Protein Conformations for Pathway Exploration in SAMSON

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If you’re studying protein dynamics, a common challenge is identifying conformational pathways between two known states. Before diving into complex simulations or heavy computations, one crucial step must be done right: loading and preparing your protein’s conformational models correctly. In…

Quickly Find and Filter Cameras in SAMSON with the NSL

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When working on complex molecular modeling projects, it’s often easy to lose track of elements in the document—especially when multiple cameras, lights, and visual nodes are involved. If you’ve ever found yourself trying to manually sift through camera nodes just…

Keeping the Good Waters: How to Remove Unwanted Crystal Waters in GROMACS Preprocessing Without Breaking Your Active Site

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Water molecules in protein structures from the Protein Data Bank (PDB) can either be essential for function or relics from crystallographic data that don’t matter for your simulation. Knowing how to selectively remove undesired water molecules while preserving those in…

Preparing Start and Goal Conformations for Protein Pathway Planning

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When modeling conformational transitions in proteins, ensuring that the start and goal structures are properly aligned and compatible is essential. If your starting and ending conformations are not set up correctly, most path-finding algorithms will either fail or return meaningless…

Cleaning Up Water Molecules Without Losing Functional Waters

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In molecular simulations, especially when preparing systems using GROMACS, it’s common to remove water molecules from the initial structure to avoid unwanted interactions or duplicate solvation. However, researchers often face a recurring dilemma: how can you quickly remove unnecessary crystal…

Prevent Simulation Failures by Validating Your Protein Structures

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Anyone who has worked with protein structures knows that small structural issues can lead to big problems down the road. Whether you’re docking ligands, running molecular dynamics simulations, or building models for drug screening, structure validation is what stands between…

Quickly Find Conformations Based on Atom Counts in SAMSON

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When you’re working with molecular structures that contain multiple conformations, it’s easy to get lost in long lists of data, especially in large systems. Whether you’re preparing datasets, designing filters for simulations, or just trying to isolate a subset of…

Why Your Molecular Models Look Flat (And How to Fix It)

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Have you ever created a molecular visualization that felt underwhelming, despite being scientifically accurate? If your model seems flat or lacks depth, you’re not alone. One of the most common problems in molecular modeling is a lack of depth perception—making…