OneAngstrom – Page 7

Quickly Select Molecular Paths with More Than 100 Atoms in SAMSON

When working on complex molecular systems in SAMSON, modelers often need to find and analyze long molecular paths—chains of atoms within molecules that represent important structural or dynamic components. Imagine having to locate all backbone paths in a protein that…

Avoiding Solvent Clashes in Coarse-Grained Systems: A Common GROMACS Pitfall

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Coarse-grained (CG) molecular dynamics is a common approach to simulate large biomolecular systems with reduced computational cost. The GROMACS Wizard in the SAMSON platform provides an intuitive interface to set up such systems, including generating periodic boxes, adding solvent, and…

Finding Aromatic Atoms Quickly in Molecular Models with NSL

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Molecular modelers often need to identify specific atomic features in complex structures, such as aromatic rings, metal atoms, or nucleic acid backbones. A common challenge is selecting atoms with shared chemical characteristics without manually inspecting or guessing their positions. This…

How to filter molecular structures by atom count in SAMSON

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When working with large molecular projects, it’s easy to get overwhelmed by the number of elements and structures loaded into your workspace. From simple ligands to multi-chain proteins and multimeric complexes, your project tree can quickly turn into a complex…

A Simple Trick to Showcase Molecular Motion with the Rock Animation

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For molecular modelers, visually communicating dynamic behavior is essential—whether it’s for presentations, publications, or team discussions. Yet, it’s often difficult to convey subtle molecular motions effectively and understandably. One recurring challenge? Showing how groups of particles move together in a…

Avoid Rework: How to Auto-Fill Input Files for NVT Equilibration in SAMSON

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When working with molecular dynamics simulations using GROMACS, setting the correct input files for each step is crucial. Whether you’re handling a protein-ligand complex, a solvated biomolecule, or a batch of systems, ensuring pipeline continuity can be tedious. One commonly…

Using NSL to Control Note Visibility in SAMSON

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As molecular models grow in size and complexity, modelers often turn to visual annotations—such as notes and labels—to document observations, mark points of interest, or organize a workspace. However, with many notes cluttering the screen, one common challenge emerges: how…

Creating Smooth Protein Transition Paths with ARAP Interpolation

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When modeling molecular processes, capturing transitions between different conformations of a protein is often essential. Whether you’re exploring activation pathways, refining docking poses, or setting up umbrella sampling simulations, intermediate structures along these conformational paths are a valuable resource. But…

Should You Minimize Ligands Before Docking? Here’s What Happens If You Do (Or Don’t)

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When preparing ligands for docking, one question consistently puzzles molecular modelers: should ligands be minimized beforehand? The answer might not be as universal as you think, but understanding the trade-offs can improve your docking reliability and save you hours of…

Entering NOESY-based distance restraints in NMR2 (without breaking a sweat)

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When modeling protein-ligand complexes from NMR data, one of the trickiest steps is translating NOESY cross-peaks into distance restraints that can be used for structure prediction. In particular, if you’re using NMR2 in SAMSON to interpret methyl-based NOESY data, you’ll…