SAMSON Blog – Page 640

Finding Aromatic Atoms Quickly in Molecular Models with NSL

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

OneAngstrom

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

OneAngstrom

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

OneAngstrom

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

OneAngstrom

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

OneAngstrom

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)

OneAngstrom

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…

Extracting Ligand Pathways as PDB Files: A Simple Way to Track Molecular Motion

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When investigating molecular recognition, drug binding, or unbinding mechanisms, tracking how a ligand moves through a protein is crucial. However, manually extracting these trajectories into formats suitable for downstream analysis or visualization can be both tedious and time-consuming. If you’ve…

Avoid Repeating Yourself: Add Custom Index Groups Once for All Your Molecular Simulations

OneAngstrom

When preparing molecular dynamics simulations in GROMACS, many modelers use gmx make_ndx to create custom index groups. You might want to separate domains, pull particular atoms, or track specific regions of a protein. However, repeating the same selection operations for…