Uncategorized – Page 564

FASTA in, Structure out: Using AlphaFold-2 in SAMSON

Many molecular modelers face a common challenge: how to obtain reliable 3D structures for proteins when experimental data isn’t available. Whether you’re trying to model a newly discovered sequence or understand domain interactions, structure prediction is your go-to route. Fortunately,…

A Simple Way to Stay Organized When Modeling Molecules

OneAngstrom

If you’ve worked on large or multi-step molecular modeling projects, you’ve probably faced the challenge of managing complex structures, reference files, scripts, and various annotations — all within a single workspace. Managing molecular data can quickly become overwhelming when everything…

Choosing the Right Discrete Color Palette for Molecular Visualization

OneAngstrom

When you’re building complex molecular models, visuals matter. Whether it’s distinguishing between different protein chains, highlighting interaction sites, or simply making your work look more readable and aesthetically pleasing, choosing the right color palette can make a big difference. Color…

Easily Control Molecular Visibility with the Shown Animation

OneAngstrom

When creating molecular animations for presentations, publications, or educational videos, one of the simplest but often underestimated challenges is managing which elements of the model the audience sees — and when. If you’ve ever wanted to reveal specific molecules or…

How to Quickly Find Hidden or Visible Nodes in Molecular Scenes

OneAngstrom

When working on large molecular models, it becomes increasingly important to manage visibility efficiently. You might be focused on just one part of the structure — a ligand binding site, a water shell, or a specific chain. But if hidden…

Efficiently Filter Charged Residues in SAMSON with NSL

OneAngstrom

When working on protein modeling workflows, one of the recurring tasks is identifying and selecting residues based on their electrical charge. Whether you’re optimizing electrostatic interactions, analyzing salt bridges, or preparing electrostatics-related simulations, filtering charged amino acids is a crucial…

A Step-by-Step Guide to Building Custom Molecules Atom by Atom in SAMSON

OneAngstrom

Molecular modelers frequently need to construct specific chemical structures not readily available in molecular libraries. Whether you’re reproducing a model from a journal article or exploring new chemical scaffolds, building molecules atom by atom is often a key part of…

Easier Custom Atom Selection in GROMACS Simulations with SAMSON

OneAngstrom

Many molecular modelers using GROMACS have run into this: you want to track or manipulate a specific set of atoms during a simulation—maybe the side chains of neutral amino acids or every non-C-alpha atom in a protein. But GROMACS only…

Quickly Find Structural Groups by Atom Count in Your Models

OneAngstrom

When building or analyzing large molecular systems, it can be a challenge to identify specific structural groups of interest — especially when dealing with hundreds or even thousands of groups. What if you want to isolate only those groups with…

Running GROMACS in the Background: How to Monitor Local Simulations with Ease

OneAngstrom

When running molecular dynamics (MD) simulations, especially those that take time to compute, a common frustration among molecular modelers is not being able to track progress easily without interrupting their workflow. Whether you’re testing new force field parameters, prepping simulations…