Author: OneAngstrom

When working with protein structures from the Protein Data Bank (PDB), researchers commonly analyze individual asymmetric units. However, much of the biological function and structural insight lies beyond the asymmetric unit — in the full biological assembly. These complete assemblies…

When setting up molecular dynamics simulations using GROMACS, one common but often confusing step is defining your system’s boundary conditions. Molecular modelers frequently ask: Which unit cell shape is best for my system?. This blog post explores this issue and…

Creating realistic animations of conformational changes in biomolecules often feels like a daunting challenge. Full molecular dynamics (MD) simulations can take days or even weeks to run, and demand high-performance computing resources. But what if you simply want to visually…

In molecular modeling, a common challenge is consistently generating clear, informative visualizations—especially when dealing with complex systems such as protein-ligand complexes, solvated structures, or multi-chain systems. Adjusting representations, selecting relevant atoms or molecules, setting color schemes, and choosing visualization models…

When preparing molecular animations—whether for a presentation, publication, or educational video—timing is crucial. A brief pause at just the right moment can give your audience the time to absorb complex molecular conformations, understand a transition, or appreciate a molecular interaction.…

For many molecular modelers, juggling multiple molecular systems during a modeling session is the norm, not the exception. Whether you’re comparing ligand binding modes, transferring fragments between structures, or running simulations on several conformations, managing multiple files effectively can be…

Collaborating on molecular modeling projects often comes with a familiar pain: file fragmentation. Between structures, scripts, analysis results, and supporting documents, tracking versions and sharing complete projects can be cumbersome. Ever forwarded a structure file and forgotten the accompanying script?…

When preparing a molecular system for simulation, especially with tools like GROMACS, one of the early and often overlooked steps is deciding which crystal waters to keep and which to remove. This may seem straightforward at first—just remove all water…

When creating animations of molecular systems, the camera view can sometimes unexpectedly shift between frames. This often happens when working on long simulation trajectories or assembling scenes over time, leading to moments of disorientation or inconsistent visual storytelling. Fortunately, the…

Whether you’re building a homology model, refining a predicted structure, or preparing a system for simulation, strained backbone conformations can introduce problems. Outliers in φ (phi) and ψ (psi) backbone dihedral angles may go unnoticed in a 3D viewer, but…