Author: OneAngstrom

Preparing systems with multiple protein replicas is a common need in coarse-grained molecular modeling, especially when studying self-assembly or concentration effects. Yet, what seems like a simple task—duplicating a single protein structure several times—can quickly turn into a frustrating experience…

When creating molecular animations, clarity is everything. Whether you’re illustrating mechanisms of action, molecular interactions, or structural rearrangements, guiding your audience’s focus without overloading the scene is a challenge. One effective way to enhance focus is by hiding parts of…

For many researchers and students working in universities, biotech companies, or public labs, installing software without administrator rights can be surprisingly difficult. IT policies, locked systems, and resource approval cycles often get in the way—preventing scientists from quickly testing or…

Visualizing molecular transformations can be challenging, especially when you want to guide your audience’s attention through a clear and digestible path. One common request from molecular modelers and presenters is the ability to create clean transitions between different components of…

One of the challenges many molecular modelers face when analyzing the flexibility and dynamics of biomolecules is keeping track of interesting conformations or motion trajectories. Whether you’re preparing a figure for publication, comparing several states of your molecule, or simply…

Adding lipid layers around proteins is a common requirement in molecular modeling, especially for studying membrane proteins and receptor dynamics. But the process often feels unintuitive, involving multiple software tools, scripts, and tedious alignment steps. If you’ve ever struggled to…

One common hurdle in molecular docking is dealing with ligand libraries pulled from various sources. Some are fully prepared, others are in 2D or have improper geometries. If docking fails or gives poor results, it’s easy to blame the algorithm…

Molecular modelers often face an overlooked but impactful challenge when creating scientific presentations: how to build smooth visual transitions that highlight what matters without distractions. While molecular animations and labels get most of the attention, the background can become a…

If you’ve ever worked with multiple protein structures—for example, when analyzing a protein family, running virtual screening, or preparing data sets for machine learning—you know how tedious it can be to clean and prepare each file manually. Removing solvents, fixing…