Author: OneAngstrom

When computing the Potential of Mean Force (PMF) in molecular simulations, there’s a crucial detail that can often be overlooked: the quality of sampling along the reaction coordinate. Poor sampling can lead to misleading energy profiles, potentially invalidating the conclusions…

One of the most common tasks molecular modelers face when preparing a simulation is cleaning up PDB structures imported from the Protein Data Bank. These files often contain crystal waters—some of which are essential for maintaining protein active sites, while…

When working on DNA nanostructures, it’s common to rely on tools like Cadnano or custom editors to design staple and scaffold strands. However, as research progresses and designs become more modular, the ability to reuse and import these components across…

When modeling complex molecular systems, selecting the right atoms is often a necessary but tedious task. Visual selection can be uncomfortable in dense structures, and name-based selection isn’t always flexible enough. But with mathematical expression-based selection, you can gain precision…

Crystallography plays a vital role in material science, nanotechnology, and structural biology. But even for experienced modelers, visualizing and interacting with crystal structures can feel abstract. A recurring challenge is analyzing how crystals look and behave along specific crystallographic planes…

One of the most common issues molecular modelers encounter during structure-based drug design is poor-quality docking results due to incorrect ligand geometries. If your ligand library includes 2D structures or molecules with unrealistic bond angles, the scoring functions used during…

If you frequently model proteins from PDB files or need to work with several different protein structures at once, you might already know how time-consuming and error-prone it can be to clean and prepare each structure individually. Protein preparation involves…

When creating animations of molecular systems, clarity and precision play a crucial role in effectively communicating scientific insights. Have you ever tried to zoom into a specific molecular region, only to realize that adjusting camera positions changed your rendering setup…

If you’ve ever tried preparing more than a handful of PDB files for simulations or docking, you know the pain: cleaning structures one by one, checking for missing atoms, removing waters, renaming residues… It’s a tedious, time-consuming task—and one that’s…