Author: OneAngstrom

Carbon nanotubes (CNTs) have become essential structures in nanotechnology, offering unique electrical, mechanical, and chemical properties. Researchers often need to create them for simulations or structural modeling. However, what should be a straightforward task often turns into a tedious one:…

In molecular simulations, molecules are constantly moving, transforming, binding, and unbinding. As a researcher or educator, you might want to focus on very specific parts of a molecular system: a ligand entering a binding site, a domain rearrangement, or an…

Creating repetitive molecular structures—such as polymers, nanotubes, or crystal lattices—can be one of the more time-consuming and error-prone tasks in molecular modeling. When you need to replicate molecular fragments with precise positioning, structure builders often find themselves tediously copying, pasting,…

One of the underestimated pain points for many molecular modelers—particularly students, researchers in large institutions, or scientists working on shared systems—is the requirement for administrative privileges to install software. Firewalls, university IT policies, and locked-down systems often add unnecessary friction…

When working with complex molecular systems, scientists and educators often need to rapidly switch between different visualization styles. Whether you want a clean look for publication, an immersive rendering for an animation, or a simplified structure for functional insight, changing…

One of the frequent challenges faced by molecular modelers using umbrella sampling is the often cumbersome post-processing stage required to compute the Potential of Mean Force (PMF). The actual simulation might already have been computationally expensive, but without a streamlined…

Creating compelling molecular animations can help researchers explain mechanisms, analyze behavior, and communicate results more effectively. But if you’ve ever tried to animate groups of atoms rotating around their center with precision, you’ve probably dealt with scripting or manual workflows…

Selecting atoms one by one is often the first bottleneck in setting up a molecular experiment or simulation. Whether you’re defining a region of interest, modifying a subset of atoms, or preparing geometric restraints, manual selection can become slow and…

If you’re working in molecular modeling, you’ve likely found yourself repeatedly diving through hierarchies of chains, residues, and atoms to apply selections—especially when dealing with large biomolecular complexes. These selections may be necessary to analyze binding sites, investigate side chain…

If you’ve ever tried to import a structure file into one tool, only to export it for another, you know the pain: data loss, conversion issues, and a lot of time spent trying to figure out which formats are supported.…