When preparing molecular animations to communicate your findings—whether in academic presentations, lectures, or research videos—clarity is essential. A common challenge faced by molecular modelers is how to gradually remove part of a complex molecular structure without overwhelming visual transitions or…

When crafting molecular animations, it’s not just about what you show—it’s about how you show it. Whether you’re preparing an animation for a presentation, a publication, or simply to better understand a structure, precise camera movement can greatly impact how…

Running molecular dynamics (MD) simulations using GROMACS often involves significant setup, hardware, and time. It’s not always easy for molecular modelers to configure local machines to handle large simulations, and setting up a remote compute environment can be daunting. The…

Sometimes, sticking with a specific version of a software can be essential — whether for compatibility reasons, validated workflows, or teaching materials built around a particular layout. If you’re working with SAMSON, the integrative molecular design platform, the good news…

Molecular modelers often face a familiar challenge: when working with intricate biomolecular assemblies or complex nanostructures, the sheer density of information in the model can make it hard to analyze or present specific parts. Whether you’re preparing a presentation, studying…

When fine-tuning a protein model before simulation, small conformational issues can turn into big problems. A single residue with unusual backbone angles can affect the outcome of minimizations or dynamics runs. But how do you spot and adjust such residues…

Molecular modeling often involves dynamic processes: ligand docking, molecular dynamics, or interactive manipulation of atomic structures during presentations. But reproducing or analyzing these movements later can become a pain, especially if you didn’t capture the atomic trajectory at the time.…

Working with molecular modeling software often comes with a common and frustrating problem: managing extensions and plug-ins. Whether you’re using a feature-limited tool or switching between machines, keeping track of which modules you’ve installed, which are under trial, or which…