When creating animations of molecular systems, one common frustration many modelers face is the inconsistency of camera angles between frames. You might carefully structure a scene, but after navigating through your document or tweaking objects, the system’s viewpoint can change…

Creating clear, informative presentations of molecular systems is one of the trickiest parts of structural modeling. Whether you’re explaining docking mechanisms in a classroom or preparing an impactful animation for a research publication, visual clarity is key. One common pain…

If you’ve ever faced the task of cleaning dozens—if not hundreds—of PDB files before running simulations or docking workflows, you’re not alone. Dealing with missing atoms, stripping waters, resolving alternate locations manually is not the most enjoyable part of molecular…

Working with large molecular systems often means wading through overwhelming layers of atoms, bonds, residues, chains, and structural groups. For molecular modelers and structural biologists, one of the most common tasks is to isolate particular regions of interest – ligands,…

When working on complex molecular models, selecting the right colors can make all the difference. Whether it’s to better highlight specific atom types, differentiate residues, or distinguish molecular groups, effective color use improves both clarity and communication. Yet, many molecular…

When working on molecular models, especially when exploring conformational changes, reaction pathways, or molecular dynamics simulations, it becomes essential to communicate these changes over time with clarity. This is where animations come in—not only as a presentation tool, but also…

Comparing entire protein structures can be useful – but sometimes, you only care about a specific segment. Whether you’re studying conserved motifs, flexible binding domains, or comparing specific helices across two species, aligning full structures may dilute the insights you’re…

When working with large molecular systems, sometimes your goal isn’t to minimize the entire structure. Instead, you may want to refine only a selected part of a molecule, like a side chain in a protein, a ligand in a binding…