One of the common frustrations in molecular modeling is the difficulty of understanding the 3D structure of large biomolecules on a 2D screen. Structures can appear flat or confusing, and subtle spatial relationships might get lost, especially when visualizing complex…

If you’ve ever worked with protein structure files downloaded from the Protein Data Bank (PDB), you’ve probably experienced one or more of the following: Manually opening and cleaning each PDB file, one at a time Writing custom scripts to remove…

When setting up GROMACS simulations, many molecular modelers reach a point where they need to define custom index groups — for example, to monitor specific residues, apply restraints, or use them as pulling groups during simulations. While gmx make_ndx is…

One common challenge molecular modelers face when building polymers is controlling the exact sequence of monomers. Whether you’re designing a repeating synthetic chain or trying to mimic the behavior of a biopolymer, sequence matters. And yet, defining and managing specific…

One of the most common frustrations for molecular modelers running energy minimization or molecular dynamics simulations is losing control over job progress. Long computations can leave users wondering whether the job is still running, if it has completed successfully, or…

When working with complex molecular systems in SAMSON, one common pain point is sifting through countless nodes (atoms, residues, structural groups, etc.) in the Document view just to find what you need. Whether you’re inspecting a specific residue type, cleaning…

If you’ve ever spent more time formatting a molecular visualization than analyzing it, you’re not alone. Adjusting colors, toggling visibility, setting rendering parameters—all these steps add up, especially when working with large systems or during presentations. Fortunately, there’s a shortcut…

Visualizing complex molecular systems can often feel overwhelming. Between selecting the right atoms, choosing the appropriate rendering styles, and tweaking color schemes, molecular modelers spend valuable time setting up visuals instead of analyzing their data. If you’ve ever asked yourself,…

Collaborating on molecular modeling projects often requires sharing not just the structural data but also the scripts and applications that process, visualize, or simulate them. However, researchers and educators frequently struggle with keeping everything organized and reproducible across different environments.…