Molecular modelers often spend a significant amount of time trying to fine-tune how molecular structures are displayed. Whether it’s for better analysis, clearer presentations, or publication-ready visuals, there’s a constant need to control how nanosystems are represented graphically. In SAMSON,…

When preparing molecular animations for presentations or publications, clarity and focus are essential. One of the common challenges molecular modelers face is how to gently de-emphasize or hide specific parts of a model without abruptly removing them. A sudden disappearance…

Complex molecular structures often overwhelm audiences when presenting biochemical mechanisms or molecular simulations. Showing every atom and bond might be accurate, but it quickly becomes counterproductive if the viewer can’t follow what’s happening. This is a challenge many molecular modelers…

If you’ve ever run into issues at the start of an equilibration step in GROMACS, you know how frustrating it can be to realize that the problem was simply an incorrect input file path or format. This is particularly common…

When building complex molecular models, one of the recurring challenges is aligning functional groups or fragments precisely and efficiently. Incorrect orientation can result in steric clashes, unrealistic geometries, or simply more work adjusting everything afterwards. If you’ve ever tried rotating…

Molecular modelers often encounter situations where automated force field parameters don’t perfectly match their specific chemical systems. Default atom types or bond orders might not reflect the intended structure, especially in complex or unusual molecules. In SAMSON, this is addressed…

One of the challenges in molecular modeling and presentation is directing the attention of your viewers. Whether you’re teaching a class, giving a talk, or recording a video, clearly visualizing molecular processes—especially the dynamic ones—can be difficult. Enter the Pulse…

One of the most common frustrations in molecular modeling arises from accidental changes, experimental edits that don’t pan out, or simply wanting to compare different model states. For molecular modelers working on complex structures, reverting changes isn’t just a nice-to-have—it…