Anyone who models biomolecular systems knows how tedious it can be to manually pick specific residues in a 3D viewport. Whether you’re selecting residues for simulations, mutations, or analysis, navigating protein structures in 3D often leads to frustration—especially when chains…
Running an Umbrella Sampling simulation can be time-consuming, especially when it comes to preparing the system correctly. One of the most critical — and often tedious — steps is choosing the right initial conformations. Missteps here can affect the reliability…
If you’ve ever built or installed a SAMSON Extension and found that it suddenly doesn’t load anymore after updating SAMSON (or if it never loaded in the first place), you’re not alone. This blog post will help you understand why…
When working with complex molecular systems, especially large biomolecules or materials, molecular modelers often face the challenge of managing and organizing large numbers of structures. One common pain point is the need to filter out parts of a system based…
If you’re working in molecular modeling or computational chemistry, your simulation tools can quickly become a digital jungle. Between installing plugins, keeping track of licenses, and updating packages, managing your modeling environment can be more time-consuming than the modeling itself.…
When setting up free energy calculations or analyzing ligand unbinding mechanisms, accessing atomic coordinates at fixed intervals along a trajectory is often a prerequisite. But extracting this data isn’t always straightforward. What if you’re interested in only a subset of…
One of the most common challenges molecular modelers face is visual overload—too many atoms, residues, or chains can make it nearly impossible to focus or communicate your scientific point effectively. Whether you’re preparing a publication figure or simply trying to…
When designing molecular models, especially with large systems or during polymer and conformational studies, you may want to quickly isolate and inspect paths that meet specific structural criteria. One common need is identifying paths based on the number of atoms…
Anyone working regularly in molecular modeling knows how repetitive and time-consuming setting up a clean, clear visualization can be. You may spend several minutes choosing representations, hiding solvent atoms, coloring chains, creating attractive figures—only to repeat the same steps a…
When preparing molecular presentations, many researchers face the challenge of pacing. Unlike classic presentation software, molecular animations often run linearly, leaving little space for pausing, discussing, or revisiting key moments on the fly. If you’ve ever tried explaining a complex…
