Creating compelling molecular animations can be one of the most time-consuming tasks for researchers preparing publications, presentations, or outreach material. While modern tools offer advanced visualization options, they often lack intuitive ways to manage complex animation timelines, leading to frustration…

Atom selection isn’t always straightforward. If you’re a molecular modeler dealing with large, complex atomic structures, manually selecting atoms that meet specific spatial or chemical criteria can be slow and error-prone. Whether you’re extracting a region of interest or preparing…

One of the common challenges in protein-protein docking is dealing with an overwhelming number of incorrect binding predictions. These false positives can distract from promising candidates and add time-consuming work for researchers manually evaluating results. Fortunately, Hex for SAMSON offers…

When running molecular simulations, a common challenge is the need to experiment interactively with the molecular system — adding or deleting atoms without resetting everything. Whether you’re exploring a reaction mechanism or preparing a structure for refinement, being able to…

If you’re working with complex molecular systems, you’ve probably encountered the challenge of selecting specific subsets of atoms that match your criteria — atoms with certain charges, elements, positions, or structural context. Doing this manually is time-consuming and error-prone, especially…

When working with proteins that undergo large conformational changes, a key challenge in simulating realistic transition paths is defining where and how atoms are allowed to move. In SAMSON’s Protein Path Finder, this is controlled by a critical setup step:…

If you’ve ever tried to generate coarse-grained (CG) models for molecular dynamics simulations with multiple copies of the same protein, you’ve probably hit a frustrating problem: topology generation errors due to non-unique residue and chain identifiers. This issue is especially…

When working with force fields like the Universal Force Field (UFF) in molecular design, default automatic typing and bonding are often quite effective. However, when modeling molecules with unusual bonding patterns or working with partially known structures, default algorithms may…