When preparing to model protein transitions—such as conformational changes or reaction pathways—many molecular modelers face a frustrating issue: their interpolation algorithm fails to run, or produces unrealistic outputs. A frequent cause? Poorly prepared structures. If you’re using the As-Rigid-As-Possible (ARAP)…
Molecular modeling projects often involve not just atoms and molecules, but hierarchical systems comprising proteins, ligands, solvents, ions, and other components. When working with such complex structures, users frequently struggle with clarity and navigation—especially when tracking changes or analyzing subcomponents.…
Preparing initial conformations for umbrella sampling can be a daunting process for molecular modelers, especially when dealing with long trajectories or custom paths. Selecting appropriate frames that are well-distributed along a reaction coordinate often requires scripting or external processing. Fortunately,…
When dealing with large biomolecular systems like proteins, DNA, or RNA, molecular modelers often face a persistent challenge: navigating and selecting specific parts within increasingly complex structures. Whether you’re adjusting specific residues, analyzing subunits, or customizing visual representations, finding your…
When working on large molecular systems, simplicity and speed are key. One common challenge among molecular modelers is quickly pinpointing the right label nodes—especially when scenes contain complex visual elements and nested structures. Whether you’re highlighting reaction intermediates or flagging…
When working with complex molecular systems in SAMSON, molecular modelers often deal with large sets of conformations. These may include snapshots from simulations, different poses from docking, or generated conformational ensembles. However, identifying conformations that meet specific structural criteria—like having…
