Author: OneAngstrom

Molecular modeling often involves working with complex biological assemblies such as protein complexes or viral capsids. For molecular modelers, understanding the symmetry of these assemblies is crucial. Symmetry not only helps identify functional interfaces but also reduces computational costs by…

Molecular modeling often involves a series of intricate operations to design precise molecular structures. But what happens when an action doesn’t yield the expected result, or you need to reverse several steps to revisit a previous state? This is where…

Molecular modeling requires intuitive tools that make complex tasks more manageable. If you frequently work with molecular structures, chances are you’ve encountered situations where selecting, transforming, or creating structures demands precision and flexibility. In SAMSON, these tasks are handled by…

Creating custom index groups is a common necessity for molecular modelers working with GROMACS. Whether you are delineating pull groups, isolating specific residues, or setting up advanced analysis workflows, custom index groups provide flexibility that standard GROMACS groups might not…

Visualizing molecular structures effectively can be a challenging task for molecular modelers. As models grow increasingly complex, it becomes critical to convey structural insights with clarity and precision. One simple yet powerful tool to enhance presentations is the Appear animation…

When working in molecular modeling, one common challenge is directing focus precisely on specific areas of a complex molecular system. Whether you are presenting an intricate protein structure to colleagues or fine-tuning visual effects for computational analysis, creating a clear…

Molecular modeling often involves selecting specific atoms, residues, or other nodes based on spatial relationships. For instance, you might need to identify atoms within a certain distance from a ligand or residues surrounding an active site. These proximity-based queries can…

Constructing complex nanoscale structures often feels like a daunting task. If you’re a molecular modeler, creating an accurate and well-structured carbon nanotube might occupy a significant amount of time and effort. But what if you had tools to make this…

Molecular modelers working with DNA nanostructures often face challenges when importing designs, whether it's compatibility issues, combining multiple components, or reusing structures from repositories. The Adenita extension for SAMSON simplifies this process by providing robust functionalities to easily import and…