Keeping track of complex molecular models can be a challenge, especially when working with large biomolecular systems or managing multiple simulation setups. Whether you’re designing a drug candidate, investigating protein-ligand interactions, or comparing molecular structures, having a clear overview and…

Adjusting atomic-level properties in molecular models often feels more complex than it should be. Whether you’re verifying atom positions, fine-tuning residue groups, or trying to undo an unexpected change, quick access to reliable attribute data is essential. This is where…

For molecular modelers working with solid-state materials, understanding and manipulating crystal structures is essential. But cutting crystals along specific directions—especially when dealing with Miller indices—can be confusing or tedious in many software environments. If you’re using SAMSON, the integrative molecular…

If you’ve ever tried to interpret complex molecular interactions from a dense 3D structure alone, you know how quickly things can become visually overwhelming. Identifying how a ligand interacts with a protein can require constant rotations, manual measurements, and lots…

One of the common challenges in setting up center-of-mass (COM) pulling simulations using GROMACS is defining the correct groups of atoms when default index groups are not sufficient. If you’re dealing with multi-chain molecular systems and want to precisely control…

Presenting molecular structures effectively is often as important as building them. Whether you’re preparing a lecture, visual abstract, or research video, storytelling through molecule animations can engage your audience in ways static images can’t. But one recurring challenge many molecular…

When communicating complex molecular models, visual clarity is essential. However, modelers often face a recurring challenge: how can you guide an audience’s attention to specific components of a system without completely deleting or permanently altering the structure? This is especially…

One of the recurring challenges when setting up molecular dynamics (MD) simulations with GROMACS is defining custom index groups. These groups provide more control during analysis and simulation by letting you specify exactly which atoms or residues you want to…