Author: OneAngstrom

When building molecular models, especially large or branched structures, one of the common frustrations for chemists and molecular designers is accidentally placing fragments too close, overlapping atoms, or misaligning critical functional groups. Even with care, fragment orientation can be tedious…

Creating custom index groups is a key step to increase flexibility and control in molecular simulations with GROMACS. From restraining specific residues to defining pull groups, index files can be crucial. But there’s a common question among SAMSON users who…

Molecular modeling often involves spending long hours analyzing complex structures, adjusting visualization settings, and preparing presentations. For many scientists, particularly those working late or in low-light environments, the bright glare of software interfaces can become tiring and distracting, even leading…

Visualizing molecular motion can be challenging when the part of interest moves rapidly or unpredictably. Adjusting the camera manually to keep focus can be tedious, especially during long animations like molecular dynamics simulations or docking sequences. That’s where the Look…

If you’ve spent time repeatedly coloring atoms, toggling representations, and organizing your molecular scenes, you’re not alone. For many molecular modelers, one of the most frustrating tasks is having to redo the same visualization settings every time they open a…

When preparing molecular presentations or molecular dynamics movies, timing is often everything. A common frustration among researchers and molecular modelers is the abrupt appearance or disappearance of molecular elements, which can be visually jarring or confusing for an audience. If…

Presenting molecular models to colleagues, students, or during talks can often lead to a common issue: overwhelming your audience with too much structural detail all at once. When atoms and bonds appear simultaneously, even well-prepared presentations can become visually confusing,…

In molecular modeling, showing how ligands bind to receptors is key when presenting your research. But visualizing this interaction clearly and smoothly can quickly become time-consuming. If you’ve ever struggled with showing how a molecule docks into a protein pocket…

Molecular modelers often know what they want to show, but not how to show it. When presenting complex molecular assemblies or dynamic motions, a static image or even a simple rotation often doesn’t do justice to the structure’s spatial features.…