Author: OneAngstrom

When working with complex macromolecular structures, especially those containing multiple chains, it can be challenging to quickly identify and select residues of interest or detect structural differences across chains. Whether you’re comparing active sites, tracing mutations, or analyzing binding interfaces,…

Many molecular modelers using SAMSON often need specific features and tools that go beyond the core installation. These capabilities usually come as SAMSON Extensions—modular add-ons that let you tailor your modeling environment to your specific needs, whether you’re simulating protein…

Molecular modelers often face the challenge of going beyond static structures to understand how biomolecules move and function. In the context of viral mechanisms, visualizing transitions between different conformational states can reveal valuable insights about infection mechanisms and antibody binding…

One of the common challenges in drug design and lead optimization is efficiently exploring chemical space by generating analogs of a parent molecule. Traditional workflows require scripting or toolchains that are time-consuming and error-prone — not ideal when you’re handling…

If you’re a molecular modeler, you’ve likely faced the challenge of setting up GROMACS for simulations. Whether it’s compiling from source to meet system-specific needs or battling dependency chains, this step can slow your workflow before any actual research begins.…

Molecular modeling often involves working with deeply nested, multi-component structures, and navigating between different elements—residues, chains, ligands, or even different molecules—can become overwhelming. If you’ve ever found yourself hunting through a jumbled 3D scene or struggling to isolate a specific…

Computational chemistry and molecular modeling software often comes with a catch: installation requires admin rights, which are typically restricted on institutional machines or shared HPC environments. This can become a significant hurdle—especially for students, researchers in restrictive IT environments, or…

When preparing molecular presentations or designing animations that highlight reaction mechanisms, structural alignment, or molecular interactions, one challenge you might encounter is the need to shift your viewpoint without rotating or redirecting focus. For example, you may want to pan…