Color is not just decoration in molecular modeling—it’s a way of encoding meaning and guiding perception. When visualizing complex structures, whether you’re comparing conformations, tracking changes in dynamics, or simply preparing a figure for publication, the color palette you choose…

As a molecular modeler, visualizing structures effectively is vital—not just for presentation purposes, but also for developing an intuitive understanding of complex nanosystems. Whether you’re analyzing protein folding, inspecting electrostatic fields, or preparing publication-quality visuals, selecting an appropriate visual model…

When working with protein conformations, it’s common to want to generate a smooth transition pathway between two structures—say, for insight into functionally relevant motions or for use in simulations like umbrella sampling. But here’s a common blocker that molecular modelers…

Designing DNA nanostructures is often only the beginning of a molecular modeling workflow. Whether you’re crafting wireframe geometries or constructing detailed double-stranded models, the next step is frequently simulation—one of the most powerful ways to assess stability, dynamics, or interactions.…

Many molecular modelers and computational scientists face the same recurring issue: needing administrator rights to install powerful simulation tools on their machines. Whether you’re using an institutional computer with limited access or a virtual machine setup, the need for admin…

As molecular modelers, we frequently compile complex projects involving not only molecular structures but also simulation scripts, datasets, papers, and custom tools. When it’s time to share our work with collaborators or transfer it to another machine, juggling all these…

Choosing the right color palette might seem like a small detail when setting up a molecular visualization, but it can make a significant difference—especially when working with large, complex systems or preparing visuals for publication. In SAMSON, the integrative molecular…

In molecular animation, it’s often important to draw attention to specific components at precise moments. Whether you’re presenting a complex assembly mechanism or highlighting a transient interaction, how you manage visibility can make the difference between clarity and confusion. This…

Running energy minimization jobs using GROMACS in SAMSON can be highly efficient, especially with the user-friendly interface of the GROMACS Wizard. But here’s a common challenge: how do you keep track of your jobs while continuing your work? Molecular modelers…

Presenting molecular structures in a compelling and understandable way can be challenging—especially when sharing models with others who may not be familiar with atomic-level geometry. While static visuals are useful, they often fail to convey spatial relationships and structural details…