Author: OneAngstrom

A molecular system can look perfectly reasonable in a viewer and still be poorly prepared for simulation. With periodic boundary conditions, the box is repeated in every direction. That means a solute is not surrounded by empty space: copies of…

Pulling one part of a molecular system away from another sounds straightforward—until periodic boundaries enter the picture. In a periodic simulation box, a molecule that travels too far can interact with its own periodic image. A box that is too…

A structure can look ready for simulation and still contain molecules that complicate preparation: alternate locations, unwanted ligands, waters, or monatomic ions. But “cleaning” is not always a matter of deleting everything that is not protein. Some waters may be…

A camera move can make a molecular scene easier to understand—or harder to follow. A common problem is moving closer to a region while also changing what the view is centered on. If the camera only has one target point…

A molecular model can look ready to simulate and still leave important questions unanswered: Are its bonds correct? Should the force field use the existing connectivity, or infer it from the atoms? What should you do if the setup reports…

A molecular structure can be difficult to inspect when a view shows only one side of a group. A short rotation can help reveal its shape and make a presentation easier to follow. In SAMSON, the Rotate animation turns a…

A molecular modeling session can accumulate more than molecular structures. It may also involve scripts, reference images, PDFs, conformations, paths, and other supporting material. When those pieces are scattered across folders or mixed into one crowded view, it becomes harder…

Starting a DNA nanostructure project often means more than finding a shape you like. A design may come as a caDNAno file, an Adenita component, or simulation files—and those formats serve different purposes. It can be easy to lose time…