Building a long molecular structure by placing every unit one at a time is tedious—and small alignment errors can accumulate as the structure grows. A more manageable approach is to make one repeat unit, arrange copies with pattern editors, then…
A molecular system can look perfectly prepared and still have a box that is too small. With periodic boundary conditions, the simulation repeats the system in every direction. If the solute is too close to its own periodic copy, it…
When a molecular scene contains several render presets, the practical problem is often not creating another one—it is identifying the right preset without confusing its name with its selection state. SAMSON’s Node Specification Language (NSL) provides a compact way to…
A molecular structure can be in the right place and still be difficult to explain. If you are preparing a presentation, a static image may show where a group of atoms or a mesh ends up, but not how it…
When a molecular scene gets busy, it can be surprisingly easy to lose track of its cameras. You may want to check a camera by name, or identify whether a camera node is marked selected, without accidentally applying a query…
A common frustration in molecular modeling is not knowing what you want to do—it is finding the right selection, command, or menu to make it happen. You may want to isolate a ligand, inspect nearby residues, remove waters, or change…
Building a nanotube atom by atom is tedious—and repeating a structure without careful alignment can leave gaps or overlaps where units should meet. A more manageable approach is to build the tube in two stages: make a circular ring from…
When a molecular scene contains many structural groups, it can be difficult to spot the ones relevant to a question: Which groups are unusually large? Which have a particular charge? Where are the carbon-rich groups? Inspecting them one by one…
A molecular system can finish energy minimization and still need time before it is ready for the next stage of a molecular dynamics workflow. A common source of uncertainty is temperature: should you continue to NPT as soon as the…
Pulling one molecular group away from another can be a useful step toward umbrella sampling—but a setup that looks reasonable in the interface can still be compromised by a too-small periodic box or incorrectly defined groups. The key is to…
