A molecular scene can become difficult to read long before the underlying model becomes complicated. A receptor, ligand, water molecules, and other structures may all be visible at once, and switching representations or colors one object at a time can turn a quick inspection into a repetitive task. The challenge is not just making one useful image—it is being able to return to a clear, consistent view when you need it again.
SAMSON visual presets address this by collecting visualization choices into an ordered set of steps. A step can specify which nodes it applies to, optional actions, a visual model, and a color scheme. Apply a preset to selected nodes, or—with nothing selected—to the whole document. This makes presets useful both for a targeted view and for a repeatable starting point across a larger molecular scene.
Think in layers, not individual clicks
When building a readable view, first decide what the viewer should notice. For a protein–ligand scene, that might be the ligand’s position, the surrounding receptor, and selected nearby atoms. Then translate those priorities into separate preset steps: choose the relevant selection, decide whether an action is needed, and add a representation or colorization where it helps.
For example, a step can target a selection such as Ligands or Receptor, use a model such as Licorice or Ribbons, and apply a color scheme. Another step can use an action such as Zoom on selection or Label atoms. These are examples of available choices, not a required recipe: the useful combination depends on what you want to inspect.
Keeping choices in distinct steps also makes the preset easier to adjust. If the ligand is hard to distinguish, revise its step’s model or colorization rather than changing the entire scene. If an action should happen before another one, use the step-order controls to move the steps up or down. Within one step, multiple actions run in the order they were added.
Build a preset around the scene you actually have
Open the editor from Home > Visual preset > Create… or Visualization > Visual preset > Create…. You can start from an existing preset and modify it, or use the plus button to create one from scratch. Starting with an existing preset can be a practical way to keep a useful setup and change only what does not suit your system.
Each new step needs a selection. The default is Any node: it applies to the whole document when nothing is selected, or to the current selection when the preset is applied. If the built-in choices—such as Receptor, Ligands, or Water—do not describe the nodes you need, use More… to compose a selection in the Find window with the Node Specification Language.
Know what the color setting affects
Colorization can be left unspecified, set to a constant color, or chosen from element- and attribute-based schemes. One detail matters when troubleshooting a result: if a visual model is specified but no colorization is chosen, that model uses its default colorization. If no visual model is specified, a chosen colorization is applied to the structural nodes selected by the step.
When a scheme has a palette, you can double-click the palette field to choose or create a palette. For a constant-color scheme, double-click the color to change it. To return to the scheme’s default palette, open the palette chooser and select Default color palette.
Apply, check, and keep the useful version
After editing, apply the preset and inspect the result on the intended selection or document. If a step affects more nodes than expected, check its selection—especially if it is set to Any node. If the scene is too busy, consider whether every step needs a model or colorization, and remove actions that do not support the view’s purpose. You can delete a step by selecting its line and choosing Delete step.
When the setup works, choose Save visual preset. You can also click Apply and choose whether to save when prompted. Saved custom presets load alongside the defaults when SAMSON launches, so a view you have refined can be reused rather than reconstructed from memory.
For the full editor instructions and additional examples, see the Visual presets documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.