Preparing a molecular structure for inspection or a figure often involves the same small chores: choosing representations, setting colors, hiding distracting nodes, and zooming to the right place. Repeating those choices by hand can slow down a workflow—and make it harder to keep views consistent across structures.
SAMSON visual presets help bundle those choices into a reusable sequence. Instead of rebuilding a view each time, you can apply an existing preset or make one that matches the way you work.
Apply a preset without changing the whole document by accident
Choose a preset from Home > Visual preset or Visualization > Visual preset. If you have selected nodes, the preset applies to that selection. If nothing is selected, it applies to the whole document. That distinction is useful when you want to restyle just a ligand or receptor, but it is worth checking your selection before applying a preset.
When applied, the preset creates a folder in the document containing the visual models it creates and node groups that correspond to selections. This makes the resulting organization easier to inspect alongside the structure.
For example, the Protein-ligand preset can quickly establish a view of a protein–ligand system such as PDB entry 1AA1:
Build a preset around a repeatable question
A useful custom preset is not just a collection of attractive settings. Start by asking what you usually need to see. Is the goal to inspect the ligand in its binding site, distinguish chains, or make a particular group of atoms easy to find? A clear purpose helps keep the preset focused.
Open the editor through Home > Visual preset > Create… or Visualization > Visual preset > Create…. You can modify an existing preset or create one from scratch. Each step combines up to four kinds of choices:
- Selection: which nodes the step affects, such as the receptor, ligands, or water.
- Actions: optional operations such as hiding nodes, labeling atoms, or zooming to a selection.
- Visual model: an optional representation, such as ribbons or licorice.
- Colorization: an optional color scheme for the selection or visual model.
Think of the steps as a small sequence: identify the relevant nodes, apply any actions, then set their representation and colors. Multiple actions in one step run in the order they were added, so order matters if one action changes what is visible or emphasized. You can move steps up or down when the sequence needs adjusting.
Make selection and color choices deliberate
The default selections cover common node types, but you are not limited to them. If the list does not match your intended group, choose More… to open the Find window and compose a selection using the Node Specification Language. Precise selections help prevent a preset from styling unrelated parts of a document.
Colorization is optional. 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 in the selection. You can also change a preset’s palette by double-clicking its color palette field, or return to the default palette for that scheme in the palette dialog.
When the preset looks right, use Save visual preset to keep it for future sessions. You can also apply it first and choose whether to save when prompted. Saving a focused preset turns repeated setup into a quick, consistent starting point—while leaving you free to make local adjustments for a particular structure.
For details on applying, editing, and saving presets, see the Visual presets documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.