A molecular structure can contain exactly the information you need and still be difficult to read. Receptor, ligands, water, and other nodes may all appear with similar visual weight, while changing representations and colors one by one can make a simple comparison feel like a repetitive setup task.
Visual presets in SAMSON address this by applying a sequence of visualization choices together. Instead of rebuilding a view from scratch each time, you can use an existing preset or create one that follows the way you work. The useful idea is not just “pick a style”: a preset can specify which nodes to affect, what actions to perform, which visual model to use, and how to color the result.
Start with the right scope
Apply a preset from Home > Visual preset or Visualization > Visual preset. If you have selected nodes, the preset is applied to that selection. If nothing is selected, it is applied to the whole document. That small detail can prevent an unexpected change to parts of a scene you meant to leave alone.
For example, if you want to adjust only a ligand or a receptor component, select it first. If your goal is to establish a view for the entire structure, clear the selection before applying the preset. The Protein-ligand preset shown below is an example of applying a preset to PDB structure 1AA1.
When a preset is applied, SAMSON creates a folder in the document named after the preset. The folder contains the visual models created by the preset and node groups corresponding to its selections. This gives you a place in the document to find the visualization elements produced by that application.
Build a view as a sequence of decisions
A custom preset is made of steps. Each step has four parts:
- Selection: which nodes the step targets, such as the receptor, ligands, or water.
- Actions: optional operations such as hiding nodes, labeling atoms, or zooming to the selection.
- Visual model: an optional representation, such as Van der Waals, Licorice, or Ribbons.
- Colorization: an optional color scheme, such as per chain, per occupancy, or a constant color.
Thinking in this order helps turn a vague goal like “make the binding site easier to inspect” into manageable choices: identify the nodes, decide what should be visible or highlighted, choose a representation, then select colors that distinguish the relevant parts. These are choices available in the editor, not a requirement to use every option in every step.
Actions within a single step run in the order they were added. If the order matters to your intended view, arrange the actions accordingly. You can remove an action with the X that appears when you hover over it. Steps can also be deleted or moved up and down, so you can refine the sequence without starting over.
Customize instead of repeating work
Open the Visual Preset Editor through Home > Visual preset > Create… or Visualization > Visual preset > Create…. You can modify an existing preset or use the plus button to make a new one from scratch. A new step defaults to Any node, meaning it applies to the whole document when nothing is selected, or to the current selection when you apply the preset to selected nodes.
If the built-in selection options do not fit your structure, choose More… in the selection list. This opens the Find window, where you can compose a selection using the Node Specification Language. For color, you can use a scheme’s default palette or double-click the palette field to choose or create another palette. A constant-color scheme can be adjusted in the same way by double-clicking its color.
One helpful distinction: when a visual model is specified but no colorization is chosen, the model uses its default colorization. When no visual model is specified, a chosen colorization applies to the structural nodes identified by the selection. Keeping that distinction in mind makes it easier to understand where a color choice will take effect.
Save a preset when you want to reuse it; saved custom presets load alongside the defaults when SAMSON launches. You can also apply a preset and then choose whether to save it. For a repeatable workflow, begin with a preset close to your goal, adjust only the selections and steps that need changing, and save the result under a useful name.
See the Visual presets documentation for the complete editor workflow and options.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.