A molecular scene can be scientifically useful and still be difficult to read. One model may show the receptor as ribbons, another may use a different ligand representation, and a third may color the same atoms differently. Rebuilding those choices every time takes attention away from the structure—and makes comparisons between images harder.
In SAMSON, a visual preset lets you save a sequence of visualization choices and apply them together. The useful idea is not just to make a scene look polished once: it is to turn a repeatable visualization workflow into something you can run again.
Start with a clear visual question
Before building a preset, decide what the image should help someone notice. For a protein–ligand scene, the question might be where the ligand sits relative to the receptor. That can guide choices such as showing the receptor as ribbons, displaying the ligand with a more detailed model, and using color to distinguish the relevant parts.
Presets are made of steps. Each step specifies a node selection and can optionally add actions, a visual model, and a color scheme. This gives you a way to treat different parts of a molecular system differently instead of applying one representation to everything.
Make the scope explicit
A common source of confusion is applying a preset to the wrong part of a document. SAMSON applies a preset to the current selection; if nothing is selected, it applies to the whole document. When you are testing a preset, check the selection first. If a step should target a specific kind of node—such as a receptor, ligand, or water—choose an appropriate selection rather than relying on the broad default of Any node.
If the available selections do not describe what you need, the editor provides a More… option that opens the Find window, where you can compose a selection using the Node Specification Language. This is useful when your visualization depends on a more specific group, such as particular atoms in a ligand.
Build the sequence deliberately
Actions in a step run in the order they were added, and steps themselves can be moved up or down. Think of the preset as a small recipe: decide which groups to select, what should be hidden or labeled, which model should represent each group, and where color will help interpretation. If you add actions such as hiding nodes, labeling atoms, or zooming on a selection, review their order and test the result on a representative document.
Colorization has an important detail: if you choose a visual model but no colorization, that model uses its default colors. If you choose colorization without a visual model, the colors are applied to the structural nodes selected by the step. You can also change the palette associated with a scheme, or return to its default palette in the palette dialog. Keeping the color choices purposeful can make a preset easier to interpret and reuse.
Save a workflow, not just a snapshot
You can start from an existing preset and adjust its steps, selections, models, or colors, or create a new preset from scratch. Save it with the Save visual preset button. Custom presets are loaded along with the defaults when SAMSON launches, so the same visualization setup is available for later work. Applying a preset also creates a folder in the document containing the visual models it created and node groups corresponding to the selections—helpful when inspecting how the result was assembled.
A practical way to refine a preset is to apply it to a representative system, check whether each selection captures the intended nodes, and adjust one choice at a time. Then apply it to another suitable system to see whether the workflow remains useful beyond the document where it was created.
For more details, see the Visual presets documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.