Visualizing complex molecular systems is often a time-consuming challenge for molecular modelers. Manually applying visual representations and color schemes to represent different elements of molecular structures can feel tedious and prone to inconsistency. If you’re looking for an efficient way to streamline this process, SAMSON’s Visual Presets can be a game-changer. This feature allows you to apply multiple illustrations and color schemes to complex systems quickly, saving both time and effort.
Visual Presets are an easy-to-use tool accessible from the Home menu and the Visualization menu in SAMSON. By leveraging these presets, you can instantly generate professional-looking molecular models, whether you are illustrating proteins, ligands, or other molecular components. Here’s everything you need to know to incorporate this feature into your workflow effectively.
How to Apply a Visual Preset
Applying a visual preset in SAMSON is simple. Navigate to Home > Visual Preset or Visualization > Visual Preset, and choose from the list of existing presets. These include a variety of default presets tailored to highlight specific molecular features.
For example, here’s how the Protein-Ligand preset transforms PDB code 1AA1:
The preset allows instant visualization, conveniently grouping visual elements into folders within the document. If nothing is selected in the molecular document, the preset applies to the entire system. This simplifies organization and ensures clarity, especially when dealing with large or complex systems.
Customizing and Creating New Presets
If the default visual presets don’t entirely suit your needs, you can create your own or modify existing presets using the Visual Preset Editor. This powerful tool enables you to tailor visualizations precisely to your preferences.
Each visual preset consists of a sequence of steps:
- A selection of nodes to target (e.g., receptors, ligands, or specific atoms).
- An optional set of actions to perform on the selection (e.g., hiding components or labeling atoms).
- A visual model to apply (e.g., ribbons, van der Waals representation).
- An optional color scheme to enhance perception (e.g., per chain, per element).
To create a new preset:
- Navigate to Home > Visual Preset > Create…, or Visualization > Visual Preset > Create….
- Click the
button to add steps, define node selections, assign actions, and customize color schemes.
Here is an example of the interface used to define a selection:
You can even create fully customized node selections using SAMSON’s Node Specification Language, making it incredibly versatile for specific research needs.
Adding Finishing Touches
Once your visual preset is complete, you can reorder or fine-tune steps, apply color palettes, and save your design for future use. These personalized presets will be loaded each time you launch SAMSON, ensuring a consistent and efficient workflow tailored to your visual style.
If you’d like to contribute your presets to SAMSON’s default library, use the Send Feedback button in the platform to get in touch.
For an in-depth guide, visit the official documentation page here.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use.