For many molecular modelers, one of the recurring challenges is efficiently visualizing complex molecular systems. The amount of time spent meticulously adjusting representations, selecting color schemes, and ensuring clarity can quickly become overwhelming—especially when there are deadlines or presentations just around the corner. Visual presets in SAMSON are designed to help with exactly this pain point, offering a powerful, customizable solution to streamline the visualization process.
What Are Visual Presets?
Visual presets in SAMSON allow you to apply a combination of visual representations and color schemes to your molecular systems in just a few clicks. Whether you’re working on proteins, ligands, or other molecular structures, these presets can help you achieve complex visualization styles without the tedious manual steps. Moreover, SAMSON provides a set of default visual presets, and you can even create your own customized ones to suit your specific needs.
Quickly Applying Visual Presets
To utilize visual presets, simply access the feature from the Home or Visualization menus by selecting Visual preset. From there, you can choose from the available list of presets. One prominent example is the Protein-ligand visual preset, which is tailored for molecular systems involving protein-ligand interactions.
Below is an example of how the Protein-ligand preset looks on the molecular structure represented by PDB code 1AA1:
When you apply a visual preset, it automatically creates a folder in your document where the associated visual models and node groups are neatly organized. This ensures your work remains clear and structured as you adapt or further customize the system’s visualization.
Customizing or Creating Visual Presets from Scratch
A particularly powerful feature of SAMSON is its flexibility to let users create and save custom visual presets. To get started:
- Go to Home > Visual preset > Create… or Visualization > Visual preset > Create….
- To create a preset from an existing one, simply select it from the list and modify the steps to suit your requirements. You can adjust node selections, actions, visual models, color schemes, and more.
- If you want to start fresh, click the
button next to the existing presets list to add a new one.
Each visual preset is composed of a series of steps, and in each step, you can:
- Select nodes to include (e.g., receptor, ligands).
- Add actions (e.g., hide, label atoms).
- Apply a visual model (e.g., Van der Waals, ribbons).
- Assign a color scheme or palette (e.g., per chain, constant color).
The flexibility and step-wise structure give complete control over the visualization process, allowing you to craft visuals tailored to your research or presentation needs. You can also reorder steps or delete them if necessary.
One example of customization is creating a step to highlight polar atoms in ligands. You can use SAMSON’s Node Specification Language to define your own selections.
Why Use Visual Presets?
Visual presets offer an efficient approach to manage visualization with minimal effort and time. Whether you’re analyzing molecular interactions or preparing visuals for reports, presets let you focus on the science without the distraction of extensive manual detailing. They’re also a great way to ensure your visualization work is consistent, especially when collaborating with teams or presenting to an audience.
Explore More
Want to dive deeper into visual presets or learn how to adapt them to your workflows in SAMSON? Visit the original documentation: Visual presets in SAMSON.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON today at https://www.samson-connect.net.