Molecular modeling can often involve managing complex systems with various components that require distinct visualization styles. Switching back and forth between different representations can feel like a daunting task, especially when working with large molecular systems or preparing visualizations for presentations. Fortunately, SAMSON’s Visual Presets feature offers a powerful solution to simplify this process and save time.
What are Visual Presets?
Visual Presets in SAMSON allow users to apply multiple visual representations and color schemes to molecular systems simultaneously, with just a few clicks. Whether you want to highlight ligands, receptors, or other molecular components, you can do so efficiently without manually configuring each visualization element. This feature is not only a time-saver but also helps create clear and consistent visualizations for analysis, reports, and presentations.
How to Apply Visual Presets
Applying Visual Presets is straightforward. Simply navigate to either the Home menu or the Visualization menu, select “Visual preset,” and choose your desired option from the list of available presets. This instantly adjusts the display of your molecular system. Here’s a snapshot of the Protein-ligand preset applied to PDB code 1AA1:
When selecting a Visual Preset, the changes apply to the currently selected nodes in your document. If nothing is selected, it will apply to the entire molecular system. The preset generates a folder in the document to organize visual models and node groups involved in the visualization—ensuring everything stays tidy.
Going Beyond: Creating Custom Visual Presets
One size doesn’t always fit all. This is why SAMSON lets users create their own Visual Presets tailored to their specific needs. By using the Visual Preset Editor, you can modify existing presets or create entirely new ones from scratch. Each Visual Preset consists of a series of steps, and each step has four customizable components:
- A selection of nodes (e.g., “Receptor,” “Ligands,” “Water,” etc.).
- Actions applied to the selection (e.g., “Hide,” “Label atoms,” “Zoom on selection,” etc.).
- A visual model for the selection (e.g., “Van der Waals,” “Licorice,” “Ribbons,” etc.).
- A color scheme for the nodes or visual model (e.g., “Constant,” “Per chain,” etc.).
Custom presets streamline repetitive workflows and ensure your visualizations are consistent across projects. Once saved, your presets load automatically with SAMSON every time for quick access.
Examples of Use
Imagine working on a protein-ligand interaction study. Instead of manually adjusting visualization settings every time, you can set up a custom preset that specifically highlights the receptor with Ribbon-style models, displays ligands in Licorice models, and uses distinct color schemes for clarity. This preset can then be reused consistently across similar studies or presentations.
Creating a visual preset only takes a few minutes and can save hours in the long run, especially when working on complex systems or collaborations where consistency is key.
Want to explore SAMSON’s Visual Presets and unleash the full potential of molecular visualization? Check out the official documentation at https://documentation.samson-connect.net/users/latest/visual-presets/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Start designing and visualizing molecular systems effortlessly today by downloading SAMSON at https://www.samson-connect.net.