For molecular modelers, creating clear, compelling visualizations of complex molecular structures can be a daunting task. Analyzing intricate systems and presenting them effectively often requires toggling between multiple visualization tools, color schemes, and rendering styles—a tedious process that can consume valuable time. Thankfully, SAMSON has a solution that simplifies this workflow: Visual Presets.
Visual Presets are pre-configured settings in SAMSON that allow users to apply multiple visual representations and color schemes to molecular systems quickly and easily. Whether you’re looking to depict a protein-ligand complex, render secondary structures, or explore intricate details, Visual Presets can streamline your work. Here’s how you can use Visual Presets to enhance your molecular visualizations effortlessly.
Applying Visual Presets
Applying a Visual Preset in SAMSON is straightforward and efficient. Here’s how you can do it:
- Go to Visualization > Visual preset in the menu.
- Select a predefined preset from the list, such as “Protein-ligand” or “Illustrative”.
For instance, the “Protein-ligand” preset provides a clear depiction of receptor-ligand interactions with visually distinct representations for proteins, ligands, and ions. Below is an example of how the “Protein-ligand” preset looks with PDB code 1AA1:
Users even have the option to create and save their own presets, allowing them to customize visualizations based on specific project needs.
Illustrative Visualization and Rendering Style
If you want to achieve striking, publication-quality visuals, the illustrative preset is particularly useful. Inspired by the style of RCSB PDB Molecule of the Month, this preset provides a textured, hand-drawn effect that can vividly showcase molecular structures.
- Apply the illustrative visualization style by selecting Visualization > Visual preset > Illustrate…. This preset highlights receptor and ligand molecules with van der Waals representations and an intuitive color scheme.
- Adjust rendering preferences to match the illustrative style via Visualization > Presets > Illustrative. This step adjusts parameters like lighting, shadows, and silhouettes to add depth to your molecular scene.
Here’s an example showcasing the “Illustrate” style:
Customizing and Creating Visual Presets
Beyond using default presets, you can modify existing settings or design your own. For instance, if you frequently work with specific color schemes or want to emphasize particular molecular components, you can tweak an existing preset and save it for reuse.
By creating custom presets, you can unify the appearance of multiple visualizations, which is particularly helpful when preparing a series of images or animations for a publication.
A Time-Saving Tip
Incorporate Visual Presets into your daily molecular modeling routine by saving your commonly used settings. Whenever you need to switch between projects or collaborations, your personalized configurations can serve as a reliable starting point, significantly boosting productivity.
Conclusion: Visual Presets are a powerful feature in SAMSON that simplify the visualization process, helping you save time while creating stunning molecular representations. Whether you’re exploring molecular systems for analysis or preparing visuals for presentations, explore Visual Presets to make the process efficient and enjoyable.
To learn more about using and customizing Visual Presets, visit the official documentation page here.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get your copy today at SAMSON Connect.