As a molecular modeler, visualizing complex molecular systems is a frequent task, but one that can be time-consuming. Iterating through various visual representations, color schemes, and selections can feel like a repetitive chore. Did you know you can save time and effort by using visual presets in SAMSON?
Visual presets allow you to apply multiple visual representations and color schemes at once with just a few clicks. This blog post will guide you through the basics of applying and creating your own visual presets to make your workflows more efficient and productive.
What Are Visual Presets?
Visual presets are predefined configurations that combine multiple visual styles and colorings for molecular systems. These presets are suitable for various visualization needs, whether you’re working on a protein-ligand complex, analyzing molecular interactions, or preparing for a presentation. You can access them from the Visualization or Home menu.
SAMSON comes with a useful set of default visual presets to get you started, such as the Protein-Ligand preset. You also have the flexibility to customize them or create entirely new ones for tailored workflows.
How to Apply Visual Presets
Applying visual presets in SAMSON is straightforward:
- Navigate to Home > Visual preset or Visualization > Visual preset.
- Select your desired preset from the list. For example, the Protein-Ligand preset can instantly provide an organized view of PDB entries, highlighting key structures and their interactions.
Here’s an example showing how the Protein-Ligand preset looks on PDB code 1AA1:
Once applied, the visual preset creates a folder in your molecular document containing visual models and node groups associated with the preset. If you’ve selected specific nodes, the preset applies only to those; otherwise, it’s applied to the entire document.
Create Your Own Visual Presets
If the default visual presets don’t meet all your needs, SAMSON allows you to create your own presets using the Visual Preset Editor. This way, you can streamline your workflows even further by tailoring visualizations to your personal preferences or project-specific requirements.
Here’s how you can get started:
- Go to Home > Visual preset > Create… or Visualization > Visual preset > Create….
- To create an entirely new preset, click the
button next to the existing presets list. - Add a step using the Add step button and configure it by specifying a selection of nodes, actions (e.g., hide or label atoms), a visual model (e.g., ribbons or licorice styles), and optional colorization (constant colors, chain-based schemes, etc.).
- If needed, you can create custom node selections using the Find window with the Node Specification Language.
- Save your customized visual preset for future use, or simply apply it directly to your current project.
Here are some interface elements from the preset creation process:
By carefully organizing your preset steps, you ensure quick and consistent visualizations that align with your workflow.
Improve Your Efficiency
Whether you’re visualizing molecular datasets for analysis or creating polished images for presentations, visual presets can dramatically simplify your task. Save time, reduce repetitive steps, and focus on the science rather than the setup.
Explore how visual presets in SAMSON can help you. For more details on applying and creating visual presets, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.