Starting a new molecular modeling project often means spending a lot of time tweaking visual representation settings. If you’ve ever wished there was a way to accelerate this part of your workflow while still producing high-quality, beautiful images, visual presets in SAMSON might be exactly what you need.
Visual presets allow users to apply a combination of visual models and color schemes to complex molecular systems in just a few clicks. These presets can dramatically improve your molecular figures for papers, presentations, or internal discussions, all while saving time.
What Are Visual Presets?
In SAMSON, a visual preset is a pre-configured style that determines how a molecular system appears in the viewport. These presets set up representations (like ribbons or van der Waals spheres), color schemes, and sometimes even rendering effects all at once.
To apply one, go to Visualization > Visual preset. SAMSON comes with several built-in presets, such as the Protein-ligand configuration, which quickly renders a biologically meaningful view.
When Should You Use Visual Presets?
Visual presets are particularly useful:
- When you need a good-looking figure quickly
- When working with large molecular systems that require consistency in representation
- As a starting point before customizing visual styles
- When generating animations where consistency helps with clarity
Example: Protein-Ligand Visualization
Here’s an example of the Protein-ligand preset applied to a protein with PDB code 1AA1:
This preset illustrates ligands and the protein environment with well-balanced transparency and coloring, instantly making the representation more insightful than default rendering.
Customizing and Saving Your Own Presets
You’re not limited to the defaults. Once you’ve modified a visual preset to your liking—added or removed visual models, changed colors, or adjusted rendering settings—you can save it as a custom preset for later use.
To create one:
- Customize your current visualization using different visual models, color schemes, and effects.
- Go to Visualization > Visual preset and choose the option to save your current configuration as a new preset.
This lets you establish a consistent style across all your projects or within a research group.
A Note on Workflow Integration
Visual presets integrate smoothly into other SAMSON workflows. For example, if you develop a script or tutorial, applying presets programmatically can standardize outputs. It also ensures other team members can replicate the same look with minimal effort.
Visit the full visualizing section of the SAMSON documentation to explore how to apply and create your own visual presets.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.