Creating high-quality molecular visualizations can often feel like a time-consuming and repetitive process. Whether you’re prepping figures for a publication or crafting an animation for a presentation, tweaking rendering settings and applying consistent visuals across structures can quickly become a chore. Fortunately, if you’re using SAMSON, there’s a much faster way: visual presets.
Visual presets in SAMSON are predefined combinations of visual models and color schemes that you can apply to your molecular systems with just a few clicks. Instead of adjusting multiple parameters every time you want to produce a specific type of visualization, you can select a preset that sets everything up for you instantly—speeding up your workflow while ensuring consistency across your images.
What Are Visual Presets?
Visual presets are SAMSON’s answer to repetitive settings adjustments. Each preset links together multiple visual elements—such as structural representations, colors, and rendering options—into a bundled configuration you can apply instantly. Want to emphasize ligands and receptors? Or perhaps showcase protein secondary structures in an illustrative style? Presets get you there fast.
Example: Below you can see SAMSON’s “Protein-ligand” visual preset applied to the protein with PDB code 1AA1. This preset automatically selects a van der Waals representation for ligands, ribbons for proteins, and assigns meaningful colors to molecular components.
How to Apply a Visual Preset
You can apply a visual preset by going to Visualization > Visual preset in the SAMSON interface. From there, simply choose the preset you need from the list. You’ll instantly see the system’s appearance update in the viewport.
If you’ve modified your system already and want to return to a clean style, you can re-apply a visual preset to reset the visual model. You can also layer additional visual models on top if needed.
Make Your Own Presets
Have a specific look that you use often? You don’t have to recreate it each time. SAMSON allows you to create and save your own visual presets. Customize an existing one by changing models, colors, transparency, and effects, then save it via Visualization > Visual preset > Save As. This is especially helpful for teams that want standardized visuals across projects.
Illustrative Style Inspired by PDB’s Molecule of the Month
Love the hand-drawn feel of RCSB PDB’s Molecule of the Month illustrations? SAMSON includes a preset called Illustrate… that mimics this style. Here’s what it looks like:
To apply both the visualization and rendering aesthetics, combine the visual preset with the rendering preset found in Visualization > Presets > Illustrative.
Why It Matters
Molecular modelers often spend significant time customizing visual elements to make their structures stand out or to emphasize specific scientific points. Visual presets simplify this process and reduce margin for error. They also make it easier to switch between different styles depending on your audience—be it researchers, students, or the general public.
By leveraging presets, you can avoid tedious manual edits, accelerate visualization setup, and streamline your workflow.
To learn more about visual presets in SAMSON, visit the full documentation page: https://documentation.samson-connect.net/users/latest/visualizing/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.