For molecular modelers, time and clarity are critical when working on complex molecular systems. One of the most common pain points is the effort required to properly visualize the system, which often involves switching between different representations, color schemes, and models to make sense of intricate data. What if you could do all of that quickly, in just a few clicks? That’s where SAMSON’s Visual Presets come in.
What Are Visual Presets?
Visual Presets in SAMSON are powerful tools designed to simultaneously apply multiple visual representations and color schemes to molecular systems. Whether you’re dealing with proteins, ligands, or intricate atomic structures, these presets help streamline the visualization process. Instead of manually configuring each part of a system, you can apply these pre-set configurations to achieve a comprehensive, meaningful view in moments.
How to Apply Visual Presets
Applying a visual preset is straightforward:
- Go to the Home or Visualization menu.
- Select Visual preset and choose from the list of available options.
For instance, the ‘Protein-ligand’ visual preset provides a clear and distinguishable representation for protein-ligand systems, as demonstrated on PDB code 1AA1 below:
When you apply a visual preset, it creates a folder in the document to organize the visual outputs and selections. This makes it easy to keep track of specific nodes and visual models.
Customizing and Creating Your Own Visual Presets
One of the biggest advantages of SAMSON’s Visual Presets is that you’re not limited to the default options. The platform allows you to customize or create your own presets from scratch using the Visual Preset Editor.
Each visual preset consists of several steps, each defining:
- The selection of nodes (e.g., “Receptor,” “Ligands,” or “Water molecules”).
- An optional set of actions (e.g., “Hide,” “Label atoms,” or “Zoom on selection”).
- An optional visual model (e.g., “Ribbons,” “Van der Waals,” or “Licorice”).
- An optional color scheme (e.g., “Per chain,” “Constant,” or “Per occupancy”).
To create a new preset, navigate to Home > Visual preset > Create…. You can start fresh or modify an existing one by adding or removing preset steps and adjusting actions, visual models, or color schemes. For instance, here’s how you can add a new step to your visual preset:
Don’t see a relevant selection in the default list? Expand your possibilities by clicking More… to create custom selections using the Node Specification Language. This allows you to tailor the visualization even further.
Why Use Visual Presets?
Visual Presets save time and enhance clarity by automating repetitive visualization tasks. Whether you’re preparing presentations, exploring structural details, or simply trying to understand complex molecular data at a glance, these presets provide a fast and organized solution. Furthermore, with the option to create your own presets, you can easily align visualizations with your specific research or communication needs.
Explore More
Ready to dive deeper into visual presets and unleash their full potential? Visit the official documentation page here: SAMSON Visual Presets Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at samson-connect.net.