For molecular modelers, visualizing intricate nanosystems effectively is a crucial part of their workflows. Whether you’re examining protein secondary structures, electron density maps, or electrostatic fields, a clear and intuitive graphical representation can make a world of difference. SAMSON, the integrative molecular design platform, provides robust tools to address this challenge: its Visual Models.
Let’s explore how SAMSON’s Visual Models help bring clarity to complex molecular systems and aid in streamlining workflow.
What are Visual Models?
Visual Models in SAMSON provide graphical representations of nanosystems, helping users analyze and interact with molecular data effectively. For instance, you might use visual models to display the secondary structure of proteins, create Gaussian surfaces, or observe isosurfaces of an electron density. They also allow you to visualize volumetric data, such as an electrostatic field.
SAMSON comes equipped with a set of default visual models, and additional models can be added via SAMSON Connect or SAMSON Extensions.
Using Visual Models in Your Workflow
Applying visual models in SAMSON is intuitive and flexible. You can apply them to selected nodes (like atoms or residues), or to the entire document when nothing is selected. The convenient ways to apply visual models include:
- Using the context toolbar menu of the selected element.
- Navigating through the menu: Visualization > Add > Visual model.
- Utilizing the shortcut
Ctrl(orCmdon Mac) +Shift+V.
To further customize this experience, some visual models allow parameter editing in the SAMSON Inspector. For instance, you can modify visualization parameters for secondary structure representation. To do so:
- Select the visual model in the Document view.
- Click on Inspect in the context menu.
As a bonus, the default visual models also facilitate selection and highlighting of atoms, residues, chains, etc., by allowing you to interact directly with surfaces based on the current selection filter.
Examples of Default Visual Models
SAMSON offers a variety of default visual models that cover common use cases. Below you can see an example of some of these visual models in action:
Tips for Developers
For those interested in crafting their own visual models, SAMSON supports extensibility through custom visual model development. By referring to the documentation about generating SAMSON Extensions, developers can create tailored visualizations aligned with specific modeling needs. More details can be found in the Documentation center.
Final Thoughts
Visual models in SAMSON make it easier to analyze and make sense of molecular complexity, enhancing the efficiency of your research and design tasks. By leveraging SAMSON’s in-built features or extending your toolkit with SAMSON Connect, you can make your molecular modeling journey much more intuitive.
To learn more about the various features of visual models and their practical applications, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.