For molecular designers and modelers, managing visual representations of molecular systems is critical. In SAMSON, the Visual Model attribute space (vm) is designed specifically to handle attributes that define how visual model nodes appear and behave. These attributes can help you control visibility, material assignment, selection, and more, which can be essential for handling large and complex molecular systems effectively.
To get started, let’s break down some key Visual Model attributes and their functionalities:
1. Controlling Visibility
The visible and hidden attributes define whether a visual model node is displayed or not. For example, you can use vm.v for checking whether a model is visible (true or false), and combine it with logical statements like not vm.v to hide structures that are not needed.
Additionally, the visibilityFlag attribute (vf) allows fine-tuning that complements the primary visibility control. For instance, setting vm.vf false will toggle a model’s immediate visibility preference.
2. Material Assignment
Materials are essential for customizing the aesthetic appearance of models. The attribute hasMaterial (hm) checks if a material is assigned to a visual model node, while ownsMaterial (om) determines whether the material is owned directly by the node itself. This allows you to control or isolate specific visual properties, such as colors or textures.
3. Labeling with Names
The name attribute (n) is a powerful way to identify or label specific visual models. You can assign strings to models using commands like vm.n "A" for better organization and search functionality. For advanced searches, wildcards can also be used. For example, vm.n "L*" matches all visual models whose names start with the letter L.
4. Selection and Interaction
Selecting and flagging nodes within your visual models ensures precise interaction. The selected attribute enables you to verify whether a visual model is selected (true or false). Pair this with the selectionFlag (sf) for advanced manipulations, like toggling the broader context of what gets highlighted or adjusted.
Effective use of these attributes can dramatically improve how molecular systems are displayed and navigated in SAMSON. Whether you are organizing a large dataset, isolating key fragments, or preparing your models for presentations, leveraging the Visual Model attribute space can streamline your workflow.
To see the complete list of Visual Model attributes and further details, visit the SAMSON Visual Model documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.