When visualizing molecular systems, researchers often struggle with a surprisingly common challenge: understanding how different parts of a structure relate to each other in space. Despite complex 3D views, depth and spatial separation can remain ambiguous—especially in crowded systems.
That’s where rendering effects come in, and in particular, shadows. Shadows provide important visual cues about the relative positions of atoms, molecules, and other objects in 3D space. Enabling them in your molecular design tool can drastically improve clarity, especially when analyzing interactions or creating explanatory visuals for publications and presentations.
Why shadows matter
Let’s take the example of the PDB structure 1YRF displayed in front of a graphene sheet. Without shadows, it can be difficult to judge whether the biomolecule is above, below, or overlapping with the graphene. The image becomes visually ambiguous, increasing the cognitive load needed to interpret spatial relationships.
However, when shadows are enabled, everything changes. Shadowing anchors the molecule in the scene. Subtle differences in lighting clearly communicate which components are closer to the light source and where objects are positioned relative to one another.
How to enable shadows in SAMSON
In SAMSON, you can find shadow settings under:
- Interface > Preferences > Rendering > Shadows – for fine-tuning parameters
- Visualization > Options – to quickly toggle shadows on or off
This flexibility allows you to choose between different quality levels, which is particularly useful if you’re working on a computer with an older graphics card. Lower-quality presets are available for maintaining smooth performance.
Without shadows:
With shadows enabled:
What to look out for
Shadows can have a performance impact depending on your hardware and the complexity of your model. This is why SAMSON allows you to easily switch between presets or disable shadows entirely when working with very large systems or under tight hardware constraints.
If shadows are not rendering smoothly, try the following:
- Switch to a lower shadow quality preset
- Disable additional rendering effects like Bloom or Depth of Field
- Ensure your graphics drivers are up to date
Final thoughts
Using shadows is a simple change that can make a significant difference in how understandable and visually compelling your molecular structures are. Whether you’re preparing figures for a paper or just trying to make sense of a complex assembly, this rendering effect is worth enabling.
Try it out yourself and experiment with different lighting conditions to see how shadows can help you better interpret your molecular data.
To learn more about shadows and other rendering effects in SAMSON, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/rendering-effects/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.