Update Visuals

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Customize the appearance of your proteins with colors and molecular representation styles.

Overview

The Visual Setup panel lets you:

• Change protein colors
• Switch between molecular representation styles
• Apply changes to selected proteins, chains, or domains

Accessing Visual Setup

1. Import a protein (see Import Proteins)
2. Find the Visual Setup panel below the Protein Outliner
3. The panel shows color and style options

Changing Colors

Apply Color to Selection

1. Select an item in the Protein Outliner (protein, chain, or domain)
2. In the Visual Setup panel, click the color picker
3. Choose your desired color
4. Click Apply Color

The color will be applied based on your selection:

• Protein selected: All chains and domains get the color
• Chain selected: All domains in that chain get the color
• Domain selected: Only that specific domain gets the color

Color Tips

• Distinct chains: Use different colors for each chain
• Functional domains: Color active sites or binding sites differently
• Emphasis: Use bright colors for regions of interest
• Publication: Use standard color schemes (e.g., blue/red for charges)

Changing Molecular Styles

Available Styles

ProteinBlender supports multiple molecular representations:

• Cartoon: Classic ribbon/cartoon representation (default)
• Surface: Molecular surface (good for visualizing shape)
• Ribbon: Simplified backbone ribbon
• Ball and Stick: Atomic detail with bonds
• Spheres: Space-filling representation
• And more: Additional styles from MolecularNodes

Apply Style to Selection

1. Select an item in the Protein Outliner
2. In the Visual Setup panel, choose a Style from the dropdown
3. Click Apply Style

Like colors, styles are applied hierarchically based on selection.

Independent Domain Styling

One of ProteinBlender’s powerful features is independent domain styling:

1. Split a chain into domains (see Domain Maker panel)
2. Select individual domains
3. Apply different colors and styles to each domain

Example: Show an active site as ball-and-stick while keeping the rest as cartoon.

Combining Colors and Styles

You can apply both colors and styles together:

1. Select your target (protein/chain/domain)
2. Choose a color
3. Choose a style
4. Apply both (or apply one at a time)

Tips and Best Practices

For Publications

• Use consistent color schemes
• High contrast for clarity
• Cartoon for overall structure, ball-and-stick for details

For Presentations

• Bold, distinct colors
• Larger molecular styles (surface, spheres)
• Color code by function or region

For Animations

• Start with simpler styles (faster rendering)
• Use color changes to highlight dynamics
• Test render times before committing

Troubleshooting

Color Doesn’t Change

• Make sure you clicked Apply Color after selecting the color
• Check that the correct item is selected in the outliner
• If domain is in a puppet, color the puppet instead

Style Doesn’t Update

• Styles may take a moment to update (especially surface)
• Check Blender console for errors
• Try switching to another style and back

Colors Look Different Than Expected

• Blender’s lighting affects color appearance
• Adjust viewport shading (top-right of viewport)
• Try Material Preview or Rendered view mode

Advanced: Custom Colors

For more advanced color control:

1. Select a domain
2. Use Blender’s shader editor to modify materials
3. ProteinBlender creates unique materials per domain

Note: Manual material edits may be overwritten if you use Apply Color again.

Next Steps

Now that you know how to style proteins, learn how to:

• Create Puppets - Group parts for coordinated changes
• Manage Poses - Save different conformations

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