Downloading and Coloring AlphaFold Structures by Confidence Level

You can download AlphaFold models directly into the workspace and evaluate their structural reliability using the predicted local distance difference test (pLDDT) confidence score.

Step 1: Download the AlphaFold Model

1. Navigate to File > Load > AlphaFold.
2. Enter the identifier for your protein to download the structure into the workspace.

Step 2: View the Confidence Coloring

Upon loading, the structure is automatically color-coded based on its pLDDT score. This allows you to visually identify the accuracy of the prediction:

• Dark Blue: Very high confidence
• Red: Low confidence

Step 3: Display the Color Legend

To view the specific numerical scale associated with the colors:

1. Open the Labels tab.
2. Check the button to enable the Rainbow Ruler.

Note: The Rainbow Ruler will appear on screen, showing the exact correspondence between the structural colors and the pLDDT confidence values.