How to color a PDB structure by the coloring in the alignment?

[Andrew Orry]

Question:

How to color a PDB structure by the coloring in the alignment?

Answer:

To color your protein molecule by the color of the alignment e.g. color by conservation.

• Extract the sequence from the PDB structure.
• Make the alignment.
• Color the alignment.
• Propagate the alignment coloring to the 3D structure by clicking and holding on the representation button (e.g. ribbon) in the display tab. Select Color by Alignment.