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7.8 Color Structure and Surface by Alignment

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.

To color a surface by the alignment conservation.

  • Make a plain solid surface using the meshes tab.
  • Make a selection in the alignment by using the options in the Alignment Editor panel and select by consensus.
  • Right click on the surface in the ICM workspace and choose Color by Selection.

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