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To superimpose proteins by 3D:
- First display and select the proteins you wish to superimpose by 3D.
- Tools/Superimpose/Proteins by 3D
- A window as shown below will be displayed.
- Select by which atoms you wish to superimpose.
- Enter the ICM selection language description for the protein structure you wish to remain static. You can also use the drop down arrow button to select it.
- Enter the sequence weight Average local sequence alignment score.
- Enter the seed length This is the similarity window size.
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