Setting up

We will be aligning the two ligands created in Task 17, 1FJS_ligand and 1FJS_ligand_copy:

• Include both structures in the Workspace
• Select both entries in the Entry List (the tool operates on selected entries)
• Click Tasks on the Selection Toolbar to open the Task Tool
• Click Browse > Structure Alignment > Flexible Ligand Alignment... to bring up the tool

Note: use Ctrl-click (Cmd-click on Mac) to include or select the second entry.

Using the Flexible Ligand Alignment tool

In the Flexible Ligand Alignment dialog:

• Choose Common scaffold alignment
• Choose Maximum common substructure
• Click Align Selected Entries; the ligands should appear well-aligned in the Workspace