Quick Start Guide: Exercise 18


Superimposing Two Ligands

Use the Flexible Ligand Alignment tool to superimpose two (or more) structurally similar ligands.

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

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