Superpose structures when you want to compare binding sites or conformations side by side in the 3D viewer.
Prerequisites: at least two structures open in the Workspace. Example: open 6OOY and 6OP0 with Home → Structure Code List.
- In the Collections panel, open Structure actions (⋮) on the structure you want as the reference, and select Set as reference.
- In the Workspace reference dialog, choose the method:
- Pocket Centric to align on a binding site. Select the pocket in the table, usually the one with the ligand you're interested in.
- Chain/Residue Centric to align on a chain. Select the chain and, if needed, enter a Residue range.
- Click Set Reference.
- Click the eye icon of the other structure to show it. It is superposed automatically.
Result: the Workspace header shows the reference (for example "6ooy | Pocket 1"), and the superposed structure shows the Matching reference superpose rule icon.
- The structure is already shown: open its Structure actions (⋮) and select Superpose by reference rule.
- Align one structure differently from the rule: open its Structure actions (⋮), select Superpose manually, choose Pocket Centric or Chain/Residue Centric, set the chains and residue ranges, and click Superpose.
- Stop automatic superposition: click the gear next to the reference in the header and clear Superpose automatically.
- Keep the alignment and share it: set a project reference instead. See Superposition in projects.
- Superpose actions are greyed out: no Workspace reference is set. Do steps 1 to 3 first.
- The superposition looks wrong: the pockets may be too different. Use Superpose manually with Chain/Residue Centric. See Superposition methods.
- The reference disappeared: the Workspace reference is not saved when you reload the page. Set it again.