To superimpoe multiple proteins:

• First display and select the proteins you wish to superimpose by 3D.
• Tools/Superimpose/Multiple Proteins
• A window as shown below will be displayed.

• Select by which method you would like to superimpose

Align Residues - Residue correspondence is established by sequence alignment using the ICM ZEGA alignment Abagyan, Batalov, 1997. Atom alignment: by atom name.

Match by Res Numbers - Residue alignment by residue number.Atom alignment: by atom name for pairs of identical residues or pairs of close residues (F with Y; B with D,N; D with N; E with Q or Z, Q with Z), for other residue pairs only the backbone atoms ca,c,n,o,hn,ha are aligned.

Exact Match - Residue alignment is by the Needleman and Wunsch method. Inside residue atoms are aligned sequentially and regardless of the name.

• Select which atoms you would like to superimpose. Visible Atoms, C alpha, Backbone, or Heavy Atoms.