[ Display and Select Proteins for Superposition | Proteins by 3D | Multiple Proteins | Arrange as Grid ]

3.8.1 Display and Select Proteins for Superposition

Before any superposition operation can be undertaken you need to select the protein structures you wish to superimpose.

One way to do this is by selecting in the ICM workspace. For other selection tools please see the Making Selections section of the manual.

• Select both receptors by double clicking on the name of the receptor in the ICM Workspace.To select two receptors use the Ctrl button or use the shift button to select a range of objects in the ICM Workspace. A receptor which is selected will be highlighted in blue in the ICM Workspace and with green crosses in the graphical display.

3.8.2 Proteins by 3D

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.

3.8.3 Multiple Proteins

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.

3.8.4 Arrange as Grid

To separate superimposed proteins:

• Tools/Superimpose/Arrange as Grid