@*~RSC_HELP_TUTORIAL_SUPERPOSITION

Introduction

This tutorial shows how protein structures can be superimposed three-dimensionally and how a multiple sequence alignment can be computed from WIKI:Structural_alignment. The three proteins of this tutorial PDB:1eje, PDB:1axj and PDB:1nrg can be loaded with the dialog HTMLDOC_BUTTON:BUT_C1(DialogFetchPdb)! (Or you can simply click).

Backbone representation

Select the three proteins and open the 3D-backbone with the tool-button HTMLDOC_BUTTON:SBUT_3D!. The three proteins are at different coordinates in 3D-space.

3D-Superposition

When the 3D-view is clicked, then the 3D-menu-bar appears which can be distinguished by its black background. Click the menu-item "Superimpose" to superimpose the proteins.
Also try the dialog HTMLDOC_BUTTON:BUT_C1(DialogSuperimpose3D)!. The result of pairwise 3D-superpositions are displayed. These are previews and the protein model is not affected. Only after pressing HTMLDOC_BUTTON:SBUTS_TAB_SUPER3D_Apply, the coordinates of the respective mobile protein are changed.

Aligning the proteins

Press the button HTMLDOC_BUTTON:SBUT_ALIGN!. Since the sequences differ, the alignment can be best evaluated with "Secondary structure" in the choice menu HTMLDOC_JCOMPONENT:HTMLDOC_JC_Strap_comboColorScheme! for residue coloring.

Visualization of 3D-distance in the alignment

3D-distances between C-alpha atoms can be visualized in the alignment pane. This option can be used for proteins that had been superimposed. If the dialog HTMLDOC_BUTTON:BUT_C1(DialogSuperimpose3D)! had been used, the buttons HTMLDOC_BUTTON:SBUTS_TAB_SUPER3D_Apply need to be pressed to change the coordinates. Select HTMLDOC_COMBO_CLASS:BUT_C1(Distance3DToCursor) in the dialog HTMLDOC_BUTTON:BUT_C1(DialogSelectionOfResidues)! and select all proteins. Click into the alignment pane. Residues in spatial neighborhood to the cursor position are highlighted. This highlighting is updated when the cursor is moved. *@