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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.
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