[ Label Residues | Label Atoms | Annotation | 2D and 3D Labels ]

29.8.1 Label Residues

In this tutorial we will label the residues surrounding the ligand binding pocket of RXR receptor - PDB code 1mvc

• Follow the instructions in the previous tutorial to select the residues surrounding the ligand binding pocket.
• Once the selection around the ligand binding pocket has been made (green crosses in the graphical display) click on the Residue Label button in the display tab.

You can change the font and coloring of the residue labels by:

• Clicking and holding on the Residue Label button in the display tab.

If the residue label is not in the position you desire you can change the label positioning by:

• Click and hold on the Residue Label button in the display tab and select either Shift to Sidechain Tips or {Shift to Calphas}. This will move all selected residue labels.
• Individual labels can be moved by clicking in the bottom left hand corner of the label and using the middle mouse buttom to move the label.

29.8.2 Label Atoms

In this example we will display the formal charge on the carboxylate group on the 1MVC ligand bm6.

• If you dont already have the 1MVC structure displayed use the pdb search tab and type 1MVC.
• Double click on the ligand bm6 in the ICM Workspace (selected will be highlighted blue in the ICM Workspace and green crosses in the graphical display).
• Click on the center button to zoom into the ligand button.

• Click on the unselect button and select the two oxygens using the pick atom button

• Click on the Atom label button and then click and hold on the Atom label button and select label style -> (formal charge).

29.8.3 Annotation

In this example we will add user-defined annotation to the ligand in 1MVC

• If you dont already have the 1MVC structure displayed use the pdb search tab and type 1MVC.
• Double click on the ligand bm6 in the ICM Workspace (selected will be highlighted blue in the ICM Workspace and green crosses in the graphical display).
• Right click on the ligand in the ICM Workspace and select Annotate selection... and a data entry box as shown below will be displayed.
• Enter text describing the ligand. The position of the arrow can be changed by clicking on the arrow-head and dragging. The level of information displayed can be changed by double-clicking on the text.

29.8.4 2D and 3D Labels

You can add 2D or 3D labels to your graphical display by using the buttons in the labels menu.