[ Coloring | Representations ]

Once you have mastered the art of making selections in the ICM graphical user interface you can then begin changing the display or graphical representations of your molecules. This was briefly introduced in the previous tutorial but there are many different options which will be covered in this section. All the representation buttons are located in the display tab and many options become available when you click and hold on the button as shown below.

29.7.1 Molecule and Background Coloring

Changing the Background Color

• PDB Search tab (PDB code 1MVC)
• The molecule will be displayed in ribbon format with a black background.
• Let us change the background color to white. To do this right click on the color panel in the display tab as shown below.

Changing the Object Color

• Select the whole 1mvc molecule. One way to do this is to double click on the name of the molecule in the ICM Workspace.
• Left click on the color panel in the display tab as shown below.

Coloring the object by secondary structure

• We can color the object by secondary structure by selecting the whole structure and then click and hold the ribbon button and select color/by-> sec.structure. The helices should be colored red, loops grey and non-canonical helices magenta by default.

Coloring the ligand by atom type

• Now let us color the ligand (bm6) according to the atom type.
• To do this select the ligand by double clicking on the name of the ligand in the ICM Workspace.
• By default the ligand is displayed in xstick therefore to change the coloring we will need to use the xstick button. Click and hold on the xstick button and select color/by-> atom type

29.7.2 Molecule Representations

In this example we will display the residues surrounding the ligand in 1MVC in wire representation:

• PDB Search tab (PDB code 1MVC)
• Right click on the ligand bm6 in the ICM Workspace.
• Select the Neighbors option

• Enter Radius 5.
• Enter type same_object_other_chains
• Choose exclude source and unselect water.
• You will see green crosses surrounding the ligand binding pocket as shown below.

• Click on the Residue selection button to change the arom selection into a residue selection.

• Click on wire representation button in the display tab.

Now we will change the ligand representation to wire

• Double click on the ligand name bm6 in the ICM Workspace to select it.
• Click on the wire representation button.
• You will notice that the ligand is currently represented in wire and xstick. These two representation buttons will be shaded blue as shown below.

• Undisplay the xstick representation by clicking on the xstick representation button in the display tab

Now we will display only the ligand and the residues surrounding the ligand binding pocket

• Remove all selections by right clicking and dragging in black space or double clicking on white space in the ICM Workspace.
• Click and hold on the wire representation button and select undisplay other representations.

• Click on the center button to get a better view.