[ Selection | Basic | Altering | Filter ]

In this section you will learn how to select parts and certain regions of molecules from the 3D graphical display. Graphical and molecule selections are required in many operations within ICM. For example, if you wanted to display graphically part of a molecule or if you wanted to perform a minimization of residues within a sphere of an imporant atom.

6.1.1 Selection Tools

The following buttons can be used to make a selection once a structure is displayed.

NOTE: All selection tool buttons are colored green. Graphical selections are represented as green crosses.

6.1.2 Basic Selections

To make a basic selection (ie nothing too complicated!) the following buttons can be used.

To unselect everything you have previously selected:

• Simply click on the Unselect icon on the selection toolbar.

OR

• Right click and drag away from the displayed structure.

To select parts of your structure:

• Click on the Rectangular selection icon and click and drag around the part of the structure you wish to select.

OR

• Click on the Lasso selection icon and click and drag your mouse around the area of the structure you wish to select, forming a lasso around it.

To pick individual atoms:

• Click on the 'pick atom' button

You may want to specify which part of your structure you will be selecting. To select by a specific part of the structure:

• Click on the Select objects , Select molecules, Select residues, or Select atoms icon, depending on which part of the structure you wish to be highlighted.

NOTE: The selection you have made is always recorded at the top of the ICM workplace. If you are familiar with using the ICM terminal (See language manual) the atoms, residues, molecules or objects selected interactively in the graphics window are automatically stored in the as_graph variable.

6.1.3 Altering a Selection

Once you have made a selection you may wish to add or remove parts of the selection. The buttons shown below allow you to accomplish this.

To add or remove from your current selection:

• Click on the Selection mode: add or Selection mode: remove icon on the toolbar.
• Click and drag around the part of your structure you wish to add or remove.

You may also wish to invert your selection in a specific part of the structure.

The parts that are currently selected will become unselected, and the unselected parts will become selected.

In order to invert a selection:

• Click on the Invert icon on the toolbar.

If you wish to select and unselect certain regions of a selection the toggle selection button is very useful.

• Click on the Toggle selection button.
• Right click around the selections you wish to select or unselect.

NOTE: The selection you have made is recorded at the top of the ICM workplace. Any selection is stored in the variable as_graph.

6.1.4 Filter Selection

You may want to be very specific about a selection you want to make. For example you may only wish to select protein backbone atoms.

The button shown below enables you to filter your selection:

Or

Right click on a selection and a menu as shown below will be displayed.

• Select the Filter Selection option.

If you wish to filter and select by residue or atom type:

• Click on the Filter graphical selection icon on the toolbar and a data entry box as shown below will be displayed.

To select just the protein or just the hetatoms as well:

• Click on the Mol tab.
• Check the appropriate boxes depending on your desired selection.

To filter by residue type or secondary structure:

• Click on the Res tab.
• Check the appropriate boxes.

NOTE: You may need to click on the button marked with a '+' symbol to expand the options.

To filter by atom type.

• Click on the Atom tab.
• Check the appropriate boxes.

NOTE: You may need to click on the button marked with a '+' symbol to expand the options.

To select neighbors to a particular selection.

• See the select neighbours section for detailed instructions.

NOTE: The selection you have made is always recorded at the top of the ICM workplace. If you are familiar with using the ICM terminal (See language manual) the atoms, residues, molecules or objects selected interactively in the graphics window are automatically s