[ Workspace | Whole | Amino ]

In the default GUI layout the workspace panel is located to the left of the 3D graphics display. It is a great tool for keeping track of all your sequences, pdb structures, objects, tables and alignments. As you will see in this section it also provides a way of making selections.

11.2.1 Workspace Navigation

Once you have mastered how to navigate the ICM workspace making a selection will become easier. Each object is divided into 3 levels:

1. Object Level - Shown in red if it is the current object. Holds details about the structure - name, X-ray, NMR, resolution etc. Importantly it will state whether the structure is an ICM object or a structure straight from the PDB. To learn how to convert a PDB into an ICM object go to the section on converting a PDB.
2. Molecular Level - Shows the individual subunits, ligands and hetatoms of a molecule.
3. Residue Level - Shows the sequence.

NOTE: You can expand each level of the ICM workspace by clicking the "+" button as shown above.

11.2.2 Selecting the Whole Object

To select the whole object:

• Double click on the object level.

11.2.3 Selecting Amino Acids

There are three options to select individual amino acid residues:

OPTION 1:

• Click and drag over the residues you wish to select in the ICM workspace. Selected residues will be highlighted in dark blue in the workspace and with green crosses in the graphical display.

OPTION 2:

• Click on the rectangular selection icon or lasso selection icon on the toolbar.
• Click and drag around the residues you wish to select. Selected residues will be displayed by green crosses on the graphical display and blue in the ICM workspace.
• Click on the Pick Atom button.

OPTION 3:

• Right click on the selected residue in the graphical display and a menu as shown here will be displayed.

• Click on Select and a further menu will be displayed.
• Click on Residue, Molecule or Object.

NOTE: Ctrl + A will select everything in the ICM workspace, and Ctrl + Shift + A will unselect your objects.

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