[ Graphics Controls | DragnDrop | Right Click | Move | Arrange | Projects | Pictures | Quick Pocket ]

This section describes some useful tips and suggestions to make life using the graphical user interface easier and more time efficient.

2.13.1 Graphics window controls

In the graphics window you can use various tools described elsewhere. It is good to know the following:

• Picking a tool: the left mouse button will function according to the selected tool
• Popup menus: right click on an atom gives a pop-up menu
• Selecting in the rotation mode: the right mouse button will select atoms
• Translating in the rotation mode: the middle mouse button will translate the scene
• Zooming and moving clipping planes in the rotation mode: the left, top and right margins of the graphics window are reserved for other actions, zoom, z-rotation, and clipping plains, respectively. That means that even if you are picking atoms, by pressing control you can still rotate your molecule with the left-mouse-button.
• Rotating in any non-rotation mode: if you press Control in any mouse mode, e.g. zoom, pick etc., it will temporarily switch to rotation
• Escaping from the connect and continuous movement modes: pressing Escape helps to get out of certain modes, such as Full Screen, Continuous rotation or rocking, the Connect mode.
• Global rotation in the Connected mode: pressing Shift will temporarily switch to the global rotation/translation mode.

See also: Graphics controls.

2.13.2 Drag and Drop

NOTE: "Drag and Drop" is a useful way of moving objects and sequences around the graphical user interface.

Sequences and objects can be moved around the graphical user interface by dragging and dropping them. All loaded sequences and objects are always displayed in the workspace panel. Select the desired object or sequence from the workspace panel by clicking and holding, move the selection to the desired location and release.

This is a useful application in the graphical user interface. For example, you may have an alignment displayed and you wish to add another sequence to the alignment. This can simply be accomplished by dragging a loaded sequence from the workspace panel into the alignment display panel. Or, you can quickly view an object by dragging and dropping it from the workspace panel into the 3D graphics window.

2.13.3 Right Click

NOTE: Use the Right Click Mouse Option

The right click mouse option can be used throughout the graphical user interface. It is a very useful means of opening up a whole new world of menus and options. Most of these options are described in this book. However, when using the graphical user interface it is always a good idea to try right clicking the mouse on an object and seeing which extra options that are available for you to use.

2.13.4 Moving Windows

It is possible to move some windows around the graphical user interface to make viewing easier.

For example, you may wish to edit an alignment by moving the alignment display into a more accessible place.

It is also possible to separate menus from the GUI.

NOTE: To return to the default display option select the 'Default layout' option in the windows menu.

OR

Click the default layout icon.

OR

Double click on the window header.

2.13.5 Arrange Windows

Sometimes when using ICM you may have many items displayed such as structures, alignments and tables. As a default the graphical display is the largest and centered in the middle of the ICM graphical user interface. However if you wish to work on an alignment or table you can place the alignment or table as the main display by clicking on the buttons shown below. The larger display generally makes it easier to manipulate the alignment or table. There are ofcourse other ways to alter the layout such as tier the windows but this option is just a simple click and can sometimes come in useful.

2.13.6 ICM Projects

Save your data in an ICM project. It is a convenient way of keeping all your structures, alignments, tables, docking results etc... in one place. A description on how to save an ICM project is described in the GUI Basics section of this manual.

2.13.7 Making a Picture

There are several ways of taking a picture of the contents of the 3D graphical display window see the write image section. However the easiest way is to simply click on the camera button in the view tools panel.

Or select /File/Quick Image

The picture will be automatically saved as a PNG file in the directory from which you loaded ICM. The default picture name is icm[n].png, where n is the number of pictures taken in one ICM session. To save in other picture formats and to change the file name see the write image section.

2.13.8 Quick Binding Pocket Display

To quickly display the binding pocket residues surrounding the ligand:

• Select the ligand in the ICM Workspace by double-clicking. A selected item will be displayed in blue.
• Right click and select the option Ligand Pocket and the pocket will be displayed with the nearest residues labeled.