May 5 2021
The Graphical User Interface (GUI) has many components. When you first use the GUI the default window layout is displayed as shown below.
There are three main ways to read in a PDB file.
Other PDB search options are described in more detail in the PDB Search section of this manual.
Available buttons and options for moving molecules around the graphical display window. This is described in more detail in the section entitled Move Buttons.
How to use the Graphics window controls
In the graphics window you can use various tools described elsewhere but it is helpful to know the following things:
The workspace panel (located on the left hand side panel of the gui) is an important place within the graphical user interface because it displays which sequences, structures, objects, tables and alignments are currently loaded into ICM. From the ICM Workspace panel you can make graphical selections and display and undisplay molecules.
Once a structure has been loaded into ICM the individual components of that structure (i.e. amino acids, metal ions, binding sites etc) are listed in the ICM workspace.
To display every component of the object except for binding sites and water atoms:
To display the whole structure in wire, ribbon, cpk, skin, surface and xstick representations:
In order to clear your graphical display:
If you only wish to display part of the structure then click in the boxes further down the tree in the ICM workspace.
To display selected regions of the molecule in wire, ribbon, cpk, skin, surface and xstick representations:
Making selections in ICM is an important skill to master (e.g. you may want to select a binding pocket for docking or a region of a molecule for coloring). The four levels of selection are:
There are several ways of making selection in ICM. The simplest is to interact directly with the graphics window - right-click, hold and drag around the area of the screen you want to select. Alternatively, in the workspace window, expand the tree of molecules and chains until the relevant protein sequences is displayed. Then left click and drag to mark residues to form a selection.
See the chapter entitled Making Selections for more information.
There are 6 main types of representation:
To change the color of the representation you need to use the buttons in the display tab.
Changing the colour of a representation works in much the same way as displaying the representation itself. The selection rationale is the same followed by clicking on a colour in the palette in the display tab. It is also possible to colour different representations of the same selection independently by clicking and holding on the representation buttons in the display tab.
To display the surface of a small molecule ligand or peptide binding pocket:
Any ICM object such as a structure, sequence, or alignment, can be saved for use at a later time.
To save an object:
All objects contained within an ICM session can be saved in a single file with the extension .icb. The file can then be read into ICM and the exact layout of the file will be preserved. To save a project file go to the File menu and select Save Project.
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.
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.
[ Arrange Windows ]
Is your graphical user interface looking a bit messy? Do you have tables, alignments, plots all over the place? Here we show you how to arrange everything to make a clearer GUI environment.
Click the default layout icon.
Double click on the window header.
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.
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 button in the view tools panel (see image below).
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.
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