[ Undisplay All | Clear-Display-and-Planes | Selection Level | Selection Mode | Fog | Side-by-Side Stereo | Hardware Stereo | Full Screen | Perspective | Full Scene Antialias | High Quality | Easy Rotate | Shadows | Animate View | Drag Res Labels | Antialias Lines | Color Background | Save Viewpoint | Center | Electrostatic Potential | Macro Shape | Select by Purple 3D Box ]

3.3.1 Undisplay All

To undisplay everything currently displayed in the graphical display

• View/Undisplay All

Note For more details on displaying structures please see the GUI Overview chapter.

3.3.2 Clear-Display-and-Planes

To clear the display and planes

• View/Clear Display and Planes

NOTE: For more details on planes please see the sections on clipping tools and mesh clipping.

3.3.3 Selection Level

There are four levels of selection - atom, residue, molecule and object. For more details on selections please see the Making Selections section.

3.3.4 Selection Mode

There are four different ways to make selections - new, add, remove and toggle. For more details on selections please see the Making Selections section.

3.3.5 Fog

Fog Toggle(Ctrl + D) : this feature creates a fog-like environment for your object, so that the part of your structure that is closer appears clear and the distant parts are faded as if they are in fog. The clipping planes control the point at which the fog begins.

• View/Fog

3.3.6 Side-by-Side Stereo

Side-by-side stereo toggle(Ctrl + S) : this feature allows you to view your structure in 3D form without any 3D goggles.

• View/Side-by-Side Stereo

3.3.7 Hardware Stereo

Hardware stereo toggle(Alt + S) - if you have 3D goggles and you wish to view your structure in 3D form, this feature will allow you to do so.

• View/Hardware Stereo

3.3.8 Full Screen

Full screen toggleAlt_F - this makes your graphical display fill the entire screen. If you wish to exit this mode, press escape.

• View/Full Screen

3.3.9 Perspective

Toggle perspective Ctrl_P this will add perspective to your structure, enhancing depth in the graphical display.

• View/Perspective

3.3.10 Full Scene Antialias

Anti-aliasing is the technique of minimizing the distortion artifacts known as aliasing when representing a high-resolution signal at a lower resolution. Always use this option before making high resolution images.

• View/Full Scene Antialias

3.3.11 High Quality

Toggle High Quality: this option will give your ICM object better resolution and higher quality. The change in quality is most visible at a high magnification. However, if your object is very large, this feature could slow down your program.

Always use this option before making high resolution images.

• View/High Quality

3.3.12 Easy Rotate

Toggle easy rotation: this feature is necessary if your structure is very large or perhaps your computer cannot quickly rotate it. It will prevent your structure from fully loading each time you rotate it, therefore speeding up the process.

• View/Easy Rotate

3.3.13 Shadows

• View/Shadows

OR

select the shadow button shown below.

3.3.14 Animate View

This tool is described in more detail in the Molecular Animations and Transitions section.

3.3.15 Drag Res Labels

To change the location of your residue label:

• Select View/Drag res labels.
• If your mouse has a middle mouse button, then click on handle (as shown) of the label you wish to move, and drag it to your desired area.

• If your mouse has no middle mouse button, then click on the Translation icon on the toolbar, and click on the handle (as shown) of the label you wish to move, and drag it to your desired area.

The +/- buttons on the side of the Residue and Atom buttons will shift the label. There are also other residue label move options available when you click and hold the residue label button. These options include Shift to Sidechain Tips, Shift to Calphas, and Restore Positions

3.3.16 Antialias Lines

Use this option to activate antialias lines. It is recommended to leave this option selected.

• View/Antialias Lines

3.3.17 Color Background

To change the background color

• View/Color Background
• Select a color from the panel and press OK.

This option is also in the more convenient display tab.

3.3.18 Save Viewpoint

It is possible to store a current view using the button shown below.

Click on the button and the current view will be stored so that you can view it later. A data entry box will be displayed asking you to name the view. All stored views can be found in the ICM workspace as shown below.

• Double click on the view in the ICM Workspace to display it.

A number of view display options are available by right clicking on the view in the ICM workspace as shown below.

The option in the right click menu called "set view smooth" returns to the view slowly showing the trajectory between the original view and the current one.

3.3.19 Center

To center on an object displayed in the graphical display

• Make a selection on the region on which you wish to center on.
• Tools/Center (or use the center button on the right hand-side of the graphical display).

3.3.20 Electrostatic potential

This option generates the skin representation of the molecular surface colored according to the electrostatic potential calculated by the REBEL method (hydrogen atoms are ignored). REBEL is a method to solve the Poisson equation for a molecule. REBEL is a powerful implementation of the boundary element method with analytical molecular surface as dielectric boundary. This method is fast (takes seconds for a protein) and accurate. REBEL stands for Rapid Exact-Boundary ELectrostatics. The energy calculated by this method consists of the Coulomb energy and the solvation energy

In order to color the skin of your molecule by electrostatic potential:

• Select View/Electrostatic potential.
• Enter the potential scale value. This is the local electrostatic potential in kcal/e.u.charge units at which the surface element is colored by extreme red or extreme blue. All higher values will have the same color. This absolute scaling is convenient to develop a feeling of electrostatic properties of molecular surfaces.
• Areas colored blue represent positive areas and red represents negative areas.

3.3.21 Macro Shape

A macroshape allows easy viewing and manipulation of a structure. A macroshape representation is ideal for large structures which allows the user to easily identify important regions of the structure and facilitate the return to the 'standard' view of a particular molecule. The level of detail displayed in the macroshape can be controled by changing the number of harmonics, gridStep, and, contour level.

• View/Macro Shape

3.3.22 Select by Purple 3D Box

An alternative way to make a make-selection{selection} is to use the purple 3D box. To do this:

• Select the display tab and the purple box button
• View/ Select by Purple 3D Box
• The atoms contained within the purple box will be selected.