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5.1 Molecule Representation
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[ Structure Representation | Wire | Stick/Ball | Ribbon | Skin | CPK | Surface | Hydrogens | Hydrogen Bond | Formal Charges ]

To change the molecule display representation:

The display tab contains tools for a variety of functions including - structural representations, coloring, labeling and superposition. This tab is shown below.

5.1.1 Structure Representation


There are six main types of structural representation in ICM. They are wire, ball and stick (Xstick), ribbon, skin, CPK and dot envelope (surface).

To display one of these representations:

To remove a displayed representation or to toggle between display and undisplay:

NOTE: The button display will change appearance (shaded) when pressed. This makes it easier to identify which representations are currently being displayed. Many characteristics of the graphical representation such as color can be changed by clicking and holding on the button or by cliking the plus(+) and minus(-) buttons next to them.

Some examples of the representations you can choose:

Wire : Thin Wire : Normal Wire : Thick
Wire : Chemistry Wire : Tree Xstick- Thin
Xstick : Thick Xstick : Stick / Ball Ribbon : Ribbon
Ribbon : Segment Ribbon : Protein Worm Ribbon : Transparent
CPK : Default Skin : Default Skin : Transparent
Surface : Tight Surface : Normal Surface - Sparse

5.1.2 Wire Representation


Click and hold on the wire representation button. A menu will be displayed as shown below.

To change the wire style:

To change the size of the wire representation:

NOTE: Clicking on the +/- next to the wire representation button also changes the thickness of the wire representation.

To undisplay representations other than wire:

If you make a mistake or you are not happy with the way your structure is displayed with the wire representation:

5.1.3 Stick and Ball (Xstick) Representation


Click and hold on the stick and ball representation button. A menu will be displayed as shown below.

To change the style of the Xstick representation:

To change the size of the Xstick representation:

NOTE: Clicking on the +/- next to the xstick representation button also changes the thickness of the xstick representation.

In order to make some parts of your picture clearer, the xstick representation can be set to transparent:

To undisplay representations other than xstick:

If you make a mistake or you are not happy with the way your structure is displayed with the xstick representation:

5.1.4 Ribbon Representation


Click and hold on the ribbon representation button. A menu will be displayed as shown below.

To change the style of the Ribbon representation:

To accurately represent the secondary structure of the molecule in ribbon representation you may wish to assign secondary structure:

To make some parts of your picture clearer, the ribbon representation can be set to transparent:

To undisplay representations other than ribbon:

If you make a mistake or you are not happy with the way your structure is displayed with the ribbon representation:

NOTE: Always use the ICM assign sec.** structure tool in the ribbon right click menu to get accurate secondary structure assignment. This is particularly important when studying helices which may have non-cannonical elements within them such as 3/10 or pi. To view non-cannonical helix segments use the segment option in the ribbon right click menu.

To change the display of chain breaks (dotted lines):

5.1.5 Skin Representation


Click and hold on the skin representation button. A menu will be displayed as shown below.

To make some parts of your picture clearer, the skin representation can be set to tight, normal or sparse:

To undisplay representations other than skin:

If you make a mistake or you are not happy with the way your structure is displayed with the skin representation:

NOTE: Sometimes due to singularity problems holes may appear within the skin surface. To cure this infliction select atoms nearby and right click select Advanced->RandomizeAtoms

5.1.6 CPK Representation


Click and hold on the CPK representation button. A menu will be displayed as shown below.

To undisplay representations other than CPK:

If you make a mistake or you are not happy with the way your structure is displayed with the cpk representation.

5.1.7 Surface Representation


Click and hold on the surface representation button. A menu will be displayed as shown below.

To change the style of the surface representation:

To undisplay representations other than surface:

If you make a mistake or you are not happy with the way your structure is displayed with the surface representation:

5.1.8 Display and Undisplay Hydrogens


To display and undisplay hydrogens. Click and hold on the "Change Hydrogen Display" button shown below. Multiple single clicks will toggle through the hyrogen display options.

5.1.9 Display Hydrogen Bond


NOTE: The method by which hydrogen bonds are calculated is described here in the command line manual. The GRAPHICS.hbondMinStrength parameter determines the hbond strength threshold for hbond display. The strength value is between 0. and 2. By changing 1. to 0.2 you will see more weak hydrogen bonds.

In order to display potential hydrogen bonds in your structure:

What do the default coloring of the H-bond represent?

Longer and shorter H-X distances in the hydrogen bond are color-coded, from red to blue, respectively.

NOTE Dynamic hydrogen bonds can be set by clicking and holding on the H-bond toggle button in the Display tab. Hydrogen bonds will then respond to any changes made to the ligand.

5.1.10 Display Formal Charges


You can display formal charges by clicking and holding on the "Change Hydrogen Display" button in the Display tab.


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