[ Hydrogens | Structure Representation | Wire | Stick/Ball | Ribbon | Skin | CPK | Surface | H-Bond | Coloring | Color/BG | Background | Labeling | Atoms | Residues | Move | Variables | Sites | Annotation | Color | Distance Atoms | Planar Angle | Dihedral Angle | Delete Label | Display Gradient | Tethers | Dist/Restraints | Superimpose | Display Clash | Toggle ]

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 Display and Undisplay Hydrogens

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

• Display Tab
• Click and hold on the button shown below.

5.1.2 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:

• Click on the representation button you desire in the display tab.

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

• Click on the corresponding representation button in the display tab.

NOTE: The button display will change appearance slightly 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.

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

5.1.3 Wire Representation

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

To change the wire style:

• Click and hold on the wire representation button and then click on wire, chemistry or tree.

To change the size of the wire representation:

• Click and hold on the wire representation button and then click on thin, normal or thick.

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

To undisplay representations other than wire:

• Click and hold on the wire representation button and then click on undisplay other representations.

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

• Click and hold on the wire representation button and then click on reset to default.

5.1.4 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:

• Click and hold on the stick and ball representation button and then click on style. Choose a style as shown below.

To change the size of the Xstick representation:

• Click and hold on the stick and ball representation button and then click on set thickness and set ball/stick ratio

NOTE: Clicking on the arrow next to the Stick and ball representation button can also change the thickness of the xstick representation.

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

• Click and hold on the stick and ball representation button and then click on transparent.

To undisplay representations other than xstick:

• Click and hold on the stick and ball representation button and then click on undisplay other representations.

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

• Click and hold on the stick and ball representation button and then click on reset to default.

5.1.5 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:

• Click and hold on the ribbon representation button and then click on a style option.

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

• Click and hold on the ribbon representation button and then click on assign sec. structure. New in version 3.5-2 is they smooth ribbon style.

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

• Click and hold on the ribbon representation button and then click on transparent.

To undisplay representations other than ribbon:

• Click and hold on the ribbon representation button and then click on undisplay other representations.

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

• Click and hold on the ribbon representation button and then click on reset to default.

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):

• Click and hold on the ribbon represenation button.
• Select the options Display Chain Breaks or Display Chain Break label.

The helices in rhodopsin and bacteriorhodopsin are shown below in segment representation. Non-cannonical regions are represented as breaks in the helix segment.

5.1.6 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:

• Click and hold on the skin representation button and then click on either tight, normal or sparse.

To undisplay representations other than skin:

• Click and hold on the skin representation button and then click on undisplay other representations.

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

• Click and hold on the skin representation button and then click on ** reset to default**.

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

5.1.7 CPK Representation

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

To undisplay representations other than CPK:

• Click and hold on the CPK representation button and then click on undisplay other representations.

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

• Click and hold on the CPK representation button and then click on reset to default.

5.1.8 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:

• Click and hold on the surface representation button and then click on tight, normal, or surface.

To undisplay representations other than surface:

• Click and hold on the surface representation button and then click on undisplay other representations.

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

• Click and hold on the surface representation button and then click on reset to default.

5.1.9 Hydrogen Bonding

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:

• Convert to an ICM Object
• Make a selection - if you are trying to display the H-bonds between a ligand and the receptor make sure the ligand is part of the selection.
• Click the Display Tab.
• Click on the Toggle H-bonds icon in the display tab.

• Click the +/- on the right of the H-Bond button to change thickness of H-bond representation.
• Click and hold the button to change representation or use the hbondpairs option in the ICM Workspace.

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 Coloring

To change the color of a structural representation such as CPK, Xstick, wire or ribbon.

• Click and hold on the structural representation buttons in the Display tab.
• Select a color by clicking color.

OR, if you wish to color by a particular parameter such as atom type, b-factor etc...

• Right click on the structural representation buttons in the Display tab.
• Select ..by-> option

To change the color of the whole of your displayed structure:

• Click on the color palate displayed on the toolbar.
• If you are not satisfied with these colors, click on the color wheel on the toolbar. A window as shown below will be displayed. Select the desired color by either clicking on one of the basic colors or by selecting the desired color on the right hand side of the window.

• Once the desired color has been selected it can be added to custom colors for future use by clicking on the Add to Custom Colors button.
• Click the OK button and the color will be applied to the structure.

To change the color of the desired representation by a defined structural characteristic:

• Click and hold on the wire representation button and then click ..by->. A menu as shown below will be displayed.

• Select the characteristic that you wish to color by and click on it.

5.1.11 Coloring Background

In order to change the color of your background:

• Select View/Color background.

• Click on the square of your desired color. If you are not satisfied with the color palate, click on the arrow next to the colors to customize a color.

OR

• Right click on a color in the colors panel in the display tab.

5.1.12 Background Image

A background image can be added to the graphical display. This can be useful for making cool images or for comparing structures (e.g.compare displayed object with background image of object).

To add a background image from an image file (png or jpeg):

• File/Open Image
• Right click on the image in the ICM Workspace and select "Set as Background in Graphics."

To set currently display as background image:

• Click and hold on the "Copy Image to Clipboard" button at the bottom of the gui and select the "Set as Background" option.

To remove a background image:

• Select the display tab and then click and hold on the color sphere button and select "Remove Background Image".

5.1.13 Labeling

Labeling options are contained within the Labels or Display Tab. In many cases clicking and holding a label button will allow you to view more options.

5.1.14 Labeling Atoms

Select the atoms you wish to label (see display structure or selection toolbar).

• Select the display tab.
• Click the label ATOM button.

To change the level of label detail:

• Click and hold the label ATOM button and select the desired level of label detail, color or style.

5.1.15 Labeling Residues

To label residues:

• Select the display tab.
• Select the residues you wish to label (see display structure or selection toolbar).
• Click the label RES button.

To change the level of label detail:

• Click and hold the label RES button and select the desired level of label detail or style.

5.1.16 Move Residue Label

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

5.1.17 Label Variables

To label variable angles (dihedral-torsion, planar and phase angle) the molecule needs to be converted into an ICM object.

• Convert the molecle to an ICM object.
• Select the atoms for which you would like to display the variables (see display structure or selection toolbar).
• Click on the toggle variable label button shown above located in the display tab.
• Change the font size by using the +/- buttons.
• Change the font and color by clicking and holding on the variable atom label button.

To change the variable label style click and hold the variable atom label button as shown below.

Rings of varying diameter and color are superimiposed on rotatable bonds. Green rings with large diameter are considered less constrained than rings with small green rings. Red rings are highly constrained and non-rotatable. When the Label Style/Energy option is selected the first number displayed represents the bond angle, the second the energy and the third the worst energy that could be achieved by rotating the bond.

5.1.18 Labeling Sites

To display and undisplay sites use the Toggle Site Label button shown below

• Click the label SITE button.

To change the level of label detail:

• Click and hold the label SITE button and select the desired level of label detail or style.

NOTE: To create your own site labels see the Label Annotation section.

5.1.19 Label Annotation

To annotate a protein structure. Select the region you wish to annotate (see Selection Toolbar).

• Right click on the selection.
• Select the option Annotate Selection.
• Enter the annotation into the text box and select ok

To change the detail (such as residue number) contained within the annotation.

• Click in the bottom left hand corner of your annotation.

To undisplay an annotation click on the site button in the Display tab.

To permanently delete an annotation.

• Right click on the Sites box in the ICM Workspace and select delete (see below).

To change the direction the arrow is pointing or move the arrow.

• Click on the translation button (or use the middle mouse button).
• Click on the end of the arrow and drag to the desired position.

5.1.20 Changing Label Colors

To change the color of any label:

• Click and hold down the required label button and a menu as shown below will be displayed.

• Select color.

5.1.21 Display Distance Between Two Atoms - the quick way

• Click on the Display tab
• Click on the Distance between two atoms button shown below.
• Click on the atoms you wish to measure.
• Distance will be displayed in the graphical display. You can turn this on and off in the ICM Workspace panel under the heading 3D labels.

5.1.22 Display Planar Angle

• Select the display tab.
• Select three atoms.
• Select the button shown below.

NOTE: This option is also available in the Tools/Analysis menu.

5.1.23 Display Dihedral Angle

• Select the display tab.
• Select four atoms.
• Select the button shown below.

NOTE: This option is also available in the Tools/Analysi s menu.

5.1.24 Delete Label

To delete distance or angle labels

• Select the display tab.
• Select the delete distance or angle label button shown below.

5.1.25 Display Gradient

This button is located in the display tab.

This option is described in detail in the language manual http://www.molsoft.com/man/icm-commands.html#display-gradient

5.1.26 Displaying Tethers

Theory

A tether is a harmonic restraint pulling an atom in the current object to a static point in space. This point is represented by an atom in another object. Typically, it is used to relate the geometry of an ICM molecular object with that of, say, an X-ray structure whose geometry is considered as a target. Tethers can be imposed between atoms of an ICM-object and atoms belonging to another object, which is static and may be a non-ICM-object. You cannot create tethers in ICM-Browser, however, if the project that you have loaded contains tethers between two objects, then they can be displayed:

• Click on the display tab (previously called advanced tab).
• Click on the 'Toggle Tethers' button.

5.1.27 Displaying Distance Restraints

Theory

A distance restraint imposes a penalty function on the distance between two atoms in the same object. You cannot create distance restraints in ICM-Browser, however, if the project that you have loaded contains distance restraints, then they can be displayed:

• Click on the display tab (previously called advanced tab).
• Click on the 'Toggle distance restraints' button.

5.1.28 Superimpose

In order to calculate the root mean square deviation (RMSD) between two structures it is necesary to superimpose them. By using the superimpose button in the display tab, ICM will calculate the Ca-atom, backbone atom and heavy atom differences between the two structures. More advanced superimpose options can be found in the Tools/Superimpose menu.

To superimpose two structures which have the same number of residues and atoms:

• First load the two structures into ICM.
• Select which parts or all of the two structure you wish to superimpose (see selection toolbar).
• Select the display tab (previously called Advanced tab) at the top of the GUI.
• Select the superimpose button.

The rmsd will be displayed in the terminal window as shown below:

5.1.29 Display Clash

To display a clash the file needs to be an ICM Object.

• Select the region around which you would like to identify clashes.
• Select the display tabs and the "toggle clashes" button shown below.

5.1.30 Display Rainbow, Box, Ruler

To (un)display a rainbow key, box or ruler use the buttons shown below located i n the display tab.