5.3.1 How to Display Hydrogen Bonds

[ Edit Hydrogen Bond Label | Move Hydrogen Bond Label ]

NOTE: The method by which hydrogen bonds are calculated is described here in the command line manual.

To display any energy-related interaction properties such as h-bonds, first convert the PDB structure into an ICM object. In this example we will Convert` 1STP into an ICM object.
Right-click on the ligand 'abtn' in the ICM Workspace and select Neighbors**.
Enter 3 angstroms for the distance and set Type = Visible**.
Leave the ligand included in the selection by clearing the Exclude Source** checkbox.
Open the Display** tab and click the Display H-Bond** button.
You will then see the h-bonds displayed in the graphics window and the individual h-bondpairs in the 3D labels section of the ICM workspace.

You can control different h-bonds options by clicking and holding on the h-bond button in the Display tab.

Text label - Displays a text label identifying the atoms involved in each hydrogen bond.
Distance [Å] - Displays the hydrogen bond distance, in Angstroms, as a label.
Solid line - Displays hydrogen bonds as solid lines between the interacting atoms.
Dotted line - Displays hydrogen bonds as dotted lines between the interacting atoms.
Spheres - Displays hydrogen bonds as a series of spheres between the interacting atoms.
Set Sphere Period... - Controls the spacing between the spheres used to represent hydrogen bonds.
Change Color... - Changes the color used to display the hydrogen bonds.
Dynamic Hbonds in One Obj - Dynamically updates hydrogen bonds within a single ICM object as the molecular geometry changes. Ideal for use with stacks.
Show Intermolecular HBonds Only - Displays only hydrogen bonds formed between different molecules or molecular components and hides intramolecular hydrogen bonds.
Hbond Ball Style - Controls the graphical style of the spheres used to display hydrogen bonds.
Hbond Min Energy - Controls the threshold used to determine which hydrogen bonds are displayed. Adjusting this value can include or exclude weaker hydrogen bonds.

Right-click on the hbondpairs group in the ICM Workspace to access additional options for managing and analyzing the displayed hydrogen bonds.

Select - Selects all hydrogen bonds contained in the hbondpairs group. This is useful for modifying, recoloring, exporting, or deleting the complete set of displayed hydrogen bonds.
Protect - Protects the hbondpairs group from accidental modification or deletion.
Change Color... - Changes the display color of all hydrogen bonds in the selected hbondpairs group.
Export to Table - Exports information for the hydrogen bonds in the group to an ICM table for further inspection, sorting, or analysis. Includes distance and color used.
Select atom pairs - Selects the atoms involved in the displayed hydrogen bonds. Both atoms participating in each hydrogen-bond interaction are included in the selection.
Undisplay - Hides the hydrogen-bond graphics from the 3D display without deleting the hbondpairs group. The hydrogen bonds can be displayed again later from the ICM Workspace.
Delete - Deletes the hbondpairs group and removes the corresponding hydrogen-bond display from the Workspace.
Rename... - Renames the hbondpairs group. This is useful when several hydrogen-bond sets are displayed and clearer identification is required.

NOTE:

Different options for displaying the H-bond can be accessed by clicking and holding on the H-bond button in the "Display" tab.
The coloring of the H-bonds are red (strong hydrogen bonds - thick spheres) to blue (weak hydrogen bonds - thin spheres).
Once the hydrogen bonds have been displayed they can be displayed and undisplayed in the 3D labels section of the ICM Workspace (left hand side of graphical window).
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.

5.3.1.1 Edit Hydrogen Bond Label

To edit a hydrogen bond label

Right click on the label.
Choose Edit Label.
Make changes in the dialog box and press OK.

5.3.1.2 Move Hydrogen Bond Label

To move a hydrogen bond label

Right click on the label.
Click on the label using the middle mouse button.
Hold the middle mouse button down and drag.

5.3.2 Pi-Pi and Pi-Cation Interactions.

Follow the steps below to display Pi-Pi and Pi-Cation interactions in your molecule.Any aromatic ring pair with distance between centers <= GRAPHICS.piIntMaxDistance (default 5.) is considered as interaction. relative position of ring planes is not taken into an account.

Read in the molecule of interest.
Click on the Pi-Pi interactions button in the dispay tab. See image below.
All pi-pi interactions will be shown in the display as dotted lines and listed in the ICM workspace.
You can change the pi-pi maximum distance parameter by clicking and holding on the pi-pi interaction button.
To display the distance of the pi-pi or pi-cation - open the 3D labels panel in the ICM workspace and locate the interaction. Right click on the blue box which controls the display and choose 'number'.