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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
 Setup Ligand and Receptor
 Preferences
 Display Options
  Pocket Surface
  Ligand Surface
  Hydrogen Atoms
  Display Hbonds
  Energy Circles
  Pretty View
  2D Interactions
  Unsatisfied Hydrogen Bonds
  Display Relaxed Ligand
  Visualize Ligand Strain
  APF Field & Excluded Volume
  Contacts
  Center
 Score and Strain
 Edit Ligand
 Screen Replacement Group
 Scan
 Bioisostere Scan
 Dock or Minimize
 Dock Table
 Fragment Linking
 Restraints
 Docking Templates
 Flexible Groups
 Refinement
 Multiple Receptor Docking
 Covalent Docking
 Dock to APF
 Save Docked Complex
 Export Docking Project
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Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
15.3 Display Options
Next

[ Pocket Surface | Ligand Surface | Hydrogen Atoms | Display Hbonds | Energy Circles | Pretty View | 2D Interactions | Unsatisfied Hydrogen Bonds | Display Relaxed Ligand | Visualize Ligand Strain | APF Field & Excluded Volume | Contacts | Center ]

Available in the following product(s): ICM-Pro | ICM-VLS | ICM-Chemist-Pro

Video |

15.3.1 Display the receptor pocket surface


This option makes a surface based on the properties of the pocket.

About the Receptor Pocket Surface: White=aromatic lipophilic, Green=non-aromatic other (mostly aliphatic) lipophilic surface, Red=hydrogen bonding acceptor potential, Blue=hydrogen bond donor potential

15.3.2 Display the ligand pocket surface


The Ligand Surface option allows you to visualize cavities that are open for ligand modifications.

About the Ligand Pocket Surface: White=aromatic lipophilic, Green=non-aromatic other (mostly aliphatic) lipophilic surface, Red=hydrogen bonding acceptor potential, Blue=hydrogen bond donor potential

15.3.3 Display Hydrogen Atoms


To display hydrogen atoms:

  • Single click on the hydrogen atom display button will toggle the display between: no hydrogens, polar hydrogens, all hydrogens, all hydrogens in ligand and polar hydrgens in receptor.
  • Click and hold on the button and you can choose the option rather than using the toggle.

15.3.4 Display Hydrogen Bonds


To display hydrogen bonds:

About Hydrogen Bonds: The coloring of the H-bonds are red (strong - thick spheres) to green (intermediate) to blue (weak - 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).

15.3.5 Display Atomic Energy Circles


To display atomic energy circles:

About the Atomic Energy Circles: Good ligand-receptor interactions are highlighted by green spheres and low values. Poor energy interactions are displayed as orange-->red stars - red being a major clash and a very poor energy contribution. Each atom is given an energy value relating to its contribution to the total receptor-ligand interaction energy. Low values colored green are considered favorable. The green values on each atom are per-atom contribution to the total energy in the receptor grid ('show energy atom' command). The score/energy can not be partitioned into per-atomic contributions because several terms/contributions are not pairwise (in particular solvation-related, as well as the strain). However, grid-based approximate interaction energy is calculated per-atom and reflects, to an extent, favorable/unfavorable contributions from things like van der waals, hydrogen bonds, coulomb part of electrostatics and some approximation of lipophilicity.

15.3.6 Display Pretty View


To display the default "Pretty View":

  • Setup the ligand and receptor.
  • Click and hold on the button shown below and choose "Pretty View".

15.3.7 2D Interaction Diagram


To create a 2D interaction diagram - click on the 2D interaction diagram button shown below. More details regarding this option can be found here.

15.3.8 Unsatisfied Hydrogen Bonds


To display unsatisfied hydrogen bonds:

  • Setup the ligand and receptor.
  • Click and hold on the button shown below and choose "Unsatisfied H-bonds".

15.3.9 Display Relaxed Ligand


The relaxed ligand is is the closest local minimum after minimization in the Merck Molecular Force Field (MMFF) outside of the receptor.

To display the relaxed ligand:

  • Setup the ligand and receptor.
  • Click and hold on the button shown below and choose "Display Relaxed Ligand".

15.3.10 Visualize Ligand Strain


If you are seeing a high ligand strain value when you calculate the score you can visualize the cause of this by viewing the variable angles.

To view the variable angles:

  • Click on the variable angle buton in the ligand editor tool panel.

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/yellow/red rings. Red rings are highly constrained. You can also compare your strained ligand with the relaxed ligand.

15.3.11 Visualize APF Field and Excluded Volume


If you are docking to Atomic Property Fields (APF - 3D Pharmacophore) as described here you can visualize the APF fields. Click on the button shown below and choose Visualize APF. The fields will be displayed and they can be toggled on and off in the ICM workspace - right click in the display box in the ICM workspace to change the surface display (e.g from mesh to transparent surface).

APF is a ligand based method but you can use a protein structure to represent an excluded volume - if you chose this option when performing APF docking then you can display the excluded volume.

15.3.12 Identify Ligand-Receptor Contacts


To display ligand-receptor contacts:

  • Click on the button shown below.
  • Select "Analyze Contacts".
  • The xstick display in the region will be scaled according to the atom/residue contact area. For example residues making large contacts with a ligand will be displayed in thicker xstick representation (and colored yellow) than those making less significant contacts.
  • A table as shown below will be displayed.The table lists the contact area, exposed area, percentage of contact area compared to exposed, the nearest atom of a residue and the distance.

15.3.13 Center on Ligand


To center on a ligand in the graphical display:

  • Click on the center button in the ligedit tab.


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