Jul 23 2008
Contents
 
Introduction
Overview - RECOMMENDED READING FOR NEW ICM USERS
 Load PDB
 Move
 Selections
 Selection Levels
 What is Selected
 Workspace Panel
 Display
 representation
 Color
 Pocket
 Save Object
 Saving an ICM Project File
 Window Menu
 Tips
 Sequences and Alignments
 Protein Structure
 Cheminformatics
File Menu
Graphics Move Tools
Display Tab
Light Tab
Labels Tab
PDB Search Tab
Meshes Tab
View Menu
Selections
Tables
Local DB
Sequences
Bioinfo Menu
Tools Menu - Xray
Tools Menu - 3D Predict
Tools Menu - Analysis
Tools Menu - Superimpose
Homology and Modelling
Working with Chemistry Tools
Chemsitry Menu
Docking
Ligand Editor
Animations, Slides, & Documents
ActiveICM
Movie Making
Frequently Asked Questions
Tutorial - Graphical Display
Molecular Document
Tutorial - Working with PDB Protein Structures
Tutorial - Working with Sequence Alignments
Tutorial - Ligand Binding Pocket Analysis
Tutorial - Homology and Modeling Tools
Tutorial - Crystallographic Analysis Tools
Tutorial - Working with Chemical Tables
Tutorial - Working with the Molecular Editor
Tutorial - Chemical Searching
Tutorial - Docking and Virtual Ligand Screening
 
Index
PrevICM User's Guide
2.7 How to Display a Molecule
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Once a structure has been loaded into ICM the individual components of that structure (i.e. amino acids, metal ions, binding sites etc) are listed in the ICM workspace.

To display every component of the object except for binding sites and water atoms:

  • Click on the white box next to the word object at the top of the ICM workspace. This box will be colored blue once the structure is displayed

To display the whole structure in wire, ribbon, cpk, skin, surface and xstick representations:

  • Right click on the blue box next to the word object. A menu will be displayed.

  • Select which representation you desire for your structure by clicking on the appropriate word. A check mark indicates the representation currently displayed. To un-display a particular representation click on the word again.

In order to clear your graphical display:

  • Select View/Undisplay All

If you only wish to display part of the structure then click in the boxes further down the tree in the ICM workspace.

To display the selected regions of the structure in wire, ribbon, cpk, skin, surface and xstick representations:

  • Right click on the appropriate box in the ICM workspace. A menu will be displayed.
  • Select which representation you desire for your structure by clicking on the appropriate word. A check mark indicates the representation currently displayed. To un-display a particular representation click on the word again.


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