Aug 8 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
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2.8 How to Change Protein Representation
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To change the representation of the protein, make a selection and then use the tools in the display tab.

There are 5 main types of representation:

  • Wire: Wires connecting covalently bound atoms of a molecule. This representation has no defined thickness as as such will not make shadows. Useful for showing the chemical structure of a (for example) small molecule.
  • Xstick: Covalent bonds are represented as cylinders whilst atoms are represented as small spheres..
  • CPK: Atoms are represented as spheres with their respective van der Waals radius and coloured according to a standard defined by Corey, Pauling and Kultun.
  • Skin: A Connolly molecular surface over the selection. This is a smooth envelope touching the van der Waals surfaceof atoms as a water probe rolls over the molecule
  • Ribbons: Cartoon representation of protein and DNA secondary structure. Protein residues marked as alpha-helices ('H') are shown as a flat, helical ribbon, those marked as beta-sheets ('E') are shown as a flat ribbon with an arrow-head, and the rest are shown as a cylindrical "worm". If secondary elements are not defined everything will be shown as a cylindrical worm. ICM can automatically assign secondary structure: Tools/3D predict /Assign Helices and Strands


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