Jul 3 2008
Contents
 
Introduction
Overview - RECOMMENDED READING FOR NEW ICM USERS
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
 RMSD
 Contact Areas
 Closed Cavities
 Surface Area
 Distance
 Planar Angle
 Dihedral Angle
 Ramachandran Plot
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
18.3 Closed Cavities		Next

This tool will identify cavities within a molecule which are completely closed,. If you are looking for buried and open pockets then use icmPocketFinder.

  • Read in a protein structure (File/Open or PDB Search)
  • Tools/Analysis/Closed Cavities
  • Enter the minimum volume of the cavities you wish to identify.
  • Click OK
  • The closed cavities will be displayed in the meshes section of the ICM Workspace and a table of the cavities will be displayed. Double click on a row in the table to jump to a particular closed cavity and select the residues surrounding it.

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Contact Areas		Home
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Surface Area

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