May 8 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
 Graphical
 Workspace
 Neighbors
 Alignment and Table
 Links
Tables
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
Animations, Slides, & Documents
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
11 Making Selections
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Note: Click Next (top right hand corner) to navigate through this chapter. Headings are listed on the left hand side (web version) or by clicking the Contents button on the left-hand-side of the help window in the graphical user interface.

There will be many occasions when you will have to make selections. For example, if you only wish part of your structure to be displayed or if you want to select residues around a binding pocket. If you have a molecule displayed in the graphics window, then selections will be displayed as green crosses. The selection you have made is also displayed at the top of the ICM Workspace. It is always a good idea to keep an eye on what is selected and what isnt.

There are four basic levels of selection

  1. Object (eg a PDB structure or ICM object)
  2. Molecule
  3. Residue
  4. Atom

You can make selections in:

  • The Graphics Display
  • The ICM Workspace (Selections are highlighted in blue)
  • Tables
  • Alignments


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