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
 Undisplay All
 Clear-Display-and-Planes
 Selection Level
 Selection Mode
 Fog
 Side-by-Side Stereo
 Hardware Stereo
 Full Screen
 Perspective
 Full Scene Antialias
 High Quality
 Easy Rotate
 Shadows
 Animate View
 Drag Res Labels
 Antialias Lines
 Color Background
 Save Viewpoint
 Center
 Macro Shape
 Select by Purple 3D Box
 Clipping Tools
 Mesh Clipping
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
10.19 Center
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To center on an object displayed in the graphical display

  • Make a selection on the region on which you wish to center on.
  • Tools/Center (or use the center button on the right hand-side of the graphical display).

>>electrostatic-potential{display.electrostatic,display.potential,charge} h2-- Electrostatic potential {Electrostatic Potential}

This option generates the skin representation of the molecular surface colored according to the electrostatic potential calculated by the REBEL method (hydrogen atoms are ignored). REBEL is a method to solve the Poisson equation for a molecule. REBEL is a powerful implementation of the boundary element method with analytical molecular surface as dielectric boundary. This method is fast (takes seconds for a protein) and accurate. REBEL stands for Rapid Exact-Boundary ELectrostatics. The energy calculated by this method consists of the Coulomb energy and the solvation energy

In order to color the skin of your molecule by electrostatic potential:

  • Select View/Electrostatic potential.
  • Enter the potential scale value. This is the local electrostatic potential in kcal/e.u.charge units at which the surface element is colored by extreme red or extreme blue. All higher values will have the same color. This absolute scaling is convenient to develop a feeling of electrostatic properties of molecular surfaces.
  • Areas colored blue represent positive areas and red represents negative areas.


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