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Contents
 
Introduction
How To Guide
Getting Started
Molecular Graphics
Slides and Documents
ActiveICM
Movie Making
Sequences & Alignments
Protein Structure Analysis
 Related Chains
 Calculate RMSD
 Contact Areas
 Closed Cavities
 Surface Area
 Distances
 Planar Angle
 Dihedral Angle
 Ramachandran Plot
 Ramachandran Export
Protein Superposition
Crystallographic Analysis
Homology & Modeling
3D Predict
Molecular Mechanics
Cheminformatics
Chemsitry Menu
Docking
Ligand Editor
Tables
Local Databases
FAQs
Tutorials
 
Index
PrevICM User's Guide
9.5 Surface Area
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This option calculates solvent accessible area of each selection in multiple objects and stores it in a table. If a molecule is specified in a multi-molecular object, the surface area of an isolated molecule is calculated and other molecules are ignored. The area is reported in square Anstroms and the probe radius is assumed to be the value set in the variable waterRadius.

Output: the macro creates table AREA . The empty comment field is added for user's future use. If the table exists, new rows are appended.

To calculate a surface area:

  • Read in a protein structure (File/Open or PDB Search)
  • Select the region you wish to analyse.
  • Tools/Analysis/Surface Area
  • A table will be displayed listing the residues in the selection along with the corresponding total surface area.


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