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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
 Homology Modeling
 Loop Modeling
 Design Loop
 Graft Loop
 Loop Preferred Residues
 Find PDB Loop Segment
 Regul
 Refine SC
 Make Disulfide Bond
 Make a Mutation
 Modify Amino Acid
 Mutation - Protein Binding
 Mutation - Protein Stability
 Protein Peptide
 Protein Ligand
 Disulfide Bond
 Sculpting
 Sample Protein
 Sample Peptide
 Molecular Mechanics
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
9.18 Sample Protein
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To generate a stack of energetically favorable protein conformers using the ICM Biased Probability Monte Carlo method:

  • Read in a protein structure and convert to an ICM object.
  • Select the residues you wish to sample.
  • MolMechanics/Sample Protein
  • Enter a value for Effort. This represents the length of the simulation - values between 1 and 10 will give a thorough sampling. A larger effort value will be needed for larger proteins.
  • Enter a value for the Angular Vicinity (default 15). Please see http://www.molsoft.com/man/reals.html#vicinity
  • Enter a Temperature value. Please see http://www.molsoft.com/man/reals.html#temperature
  • Click OK.
  • When the simulation is finished a stack of conformations will be displayed in the ICM workspace.


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