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Contents
 
Introduction
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
8.6 Find Loops in PDB
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To find loops in the PDB that have similar conformation to a loop displayed in ICM:

  • Read in a protein structure and convert to an ICM object.
  • Select the residues in the loop.
  • MolMechanics/Loop/Find PDB Segments
  • Enter a vicinity value (see: http://www.molsoft.com/man/reals.html#vicinity).
  • Enter the number of hits it should return.
  • Click OK.
  • A table of the hits containing the PDB codes containing a similar loop conformation will be displayed. The column aRMSD is angular (torsional) RMSD.


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