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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
9.4 Graft Loop
Next

Available in the following product(s): Homology

To transfer a loop from one object to another:

Step 1: Read in the structures and convert to ICM objects.
  • Read in the two structures into ICM.
  • Convert the structures to an ICM Object.
  • Superimpose the two structures.

Step 2 (Optional): To help identify and selet the gap region you can align the PDB sequences.
  • Right click on the protein molecule in each object and choose the option "Extract Sequences"
  • Select the sequences in the ICM Workspace by double clicking on one sequence- hold CTRL- and click on the other sequence.
  • Right click on the selected sequences and choose the Align option.

Step 3: Select the source loop.
  • Select the loop and the termini residues (e.g. click and drag over them in the alignment).

Step 4: Select MolMechanics/Loop/Graft

Step 5: Select the termini residues of the structure with the gap (destination).
  • Right click on the N-terminal residue flanking the gap and then left click on the top item of the menu. This will transfer the selection to the dialog box.
  • Right click on the C-terminal residue flanking the gap and then left click on the top item of the menu. This will transfer the selection to the dialog box.

Step 6: Superimpose termini backbone and assess the quality of the match.

  • You can change the sequence of the residues in the grafted gap (click on the drop down button in the Sequence dialog box).
  • Click on the superimpose terminal backbone button.
  • Use "Assess Match" button before proceeding, the RMSD and report will be displayed in the terminal box. Use adjust termini mode for cases other than Good.
  • Click OK.

Step 7: Display the grafted structure. Sometimes you may need to refresh the ribbon display to view the new loop.


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