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PrevICM User's Guide
9.4 Graft Loop

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 select 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.

Design Loop
Loop Preferred Residues

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