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[modeller_usage] loop refining of a multi chain protein

Dear User
I have a protein with multichain and I am using loop.py script for refining a protein but  a error is coming which suggests that it fails to indentify the metioned residues in pdb file. But when I am running the same loop.py script with a alignment file and PDB file without mentioning any chain, it seems to run ok.
In case of multichain proteins what should be the changes made to the loop.py script for loop refining and how the residues should be mentioned in the script.
Subarna thakur

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