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[modeller_usage] doutbs about file

My name is Amanda Maia and I´m a beginner using Modeller. I´m having some trouble finding the answers to my questions on the manual. Could you help me?
I have a sequence that aligns (BLAST pdb)with various structures on PDB within an average identity of 35%. Since I need to use as much models as I can get, I´m writing a PIR file with 5 templates. But one (1MDY) has 2 chains (out of 4) that blast quotes (B and E). Do I have to make a PIR line to each one? And a pdb file for each one too?
structureX:molde1MDYB:FIRST:@:LAST :@:myoD:myoD: 2.00:-1.00
structureX:molde1MDYA:FIRST:@:LAST :@:myoD:myoD: 2.00:-1.00
Thank you in advance!
Amanda Maia

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