Dear Modellers

I have problem in my alignment file. i want to build structure for antibody. which has matching with the corresponding chains in the template. My first chain has nearly 110 aa which match with the 220aa template chainA and again my second chain has hit with the chain B. after chain A there are 100aa gapped and again hit with ChainB, again after that gap of 100aa. The problem is in template the two chains have seperate numbering. i dont want to build the chains individually. how can I then set my alignment file? I'm attaching alignment file with this.

I already mailed to this address Modeller_usage@guitar.rockefeller.edu. but it was bounced back. so i'm sending u. sorry for the inconvenience.

Thank you. with regards

Phani Vijay