Sorry - i dont know the answer but why dont you divide the pdb into two parts, ditto the pir alignment and run two chainsaw jobs?
Clumsy but it should work..
Eleanor

Ronnie wrote:
If i want to use chainsaw to prep a pdb file that contains two chains of different sequences, how do I format the alignment .pir file to include the alignments for both chains?

thanks for in advance for your help!

Ronnie



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