Monica,

Try:

align PDB1//A/80-120+160-220/, PDB2//A/80-120+160-220/
or if you want to align using the alpha carbons,
align PDB1//A/80-120+160-220/CA, PDB2//A/80-120+160-220/CA

Cheers,
-Rajintha

On Wed, Jul 2, 2014 at 7:22 AM, Monica Mittal <monica.mittal41@gmail.com> wrote:
Dear all
I need to align lets say resi 80-120 and 160-220 from one protein to resi 80-120 and 160-220 in second protein. How can i do this.
I tried following:
align PDB1 and resi 80-120, PDB2 and resi 80-120 
this is for one set but how to do for two sets 80-120 as well as 160-220 simultaneously.
Thank you 
Monica

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