I have to model a chimeric protein of two known sequnces. I have gone through the previous archives and have come across the emails of people who have done it. 

however, I am confused with how to start the first alignment to get the following alignment file

>P1;proteinA
structureX:proteinA
aaaaaaaaaaaaaaaaaaaaaaaaaaaa----------------------------------*
>P1;proteinB
structureX:proteinB
----------------------------bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb*
>P1;chimera
sequence:chimera
aaaaaaaaaaaaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb*

is this the .ali file to give for alignment. Which script should I use. 

Kindly help with which is the correct script to use.

Thank you

Regards

Ayesha Fatima

QIUP, Ipoh, Perak