[modeller_usage] Antibody Modelling

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I want to model an antibody structure with multiple templates for specific segments from each template based on the below alignment for two chains seperately. Since I know the domain interface residues, I could able to superimpose their relative orientation after modelling seperately.

 

L-CHAIN TARGET__: AAAAAAAAAA11111AAAAAAAAAA22222AAAAAAAAAA33333AAAAAAAAAA

L-CHAIN TEMPLATE: AAAAAAAAAAxxxxxAAAAAAAAAAxxxxxAAAAAAAAAAxxxxxAAAAAAAAAA

LOOP-L1 TEMPLATE: xxxxxxxxxx11111xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

LOOP-L2 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxx22222xxxxxxxxxxxxxxxxxxxxxxxxx

LOOP-L3 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx33333xxxxxxxxxx

 

 

H-CHAIN TARGET__: BBBBBBBBBB44444BBBBBBBBBB55555BBBBBBBBBB66666BBBBBBBBBB

H-CHAIN TEMPLATE: BBBBBBBBBBxxxxxBBBBBBBBBBxxxxxBBBBBBBBBBxxxxxBBBBBBBBBB

LOOP-H1 TEMPLATE: xxxxxxxxxx44444xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

LOOP-H2 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxx55555xxxxxxxxxxxxxxxxxxxxxxxxx

LOOP-H3 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx66666xxxxxxxxxx

 

 

I wish to know how to specify the segment positions to be modeled from each template or

 

Is there anyother easy way of modelling the same?.

 

Selva

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