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