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Re: [modeller_usage] Antibody Modelling

selva@pnu.edu wrote:
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: *AAAAAAAAAA*xxxxx*AAAAAAAAAA*xxxxx*AAAAAAAAAA*xxxxx*AAAAAAAAAA* 
LOOP-L1 TEMPLATE: xxxxxxxxxx*11111*xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-L2 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxx*22222*xxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-L3 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx*33333*xxxxxxxxxx
H-CHAIN TARGET__: *BBBBBBBBBB44444BBBBBBBBBB55555BBBBBBBBBB66666BBBBBBBBBB* H-CHAIN TEMPLATE: *BBBBBBBBBB*xxxxx*BBBBBBBBBB*xxxxx*BBBBBBBBBB*xxxxx*BBBBBBBBBB* 
LOOP-H1 TEMPLATE: xxxxxxxxxx*44444*xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-H2 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxx*55555*xxxxxxxxxxxxxxxxxxxxxxxxx
LOOP-H3 TEMPLATE: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx*66666*xxxxxxxxxx
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?. 
You can just build a model using the four templates you have above, 
using essentially the alignment you show (except using - for a gap 
rather than x, of course). If your LOOP-* templates actually have 
additional structure (e.g. coordinates for the non-loop regions) then 
you can either edit the PDB file and take that structure out, or list 
that sequence in the alignment file as per usual (just align it with 
gaps in the target sequence, so that that structure isn't used in the 
model).

	Ben Webb, Modeller Caretaker
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