On 6/7/10 4:15 PM, Konstantin A. Odynets wrote: > my templates are a homodimer of the first domain and a monomer of the > second domain, > and the target protein is a homodimer. Both domains are linked by 17 aa > flexible regions > without templates. How could I do such task in Modeller 9.8?
You are going to have trouble with the 17aa linker regions - that's a little long for loop modeling. But to model the second domain, simply use two copies of your second template in your alignment, e.g. something like:
>P1;1n3l structureX:1n3l:4:A:342:B:hstyrrs-N_2x342:homo sapiens:1.18:0.18 -AAAAAAAAAA-AAAAAA-------/-BBBBBBBBBB-BBBBBB-------* >P1;1ntg-1 structureX:1ntg:2:A:170:A:hstyrrs-C_1x169:homo sapiens:2.21:0.251 -------------------CCCCCC* >P1;1ntg-2 structureX:1ntg:2:A:170:A:hstyrrs-C_1x169:homo sapiens:2.21:0.251 ---------------------------------------------------/--------------------------------------CCCCCC* >P1;hstyrrs sequence:hstyrrs:1:A:528:B:hstyrrs_2x528:homo sapiens:2.00:-1.00 AAAAAAAAAAAAAAAAAALCCCCCC/BBBBBBBBBBBBBBBBBBLCCCCCC*
Ben Webb, Modeller Caretaker