index and restraints

[sawbtte]

Hi, I am using the colabdock model recently and I think it's great.But I have some questions about the code; suppose I want to docking a antigen-antibody complex,and the complex has three chains(A\B\C);the parameter "chains" will be "A,B,C" in the config.py;and the restraints is [[4, 8]]; the restraints [[4,8]], means that the 4th residue in the chain A and the 8th residue in the chainB satisfy the distance setting and also the 4th residue in the chain B and the 8th residue in the chain C satisfy the distance setting ? or just the first two chain will satisfy this setting?

[sawbtte]

and if I input three chains, but only need input the restraints between just two chains, how can I modify the config.py.

[sawbtte]

and thinks for your help!

[JeffSHF]

Hi, there. As stated in the description in the config.py, the order number in a restraint refers to the residue in the complex sequence. The complex sequence is comprised of the chain sequences and the order is determined by the "chains" variable. Thus, in your case, if the lengths of chain A, B, C are 5, 10, and 15, respectively, and 4th residue in chain A has contact with 8th residue in chain B, then, your restraint should be set as [4, 13]. If 4th residue in chain B also has contact with 8th residue in chain C, then the restraint should be set as [[4, 13], [9, 23]].

[sawbtte]

thank you for your help!!!!