
Dear Ben
Thank you so much for your swift/comprehensive answers!
regarding the antibody/IGG modelling, one more question: I understand, with modeller, you can define S-S bonds, and modelling the FC-part plus hinge (including di-sulfide bonds) does work if you have a decent template for the FC (without hinge) - of which there are many. I tried this and it does give the expected result. To get the full length antibody, this would require including the two Fab domains, ideally as rigid bodies. I understand rigid bodies can be defined in modeller, but I wonder: is there a way to define these two Fab domains, and perhaps also the FC, as rigid bodies, have their initial structures be random positions/orientations, and then ask modeller to construct a model of the three domains (one FC, two Fabs) with only the hinge (including the S-S constraints) being sampled, with the constraint that there are supposed to be no overlaps/clashes between the three domains?
I should add, that this random initial position/orientation is important here, since I don't want to bias the algorithm towards any particular conformation (mutual orientation of the 3 domains) and also, I am in the process of generating a large number of structures, and here generating, for each case, a viable initial structure with the three domains positioned/oriented in a physically plausible way would require a lot of manual work using some editor. like pymol or chimera.
best regards, Michael