Hi,
I would like to know the appropìate way to define rigid bodies with PMI. Let's say I am working with a multimeric complex of 8 chains, grouped in 2 subcomplex of 4 chains each (subcpx1 "ABCD" and subcpx2 "EFGH"). At the same time, each subcomplex is bound in a coiled coil region, which is fixed, and I name it CorEX (coiled coils of chains "ABCD" and coiled coils of chains "EFGH"). I would like to explore different conformations of this protein complex by allowing each chain to move in the space, but imposing that coiled coil regions must be rigid (coiled coils of chain "ABCD" must move together and cannot break, e.g). My doubt is how to define this behaviour:
1- Define 3 rigid regions per chain (N-ter; CoiledCoil; C-ter) plus define each CorEX as another rigid body. 2- Define 2 rigid regions per chain (N-ter and C-ter) and then define the 2 CorEX regions.
It seems that IMP.pmi does not allow to define it as in 1, some errors occur. I guess I cannot define two times a given region as a rigid body if it is already defined.
I hope it is well explained :)
Thanks!
Altair