On 4/4/20 9:23 AM, Чугунов Антон wrote: > I want to perform task almost as in the FAQ #1 > https://salilab.org/modeller/FAQ.html#1: I have two separate proteins, > and want to receive one -- where these two are joined by the [G4S]n > linker. The major difference from the example in FAQ that I have the > exact orientation of both domains (they are docked onto the same > receptor at different sites), and I want them to be prohibited from > movement. The common protocol moves the downstream domain so it changes > its position and orientation, but I have to basically "freeze" the both > domains, allowing the linker to fullfill the space between them.

Either merge the two domains into one PDB file and treat them as a single template with two chains (in which case Modeller will generate inter-chain restraints and keep the input orientation), or deselect those two domains so that Modeller does not refine them, as per https://salilab.org/modeller/9.23/manual/node23.html

Ben Webb, Modeller Caretaker