Reply To: loop remodelling with a fixed bound DNA

[Anonymous]

I would guess that the loop modeling app is throwing out your non-protein atoms. It has some poorly thought out assumptions…

PyRosetta is likely to be an reasonable way around this problem. You can pick apart the loop modeling executeable to see the Movers it calls; if you set up your Pose yourself (and FoldTree, and MoveMap) to handle the DNA and then call those Movers yourself I bet it will work. Worst comes to worst, directly call the KinematicMover and/or (Small/Shear/Frag + CCDLoopClosureMover) directly.

I haven’t played around with PyRosetta but I’m reasonably certain all the necessary parts are present.