I am running some flexible backbone design on a transmembrane four-helix bundle heme protein via RosettaScripts. I'm finding that the membrane residue is moving a lot during design, and I have to optimize the embedding with mp_transform post-design to reposition the mem residue. I have a few questions about this:
1. Is there any way to implement an embedding optimization step at the end of a Rosetta script? I've found the OptimizeMembraneEmbedding mover but it says its currently not compatible with RosettaScripts in the documentation.
2. After optimization, the score is reported using the old score function (mpframework_smooth_fa_2012.wts), but I'm using franklin2019 for my designs. Is there any way for mp_transform to report the score, or perform optimization, with franklin2019? I've added "-score:weights franklin2019" to my flags but it seems to ignore it.
3. Is there any way to prevent movement of the protein within the membrane during design?