I would like to add a filter to my XML Rosetta design script that allows me to implement negative design.
Specifically, I want a filter that can take my designed and minimized input structure, apply a symmetry operation to it (i.e. rotate & translate a domain), minimized the transformed structure and compare the energy to the unmodified input structure. Is this possible with the XML-based Rosetta scripts (I couldn't find a filter operation that allowed me to modify a structure, apply a minimization mover while "remembering" the input structure).
I could do something similar in two separate steps: step 1 (design, minimize and write to disk), followed by step 2, read in structures from disk (computed in step 1), apply symmetry operation, minimize and then compare to the input structure. However, this is not particularly satisfactory as I would like to use the negative design filter to guide a simulated annealing search of sequence space to find sequences that show a strong preference for the desired binding mode.