Member Site Forums Rosetta 3 Rosetta 3 – General using constraints with AbinitioRelax (Rosetta 3.1) Reply To: using constraints with AbinitioRelax (Rosetta 3.1)


    Smlewis, thanks for your quick responses.

    Actually, the C-alpha trace RMSD is what I need. Can I set the RMSD score term for a subset of the C-alphas? I want to constrain only the secondary structure elements.

    The coordinates of the constraint are superimposed (best-fit) on the native structure (makes it easier to view the two structures together in VMD), and hence they are far from the Rosetta model. I will try to re-align the constraints to the Rosetta models ex post facto and see if this helps.