I'm running into some issues applying the DRRAFTER instructions to model RNA loops between several distinct rigid-body helices, and am asking for advice here on how to proceed.
My goal is to rebuild the loop structures between two base-paired regions opf a stem loop. A fake secondary structure is like so:
(1) To get ROSETTA to parse, I have had to break up the double-helix part into its 5-prime and 3-prime strands so that rna_denovo will see the residues in the correct order. This results in effectively 3 pieces. Is there a better way to organise the rigid bodies, or is this correct?
Now, I have tentatively assigned the first RNA piece as the
absolute_coordinates_rigid_body_structure. However, if I don't put in -no_csts DRRAFTER cannot proceed, as it complains about not having a protein component to automatically configure constraints. It will only work with -no_csts, for instance:
-residues_to_model A:1-59 -map_file <mrc> -map_reso 10 -start_struct ./concat.pdb
-include_as_rigid_body_structures pieceA-5prime.pdb pieceB-stemloop.pdb pieceA-3prime.pdb -absolute_coordinates_rigid_body_structure pieceA-5prime.pdb -no_csts
(2) Is there a work around for this or should I give a custom constraint file?
(3) In the custom constraint file given to rna_denovo by -extra_flags cst_file ./constraints.txt , when I give a CoordinateConstraint , which reference atom2 should I be looking at using? I have currently tried to pair atom1 and atom2 from different rigid bodies, but it doesn't seem to keep the strands together.