Unsolved

Hi, 

I submitted a job to the ROSIE antibody queue, which ran successfully, but all the result files now have a discontinuity in the backbone 2 residues before the start of CDR L2. No residues are missing. I ran it again without the H3 modeling, and the discontinuity isn't there, so it's something during the high resolution modeling that is causing a problem. Is there anything I can do to prevent this from happening? Should I use the light chain structure from the grafted model as correct, and use the heavy chains from the more rigorous protocol?

When I use

pose = pose_from_pdb("1YY8.clean.pdb")

it results in an error:

RuntimeError Traceback (most recent call last)
<ipython-input-9-755d9c16f3f1> in <module>()
----> 1 pose = pose_from_pdb("1YY8.clean.pdb")

RuntimeError: unidentifiable C++ exception in both linux and window.

I need help in this regard...........................................

I am doing SymDock using Rosetta 3.5. I wonder what the option really does:

-symmetry:initialize_rigid_body_dofs - Initialize the rigid body configuration according to the symmetry definition file.

I actually ran SymDock using diff. option combinations. When initialize_rigid_body_dofs is set, the assemblies look very different, otherwise more homogeneous. So I concluded that the option does initialization.

I am doing SymDock using Rosetta 3.5. I played with dock_lowres_filter so decoys were generated. Now the program reports that 

protocols.symmetric_docking.SymDockProtocol: STRUCTURE FAILED HIGH-RES FILTER