Unsolved

Dear Rosetta users, 

I'm using RASREC CS-Rosetta 3.5 to pridect the structure of a membrane protein. So far I've added the following files to the setup_run: CS file (NMR data), FASTA and Fragment files. I've tried to add the Span and Lips files in the setup_run, but I didn't know the commands for these types of files; I've tried -span <spanfile>  (and ) -lips <lipsfile>, but they weren't excepted this way! So what I did is add them manually to the flags_denovo file. 

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.