I am new to the Rosetta software and I would really appreciate some help from someone with experience in RNA Denovo. I am using the rna_denovo application on a cluster with Rosetta 3.3 and I want to predict 3D structures for a large number of RNA molecules.
Initially I predict 3D structures for which there is NMR data available so that I can determine how well the algorithm works. I am supplying the NMR structure as the native structure in order to plot RMSD vs. energy (score).
I would like to generate similar plots when predicting structures where I am not supplying a native structure. As I understand it from the RNA Denovo Server documentation, RMSD is calculated between the models and the lowest energy model (best scoring model) when no native pdb is supplied, however, I do not obtain any RMSD data in my out file when I run without a native structure. How can I calculate this? Are there any significant differences between the RNA Denovo server application and the one included in the Rosetta package?
Also, are there any post-processing scripts available that can be useful for analyzing data from RNA Denovo?
I hope that someone could clarify these points to me. Thank you.