Comparing a prediction to the native structure and calculate RMSD for RNA
Hi all,
I am new to Rosetta and FARFAR2. I have attempted modelling the structure of PDB:1KXK using the following command line:
rna_denovo -sequence gucuaccuaucgggcuaaggagccguaugcgaugaaagucgcacguacgguucuaugcccgggggaaaac -cycles 20000 -nstruct 3 -bps_moves false -minimize_rna true -secstruct ".....(((.((((((...(((((((((((((((....))))))..)))))))))..)))))))))....."
Now I want to compare the obtained structure to the original PDB and to calculate the RMSD. I ran the following: