I wnated to solve this in PyRosetta because of the possibility of easy Windows instalation, but I recieved advice to do it in Rosetta ( https://www.rosettacommons.org/node/9517 ).
So what I need (also described in a link above) is that I have RNA pdb file with hundreds of residues in witch I miss usually about ten segments each max 40 but often 3-4 residues ( I have only FASTA sequence of the missing parts). I want to predict the missing parts and insert it into my pdb.
I found rna_denovo_setup.py (https://www.rosettacommons.org/docs/latest/application_documentation/rna/rna-denovo-setup) which I could use to predict the missing parts of sequence and then using the same protocol ( option "-s" ) to join all pdb-s together (I am not sure if this works as i think).
Or is here a better way to do this? (maybe provide the pdb when the missing parts are predictet so the prediction software could consider residues which I dont want to predict).
I appriciate any advice or idea.
That should be the protocol to use, unless you want to look at the stepwise modeling protocol. The stepwise protocol is a bit more involved in stringing together, though, as it requires a bunch of file manipulations and organization on your part.
With either protocol, my suggestion would be to - at least for your first run - not try to fill in all 10 sections at once, but instead look at remodeling just a single segment, probably one in the 5-7 nt range. Once you've figured out the protocol for modeling a single missing segment and have results for that segment which are looking reasonable, only then would I suggest trying to move on to the more complicated protocol of filling the multiple other missing segments.