I have recently started using Rosetta and I wanted to generate the 3-mer and 9-mer fragments for Abinitio (without using the Robetta server).
I used the make_fragment.pl files provided under the fragment_tools folder in Rosetta to generate the files (by giving just the fasta file as an input). However, the result that I gathered was not the same, as what is generated by the Robetta server.
I would really appreciate any help on what I am doing wrong or how I can verify the results or are there any other ways to generate the 3-mer, 9-mer file without having to use the Robetta server.
In addition to the configuration changes in the make_fragment.pl file, I once changed the default database from nr to uniref50, but I later reversed it.