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Job short description (visible in queue):

Input fasta file of the target sequence. Must correspond to input.

Dot-bracket secondary structure of the target. Must be the same length as the target fasta. May use []{}<> for pseudoknots. Use . for any regions specified explicitly as starting PDBs, even if those regions are helical.

Number of structures to generate:

PDB Inputs

Input PDB file(s) of RNA. (Waters and unrecognized small molecules will NOT be removed)

PDB file containing part of the target model to which to align the simulation, using 4.0 A RMSD constraints.

Native PDB file.

High Resolution Settings

After fragment assembly, run full-atom refinement in a high-resolution scorefunction

Use the original FARFAR scorefunction
Use the most recently published scoring function for FARFAR2 (recommended)
Use the BETA scoring function currently under active evaluation and development (not recommended)

Low Resolution Settings

Use the ribosome fragments from 1jj2 (FARNA paper)
Use the Rosetta default fragment library (Richardson 2009)
Use the new fragments from the FARFAR2 paper (Das 2018)

Job Description (for your own records):