rna_design.macosgccrelease -s chunk001_uucg_RNA.pdb -nstruct 3 -ex1:level 4 -dump -score:weights rna_hires.wts
command Command lines and Options: In the new release, user can simply use a flag file to instead of enter bunch of flags everytime.flag file is a plain txt file which holds a list of options
-database Path to rosetta3 databases. [PathVector] -in:file:s Name(s) of single PDB file(s) to process. [FileVector] -nstruct Number of times to process each input PDB. [Integer] -ex1:level <n> Use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff. [Boolean] The integers that follow the ex flags specify the pattern for chi dihedral angle sampling. There are currently 8 options; they all include the original chi dihedral angle No. 4 means: EX_TWO_HALF_STEP_STDDEVS [-1,-1/2,0,1/2,1 standard deviations]. -dump Generate pdb output,default:false. [Boolean] -score:weights rna_hires.wts Name of weights file, default is standard. [String]
***Energy interpreter for fullatom silent output: score Final total score fa_atr lennard-jones attractive fa_rep lennard-jones repulsive fa_intra_rep Lennard-jones repulsive between atoms in the same residue lk_nonpolar lazaridis-karplus non-polar solvation energy hack_elec_rna_phos_phos Simple electrostatic repulsion term between phosphates hbond_sr_bb_sc backbone-sidechain hbonds close in primary sequence hbond_lr_bb_sc backbone-sidechain hbonds distant in primary sequence hbond_sc sidechain-sidechain and sidechain-backbone hydrogen bond energy ch_bond Carbon hydrogen bonds geom_sol Geometric Solvation energy for polar atoms rna_torsion RNA torsional potential. atom_pair_constraint Atom pair distance constraints score? angle_constraint (not in use) rms rmsd ***If you use the sample flag files, there are also other output files generated. start.pdb: Idealized structure S_000*.pdb: Output of the rna denovo design. chunk001_uucg_RNA.sequence_recovery.txt: This is a simple report for design identity of each RNA residue and structure.