Author: Andrew Watkins

# Code and Demo

The central code for the rna_score application is in apps/public/rna/util/rna_score.cc

# Application purpose

This code is intended to score RNA-containing silent files in a way that provides extra functionality in ways that RNA workflows may expect.

# Input Files

## Required files

• A silent file (and tags) or PDB file(s) containing RNA (or, properly, anything) to score

## Tips

• This program can be made aware of what PDBs may once have contributed to the full modeling problem that resulted in the silent file to be scored; use the option -original_input to pass some PDBs
• RNA chemical mapping data options are also respected (by passing -rna:data_file)
• Will convert protein part to centroid if requested
• Can be used to recompute RMSDs for entire poses or subsets of the pose
• Can be used with superimposition over all residues, or over a particular fixed domain (especially useful if you are rescoring a silent file from a run that had used a superimposition-standard you are now regretting)

# Options

-in:file:s                     Name of single PDB file with template coordinates
-in:file:native                A native PDB (for RMS calculation)
-stepwise:virtualize_free_moieties_in_native    Will virtualize groups in the native PDB that
aren't making any contacts (thus omitted from RMSD computation)
-in:file:fasta                 The fasta will allow a FullModelInfo setup based on each input
pose, even if some or all of the input poses are incomplete
(necessary for some RNA score terms like loop_close)
-rmsd_nosuper                  Calculate RMSD without superimposing to the native (good for
density cases, where there IS a privileged reference frame
-rmsd_residues                 Specification of a subset of residues over which to calculate RMSD
-just_calc_rmsd                Do nothing but calculate RMSD
-color_by_score                Set the temperature of each atom in the PDBInfo to the score
so that you can color by score in PyMOL
-stepwise:superimpose_over_all    Will superimpose over every residue if true. If false, will try
to figure out a reasonable fixed domain to use instead.
-stepwise:alignment_anchor_res    Help out the superimposition by giving a residue from the fixed
domain over which superposition should take place