Metadata

Author: Andrew Watkins

Added to documentation: Feb 2018

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

Documentation for rna_score