Author: Andrew Watkins
Added to documentation: Feb 2018
The central code for the
rna_score application is in
This code is intended to score RNA-containing silent files in a way that provides extra functionality in ways that RNA workflows may expect.
-original_inputto pass some PDBs
-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