As of v1.0.3-2014mar09, DSSR has a decent user manual in PDF! Currently of 45 pages long, the DSSR manual contains everything a typical user needs to know to get started using the program effectively. The contents the manual are listed below.
Table of Contents List of Figures Introduction Download and installation Usages Command-line help Default run on PDB entry 1msy – detailed explanations Summary section List of base pairs List of multiplets List of helices List of stems List of lone canonical pairs List of various loops List of single-stranded fragments Secondary structure in dot-bracket notation List of backbone torsion angles and suite names Default run on PDB entry 1ehz (tRNAPhe) – summary notes Brief summary Specific features Default run on PDB entry 1jj2 – four auto-checked motifs Kissing loops A-minor (types I and II) motifs Ribose zippers Kink turns The --more option Extra parameters for base pairs Extra parameters for helices/stems The –-non-pair option The –-u-turn option The --po4 option The –-long-idstr option Frequently asked questions How to cite DSSR? Does DSSR work for DNA? Does DSSR detect RNA tertiary interactions? Revision history Acknowledgements References
With the User Manual available, I feel confident to claim that DSSR is now mature, stable, ready for real world applications. While only time would tell, I have no doubt that DSSR will become an essential tool in RNA structural bioinformatics.