Fixed problems processing nucleic acids
Added option to delete heterogens
Merge branch 'master' of https://github.com/peastman/pdbfixer
Minor improvements to correctly handle more PDB files
Use MODRES records to identify modified residues
Bug fixes
Added option to download files directly from RCSB
Improved handling of nonstandard nucleotides
Show 'processing' message while doing computations
Added option to add a water box
Added docstrings
Created a more full featured command line interface
Display a warning message when Javascript is disabled
Created User Manual
Added lots of examples to the manual, plus some other fixes.