Updated HTML docs.

Manual.html

@@ -98,6 +98,8 @@ When run with no arguments, it launches the user interface.  If any arguments ar
 
 
 Options:
 Options:
   -h, --help            show this help message and exit
   -h, --help            show this help message and exit
+  --pdbid=PDBID         PDB id to retrieve from RCSB [default: None]
+  --url=URL             URL to retrieve PDB from [default: None]
   --output=FILENAME     output pdb file [default: output.pdb]
   --output=FILENAME     output pdb file [default: output.pdb]
   --add-atoms=ATOMS     which missing atoms to add: all, heavy, hydrogen, or
   --add-atoms=ATOMS     which missing atoms to add: all, heavy, hydrogen, or
                         none [default: all]
                         none [default: all]