Rosetta Input/Output Paths (order essential)
path is first '/', './',or  '../' to next whitespace, must end with /
INPUT PATHS:
pdb1	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
pdb2	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
pdb3	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
fragments	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
structure	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
sequence	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
constraints	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
starting structure	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
data files	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/rosetta_scripts/abinitio/bin/../../../rosetta_database/
OUTPUT PATHS:
movie	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
pdb	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
score	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
status	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
user	/Users/ion/Projects/rosetta/branches/releases/rosetta-2.1/RosettaAbinitio/examples/test/./
FRAGMENTS:
2  number of fragment files
3  file 1 size
aa*****03_05.200_v1_3
9  file 2 size
aa*****09_05.200_v1_3
