The files in this directory walks you through an example to help you run the antibody modeler mode. 
Before proceeding you need to make sure that you have done the following:
1. Updated your code to make sure that you have the latest developments
2. Make sure that you have the "antibody" directory.
3. Read the "antibody_readme.txt" file in the "antibody" directory and make sure that you follow 
   all the instructions

After all the scripts and supporting files are in place:
a. grafting_input <directory>		
   This contains all the fasta sequence
   
   files for the query. 
   --------------------
   i.   launcher.bash		A bash file to invoke the master wrapper script. 
				The script takes the fasta files as an input and outputs 
				a framework with everything except the CDR-H3. It also 
				generates the fragment files for H3 modeling. It also 
				creates a build directory with a condor script to actually 
				build <nstruct> number of homology models
   ii.  query_h.fasta		Fasta file containing the heavy chain	sequence.
   iii. query_l.fasta		Fasta file containing the light chain sequence 
   iv.  rampaths.txt		Paths for various files needed by scripts 
   v.   utilities.txt		Supporting file

b. build_input <directory>	This contains the files needed for modeling the CDR H3. 
				These files are the output files generated by "launcher.bash".
   i.   1xyz_build_loops.bash   Bash script that invokes rosetta to actually model the CDR-H3 loops. 
				This is the most time consuming part of the protocol. For 
				simplicity the nstruct is set to 1. However, for a normal run
				it should be 2000. The file created by "laucher.bash" actually 
				has nstruct 2000. I manually changed it to 1 for the purposes of 
				this example.
   ii.  aaFR02_09_05.200_v1_3   Standard rosetta 9-mer fragment file
   iii. aaFR02_03_05.200_v1_3   Rosetta 3-mer fragment file appended with antibody fragments
   iv.  H3_CTERM		Special fragment file containing H3 base fragments 
   v.   hfr.pdb			Template structure from which heavy chain of query has been obtained 
   vi.  lfr.pdb                 Template structure from which light chain of query has been obtained   
   vii. paths.txt               Standard rosetta paths file. Make sure this matches with your paths. 
				Once again this should be set if you have followed instructions in 
				"antibody_readme.txt"
   viii.FR02.pdb                The output file of "launcher.bash" which has the all non-H3 CDRs grafted
				onto the framework regions. It contains the CDR-H3 region with the
				coordinates blanked out.

c. build_output <directory>     Files generated by the "1xyz_build_loops.bash" 
   i.  	aaFR02_0001.pdb		Output decoy with ab initio built CDR-H3. The non-H3 CDRs alongwith the
				relative orientation of the light and heavy chains has been optimized
   ii.  FR02_dummy_loop_01_0001 A fragment generated for the CDR-H3 loop modeled plus one flanking residue
				on either side. The three columns are for the phi-psi-omega angles for each
				residue. This is helpful in recreating the loop using other command line
				options like "refine_loop".
   iii. aaFR02.fasc             Scorefile with special columns:
				a. rmsg         Global rmsd of CDR H3 if native was specified, otherwise -1.00
				b. hydrphbc     A hydrophobic score adapted from Friesner's long loop modeling paper
				c. Brms         Global rmsd of the CDR H3 base region
				d. Rrms         Global rmsd of the CDR H3 non-base region
				e. Gap          Separation at the loop cutpoint. Useful in detecting broken loops. 
						Has to be less than 1.9 Ang.
				f. H3           Binary variable is true if decoy satisfies Shirai rules
			        e. N--O         Distances between the backbone oxygen of the (n-2)th residue and the 
						NEl atom of the (n+l)th Trp side chain. (Shirai)
				f. HH   	Number of hydrogen bonds in the	CDR-H3. This is purely based on a
						distance based criteria and does not use Rosetta's sophisticated 
						hydrogen bond stuff. Helpful in detecting H ladder formation
				e. St           Checks if Stem follows Shirai's rule for extra bulge.

Make sure that launcher.bash and rampaths.txt are modified to match your paths. You should have completed this 
already if you have read "antibody_readme.txt" in the "antibody" directory. You can merely copy the rampaths.txt 
from "antibody/scripts/rampaths.txt" to overwrite this local copy.

Once you have modified the "launcher.bash", after the run finishes,you should have a build directory. 
There are thousands of files in there, but then I have placed the key files in the "build_input" directory. 
You only need these files to be able to build the CDR-H3 into the antibody scaffold. 

Finally, on execution of the "1xyz_build_loops.bash" script, we actually generate the final homology models. 
We generally build 2000 of this (in this example, we build just one) and choose the top ten. 
