1. Checkout trunk/antibody
2. Change ~/antibody/scripts/rampaths.txt to set the paths to
	 match your directory structure
3. Copy the following files to directory where simulation will be run:
	 a. ~/antibody/scripts/rampaths.txt
	 b. ~/antibody/scripts/utilities.txt
4. Have the following files ready for input in the simulation directory:
	 a. query_l.fasta: sequence of light chain
	 b. query_h.fasta: sequence of heavy chain
	 Note: The fasta files should conform to the following format:
				 i.  The header line with > should not be there
				 ii. There should not be any hyphens for breaks
				 iii.There should not be any newline charchter - all on one
						 line		 
5. Make sure that Profit is installed on your system and it is set up
	 such that it can be called from any subfolder by typing "profit".
6. Change the paths.txt in  ~/antibody/scripts/paths.txt
	 such that in all cases it points to your local copy of the
	 rosetta_database directory
7. Change the hardcoded paths in the file ~/antibody/scripts/ram_blankcdrs.pl
   They should point to two files located in ~/antibody/scripts/. Make
	 sure that the full absolute paths (non-relative) are provided. For
	 some strange reason incorporating rampaths.txt does not work here,
	 more details are provided in ram_blankcdrs.pl
8. Change the hardcodes paths in the following file to match your directory
   structure:
	 ~/antibody/scripts/get_top10_scoring.pl
9. Also ensure that you have the most updated version of the rosetta_database
	 directory
10. Change paths for sam/jufo/blosum etc in the following file:
	  ~antibody/scripts/make_rosetta_fragments.pl
11.In the folder in which simulations will be run,which already contains:
   i.   rampaths.txt
	 ii.  utilities.txt
	 iii. query_l.fasta
	 iv.  quary_l.fasta
	 Launch the following command:
	 perl -P ~/antibody/scripts/ram_buildloop_wrapper.pl pdb1xyz_chothia.pdb bit 1 1 1 1 1 1 1 2000 query_l.fasta query_h.fasta
12.The simulations folder will have a new directory named "build". Some of the
	 important files in the directory are:
	 i.   FR02.pdb: The framework region with the non-H3 CDRs grafted in
	 ii.  H3_CTERM: Fragment files for the CDR H3 base region
	 iii. aaFR02_03_05.200_v1_3: 3-mer fragment file for the H3 loop region 
				  										 with antibody fragments appended
	 iv.  aaFR02_09_05.200_v1_3: 9-mer standard rosetta fragment
   v.   lfr.pdb: light chain template from which light chain of
								 FR02.pdb has been obtained
	 vi.  hfr.pdb: heavy chain template from which heavy chain of
								 FR02.pdb has been obtained
	 vii. 1xyz_build_loops.con: The condor script file containing headers. This
				 										  is used for launching jobs on the cluster using
														  the command: "condor_submit 1xyz_build_loops.con"
   viii.1xyz_build_loops.bash: This is called by the .con file (above) and 
															 contains the actual rosetta command line needed
															 for launching a job with 2000 decoys.
13.Post processing: In the directory one level above the "build" directory
   launch the script:
   ~/antibody/scripts/get_top10_scoring.pl
	 The top ten models are outputted: model1.pdb.....model10.pdb
	 The processed scorefile void of any redundancies and containing
	 decoys which do not have broken CDR H3s is also outputted as:
	 aaFR02_unbroken.fasc

UPDATING THE ANTIBODY DATABASE:
Use the script:
~/antibody/scripts/update_RosettaAntibody_database.pl
(follow instructions in the script)

Reference:
"Toward high-resolution homology modeling of antibody Fv regions and
application to antibody-antigen docking"
Arvind Sivasubramanian*, Aroop Sircar*, Sidhartha Chaudhury & Jeffrey
J. Gray, 2008
Submitted to: Proteins: Structure, Function and Bioinformatics

