Author: Arvind Sivasubramanian
Date: Feb 8 2007.

The following are the steps that were taken to create the
*_chothia.pdb files in this directory.

1. Use -idealize Rosetta mode on the pdb files in the ../renumbered
directory to create the light (L) and the heavy (H) chains in the
../idealized(L|H) directories.The resulting chothia files in the
idealized(L|H) directories were created after the rosetta run using
chothia_mapping.pl and chothia_renumber.pl

2. Overlay the individual idealized light and heavy files on the
   native pdb structure available in ../pdbfiles. The script to do
   this is ram_idealize_combine.pl. This script makes use of Profit to
   do the superposition. Once this is done, the two files are joined
   into one chothia file using cat.

3. The file list_chothia_fv_lhdimer contains a list of L-H dimers as
   well as L and H dimers. Several of the files in the directory have
   bugs during the -idealize procedure. The following are the types of bugs

   a. failed during -idealize (1j05,1iga,1yuh,1p7k,1dvf)
   b. idealized, but incorrectly. This is a long list. See notebook
   for details.


cat list_chothia_fv_lhdimer |grep -vE
'(1j05|1iga|1yuh|1p7k|1dvf|1xf3|1r24|1rmf|2lve|1rvf|1fpt|1mam|1nsn|1a6v|8fab|1xf4|1dqm|1xf2|1ndg|1mfc|1a6w|1mfd|1mfb|1a7q|1yc7|1nj9|1bm3|1dfb|1e4w|1e4x|1fl3|1mim|1ub5|ub6)'
> list

The files in the file "list" will be used to create the dssp files and
subsequently fragments.
