WEBSERVER FOR FRAGMENTS:
http://robetta.bakerlab.org/fragmentsubmit.jsp

TO MAKE FRAGMENTS LOCALLY WITH make_fragments.pl:

0. Setup--
      Configure paths at the top of make_fragments.pl
      PSI-BLAST must be installed locally

1. Obtain a fasta file for the desired sequence. This file
   must have 60 characters/line with no white space.  First
   line can be a comment starting with the '>' character.

2. Obtain secondary structure predictions from web servers, or
   setup shareware locally so that make_fragment.pl can run 
   secondary structure predictions locally.  

   The fragment maker can use predictions from psipred (.jones or 
   .psipred extension), PhD  (.phd) and SAM-T99 rdb format (.rdb) 
   and jufo (.jufo).  Up to three predictions can be used. At least 
   one must be used. 

   The getSSpred.pl script can be used to obtain predictions
   off the web.  Edit the config portion of this script to include 
   your email address and to include the correct path to the httpget 
   script.  To use this script, provide the fasta filename and the desired
   method.   (invoke the command without arguments to see the
   usage explanation).  Retrieve the secondary structure predictions
   from your email mail box.  

3. Prepare files with NMR data-  these include .cst and .dpl files
   that are the same files that rosetta uses, and the .chsft_in file
   that contains chemical shift information.  See the file
   'data_formats.README' for the formatting information.

4. Run make_fragments.pl.  Invoke without arguments for usage options.
   Likely the only argument you need to provide is the fasta file.
   If you want to exclude homologous seqeunces from the fragment search, 
   add the -nohoms argument.  Note that if you want to exclude homologs 
   from the chemical shift/TALOS search, you need to edit the talos 
   database.  See the README in the chemshift_source directory for 
   instructions.  If you do not have a particular type of secondary structure
   prediction (say the .jufo file) and you do NOT want make_fragments to
   try to run the method locally, use the -nojufo option.

NOTES:  

1.  name all your files with a five character base name followed
    by the appropriate extension.  The base-name should be the four-letter
    pdb code and 1 letter chain id.

2   See also the nnmake.README a listing of the files involved in the 
    fragment process

3.  If a pdb file is in the directory you're making fragments in, nnmake
    will evaluate the fragment match to the pdb.  Note that if the pdbfile
    disagrees with the fasta file, the program will detect an error and 
    stop