Instruction from Author

Author  :  Carolyn M. Slupsky 
Date    :  Thu Apr  2 14:29:02 PST 1998 
Purpose :  To convert from PIPP .shift file to BMRB format 
To run  :  1.  First modify header.awk and shft2bmrb.awk to include 
           the number of residues in your protein (r_length). 
           2.  Then, modify shft2bmrb.awk to have the generic errors  
           assigned to 15N, 13C, and 1H. If there is no error given, assign these
           three values to 0 
           3.  Finally, type bmrb. 
Input   :  1.  A file with the 1-letter amino acid sequence (no breaks) 
           2.  A modified PIPP file (no header, and no '\' characters) 
Output  :  A completed file in BioMagRes Bank format.  After the progra m is 
           run, you will have to modify some of the ambiguity codes (those
           with a code of 4 or higher).....for more information, see the header
           of the output.  You may also have to alter some of the errors
           (if they are not generic errors).  Please check over the final
           result to be sure the program ran satisfactorily.  I have only accounted
           for atoms that I would normally see and assign in NMR spectra.
Note    :  I wrote this program for myself, and therefore it is not well 
           commented. I am not responsible for any incorrect results obtained
           while using this script, but I  would be happy to answer any questions 
           or to help modify it.  (My e-mail address is: cms@wolf.biochem.ubc.ca).



Additional instruction from BMRB

Using script software to convert PDB-PIPP file portion to BMRB STAR files

1. down load PDB "nmr restraint" files
2. uncompress the file, delete all "\" symbols
3. save only the PIPP (chemical shift assignment) part, delete the rest
4. files from 3 should have the following format:

(e.g.)

RES_ID		1
RES_TYPE	MET
SPIN_SYSTEM_ID	1
HETEROGENEITY	100
   N  120.0000
   HN  8.7000
   CA  54.9000
   HA  4.0000
   CB  32.5600
   HB#  2.1600
   CG  30.7400
   HG#  2.5800
END_RES_DEF

delete whatever text that is not included in this format.

If the assignments for a amino acid is missing, add into the corresponding 
position the following:

(e.g.)

RES_ID		1   # residue number    
RES_TYPE	@
SPIN_SYSTEM_ID	@
HETEROGENEITY	@
   @
END_RES_DEF


5. Edit 1-letter amino acid sequence file according to the chemical shift assignment,
name the skipped amino acid "@"; otherwise, find the aa sequence in the original
PDB coordinance file, and convert it from 3-letter code to 1-letter code.  The sequence
code should be on one unbroken line.

6. edit header.awk and shft2bmrb.awk files, change r_lgnth to the actual 
length of the peptide.

7. run bmrb by typing "bmrb", give the names of input and output files as requested



There are two files that can be used for testing:

test.seq  (aa seq, r_lgnth=8)
test.t    (PIPP file)

whose format the user should refer to.
