CHEMSHIFT
input:
.chsft_in

output:
.chsft
--------------------
NNMAKE
input:
.pdb            (optional)
.jones          psipred prediction, obtained from server (automate_jones.pl)
.rdb            SAM-T99 prediction, obtained from server (automate_sam.pl)
.phd            PhD prediction, obtained from server (automate_phd.pl)
.homolog_vall   list of homologs in the vall to be excluded (dsc_psiblast2.pl)
.homolog_nr     list of homologs in nr to be excludedA  (dsc_psiblast2.pl)  
.checkpoint     MSA sequence similarity matrix, from blast (dsc_psiblast2.pl)  
                parsed from *.checkASCII
.chsft          predicted torsion angles (pCHEMSHIFT)   
.cst            NOE constraints
.dpl            dipolar coupling constants

output: 
.dat                        sequence and secondary structure of native
aa1ubq_03_05.200_v1_3      fragment files  for '1ubq' chain '_'
aa1ubq_09_05.200_v1_3        aa= arbitrary 2 character code
                             1ubq = pdb code
                             _ = chain
                             03 (09) = fragment size
                             _ = spacer character
                             05 = fragment selection strategy used in nnmake
                                     (04 -> secondary structure only)
                                     (05 -> sequence & predicted ss)
                                     (06 -> sequence, predicted ss, nmr data)
                              . = spacer character
                             200 = depth of library
                             _ = spacer character
                             v1_3 = nnmake version number
 
additional files            score, status, names (removed by make_fragments.pl)

---------------------
ROSETTA
input:
.pdb                  (optional)  native pdb
.dat         
.fasta                (if .dat not available)
.dssp                 (optional) secondary structure 
.ssa                  (optional) alternate source of secondary structure information
aa1ubq_03_06.200_new_d        fragment files
aa1ubq_03_06.200_new_d 


additional input for refine mode:
.pdb                 starting structure
.dssp or .ssa        secondary structure (if not in pdb file)

output:
decoy pdb files
.sc, .fasc           scores of all decoys built