# stapp.par Contains Parameters for Shift Table Approach to Peak picking
#	This is not a .com file
# To run program use stapp.com


EXP_NAME  13C-NOESY  C13-NOESY  C13-NOE
SIAD_STRING     H* * C*
PK_TBL_FRMT	%9.4f
ACQ_BASE_PHASE  POSITIVE
COMPLETE_ASGNMTS TRUE
#ASGNMT_READ_ONLY TRUE
REQ_ND_SYM      FALSE 
PK_EXCLUDE_XY_DIAG  FALSE
DIM_COUNT	3
THRESHOLD	3.7e5

PDB_ATM_NM_FILTER  *
#DIST_FROM USE_NONE
MAX_NOE_DIST  10.0
PDB_FILES dimer169.pdb 
#PDB_FILES best104xplor.pdb
#PDB_FILES best100xplor.pdb
#PDB_FILES best63.pdb
#PDB_FILES best60.pdb
#PDB_FILES best51xplor.pdb
#PDB_FILES 44_1.pdb 
#PDB_FILES ave29xplor.pdb
#PDB_FILES sa6_5.pdb
#PDB_FILES xplor7_14.pdb
#PDB_FILES xplor12_15.pdb
WRITE_NOE_DIST  TRUE
#XPLR_FILE_NAME ccnewtest21.tbl
#XPLR_FILE_NAME ccnew2test21.tbl
#XPLR_FILE_NAME cntest20.tbl
#XPLR_FILE_NAME noe3dtest22.tbl 


# DATA_OFFSET (PPM) Number to be ADDED to experim. chem. shift to match assign. table
# DATA_OFFSET     0.0      0.0     0.0   
# ERROR_RANGE	0.030	 0.015   0.16 

DATA_OFFSET     0.011     0.012    -0.020
DEG_PROX_LIMIT  0.020     0.025     0.060
#ERROR_RANGE	0.040     0.050     0.120
ERROR_RANGE	0.060     0.075     0.180
#ERROR_RANGE	0.060     0.075     0.240
#ERROR_RANGE	0.060     0.075     0.440


ACQ_PRM_FRMT NMRI_PIPE

#ANTIPHASE_FOLDOVER	FALSE
ANTIPHASE_FOLDOVER      TRUE

SEQUENCE      MATSGFKHLV VVKFKEDTKV DEILKGLENL VSQIDTVKSF \ 
              EWGEDKESHD MLRQGFTHAF SMTFENKDGY VAFTSHPLHV \ 
              EFSAAFTAVI DKIVLLDFPV AAVKSSVVAT PAAAAAAAAA \
              AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA \
              AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA \
              AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA \
              AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA \
              AAAAAAAAAA AAAAAAAAAA MATSGFKHLV VVKFKEDTKV \
              DEILKGLENL VSQIDTVKSF EWGEDKESHD MLRQGFTHAF \ 
              SMTFENKDGY VAFTSHPLHV EFSAAFTAVI DKIVLLDFPV \ 
              AAVKSSVVAT P
		


# Restricting Search to contents of a .PCK File
#   These params will have NO effect to the running
#   of of pipp, they only effect stapp.

SEARCH_PCK_FILE FALSE 
# Can have Multiple PCK files, MUST specify .PCK in file name
#       This is PCK file(s) that will be used to restrict
#       stapp peak picking.

PCK_DO_INTERP FALSE
# PCK_DO_INTERP  if TRUE forces stapp to find closest peak
#       in xtrma list, this also re-determines intensity

PCK_KEAP_SIGN TRUE
# PCK_KEAP_SIGN  if TRUE forces stapp to keap the same
#       sign from from the intensity in the .PCK file

PCK_DO_ASSIGN TRUE
# PCK_DO_ASSIGN  if TRUE forces stapp to re-assign
#       the peak, using all the filters that are set.
#       otherwise assignment label will be kept as is.

PCK_SHOW_LOST TRUE
# PCK_SHOW_LOST  if TRUE forces stapp to keap track of
#       peaks that get filtered out and put them
#       in a file .LOST so user can judge
#       otherwise lost peaks are truely LOST


# Post Search Processing functions
#  performs Processing after Search is complete

# PSP_MATCH_ATOMS   CA    CB
# PSP_MATCH_ERROR  0.20  0.20
# PSP_SEQ_SS_FL    act2_cbca_seq
# PSP_MIN_SEQ_SZ   1