# 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-TOCSY_T  C13-TOCSY_T 
SIAD_STRING     H*  H*  C*
PK_FILE_NAME    tocsy
PK_TBL_FRMT     %9.4f
ACQ_BASE_PHASE  POSITIVE
COMPLETE_ASGNMTS FALSE
# ASGNMT_READ_ONLY TRUE
REQ_ND_SYM      FALSE
PK_EXCLUDE_XY_DIAG  FALSE
DIM_COUNT       3
THRESHOLD       1.13e6

AXIS_ATOM_TABLE
 AXIS		ATOM_NAME	FOLD_TYPE	FOLD_FUNC
X_AXIS		   H*.j		 IGNORE		  NONE
Y_AXIS		   H*.i		 IGNORE		  NONE
Z_AXIS		   C*		POS_PHASE	   SW


# DATA_OFFSET (PPM) Number to Add to Shift From 3D Exp to Match Table
# DATA_OFFSET     0.0      0.0     0.0   
# ERROR_RANGE	0.030	 0.015   0.16 

DATA_OFFSET    -0.004    -0.002     0.000
DEG_PROX_LIMIT  0.020     0.030     0.050
ERROR_RANGE	0.060	  0.090     0.300 

ACQ_PRM_FRMT NMRI_PIPE

ANTIPHASE_FOLDOVER	FALSE

SEQUENCE      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 
PCK_IN_FILE   B.PCK.orig
# 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