# 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  H-DIPSI(CO)NH  H-DIPSI(CO)NH
	SIAD_STRING	* HN N
	DIM_COUNT 	3
	SORT_ATOMS	N.i
	ATOMS_BONDED	HN.i N.i
	RESID_RELAT	*.j *.i -1
	USE_PROX_PRIO    FALSE
	EXCLUDE_AUTO_PK TRUE
#	SYM_ATOMS       HN.i   H*.i
	AUTO_AXIS	X_AXIS  Y_AXIS
	AVERAGE_SHIFT	HN.i  H*.i   N.i
	LBL_PEAK_WITH   HN.i H*.j
#AXIS_ATOM_TABLE
# AXIS		ATOM_NAME	FOLD_TYPE	FOLD_FUNC
#X_AXIS		   HN.i		 IGNORE		  NONE
#Y_AXIS		   H*.j		 IGNORE	   	  NONE 
#Z_AXIS		   N.i		NEG_PHASE	   SW

PK_TBL_FRMT	%9.4f
ACQ_BASE_PHASE  POSITIVE
COMPLETE_ASGNMTS FALSE
THRESHOLD	2.2e5

#MAX_NOE_DIST  20.0
#PDB_ATM_NM_FILTER  H*
#PDB_FILES gaip21_refine2.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 Add to Shift From 3D Exp to Match Table
DATA_OFFSET     0.001    0.001  -0.020
ERROR_RANGE	0.08     0.10    0.30
DEG_PROX_LIMIT  0.02     0.03    0.05

ACQ_PRM_FRMT NMRI_PIPE

ANTIPHASE_FOLDOVER	FALSE

SEQUENCE        MGHHHHHHLE AEESRVPSSV SVTVAHDLLL AGHRYLDVRT \ 
                PEEFSQGHAC GAINVPYMNR GASGMSKNTD FLEQVSSHFG \ 
                QSDNIIVGCQ SGGRSIKATT DLLHAGFTGV KDIVGGYSAW \ 
                AKNGLPTKA

# 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