# 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        CBCANH 
SIAD_STRING	HN CA|CB:0|-1 N         
#SIAD_STRING     HN CA|CB:-1 N
#SIAD_STRING     HN CA|CB:0 N
PK_TBL_FRMT	%9.4f
ACQ_BASE_PHASE  POSITIVE
COMPLETE_ASGNMTS TRUE
# ASGNMT_READ_ONLY TRUE
REQ_ND_SYM      TRUE 
PK_EXCLUDE_XY_DIAG  FALSE
DIM_COUNT	3
THRESHOLD	4.4e5

#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     0.0      0.0     0.0   
# ERROR_RANGE	0.030	 0.015   0.16 


DATA_OFFSET     0.001     0.036   -0.018
ERROR_RANGE	0.06      0.30     0.30
DEG_PROX_LIMIT  0.03      0.15     0.10


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 FALSE
# 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