# 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        15N-NOESY 15N-NOESY
#SIAD_STRING	HN * N
#PK_FILE_NAME stapp_n15
#PK_TBL_FRMT	%9.4f
ACQ_BASE_PHASE  POSITIVE
COMPLETE_ASGNMTS TRUE
#ASGNMT_READ_ONLY TRUE
REQ_ND_SYM      FALSE 
#SMW_FILTER      UNKNOWN 
PK_EXCLUDE_XY_DIAG  TRUE
DIM_COUNT	3
THRESHOLD	4800

PDB_ATM_NM_FILTER  H*
#DIST_FROM USE_NONE
MAX_NOE_DIST  8.0
PDB_FILES x146-ivm5cys.pdb
#PDB_FILES x144-ivm10cys.pdb
#PDB_FILES x137-ivm4cys.pdb
#PDB_FILES x135-ivm9cys.pdb
#PDB_FILES x131-ivm9cys.pdb
#PDB_FILES x128-ivm15cys.pdb
#PDB_FILES x118-ivm1-cys.pdb
#PDB_FILES x112-ivm5.pdb
#PDB_FILES x110-ivm15.pdb
#PDB_FILES x109-ivm9.pdb
#PDB_FILES x108-ivm8.pdb
#PDB_FILES x107-ivm20.pdb
#PDB_FILES x106-ivm7.pdb
#PDB_FILES model.pdb
#PDB_FILES lowest_164-CYS.pdb
#PDB_FILES xivm43-20.pdb
#PDB_FILES refine6-z-51-long.pdb
#WRITE_NOE_DIST  TRUE

# DATA_OFFSET (PPM) Number to be ADDED to experim. chem. shift to match assign. table
DATA_OFFSET     0.001	  0.002     0.012   
DEG_PROX_LIMIT  0.008     0.015     0.047
#ERROR_RANGE	0.016     0.030     0.094
#ERROR_RANGE	0.025     0.040     0.200
#ERROR_RANGE	0.030     0.050     0.250
ERROR_RANGE	0.030     0.050     0.350

ACQ_PRM_FRMT NMRI_PIPE

ANTIPHASE_FOLDOVER	FALSE

SEQUENCE        MAAVQLSELR DRQAIFETLV AKGRELLACD RVIVYAFDDN \
                YVGTVVAESV AEGWPQARDQ VIEDPCFREH WVEAYRQGRI \
                QATTDIFKAG LTECHLNQLR PLKVRANLVV PMVIDDQLFG \
                LLIAHQASEP RQWQEIEIDQ FSELASTGSL VLERLHFLEQ \
                TIASLHHHHH H

SHIFT_TBL_TYPE  EXPLICIT

# 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