shifts.lib # chemical shift library aldolase.seq # protein sequence 100 100.0 4 0.01 0.001 0.01 15 # A B C D E F G # Parameters: # A = maximal number of possible individual mappings ("Ind" in Fig. 2 of the paper) # B = maximally accepted value for 0.5*(shift(obs)-shift(library)/stddev(library))^2 # C = maximal number of fragments considered simultaneously in the consistency check # D = minimal absolute probability of an individual mapping ("Q0" in the paper) # E = minimal relative probability of an individual mapping # F = minimal probability of a global mapping # G = maximal number of global mappings in the output # THE FOLLOWING PARAMETERS ARE GIVEN IN COLUMNS OF 8 CHARACTERS: CA CB # atoms with chemical shifts 0.300 0.500 # ppm tolerance for matching shifts 2.000 1.000 # additional offset for residues preceding PRO abs abs # scoring mode # Offsets that will be added to the observed chemical shifts (or subtracted from the # chemical shifts in the library) can be applied by uncommenting the block of lines # starting with the keyword "offsets" below. Offsets can be used, for instance, in the # case of known secondary structure. If a residue is followed by a proline then the # additional offsets given above will be applied. #offsets # -1.25 0.75 20..25 40..45 54..65 73..87 # alpha-helices in aldolase # 0.75 -1.25 4..13 27..37 91..100 112..119 # beta-sheets in aldolase # --------------------------------------------------------------------------------- # From here to the end of the input comes the data for each fragment: # # Chemical shift and other data form a block of non-empty lines for each fragment. # Data for different fragments are separated by empty lines. # The fragment number, given after the keyword "fragment", is used to identify the # fragment in the output. Fragments should have unique fragment numbers between # 1 and 999. Fragments with negative fragment numbers are skipped. # CHEMICAL SHIFTS ARE GIVEN IN FIXED FORTRAN FORMAT 4F8.2, followed, possibly by # a selection of residues in the sequence (residue numbers, residue number ranges, # residue names in three letter code; an initial "!" indicates negation) to which # the residue in the fragment may be mapped. Missing chemical shift values are left # blank. # THE INPUT MUST NOT CONTAIN CHARACTERS. # The first or the last residue of a fragment may carry the "overlap" attribute to # indicate that it can be mapped to a position in the sequence that is already # occupied by another fragment. fragment 102 61.33 # First residue in sequence; CB shift is missing. 56.88 39.61 overlap # Second (and last) residue in sequence. fragment 105 57.08 55.47 54.58 58.12 29.08 58.13 29.09 ! PRO overlap # Cannot be mapped to proline, and may overlap. fragment 106 29.54 54.30 40.50 58.75 59.18 overlap # May overlap with 1st residue of another fragment. fragment 107 51.48 56.05 ! PRO overlap fragment 108 54.28 56.34 overlap fragment 201 56.35 42.65 LEU 7 # Fixed to residue LEU 7 in the sequence. 53.93 34.09 46.40 55.52 34.39 54.00 32.16 54.90 42.29 57.86 36.86 43.32 57.96 54.45 30.53 44.83 51.45 18.29 52.68 41.40 ! PRO overlap fragment 203 #ok 52.67 60.85 54.70 19.02 58.65 30.19 54.00 38.11 57.70 61.78 45.56 54.23 30.25 56.81 34.80 56.11 42.07 ! PRO overlap fragment 211 #ok 53.70 59.78 51.85 43.31 60.00 34.48 61.48 69.28 51.88 41.88 55.22 59.39 36.00 54.09 39.40 ! PRO overlap fragment 212 #ok 54.07 54.08 39.10 61.29 ! PRO overlap fragment 213 #ok 61.24 66.75 59.03 27.72 53.36 17.80 45.63 57.70 62.48 69.09 55.46 40.90 50.86 38.47 63.34 30.58 61.87 36.36 54.30 40.45 57.40 60.04 32.13 ! PRO overlap fragment 214 60.02 32.11 55.16 29.71 58.43 46.47 58.21 66.00 61.96 37.92 58.16 27.97 57.50 27.68 ! PRO overlap fragment 221 #ok 65.75 58.36 31.16 60.02 61.61 63.00 37.47 54.70 55.33 27.55 43.32 56.24 31.31 51.59 17.99 58.06 31.30 55.86 53.26 45.38 56.81 41.62 60.28 57.16 ! PRO overlap fragment 230 59.18 41.68 54.42 55.30 37.92 57.00 29.48 64.27 ! PRO overlap fragment 231 64.10 54.30 35.47 60.09 62.38 55.74 29.68 55.75 37.84 54.80 36.98 56.17 29.38 62.38 30.11 56.18 32.64 55.26 32.73 62.52 68.70 53.39 33.37 ! PRO overlap fragment 232 53.28 59.98 53.35 59.94 60.85 69.93 ! PRO overlap fragment 233 60.63 70.07 54.70 33.04 56.68 29.41 50.94 ! PRO overlap fragment 251 60.09 29.29 43.67 53.99 29.94 53.98 36.93 54.89 40.38 45.09 57.00 33.30 45.69 ! PRO overlap fragment 253 57.79 40.45 ILE 116 61.22 32.85 VAL 117 51.04 29.62 ARG 118 56.15 29.63 GLU 119 51.12 36.62 ASN 120 56.59 32.64 LYS 121 # Example input file for MAPPER 2.0 # Copyright (c) 2002 Peter Guntert. # All rights reserved.