diff --git a/actions/pm-build-model b/actions/pm-build-model
index 80b3b270606f37e6ce7ee8cce0e32e9467b42597..d12f644831fae5238d6a62ad1521931975c201bd 100755
--- a/actions/pm-build-model
+++ b/actions/pm-build-model
@@ -40,6 +40,7 @@ parser = pm3argparse.PM3ArgumentParser(__doc__, action=True)
parser.AddAlignment()
parser.AddStructure(attach_views=True)
parser.AddProfile()
+parser.AddFragments()
parser.AssembleParser()
parser.add_argument('-o', '--model-file', metavar='<FILENAME>', type=str,
default='model.pdb', help='File to store model coordinates'+
@@ -70,6 +71,12 @@ try:
# pssm files would not be sufficient and we would be restricted to hhm.
if len(opts.profiles) > 0:
modelling.SetSequenceProfiles(mhandle, opts.profiles)
+ # add fragment support for Monte Carlo sampling. The fragment search
+ # is setup in the argument parser. If activated you get fragment support
+ # in any case but for optimal performance you should provide profiles
+ # in hhm format (for profile AND secondary structure information).
+ if len(opts.fragger_handles) > 0:
+ modelling.SetFraggerHandles(mhandle, opts.fragger_handles)
# build final model
final_model = modelling.BuildFromRawModel(mhandle)
except Exception as ex:
diff --git a/extras/external_scripts/CAMEO_bst/model.pdb b/extras/external_scripts/CAMEO_bst/model.pdb
index 38c277b9af45f9d437ab762e8a8b0754d4245e6b..2aad8113ba471668f4affd93be8b9a43d66c141d 100644
--- a/extras/external_scripts/CAMEO_bst/model.pdb
+++ b/extras/external_scripts/CAMEO_bst/model.pdb
@@ -1,329 +1,253 @@
-ATOM 1 N THR A 1 17.087 14.220 3.252 1.00 0.00 N
-ATOM 2 CA THR A 1 17.037 12.923 4.052 1.00 0.00 C
-ATOM 3 C THR A 1 15.783 12.865 4.876 1.00 0.00 C
-ATOM 4 O THR A 1 15.387 13.876 5.435 1.00 0.00 O
-ATOM 5 CB THR A 1 18.241 12.815 4.991 1.00 0.00 C
-ATOM 6 OG1 THR A 1 19.425 12.788 4.208 1.00 0.00 O
-ATOM 7 CG2 THR A 1 18.268 11.550 5.871 1.00 0.00 C
-ATOM 8 N THR A 2 15.115 11.692 4.960 1.00 0.00 N
-ATOM 9 CA THR A 2 13.915 11.525 5.764 1.00 0.00 C
-ATOM 10 C THR A 2 14.298 10.890 7.078 1.00 0.00 C
-ATOM 11 O THR A 2 15.241 10.110 7.157 1.00 0.00 O
-ATOM 12 CB THR A 2 12.818 10.709 5.077 1.00 0.00 C
-ATOM 13 OG1 THR A 2 13.245 9.420 4.663 1.00 0.00 O
-ATOM 14 CG2 THR A 2 12.428 11.452 3.799 1.00 0.00 C
-ATOM 15 N CYS A 3 13.585 11.258 8.155 1.00 0.00 N
-ATOM 16 CA CYS A 3 13.791 10.708 9.482 1.00 0.00 C
-ATOM 17 C CYS A 3 12.412 10.508 10.077 1.00 0.00 C
-ATOM 18 O CYS A 3 11.545 11.360 9.914 1.00 0.00 O
-ATOM 19 CB CYS A 3 14.532 11.695 10.424 1.00 0.00 C
-ATOM 20 SG CYS A 3 16.117 12.327 9.789 1.00 0.00 S
-ATOM 21 N CYS A 4 12.147 9.380 10.764 1.00 0.00 N
-ATOM 22 CA CYS A 4 10.821 9.055 11.254 1.00 0.00 C
-ATOM 23 C CYS A 4 10.813 8.849 12.770 1.00 0.00 C
-ATOM 24 O CYS A 4 11.806 8.410 13.340 1.00 0.00 O
-ATOM 25 CB CYS A 4 10.319 7.779 10.550 1.00 0.00 C
-ATOM 26 SG CYS A 4 9.917 8.095 8.809 1.00 0.00 S
-ATOM 27 N PRO A 5 9.733 9.154 13.496 1.00 0.00 N
-ATOM 28 CA PRO A 5 9.723 9.104 14.960 1.00 0.00 C
-ATOM 29 C PRO A 5 9.544 7.694 15.467 1.00 0.00 C
-ATOM 30 O PRO A 5 9.753 7.433 16.647 1.00 0.00 O
-ATOM 31 CB PRO A 5 8.545 10.015 15.343 1.00 0.00 C
-ATOM 32 CG PRO A 5 7.586 9.959 14.149 1.00 0.00 C
-ATOM 33 CD PRO A 5 8.510 9.744 12.953 1.00 0.00 C
-ATOM 34 N SER A 6 9.115 6.765 14.605 1.00 0.00 N
-ATOM 35 CA SER A 6 8.836 5.414 15.029 1.00 0.00 C
-ATOM 36 C SER A 6 8.883 4.483 13.848 1.00 0.00 C
-ATOM 37 O SER A 6 8.864 4.909 12.690 1.00 0.00 O
-ATOM 38 CB SER A 6 7.471 5.260 15.776 1.00 0.00 C
-ATOM 39 OG SER A 6 6.324 5.341 14.916 1.00 0.00 O
-ATOM 40 N ILE A 7 8.919 3.162 14.124 1.00 0.00 N
-ATOM 41 CA ILE A 7 8.829 2.103 13.123 1.00 0.00 C
-ATOM 42 C ILE A 7 7.578 2.229 12.276 1.00 0.00 C
-ATOM 43 O ILE A 7 7.633 2.200 11.047 1.00 0.00 O
-ATOM 44 CB ILE A 7 8.781 0.736 13.813 1.00 0.00 C
-ATOM 45 CG1 ILE A 7 10.163 0.413 14.419 1.00 0.00 C
-ATOM 46 CG2 ILE A 7 8.308 -0.393 12.852 1.00 0.00 C
-ATOM 47 CD1 ILE A 7 10.112 -0.789 15.368 1.00 0.00 C
-ATOM 48 N VAL A 8 6.414 2.426 12.932 1.00 0.00 N
-ATOM 49 CA VAL A 8 5.104 2.532 12.313 1.00 0.00 C
-ATOM 50 C VAL A 8 5.057 3.683 11.327 1.00 0.00 C
-ATOM 51 O VAL A 8 4.581 3.551 10.211 1.00 0.00 O
-ATOM 52 CB VAL A 8 4.014 2.749 13.365 1.00 0.00 C
-ATOM 53 CG1 VAL A 8 2.649 3.057 12.709 1.00 0.00 C
-ATOM 54 CG2 VAL A 8 3.895 1.497 14.254 1.00 0.00 C
-ATOM 55 N ALA A 9 5.610 4.846 11.731 1.00 0.00 N
-ATOM 56 CA ALA A 9 5.696 6.019 10.898 1.00 0.00 C
-ATOM 57 C ALA A 9 6.539 5.811 9.643 1.00 0.00 C
-ATOM 58 O ALA A 9 6.096 6.158 8.545 1.00 0.00 O
-ATOM 59 CB ALA A 9 6.276 7.160 11.750 1.00 0.00 C
-ATOM 60 N ARG A 10 7.735 5.190 9.750 1.00 0.00 N
-ATOM 61 CA ARG A 10 8.578 4.826 8.617 1.00 0.00 C
-ATOM 62 C ARG A 10 7.943 3.775 7.711 1.00 0.00 C
-ATOM 63 O ARG A 10 7.980 3.883 6.484 1.00 0.00 O
-ATOM 64 CB ARG A 10 9.976 4.331 9.072 1.00 0.00 C
-ATOM 65 CG ARG A 10 10.983 4.123 7.920 1.00 0.00 C
-ATOM 66 CD ARG A 10 11.658 5.412 7.440 1.00 0.00 C
-ATOM 67 NE ARG A 10 12.600 5.010 6.351 1.00 0.00 N
-ATOM 68 CZ ARG A 10 13.839 4.565 6.601 1.00 0.00 C
-ATOM 69 NH1 ARG A 10 14.593 4.179 5.570 1.00 0.00 N
-ATOM 70 NH2 ARG A 10 14.329 4.487 7.836 1.00 0.00 N
-ATOM 71 N SER A 11 7.309 2.734 8.277 1.00 0.00 N
-ATOM 72 CA SER A 11 6.585 1.715 7.519 1.00 0.00 C
-ATOM 73 C SER A 11 5.411 2.276 6.743 1.00 0.00 C
-ATOM 74 O SER A 11 5.250 1.992 5.550 1.00 0.00 O
-ATOM 75 CB SER A 11 6.055 0.578 8.426 1.00 0.00 C
-ATOM 76 OG SER A 11 7.160 -0.132 8.984 1.00 0.00 O
-ATOM 77 N ASN A 12 4.606 3.152 7.375 1.00 3.54 N
-ATOM 78 CA ASN A 12 3.547 3.925 6.740 1.00 4.57 C
-ATOM 79 C ASN A 12 4.082 4.862 5.657 1.00 4.14 C
-ATOM 80 O ASN A 12 3.493 5.002 4.585 1.00 5.52 O
-ATOM 81 CB ASN A 12 2.762 4.782 7.776 1.00 6.42 C
-ATOM 82 CG ASN A 12 1.946 3.904 8.716 1.00 0.00 C
-ATOM 83 OD1 ASN A 12 1.690 2.723 8.473 1.00 0.00 O
-ATOM 84 ND2 ASN A 12 1.489 4.503 9.839 1.00 0.00 N
-ATOM 85 N PHE A 13 5.241 5.509 5.909 1.00 3.43 N
-ATOM 86 CA PHE A 13 5.966 6.370 4.982 1.00 3.49 C
-ATOM 87 C PHE A 13 6.398 5.648 3.725 1.00 3.40 C
-ATOM 88 O PHE A 13 6.205 6.147 2.615 1.00 4.07 O
-ATOM 89 CB PHE A 13 7.213 6.970 5.711 1.00 5.48 C
-ATOM 90 CG PHE A 13 7.966 7.991 4.911 1.00 5.57 C
-ATOM 91 CD1 PHE A 13 8.969 7.589 4.013 1.00 6.99 C
-ATOM 92 CD2 PHE A 13 7.680 9.356 5.046 1.00 6.52 C
-ATOM 93 CE1 PHE A 13 9.604 8.527 3.193 1.00 8.20 C
-ATOM 94 CE2 PHE A 13 8.361 10.303 4.274 1.00 6.34 C
-ATOM 95 CZ PHE A 13 9.273 9.882 3.304 1.00 6.84 C
-ATOM 96 N ASN A 14 6.959 4.437 3.863 1.00 3.64 N
-ATOM 97 CA ASN A 14 7.364 3.607 2.748 1.00 4.31 C
-ATOM 98 C ASN A 14 6.182 3.181 1.878 1.00 3.98 C
-ATOM 99 O ASN A 14 6.271 3.229 0.656 1.00 6.22 O
-ATOM 100 CB ASN A 14 8.161 2.373 3.238 1.00 5.81 C
-ATOM 101 CG ASN A 14 9.527 2.808 3.779 1.00 6.82 C
-ATOM 102 OD1 ASN A 14 10.067 3.864 3.498 1.00 9.43 O
-ATOM 103 ND2 ASN A 14 10.144 1.910 4.594 1.00 8.21 N
-ATOM 104 N VAL A 15 5.024 2.812 2.479 1.00 3.76 N
-ATOM 105 CA VAL A 15 3.789 2.556 1.733 1.00 3.98 C
-ATOM 106 C VAL A 15 3.263 3.803 1.036 1.00 3.80 C
-ATOM 107 O VAL A 15 2.881 3.759 -0.134 1.00 4.85 O
-ATOM 108 CB VAL A 15 2.692 1.939 2.601 1.00 4.71 C
-ATOM 109 CG1 VAL A 15 1.358 1.799 1.827 1.00 6.67 C
-ATOM 110 CG2 VAL A 15 3.178 0.546 3.043 1.00 6.26 C
-ATOM 111 N CYS A 16 3.278 4.974 1.712 1.00 3.79 N
-ATOM 112 CA CYS A 16 2.874 6.252 1.132 1.00 3.54 C
-ATOM 113 C CYS A 16 3.729 6.650 -0.072 1.00 3.48 C
-ATOM 114 O CYS A 16 3.239 7.258 -1.020 1.00 4.63 O
-ATOM 115 CB CYS A 16 2.893 7.391 2.196 1.00 4.58 C
-ATOM 116 SG CYS A 16 2.008 8.921 1.742 1.00 0.00 S
-ATOM 117 N ARG A 17 5.030 6.297 -0.080 1.00 3.99 N
-ATOM 118 CA ARG A 17 5.938 6.540 -1.187 1.00 3.83 C
-ATOM 119 C ARG A 17 5.822 5.585 -2.364 1.00 3.79 C
-ATOM 120 O ARG A 17 6.314 5.915 -3.441 1.00 5.39 O
-ATOM 121 CB ARG A 17 7.406 6.486 -0.699 1.00 4.11 C
-ATOM 122 CG ARG A 17 7.774 7.689 0.188 1.00 4.69 C
-ATOM 123 CD ARG A 17 7.948 8.999 -0.586 1.00 5.10 C
-ATOM 124 NE ARG A 17 9.237 8.889 -1.331 1.00 4.71 N
-ATOM 125 CZ ARG A 17 9.547 9.579 -2.432 1.00 5.28 C
-ATOM 126 NH1 ARG A 17 8.677 10.383 -3.036 1.00 6.67 N
-ATOM 127 NH2 ARG A 17 10.775 9.467 -2.931 1.00 6.41 N
-ATOM 128 N LEU A 18 5.159 4.414 -2.231 1.00 4.70 N
-ATOM 129 CA LEU A 18 5.005 3.459 -3.328 1.00 5.46 C
-ATOM 130 C LEU A 18 4.340 3.994 -4.607 1.00 5.13 C
-ATOM 131 O LEU A 18 4.864 3.691 -5.678 1.00 5.55 O
-ATOM 132 CB LEU A 18 4.207 2.195 -2.900 1.00 6.47 C
-ATOM 133 CG LEU A 18 4.948 1.169 -2.027 1.00 7.43 C
-ATOM 134 CD1 LEU A 18 3.956 0.073 -1.598 1.00 8.70 C
-ATOM 135 CD2 LEU A 18 6.149 0.546 -2.759 1.00 9.39 C
-ATOM 136 N PRO A 19 3.247 4.775 -4.623 1.00 4.28 N
-ATOM 137 CA PRO A 19 2.728 5.364 -5.854 1.00 5.38 C
-ATOM 138 C PRO A 19 3.551 6.543 -6.351 1.00 6.30 C
-ATOM 139 O PRO A 19 3.236 7.059 -7.424 1.00 9.62 O
-ATOM 140 CB PRO A 19 1.274 5.774 -5.525 1.00 5.87 C
-ATOM 141 CG PRO A 19 1.134 5.754 -3.996 1.00 6.47 C
-ATOM 142 CD PRO A 19 2.329 4.947 -3.494 1.00 6.45 C
-ATOM 143 N GLY A 20 4.580 7.017 -5.620 1.00 4.94 N
-ATOM 144 CA GLY A 20 5.393 8.149 -6.055 1.00 5.39 C
-ATOM 145 C GLY A 20 5.045 9.428 -5.371 1.00 5.03 C
-ATOM 146 O GLY A 20 5.550 10.490 -5.750 1.00 7.34 O
-ATOM 147 N THR A 21 4.198 9.381 -4.327 1.00 4.10 N
-ATOM 148 CA THR A 21 3.797 10.527 -3.511 1.00 3.94 C
-ATOM 149 C THR A 21 5.009 11.348 -3.050 1.00 3.96 C
-ATOM 150 O THR A 21 5.954 10.758 -2.515 1.00 5.82 O
-ATOM 151 CB THR A 21 2.995 10.129 -2.280 1.00 4.13 C
-ATOM 152 OG1 THR A 21 1.938 9.257 -2.636 1.00 5.45 O
-ATOM 153 CG2 THR A 21 2.313 11.322 -1.612 1.00 5.41 C
-ATOM 154 N PRO A 22 5.105 12.667 -3.256 1.00 5.04 N
-ATOM 155 CA PRO A 22 6.162 13.520 -2.716 1.00 4.69 C
-ATOM 156 C PRO A 22 6.460 13.295 -1.242 1.00 4.19 C
-ATOM 157 O PRO A 22 5.530 13.138 -0.464 1.00 4.47 O
-ATOM 158 CB PRO A 22 5.672 14.959 -2.953 1.00 7.12 C
-ATOM 159 CG PRO A 22 4.668 14.860 -4.107 1.00 7.03 C
-ATOM 160 CD PRO A 22 4.139 13.427 -4.041 1.00 4.90 C
-ATOM 161 N GLU A 23 7.742 13.336 -0.825 1.00 5.16 N
-ATOM 162 CA GLU A 23 8.149 13.151 0.560 1.00 5.31 C
-ATOM 163 C GLU A 23 7.524 14.138 1.533 1.00 4.11 C
-ATOM 164 O GLU A 23 7.262 13.805 2.698 1.00 5.11 O
-ATOM 165 CB GLU A 23 9.685 13.264 0.662 1.00 6.16 C
-ATOM 166 CG GLU A 23 10.439 12.083 0.016 1.00 7.48 C
-ATOM 167 CD GLU A 23 11.930 12.089 0.344 1.00 9.40 C
-ATOM 168 OE1 GLU A 23 12.466 13.139 0.774 1.00 10.40 O
-ATOM 169 OE2 GLU A 23 12.528 10.995 0.171 1.00 13.32 O
-ATOM 170 N ALA A 24 7.268 15.385 1.102 1.00 4.56 N
-ATOM 171 CA ALA A 24 6.639 16.422 1.903 1.00 4.49 C
-ATOM 172 C ALA A 24 5.212 16.108 2.301 1.00 4.10 C
-ATOM 173 O ALA A 24 4.814 16.316 3.444 1.00 5.64 O
-ATOM 174 CB ALA A 24 6.650 17.775 1.167 1.00 5.80 C
-ATOM 175 N ILE A 25 4.414 15.541 1.370 1.00 0.00 N
-ATOM 176 CA ILE A 25 3.085 15.024 1.646 1.00 0.00 C
-ATOM 177 C ILE A 25 3.174 13.926 2.682 1.00 0.00 C
-ATOM 178 O ILE A 25 2.489 13.941 3.673 1.00 0.00 O
-ATOM 179 CB ILE A 25 2.418 14.512 0.375 1.00 0.00 C
-ATOM 180 CG1 ILE A 25 2.022 15.726 -0.488 1.00 0.00 C
-ATOM 181 CG2 ILE A 25 1.185 13.622 0.673 1.00 0.00 C
-ATOM 182 CD1 ILE A 25 1.548 15.323 -1.882 1.00 0.00 C
-ATOM 183 N CYS A 26 4.144 13.003 2.520 1.00 0.00 N
-ATOM 184 CA CYS A 26 4.340 11.898 3.431 1.00 0.00 C
-ATOM 185 C CYS A 26 4.571 12.314 4.884 1.00 0.00 C
-ATOM 186 O CYS A 26 4.099 11.609 5.771 1.00 0.00 O
-ATOM 187 CB CYS A 26 5.477 10.972 2.949 1.00 0.00 C
-ATOM 188 SG CYS A 26 5.324 10.350 1.265 1.00 0.00 S
-ATOM 189 N ALA A 27 5.211 13.474 5.184 1.00 0.00 N
-ATOM 190 CA ALA A 27 5.344 14.027 6.532 1.00 0.00 C
-ATOM 191 C ALA A 27 3.996 14.248 7.229 1.00 0.00 C
-ATOM 192 O ALA A 27 3.789 13.844 8.377 1.00 0.00 O
-ATOM 193 CB ALA A 27 6.095 15.383 6.461 1.00 0.00 C
-ATOM 194 N THR A 28 3.020 14.812 6.490 1.00 0.00 N
-ATOM 195 CA THR A 28 1.612 15.016 6.858 1.00 0.00 C
-ATOM 196 C THR A 28 0.899 13.710 7.170 1.00 0.00 C
-ATOM 197 O THR A 28 0.020 13.652 8.029 1.00 0.00 O
-ATOM 198 CB THR A 28 0.840 15.777 5.771 1.00 0.00 C
-ATOM 199 OG1 THR A 28 1.413 17.063 5.603 1.00 0.00 O
-ATOM 200 CG2 THR A 28 -0.639 16.013 6.114 1.00 0.00 C
-ATOM 201 N TYR A 29 1.273 12.608 6.489 1.00 0.00 N
-ATOM 202 CA TYR A 29 0.608 11.315 6.582 1.00 0.00 C
-ATOM 203 C TYR A 29 1.293 10.353 7.549 1.00 0.00 C
-ATOM 204 O TYR A 29 0.795 9.248 7.771 1.00 0.00 O
-ATOM 205 CB TYR A 29 0.561 10.621 5.187 1.00 0.00 C
-ATOM 206 CG TYR A 29 -0.565 11.180 4.364 1.00 0.00 C
-ATOM 207 CD1 TYR A 29 -0.432 12.424 3.741 1.00 0.00 C
-ATOM 208 CD2 TYR A 29 -1.778 10.485 4.215 1.00 0.00 C
-ATOM 209 CE1 TYR A 29 -1.453 12.957 2.953 1.00 0.00 C
-ATOM 210 CE2 TYR A 29 -2.811 11.013 3.423 1.00 0.00 C
-ATOM 211 CZ TYR A 29 -2.634 12.244 2.776 1.00 0.00 C
-ATOM 212 OH TYR A 29 -3.628 12.799 1.950 1.00 0.00 O
-ATOM 213 N THR A 30 2.447 10.710 8.156 1.00 0.00 N
-ATOM 214 CA THR A 30 3.191 9.765 8.998 1.00 0.00 C
-ATOM 215 C THR A 30 3.765 10.358 10.256 1.00 0.00 C
-ATOM 216 O THR A 30 4.072 9.630 11.199 1.00 0.00 O
-ATOM 217 CB THR A 30 4.403 9.162 8.299 1.00 0.00 C
-ATOM 218 OG1 THR A 30 5.350 10.136 7.888 1.00 0.00 O
-ATOM 219 CG2 THR A 30 3.943 8.465 7.026 1.00 0.00 C
-ATOM 220 N GLY A 31 3.987 11.685 10.298 1.00 4.99 N
-ATOM 221 CA GLY A 31 4.740 12.329 11.360 1.00 5.50 C
-ATOM 222 C GLY A 31 6.236 12.244 11.177 1.00 4.19 C
-ATOM 223 O GLY A 31 6.992 12.703 12.018 1.00 6.12 O
-ATOM 224 N CYS A 32 6.713 11.656 10.055 1.00 4.30 N
-ATOM 225 CA CYS A 32 8.111 11.727 9.648 1.00 4.89 C
-ATOM 226 C CYS A 32 8.490 13.111 9.182 1.00 5.50 C
-ATOM 227 O CYS A 32 7.644 13.915 8.805 1.00 5.82 O
-ATOM 228 CB CYS A 32 8.501 10.747 8.517 1.00 4.66 C
-ATOM 229 SG CYS A 32 8.130 9.020 8.923 1.00 0.00 S
-ATOM 230 N ILE A 33 9.789 13.432 9.202 1.00 6.02 N
-ATOM 231 CA ILE A 33 10.262 14.754 8.864 1.00 5.24 C
-ATOM 232 C ILE A 33 11.308 14.646 7.778 1.00 5.16 C
-ATOM 233 O ILE A 33 11.928 13.601 7.575 1.00 7.19 O
-ATOM 234 CB ILE A 33 10.824 15.508 10.070 1.00 5.49 C
-ATOM 235 CG1 ILE A 33 12.060 14.815 10.700 1.00 6.85 C
-ATOM 236 CG2 ILE A 33 9.676 15.683 11.093 1.00 6.45 C
-ATOM 237 CD1 ILE A 33 12.741 15.658 11.787 1.00 8.94 C
-ATOM 238 N ILE A 34 11.527 15.749 7.041 1.00 5.52 N
-ATOM 239 CA ILE A 34 12.553 15.850 6.023 1.00 6.82 C
-ATOM 240 C ILE A 34 13.545 16.857 6.548 1.00 6.92 C
-ATOM 241 O ILE A 34 13.176 17.950 6.948 1.00 9.22 O
-ATOM 242 CB ILE A 34 12.017 16.374 4.693 1.00 8.11 C
-ATOM 243 CG1 ILE A 34 10.932 15.433 4.141 1.00 9.59 C
-ATOM 244 CG2 ILE A 34 13.170 16.518 3.668 1.00 9.73 C
-ATOM 245 CD1 ILE A 34 10.165 16.054 2.977 1.00 13.41 C
-ATOM 246 N ILE A 35 14.844 16.494 6.561 1.00 7.06 N
-ATOM 247 CA ILE A 35 15.903 17.393 6.980 1.00 7.52 C
-ATOM 248 C ILE A 35 16.891 17.560 5.822 1.00 6.63 C
-ATOM 249 O ILE A 35 16.984 16.668 4.965 1.00 7.90 O
-ATOM 250 CB ILE A 35 16.631 16.931 8.245 1.00 8.07 C
-ATOM 251 CG1 ILE A 35 17.350 15.569 8.072 1.00 9.41 C
-ATOM 252 CG2 ILE A 35 15.608 16.933 9.406 1.00 9.46 C
-ATOM 253 CD1 ILE A 35 18.272 15.214 9.244 1.00 9.85 C
-ATOM 254 N PRO A 36 17.642 18.672 5.736 1.00 8.07 N
-ATOM 255 CA PRO A 36 18.640 18.875 4.691 1.00 8.78 C
-ATOM 256 C PRO A 36 19.891 18.043 4.923 1.00 8.31 C
-ATOM 257 O PRO A 36 20.558 17.689 3.958 1.00 9.09 O
-ATOM 258 CB PRO A 36 18.971 20.386 4.709 1.00 9.67 C
-ATOM 259 CG PRO A 36 18.250 21.004 5.921 1.00 10.15 C
-ATOM 260 CD PRO A 36 17.393 19.885 6.519 1.00 9.53 C
-ATOM 261 N GLY A 37 20.253 17.770 6.196 1.00 8.48 N
-ATOM 262 CA GLY A 37 21.424 16.977 6.564 1.00 9.20 C
-ATOM 263 C GLY A 37 21.186 15.489 6.495 1.00 10.41 C
-ATOM 264 O GLY A 37 20.187 15.019 5.979 1.00 12.06 O
-ATOM 265 N ALA A 38 22.121 14.683 7.032 1.00 9.24 N
-ATOM 266 CA ALA A 38 22.009 13.237 6.979 1.00 9.24 C
-ATOM 267 C ALA A 38 21.910 12.613 8.358 1.00 9.60 C
-ATOM 268 O ALA A 38 21.821 11.392 8.497 1.00 13.65 O
-ATOM 269 CB ALA A 38 23.255 12.705 6.253 1.00 10.43 C
-ATOM 270 N THR A 39 21.882 13.426 9.421 1.00 8.70 N
-ATOM 271 CA THR A 39 21.996 12.914 10.774 1.00 9.46 C
-ATOM 272 C THR A 39 20.695 13.206 11.463 1.00 8.32 C
-ATOM 273 O THR A 39 20.402 14.338 11.823 1.00 9.89 O
-ATOM 274 CB THR A 39 23.119 13.580 11.551 1.00 10.72 C
-ATOM 275 OG1 THR A 39 24.347 13.435 10.855 1.00 11.66 O
-ATOM 276 CG2 THR A 39 23.328 12.909 12.913 1.00 11.81 C
-ATOM 277 N CYS A 40 19.853 12.167 11.620 1.00 7.64 N
-ATOM 278 CA CYS A 40 18.557 12.284 12.255 1.00 8.05 C
-ATOM 279 C CYS A 40 18.669 12.470 13.770 1.00 7.63 C
-ATOM 280 O CYS A 40 19.532 11.836 14.381 1.00 9.64 O
-ATOM 281 CB CYS A 40 17.680 11.052 11.930 1.00 7.80 C
-ATOM 282 SG CYS A 40 17.426 10.832 10.149 1.00 0.00 S
-ATOM 283 N PRO A 41 17.885 13.319 14.437 1.00 8.00 N
-ATOM 284 CA PRO A 41 17.922 13.459 15.888 1.00 8.96 C
-ATOM 285 C PRO A 41 17.393 12.230 16.608 1.00 9.06 C
-ATOM 286 O PRO A 41 16.730 11.385 16.007 1.00 8.82 O
-ATOM 287 CB PRO A 41 17.062 14.706 16.157 1.00 10.39 C
-ATOM 288 CG PRO A 41 16.061 14.733 14.999 1.00 10.99 C
-ATOM 289 CD PRO A 41 16.855 14.160 13.827 1.00 10.49 C
-ATOM 290 N GLY A 42 17.676 12.106 17.920 1.00 7.55 N
-ATOM 291 CA GLY A 42 17.331 10.936 18.725 1.00 8.00 C
-ATOM 292 C GLY A 42 15.860 10.673 18.944 1.00 7.22 C
-ATOM 293 O GLY A 42 15.496 9.548 19.281 1.00 8.41 O
-ATOM 294 N ASP A 43 14.969 11.661 18.755 1.00 5.54 N
-ATOM 295 CA ASP A 43 13.535 11.507 18.862 1.00 5.85 C
-ATOM 296 C ASP A 43 12.911 11.246 17.484 1.00 5.87 C
-ATOM 297 O ASP A 43 11.713 10.982 17.363 1.00 7.29 O
-ATOM 298 CB ASP A 43 12.926 12.756 19.577 1.00 6.72 C
-ATOM 299 CG ASP A 43 13.241 14.094 18.912 1.00 8.59 C
-ATOM 300 OD1 ASP A 43 14.281 14.194 18.206 1.00 9.59 O
-ATOM 301 OD2 ASP A 43 12.459 15.046 19.146 1.00 11.45 O
-ATOM 302 N TYR A 44 13.733 11.209 16.413 1.00 5.22 N
-ATOM 303 CA TYR A 44 13.320 10.810 15.080 1.00 5.56 C
-ATOM 304 C TYR A 44 14.306 9.770 14.591 1.00 4.61 C
-ATOM 305 O TYR A 44 14.987 9.936 13.585 1.00 6.04 O
-ATOM 306 CB TYR A 44 13.218 11.977 14.058 1.00 5.41 C
-ATOM 307 CG TYR A 44 12.047 12.862 14.373 1.00 5.34 C
-ATOM 308 CD1 TYR A 44 12.144 13.893 15.322 1.00 6.59 C
-ATOM 309 CD2 TYR A 44 10.819 12.649 13.728 1.00 5.94 C
-ATOM 310 CE1 TYR A 44 11.034 14.696 15.620 1.00 5.97 C
-ATOM 311 CE2 TYR A 44 9.709 13.448 14.027 1.00 5.17 C
-ATOM 312 CZ TYR A 44 9.821 14.483 14.960 1.00 5.96 C
-ATOM 313 OH TYR A 44 8.703 15.296 15.231 1.00 8.60 O
-ATOM 314 N ALA A 45 14.401 8.656 15.343 1.00 4.76 N
-ATOM 315 CA ALA A 45 15.473 7.694 15.230 1.00 5.89 C
-ATOM 316 C ALA A 45 15.179 6.522 14.290 1.00 6.67 C
-ATOM 317 O ALA A 45 16.008 5.611 14.167 1.00 7.56 O
-ATOM 318 CB ALA A 45 15.707 7.118 16.644 1.00 6.82 C
-ATOM 319 N ASN A 46 14.017 6.484 13.616 1.00 5.80 N
-ATOM 320 CA ASN A 46 13.600 5.371 12.780 1.00 6.15 C
-ATOM 321 C ASN A 46 13.399 5.776 11.282 1.00 6.61 C
-ATOM 322 O ASN A 46 13.560 6.976 10.932 1.00 7.18 O
-ATOM 323 CB ASN A 46 12.305 4.765 13.387 1.00 7.27 C
-ATOM 324 CG ASN A 46 12.544 4.245 14.801 1.00 7.98 C
-ATOM 325 OD1 ASN A 46 11.952 4.707 15.781 1.00 11.00 O
-ATOM 326 ND2 ASN A 46 13.409 3.222 14.959 1.00 10.32 N
-ATOM 327 OXT ASN A 46 13.101 4.877 10.442 1.00 0.00 O
-TER 328 ASN A 46
+ATOM 1 N ASN A 12 4.554 3.051 7.524 1.00 3.54 N
+ATOM 2 CA ASN A 12 3.554 3.930 6.792 1.00 4.57 C
+ATOM 3 C ASN A 12 4.154 4.829 5.728 1.00 4.14 C
+ATOM 4 O ASN A 12 3.644 4.873 4.614 1.00 5.52 O
+ATOM 5 CB ASN A 12 2.698 4.766 7.785 1.00 6.42 C
+ATOM 6 CG ASN A 12 1.918 3.796 8.664 1.00 8.25 C
+ATOM 7 OD1 ASN A 12 1.927 2.605 8.332 1.00 12.72 O
+ATOM 8 ND2 ASN A 12 1.340 4.242 9.791 1.00 9.92 N
+ATOM 9 N PHE A 13 5.280 5.524 6.007 1.00 3.43 N
+ATOM 10 CA PHE A 13 5.969 6.383 5.048 1.00 3.49 C
+ATOM 11 C PHE A 13 6.370 5.655 3.766 1.00 3.40 C
+ATOM 12 O PHE A 13 6.097 6.132 2.667 1.00 4.07 O
+ATOM 13 CB PHE A 13 7.212 6.973 5.774 1.00 5.48 C
+ATOM 14 CG PHE A 13 7.966 7.985 4.951 1.00 5.57 C
+ATOM 15 CD1 PHE A 13 8.949 7.575 4.031 1.00 6.99 C
+ATOM 16 CD2 PHE A 13 7.714 9.358 5.101 1.00 6.52 C
+ATOM 17 CE1 PHE A 13 9.602 8.511 3.220 1.00 8.20 C
+ATOM 18 CE2 PHE A 13 8.395 10.296 4.314 1.00 6.34 C
+ATOM 19 CZ PHE A 13 9.307 9.870 3.348 1.00 6.84 C
+ATOM 20 N ASN A 14 6.957 4.446 3.885 1.00 3.64 N
+ATOM 21 CA ASN A 14 7.340 3.613 2.749 1.00 4.31 C
+ATOM 22 C ASN A 14 6.168 3.200 1.863 1.00 3.98 C
+ATOM 23 O ASN A 14 6.272 3.231 0.638 1.00 6.22 O
+ATOM 24 CB ASN A 14 8.128 2.359 3.219 1.00 5.81 C
+ATOM 25 CG ASN A 14 9.484 2.797 3.770 1.00 6.82 C
+ATOM 26 OD1 ASN A 14 9.939 3.911 3.493 1.00 9.43 O
+ATOM 27 ND2 ASN A 14 10.150 1.947 4.580 1.00 8.21 N
+ATOM 28 N VAL A 15 5.007 2.844 2.449 1.00 3.76 N
+ATOM 29 CA VAL A 15 3.779 2.564 1.706 1.00 3.98 C
+ATOM 30 C VAL A 15 3.251 3.808 1.007 1.00 3.80 C
+ATOM 31 O VAL A 15 2.875 3.772 -0.164 1.00 4.85 O
+ATOM 32 CB VAL A 15 2.697 1.943 2.587 1.00 4.71 C
+ATOM 33 CG1 VAL A 15 1.363 1.794 1.823 1.00 6.67 C
+ATOM 34 CG2 VAL A 15 3.180 0.551 3.038 1.00 6.26 C
+ATOM 35 N CYS A 16 3.266 4.970 1.690 1.00 3.79 N
+ATOM 36 CA CYS A 16 2.856 6.243 1.112 1.00 3.54 C
+ATOM 37 C CYS A 16 3.716 6.656 -0.083 1.00 3.48 C
+ATOM 38 O CYS A 16 3.228 7.276 -1.022 1.00 4.63 O
+ATOM 39 CB CYS A 16 2.848 7.364 2.195 1.00 4.58 C
+ATOM 40 SG CYS A 16 1.884 8.861 1.768 1.00 0.00 S
+ATOM 41 N ARG A 17 5.016 6.295 -0.088 1.00 3.99 N
+ATOM 42 CA ARG A 17 5.931 6.536 -1.192 1.00 3.83 C
+ATOM 43 C ARG A 17 5.812 5.586 -2.372 1.00 3.79 C
+ATOM 44 O ARG A 17 6.306 5.912 -3.451 1.00 5.39 O
+ATOM 45 CB ARG A 17 7.399 6.486 -0.702 1.00 4.11 C
+ATOM 46 CG ARG A 17 7.777 7.683 0.189 1.00 4.69 C
+ATOM 47 CD ARG A 17 7.946 8.994 -0.580 1.00 5.10 C
+ATOM 48 NE ARG A 17 9.235 8.886 -1.325 1.00 4.71 N
+ATOM 49 CZ ARG A 17 9.545 9.576 -2.428 1.00 5.28 C
+ATOM 50 NH1 ARG A 17 8.670 10.368 -3.045 1.00 6.67 N
+ATOM 51 NH2 ARG A 17 10.781 9.478 -2.915 1.00 6.41 N
+ATOM 52 N LEU A 18 5.146 4.421 -2.238 1.00 4.70 N
+ATOM 53 CA LEU A 18 4.994 3.464 -3.332 1.00 5.46 C
+ATOM 54 C LEU A 18 4.339 3.997 -4.613 1.00 5.13 C
+ATOM 55 O LEU A 18 4.867 3.695 -5.686 1.00 5.55 O
+ATOM 56 CB LEU A 18 4.210 2.196 -2.903 1.00 6.47 C
+ATOM 57 CG LEU A 18 4.950 1.170 -2.027 1.00 7.43 C
+ATOM 58 CD1 LEU A 18 3.956 0.075 -1.602 1.00 8.70 C
+ATOM 59 CD2 LEU A 18 6.147 0.547 -2.760 1.00 9.39 C
+ATOM 60 N PRO A 19 3.252 4.779 -4.623 1.00 4.28 N
+ATOM 61 CA PRO A 19 2.731 5.370 -5.850 1.00 5.38 C
+ATOM 62 C PRO A 19 3.551 6.545 -6.351 1.00 6.30 C
+ATOM 63 O PRO A 19 3.232 7.058 -7.424 1.00 9.62 O
+ATOM 64 CB PRO A 19 1.280 5.772 -5.524 1.00 5.87 C
+ATOM 65 CG PRO A 19 1.140 5.752 -3.998 1.00 6.47 C
+ATOM 66 CD PRO A 19 2.333 4.946 -3.492 1.00 6.45 C
+ATOM 67 N GLY A 20 4.581 7.015 -5.620 1.00 4.94 N
+ATOM 68 CA GLY A 20 5.392 8.147 -6.053 1.00 5.39 C
+ATOM 69 C GLY A 20 5.045 9.432 -5.376 1.00 5.03 C
+ATOM 70 O GLY A 20 5.553 10.488 -5.753 1.00 7.34 O
+ATOM 71 N THR A 21 4.191 9.388 -4.336 1.00 4.10 N
+ATOM 72 CA THR A 21 3.790 10.539 -3.528 1.00 3.94 C
+ATOM 73 C THR A 21 4.998 11.363 -3.053 1.00 3.96 C
+ATOM 74 O THR A 21 5.943 10.766 -2.530 1.00 5.82 O
+ATOM 75 CB THR A 21 2.989 10.115 -2.296 1.00 4.13 C
+ATOM 76 OG1 THR A 21 1.946 9.228 -2.653 1.00 5.45 O
+ATOM 77 CG2 THR A 21 2.314 11.309 -1.619 1.00 5.41 C
+ATOM 78 N PRO A 22 5.092 12.684 -3.238 1.00 5.04 N
+ATOM 79 CA PRO A 22 6.163 13.520 -2.703 1.00 4.69 C
+ATOM 80 C PRO A 22 6.459 13.283 -1.234 1.00 4.19 C
+ATOM 81 O PRO A 22 5.524 13.099 -0.456 1.00 4.47 O
+ATOM 82 CB PRO A 22 5.693 14.962 -2.950 1.00 7.12 C
+ATOM 83 CG PRO A 22 4.710 14.887 -4.121 1.00 7.03 C
+ATOM 84 CD PRO A 22 4.167 13.456 -4.073 1.00 4.90 C
+ATOM 85 N GLU A 23 7.733 13.334 -0.815 1.00 5.16 N
+ATOM 86 CA GLU A 23 8.134 13.129 0.567 1.00 5.31 C
+ATOM 87 C GLU A 23 7.488 14.084 1.561 1.00 4.11 C
+ATOM 88 O GLU A 23 7.181 13.718 2.697 1.00 5.11 O
+ATOM 89 CB GLU A 23 9.664 13.247 0.669 1.00 6.16 C
+ATOM 90 CG GLU A 23 10.393 12.064 0.003 1.00 7.48 C
+ATOM 91 CD GLU A 23 11.894 12.081 0.271 1.00 9.40 C
+ATOM 92 OE1 GLU A 23 12.425 13.140 0.669 1.00 10.40 O
+ATOM 93 OE2 GLU A 23 12.497 10.997 0.038 1.00 13.32 O
+ATOM 94 N ALA A 24 7.245 15.342 1.143 1.00 4.56 N
+ATOM 95 CA ALA A 24 6.599 16.367 1.944 1.00 4.49 C
+ATOM 96 C ALA A 24 5.178 16.000 2.369 1.00 4.10 C
+ATOM 97 O ALA A 24 4.775 16.231 3.508 1.00 5.64 O
+ATOM 98 CB ALA A 24 6.614 17.719 1.196 1.00 5.80 C
+ATOM 99 N ILE A 25 4.390 15.368 1.474 1.00 0.00 N
+ATOM 100 CA ILE A 25 3.056 14.860 1.783 1.00 0.00 C
+ATOM 101 C ILE A 25 3.117 13.767 2.813 1.00 0.00 C
+ATOM 102 O ILE A 25 2.337 13.711 3.764 1.00 0.00 O
+ATOM 103 CB ILE A 25 2.391 14.300 0.539 1.00 0.00 C
+ATOM 104 CG1 ILE A 25 2.063 15.455 -0.422 1.00 0.00 C
+ATOM 105 CG2 ILE A 25 1.142 13.435 0.874 1.00 0.00 C
+ATOM 106 CD1 ILE A 25 1.416 14.939 -1.710 1.00 0.00 C
+ATOM 107 N CYS A 26 4.090 12.862 2.640 1.00 0.00 N
+ATOM 108 CA CYS A 26 4.308 11.767 3.551 1.00 0.00 C
+ATOM 109 C CYS A 26 4.649 12.228 4.960 1.00 0.00 C
+ATOM 110 O CYS A 26 4.117 11.670 5.917 1.00 0.00 O
+ATOM 111 CB CYS A 26 5.439 10.848 3.053 1.00 0.00 C
+ATOM 112 SG CYS A 26 5.256 10.214 1.378 1.00 0.00 S
+ATOM 113 N ALA A 27 5.482 13.280 5.126 1.00 0.00 N
+ATOM 114 CA ALA A 27 5.801 13.899 6.405 1.00 0.00 C
+ATOM 115 C ALA A 27 4.559 14.356 7.171 1.00 0.00 C
+ATOM 116 O ALA A 27 4.380 14.071 8.358 1.00 0.00 O
+ATOM 117 CB ALA A 27 6.729 15.120 6.167 1.00 0.00 C
+ATOM 118 N THR A 28 3.633 15.017 6.456 1.00 0.00 N
+ATOM 119 CA THR A 28 2.321 15.446 6.937 1.00 0.00 C
+ATOM 120 C THR A 28 1.404 14.294 7.323 1.00 0.00 C
+ATOM 121 O THR A 28 0.712 14.345 8.336 1.00 0.00 O
+ATOM 122 CB THR A 28 1.626 16.343 5.912 1.00 0.00 C
+ATOM 123 OG1 THR A 28 2.409 17.510 5.702 1.00 0.00 O
+ATOM 124 CG2 THR A 28 0.252 16.831 6.389 1.00 0.00 C
+ATOM 125 N TYR A 29 1.378 13.211 6.519 1.00 0.00 N
+ATOM 126 CA TYR A 29 0.552 12.036 6.752 1.00 0.00 C
+ATOM 127 C TYR A 29 1.026 11.150 7.913 1.00 0.00 C
+ATOM 128 O TYR A 29 0.217 10.575 8.639 1.00 0.00 O
+ATOM 129 CB TYR A 29 0.428 11.216 5.432 1.00 0.00 C
+ATOM 130 CG TYR A 29 -0.622 10.133 5.517 1.00 0.00 C
+ATOM 131 CD1 TYR A 29 -0.251 8.780 5.590 1.00 0.00 C
+ATOM 132 CD2 TYR A 29 -1.988 10.459 5.548 1.00 0.00 C
+ATOM 133 CE1 TYR A 29 -1.223 7.779 5.722 1.00 0.00 C
+ATOM 134 CE2 TYR A 29 -2.963 9.455 5.658 1.00 0.00 C
+ATOM 135 CZ TYR A 29 -2.578 8.114 5.748 1.00 0.00 C
+ATOM 136 OH TYR A 29 -3.540 7.090 5.859 1.00 0.00 O
+ATOM 137 N THR A 30 2.357 10.982 8.093 1.00 0.00 N
+ATOM 138 CA THR A 30 2.914 9.976 8.999 1.00 0.00 C
+ATOM 139 C THR A 30 3.686 10.510 10.182 1.00 0.00 C
+ATOM 140 O THR A 30 4.066 9.739 11.064 1.00 0.00 O
+ATOM 141 CB THR A 30 3.862 9.005 8.296 1.00 0.00 C
+ATOM 142 OG1 THR A 30 4.986 9.650 7.716 1.00 0.00 O
+ATOM 143 CG2 THR A 30 3.095 8.337 7.153 1.00 0.00 C
+ATOM 144 N GLY A 31 3.951 11.824 10.255 1.00 4.99 N
+ATOM 145 CA GLY A 31 4.741 12.411 11.334 1.00 5.50 C
+ATOM 146 C GLY A 31 6.229 12.273 11.162 1.00 4.19 C
+ATOM 147 O GLY A 31 6.997 12.715 12.015 1.00 6.12 O
+ATOM 148 N CYS A 32 6.696 11.684 10.044 1.00 4.30 N
+ATOM 149 CA CYS A 32 8.101 11.682 9.664 1.00 4.89 C
+ATOM 150 C CYS A 32 8.520 13.077 9.218 1.00 5.50 C
+ATOM 151 O CYS A 32 7.680 13.916 8.906 1.00 5.82 O
+ATOM 152 CB CYS A 32 8.438 10.657 8.546 1.00 4.66 C
+ATOM 153 SG CYS A 32 7.969 8.946 8.965 1.00 5.33 S
+ATOM 154 N ILE A 33 9.825 13.398 9.191 1.00 6.02 N
+ATOM 155 CA ILE A 33 10.271 14.742 8.869 1.00 5.24 C
+ATOM 156 C ILE A 33 11.316 14.662 7.783 1.00 5.16 C
+ATOM 157 O ILE A 33 11.951 13.625 7.588 1.00 7.19 O
+ATOM 158 CB ILE A 33 10.825 15.505 10.076 1.00 5.49 C
+ATOM 159 CG1 ILE A 33 12.061 14.816 10.706 1.00 6.85 C
+ATOM 160 CG2 ILE A 33 9.677 15.684 11.094 1.00 6.45 C
+ATOM 161 CD1 ILE A 33 12.740 15.663 11.789 1.00 8.94 C
+ATOM 162 N ILE A 34 11.525 15.763 7.043 1.00 5.52 N
+ATOM 163 CA ILE A 34 12.553 15.857 6.024 1.00 6.82 C
+ATOM 164 C ILE A 34 13.547 16.865 6.552 1.00 6.92 C
+ATOM 165 O ILE A 34 13.161 17.949 6.983 1.00 9.22 O
+ATOM 166 CB ILE A 34 12.018 16.369 4.691 1.00 8.11 C
+ATOM 167 CG1 ILE A 34 10.935 15.424 4.141 1.00 9.59 C
+ATOM 168 CG2 ILE A 34 13.167 16.520 3.666 1.00 9.73 C
+ATOM 169 CD1 ILE A 34 10.162 16.044 2.977 1.00 13.41 C
+ATOM 170 N ILE A 35 14.851 16.529 6.553 1.00 7.06 N
+ATOM 171 CA ILE A 35 15.898 17.427 7.004 1.00 7.52 C
+ATOM 172 C ILE A 35 16.885 17.612 5.857 1.00 6.63 C
+ATOM 173 O ILE A 35 16.943 16.752 4.978 1.00 7.90 O
+ATOM 174 CB ILE A 35 16.626 16.941 8.263 1.00 8.07 C
+ATOM 175 CG1 ILE A 35 17.338 15.577 8.082 1.00 9.41 C
+ATOM 176 CG2 ILE A 35 15.605 16.940 9.421 1.00 9.46 C
+ATOM 177 CD1 ILE A 35 18.265 15.211 9.249 1.00 9.85 C
+ATOM 178 N PRO A 36 17.670 18.690 5.789 1.00 8.07 N
+ATOM 179 CA PRO A 36 18.640 18.880 4.713 1.00 8.78 C
+ATOM 180 C PRO A 36 19.907 18.075 4.930 1.00 8.31 C
+ATOM 181 O PRO A 36 20.626 17.818 3.969 1.00 9.09 O
+ATOM 182 CB PRO A 36 18.964 20.390 4.709 1.00 9.67 C
+ATOM 183 CG PRO A 36 18.255 21.019 5.918 1.00 10.15 C
+ATOM 184 CD PRO A 36 17.402 19.915 6.539 1.00 9.53 C
+ATOM 185 N GLY A 37 20.241 17.753 6.195 1.00 8.48 N
+ATOM 186 CA GLY A 37 21.408 16.954 6.554 1.00 9.20 C
+ATOM 187 C GLY A 37 21.154 15.469 6.484 1.00 10.41 C
+ATOM 188 O GLY A 37 20.133 15.005 5.995 1.00 12.06 O
+ATOM 189 N ALA A 38 22.097 14.668 7.015 1.00 9.24 N
+ATOM 190 CA ALA A 38 21.999 13.224 6.970 1.00 9.24 C
+ATOM 191 C ALA A 38 21.916 12.601 8.351 1.00 9.60 C
+ATOM 192 O ALA A 38 21.860 11.377 8.493 1.00 13.65 O
+ATOM 193 CB ALA A 38 23.251 12.700 6.251 1.00 10.43 C
+ATOM 194 N THR A 39 21.877 13.417 9.413 1.00 8.70 N
+ATOM 195 CA THR A 39 21.992 12.914 10.771 1.00 9.46 C
+ATOM 196 C THR A 39 20.690 13.195 11.469 1.00 8.32 C
+ATOM 197 O THR A 39 20.401 14.325 11.853 1.00 9.89 O
+ATOM 198 CB THR A 39 23.122 13.579 11.548 1.00 10.72 C
+ATOM 199 OG1 THR A 39 24.349 13.438 10.850 1.00 11.66 O
+ATOM 200 CG2 THR A 39 23.325 12.911 12.913 1.00 11.81 C
+ATOM 201 N CYS A 40 19.847 12.160 11.624 1.00 7.64 N
+ATOM 202 CA CYS A 40 18.552 12.292 12.269 1.00 8.05 C
+ATOM 203 C CYS A 40 18.674 12.464 13.784 1.00 7.63 C
+ATOM 204 O CYS A 40 19.539 11.828 14.396 1.00 9.64 O
+ATOM 205 CB CYS A 40 17.612 11.109 11.922 1.00 7.80 C
+ATOM 206 SG CYS A 40 17.269 10.997 10.134 1.00 7.30 S
+ATOM 207 N PRO A 41 17.890 13.314 14.448 1.00 8.00 N
+ATOM 208 CA PRO A 41 17.918 13.458 15.898 1.00 8.96 C
+ATOM 209 C PRO A 41 17.386 12.232 16.618 1.00 9.06 C
+ATOM 210 O PRO A 41 16.717 11.388 16.021 1.00 8.82 O
+ATOM 211 CB PRO A 41 17.062 14.707 16.161 1.00 10.39 C
+ATOM 212 CG PRO A 41 16.065 14.730 15.003 1.00 10.99 C
+ATOM 213 CD PRO A 41 16.861 14.157 13.834 1.00 10.49 C
+ATOM 214 N GLY A 42 17.676 12.111 17.927 1.00 7.55 N
+ATOM 215 CA GLY A 42 17.327 10.937 18.725 1.00 8.00 C
+ATOM 216 C GLY A 42 15.855 10.669 18.938 1.00 7.22 C
+ATOM 217 O GLY A 42 15.484 9.546 19.273 1.00 8.41 O
+ATOM 218 N ASP A 43 14.969 11.660 18.744 1.00 5.54 N
+ATOM 219 CA ASP A 43 13.536 11.507 18.859 1.00 5.85 C
+ATOM 220 C ASP A 43 12.886 11.217 17.501 1.00 5.87 C
+ATOM 221 O ASP A 43 11.691 10.932 17.417 1.00 7.29 O
+ATOM 222 CB ASP A 43 12.929 12.754 19.572 1.00 6.72 C
+ATOM 223 CG ASP A 43 13.245 14.091 18.908 1.00 8.59 C
+ATOM 224 OD1 ASP A 43 14.282 14.193 18.201 1.00 9.59 O
+ATOM 225 OD2 ASP A 43 12.461 15.040 19.153 1.00 11.45 O
+ATOM 226 N TYR A 44 13.684 11.173 16.414 1.00 5.22 N
+ATOM 227 CA TYR A 44 13.250 10.771 15.088 1.00 5.56 C
+ATOM 228 C TYR A 44 14.257 9.746 14.610 1.00 4.61 C
+ATOM 229 O TYR A 44 14.941 9.918 13.603 1.00 6.04 O
+ATOM 230 CB TYR A 44 13.186 11.943 14.075 1.00 5.41 C
+ATOM 231 CG TYR A 44 12.028 12.844 14.383 1.00 5.34 C
+ATOM 232 CD1 TYR A 44 12.137 13.887 15.315 1.00 6.59 C
+ATOM 233 CD2 TYR A 44 10.795 12.629 13.750 1.00 5.94 C
+ATOM 234 CE1 TYR A 44 11.033 14.699 15.612 1.00 5.97 C
+ATOM 235 CE2 TYR A 44 9.694 13.443 14.039 1.00 5.17 C
+ATOM 236 CZ TYR A 44 9.816 14.487 14.959 1.00 5.96 C
+ATOM 237 OH TYR A 44 8.700 15.304 15.220 1.00 8.60 O
+ATOM 238 N ALA A 45 14.382 8.644 15.369 1.00 4.76 N
+ATOM 239 CA ALA A 45 15.471 7.700 15.249 1.00 5.89 C
+ATOM 240 C ALA A 45 15.182 6.516 14.332 1.00 6.67 C
+ATOM 241 O ALA A 45 16.018 5.614 14.201 1.00 7.56 O
+ATOM 242 CB ALA A 45 15.715 7.125 16.659 1.00 6.82 C
+ATOM 243 N ASN A 46 14.005 6.481 13.693 1.00 5.80 N
+ATOM 244 CA ASN A 46 13.544 5.386 12.865 1.00 6.15 C
+ATOM 245 C ASN A 46 13.202 5.858 11.431 1.00 6.61 C
+ATOM 246 O ASN A 46 13.307 7.080 11.150 1.00 7.18 O
+ATOM 247 CB ASN A 46 12.259 4.765 13.459 1.00 7.27 C
+ATOM 248 CG ASN A 46 12.521 4.274 14.869 1.00 7.98 C
+ATOM 249 OD1 ASN A 46 11.984 4.792 15.854 1.00 11.00 O
+ATOM 250 ND2 ASN A 46 13.379 3.239 15.000 1.00 10.32 N
+ATOM 251 OXT ASN A 46 12.807 4.982 10.613 1.00 0.00 O
+TER 252 ASN A 46
END
diff --git a/modelling/doc/pipeline.rst b/modelling/doc/pipeline.rst
index 54d86037d316ed87434fea7ae1cca2e3a2ae11d0..f5fa202666feef0d0c7bc1482cdc15f7238288a6 100644
--- a/modelling/doc/pipeline.rst
+++ b/modelling/doc/pipeline.rst
@@ -400,6 +400,7 @@ Modelling Steps
with seqres in **mhandle**
+.. autofunction:: SetFraggerHandles
.. autofunction:: CloseGaps
diff --git a/modelling/pymod/CMakeLists.txt b/modelling/pymod/CMakeLists.txt
index 5e44247d6bd03f7f80cbaee99fe973700ce4dcda..9d0648c9f8055a113dffc32e93a2cddae113c0c7 100644
--- a/modelling/pymod/CMakeLists.txt
+++ b/modelling/pymod/CMakeLists.txt
@@ -23,6 +23,7 @@ set(MODELLING_PYMOD
_fragger_handle.py
_reconstruct_sidechains.py
_monte_carlo.py
+ _mhandle_helper.py
)
pymod(NAME modelling
diff --git a/modelling/pymod/__init__.py b/modelling/pymod/__init__.py
index d81fc6ee63f97c01c6810036749a957c53f35205..e271378977183e94d53c492d7d465bdad762b378 100644
--- a/modelling/pymod/__init__.py
+++ b/modelling/pymod/__init__.py
@@ -24,3 +24,4 @@ from _ring_punches import *
from _denovo import *
from _fragger_handle import *
from _monte_carlo import *
+from _mhandle_helper import *
diff --git a/modelling/pymod/_mhandle_helper.py b/modelling/pymod/_mhandle_helper.py
new file mode 100644
index 0000000000000000000000000000000000000000..8e91ce760be66816ff2844f7088e9c16990e8d5a
--- /dev/null
+++ b/modelling/pymod/_mhandle_helper.py
@@ -0,0 +1,36 @@
+# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+# Biozentrum - University of Basel
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+def SetFraggerHandles(mhandle, fragger_handles):
+ """ Sets the :attr:`fragger_handles` in **mhandle** while ensuring
+ consistency with the :attr:`ModellingHandle.seqres`
+
+ :param mhandle: Will have the fragger handles attached afterwards
+ :param fragger_handles: The fragger handles to attach
+
+ :type mhandle: :class:`ModellingHandle`
+ :type fragger_handles: :class:`list` of :class:`FraggerHandle`
+
+ :raises: :class:`ValueError` when the given **fragger_handles** are not
+ consistent with seqres in **mhandle**
+ """
+
+ if len(mhandle.seqres) != len(mhandle.fragger_handles):
+ raise RuntimeError("Must have one FraggerHandle per chain!")
+ for a,b in zip(mhandle.seqres, mhandle.fragger_handles):
+ if str(a) != str(b.sequence):
+ raise RuntimeError("Sequence in FraggerHandle must match sequence "+
+ "in SEQRES!")
+ mhandle.fragger_handles = fragger_handles
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index 56cc847c61da1238af93114613208ab3061fe2a6..ecb968ba34349b7c60770cdcb5b7c54ae3efa4e7 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -445,6 +445,13 @@ def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list()):
and adapt the default scoring members. Alternatively, you can setup the
scoring manually, but you must ensure consistency yourself!
+ By default, a simple backbone dihedral sampling is performed when entering
+ Monte Carlo. If *mhandle* has a list of :class:`FraggerHandle` objects
+ attached as "fragger_handles" attribute, the sampling will be performed with
+ structural fragments. To ensure consistency, the fragger handles should be
+ attached using :meth:`SetFraggerHandles`.
+ But be aware of increased runtime due to the fragment search step.
+
If the function fails to close all gaps, it will produce a warning and
return an incomplete model.
@@ -489,10 +496,16 @@ def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list()):
# remove terminal gaps
RemoveTerminalGaps(mhandle)
+ # check whether we have fragger handles
+ fragger_handles = None
+ if hasattr(mhandle, "fragger_handles"):
+ fragger_handles = mhandle.fragger_handles
+ ost.LogInfo("Use fragments for Monte Carlo sampling")
+
# close gaps
CloseGaps(mhandle, merge_distance=merge_distance,
fragment_db=fragment_db, structure_db=structure_db,
- torsion_sampler=torsion_sampler)
+ torsion_sampler=torsion_sampler, fragger_handles=fragger_handles)
# build sidechains
BuildSidechains(mhandle, merge_distance, fragment_db,