Author: bugman
Date: Mon Oct 24 15:44:36 2011
New Revision: 14902
URL: http://svn.gna.org/viewcvs/relax?rev=14902&view=rev
Log:
Added the frame order free rotor optimisation script and its results.
Added:
1.3/test_suite/shared_data/frame_order/free_rotor/ave_pos.pdb
1.3/test_suite/shared_data/frame_order/free_rotor/cone.pdb
1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.bz2 (with
props)
1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.log.bz2
(with props)
1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.py
- copied, changed from r14894,
1.3/test_suite/shared_data/frame_order/rigid/frame_order.py
Added: 1.3/test_suite/shared_data/frame_order/free_rotor/ave_pos.pdb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/frame_order/free_rotor/ave_pos.pdb?rev=14902&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/frame_order/free_rotor/ave_pos.pdb (added)
+++ 1.3/test_suite/shared_data/frame_order/free_rotor/ave_pos.pdb Mon Oct 24
15:44:36 2011
@@ -1,0 +1,144 @@
+REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.1, 1-AUG-2007
+REMARK 40 CREATED BY RELAX (HTTP://NMR-RELAX.COM)
+HET A CA1000 1
+HET A CA1001 1
+HETNAM CA Unknown
+FORMUL 1000 CA CA1
+ATOM 1 N GLU A 82 34.284 -3.066 17.436 1.00 0.00
N
+ATOM 2 N GLU A 83 33.511 -0.947 19.195 1.00 0.00
N
+ATOM 3 H GLU A 83 33.907 -0.643 18.350 1.00 0.00
H
+ATOM 4 N GLU A 84 30.775 -1.299 18.977 1.00 0.00
N
+ATOM 5 H GLU A 84 31.327 -1.339 18.167 1.00 0.00
H
+ATOM 6 N ILE A 85 30.503 -3.818 20.117 1.00 0.00
N
+ATOM 7 H ILE A 85 31.244 -3.678 19.492 1.00 0.00
H
+ATOM 8 N ARG A 86 31.539 -3.296 22.678 1.00 0.00
N
+ATOM 9 H ARG A 86 32.051 -2.963 21.911 1.00 0.00
H
+ATOM 10 N GLU A 87 29.826 -1.183 23.570 1.00 0.00
N
+ATOM 11 H GLU A 87 30.235 -1.018 22.693 1.00 0.00
H
+ATOM 12 N ALA A 88 27.444 -2.613 23.440 1.00 0.00
N
+ATOM 13 H ALA A 88 28.035 -2.656 22.658 1.00 0.00
H
+ATOM 14 N PHE A 89 28.103 -4.549 25.307 1.00 0.00
N
+ATOM 15 H PHE A 89 28.787 -4.295 24.653 1.00 0.00
H
+ATOM 16 N ARG A 90 28.240 -2.951 27.590 1.00 0.00
N
+ATOM 17 H ARG A 90 28.606 -2.595 26.754 1.00 0.00
H
+ATOM 18 N VAL A 91 25.620 -2.193 27.700 1.00 0.00
N
+ATOM 19 H VAL A 91 26.078 -2.313 26.842 1.00 0.00
H
+ATOM 20 N PHE A 92 24.290 -4.514 28.459 1.00 0.00
N
+ATOM 21 H PHE A 92 25.075 -4.577 27.875 1.00 0.00
H
+ATOM 22 N ASP A 93 25.395 -4.882 30.906 1.00 0.00
N
+ATOM 23 H ASP A 93 25.861 -4.444 30.163 1.00 0.00
H
+ATOM 24 N LYS A 94 23.850 -4.003 33.345 1.00 0.00
N
+ATOM 25 H LYS A 94 23.536 -4.909 33.142 1.00 0.00
H
+ATOM 26 N ASP A 95 24.337 -3.231 36.008 1.00 0.00
N
+ATOM 27 H ASP A 95 24.449 -4.170 35.752 1.00 0.00
H
+ATOM 28 N GLY A 96 26.825 -2.219 35.739 1.00 0.00
N
+ATOM 29 H GLY A 96 26.297 -2.667 35.047 1.00 0.00
H
+ATOM 30 N ASN A 97 29.008 -3.639 36.491 1.00 0.00
N
+ATOM 31 H ASN A 97 28.129 -4.028 36.301 1.00 0.00
H
+ATOM 32 N GLY A 98 30.975 -4.694 34.974 1.00 0.00
N
+ATOM 33 H GLY A 98 30.208 -4.179 34.642 1.00 0.00
H
+ATOM 34 N TYR A 99 30.775 -7.242 34.187 1.00 0.00
N
+ATOM 35 H TYR A 99 30.141 -6.744 34.745 1.00 0.00
H
+ATOM 36 N ILE A 100 28.738 -9.760 32.680 1.00 0.00
N
+ATOM 37 H ILE A 100 29.445 -10.189 32.156 1.00 0.00
H
+ATOM 38 N SER A 101 25.887 -11.260 33.913 1.00 0.00
N
+ATOM 39 H SER A 101 25.441 -10.398 34.049 1.00 0.00
H
+ATOM 40 N ALA A 102 24.280 -14.517 34.074 1.00 0.00
N
+ATOM 41 H ALA A 102 24.772 -14.915 34.823 1.00 0.00
H
+ATOM 42 N ALA A 103 21.495 -14.351 34.449 1.00 0.00
N
+ATOM 43 H ALA A 103 22.043 -14.447 35.256 1.00 0.00
H
+ATOM 44 N GLU A 104 21.199 -11.731 33.696 1.00 0.00
N
+ATOM 45 H GLU A 104 22.004 -12.027 34.169 1.00 0.00
H
+ATOM 46 N LEU A 105 21.667 -11.985 31.045 1.00 0.00
N
+ATOM 47 H LEU A 105 22.179 -12.513 31.695 1.00 0.00
H
+ATOM 48 N ARG A 106 19.403 -13.323 30.312 1.00 0.00
N
+ATOM 49 H ARG A 106 19.843 -13.521 31.167 1.00 0.00
H
+ATOM 50 N HIS A 107 17.545 -11.323 30.595 1.00 0.00
N
+ATOM 51 H HIS A 107 18.316 -11.375 31.203 1.00 0.00
H
+ATOM 52 N VAL A 108 18.253 -9.457 28.556 1.00 0.00
N
+ATOM 53 H VAL A 108 18.999 -9.733 29.129 1.00 0.00
H
+ATOM 54 N MET A 109 18.176 -11.158 26.275 1.00 0.00
N
+ATOM 55 H MET A 109 18.711 -11.474 27.033 1.00 0.00
H
+ATOM 56 N THR A 110 15.540 -12.164 26.438 1.00 0.00
N
+ATOM 57 H THR A 110 16.063 -12.112 27.265 1.00 0.00
H
+ATOM 58 N ASN A 111 13.930 -9.814 26.179 1.00 0.00
N
+ATOM 59 H ASN A 111 14.686 -9.740 26.802 1.00 0.00
H
+ATOM 60 N LEU A 112 14.976 -8.936 23.818 1.00 0.00
N
+ATOM 61 H LEU A 112 15.519 -9.378 24.505 1.00 0.00
H
+ATOM 62 N GLY A 113 13.737 -10.492 22.081 1.00 0.00
N
+ATOM 63 H GLY A 113 13.624 -10.458 23.053 1.00 0.00
H
+ATOM 64 N GLU A 114 14.439 -13.072 22.015 1.00 0.00
N
+ATOM 65 H GLU A 114 14.933 -12.328 22.420 1.00 0.00
H
+ATOM 66 N LYS A 115 13.713 -15.962 23.662 1.00 0.00
N
+ATOM 67 H LYS A 115 13.350 -16.378 22.852 1.00 0.00
H
+ATOM 68 N LEU A 116 15.110 -17.698 26.094 1.00 0.00
N
+ATOM 69 H LEU A 116 15.336 -16.834 26.496 1.00 0.00
H
+ATOM 70 N THR A 117 15.704 -20.694 27.995 1.00 0.00
N
+ATOM 71 H THR A 117 15.987 -21.277 27.260 1.00 0.00
H
+ATOM 72 N ASP A 118 16.593 -21.349 31.464 1.00 0.00
N
+ATOM 73 H ASP A 118 15.718 -21.519 31.872 1.00 0.00
H
+ATOM 74 N GLU A 119 18.440 -23.380 31.319 1.00 0.00
N
+ATOM 75 H GLU A 119 17.481 -23.568 31.240 1.00 0.00
H
+ATOM 76 N GLU A 120 19.240 -23.372 28.636 1.00 0.00
N
+ATOM 77 H GLU A 120 18.284 -23.283 28.832 1.00 0.00
H
+ATOM 78 N VAL A 121 20.548 -20.944 28.597 1.00 0.00
N
+ATOM 79 H VAL A 121 19.728 -21.045 29.126 1.00 0.00
H
+ATOM 80 N ASP A 122 22.495 -21.548 30.370 1.00 0.00
N
+ATOM 81 H ASP A 122 21.577 -21.856 30.515 1.00 0.00
H
+ATOM 82 N GLU A 123 23.974 -23.284 28.839 1.00 0.00
N
+ATOM 83 H GLU A 123 22.998 -23.351 28.785 1.00 0.00
H
+ATOM 84 N MET A 124 24.949 -21.494 26.883 1.00 0.00
N
+ATOM 85 H MET A 124 23.989 -21.425 27.089 1.00 0.00
H
+ATOM 86 N ILE A 125 26.360 -19.765 28.566 1.00 0.00
N
+ATOM 87 H ILE A 125 25.454 -20.029 28.825 1.00 0.00
H
+ATOM 88 N ARG A 126 28.181 -21.537 29.825 1.00 0.00
N
+ATOM 89 H ARG A 126 27.243 -21.819 29.847 1.00 0.00
H
+ATOM 90 N GLU A 127 29.540 -22.333 27.531 1.00 0.00
N
+ATOM 91 H GLU A 127 28.568 -22.215 27.491 1.00 0.00
H
+ATOM 92 N ALA A 128 30.570 -19.904 26.574 1.00 0.00
N
+ATOM 93 H ALA A 128 29.633 -19.917 26.861 1.00 0.00
H
+ATOM 94 N ASP A 129 31.749 -19.069 28.869 1.00 0.00
N
+ATOM 95 H ASP A 129 30.967 -19.658 28.832 1.00 0.00
H
+ATOM 96 N ILE A 130 34.882 -19.250 29.825 1.00 0.00
N
+ATOM 97 H ILE A 130 34.914 -18.282 29.673 1.00 0.00
H
+ATOM 98 N ASP A 131 36.550 -19.313 32.020 1.00 0.00
N
+ATOM 99 H ASP A 131 35.996 -18.531 31.817 1.00 0.00
H
+ATOM 100 N GLY A 132 35.076 -20.646 33.747 1.00 0.00
N
+ATOM 101 H GLY A 132 34.881 -20.450 32.806 1.00 0.00
H
+ATOM 102 N ASP A 133 33.635 -19.253 35.581 1.00 0.00
N
+ATOM 103 H ASP A 133 34.007 -18.859 34.765 1.00 0.00
H
+ATOM 104 N GLY A 134 31.014 -18.763 35.569 1.00 0.00
N
+ATOM 105 H GLY A 134 31.553 -19.083 34.815 1.00 0.00
H
+ATOM 106 N GLN A 135 29.883 -16.599 34.433 1.00 0.00
N
+ATOM 107 H GLN A 135 30.835 -16.834 34.431 1.00 0.00
H
+ATOM 108 N VAL A 136 29.775 -14.077 31.778 1.00 0.00
N
+ATOM 109 H VAL A 136 28.912 -13.651 31.969 1.00 0.00
H
+ATOM 110 N ASN A 137 32.512 -12.332 30.539 1.00 0.00
N
+ATOM 111 H ASN A 137 32.993 -13.153 30.308 1.00 0.00
H
+ATOM 112 N TYR A 138 33.946 -9.259 29.172 1.00 0.00
N
+ATOM 113 H TYR A 138 34.217 -8.778 29.981 1.00 0.00
H
+ATOM 114 N GLU A 139 36.026 -10.064 27.343 1.00 0.00
N
+ATOM 115 H GLU A 139 36.326 -9.904 28.260 1.00 0.00
H
+ATOM 116 N GLU A 140 35.316 -12.771 26.871 1.00 0.00
N
+ATOM 117 H GLU A 140 35.337 -12.471 27.805 1.00 0.00
H
+ATOM 118 N PHE A 141 32.761 -12.364 25.844 1.00 0.00
N
+ATOM 119 H PHE A 141 33.050 -11.833 26.614 1.00 0.00
H
+ATOM 120 N VAL A 142 33.332 -11.038 23.441 1.00 0.00
N
+ATOM 121 H VAL A 142 33.820 -10.740 24.238 1.00 0.00
H
+ATOM 122 N GLN A 143 34.738 -13.071 22.010 1.00 0.00
N
+ATOM 123 H GLN A 143 35.079 -12.915 22.917 1.00 0.00
H
+ATOM 124 N MET A 144 32.691 -15.026 21.926 1.00 0.00
N
+ATOM 125 H MET A 144 32.851 -14.575 22.782 1.00 0.00
H
+ATOM 126 N MET A 145 30.681 -13.716 20.415 1.00 0.00
N
+ATOM 127 H MET A 145 31.151 -13.194 21.098 1.00 0.00
H
+ATOM 128 N THR A 146 32.233 -12.819 18.384 1.00 0.00
N
+ATOM 129 H THR A 146 32.533 -12.953 19.308 1.00 0.00
H
+ATOM 130 N ALA A 147 33.361 -15.073 17.459 1.00 0.00
N
+ATOM 131 H ALA A 147 32.461 -15.022 17.845 1.00 0.00
H
+ATOM 132 N LYS A 148 35.654 -16.178 15.496 1.00 0.00
N
+ATOM 133 H LYS A 148 36.251 -15.805 16.177 1.00 0.00
H
+TER 134 CA A1001
+HETATM 135 CA CA A1000 26.319 -7.065 35.514 1.00 0.00
CA
+HETATM 136 CA CA A1001 33.889 -15.886 32.605 1.00 0.00
CA
+MASTER 0 0 2 0 0 0 0 0 135 1 0 0
+END
Added: 1.3/test_suite/shared_data/frame_order/free_rotor/cone.pdb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/frame_order/free_rotor/cone.pdb?rev=14902&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/frame_order/free_rotor/cone.pdb (added)
+++ 1.3/test_suite/shared_data/frame_order/free_rotor/cone.pdb Mon Oct 24
15:44:36 2011
@@ -1,0 +1,22 @@
+REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.1, 1-AUG-2007
+REMARK 40 CREATED BY RELAX (HTTP://NMR-RELAX.COM)
+HET PIV 1 1
+HET ZAX 2 3
+HET ZAX 3 3
+HETNAM PIV Pivot point
+HETNAM ZAX Unknown
+FORMUL 1 PIV C1
+FORMUL 2 ZAX C2N1
+HETATM 1 R PIV 1 37.254 0.500 16.747 1.00 0.00
C
+HETATM 2 R ZAX 2 37.254 0.500 16.747 1.00 0.00
C
+HETATM 3 z-ax ZAX 2 21.780 -18.562 33.986 1.00 0.00
C
+HETATM 4 z-ax ZAX 2 20.232 -20.468 35.710 1.00 0.00
N
+HETATM 5 R ZAX 3 37.254 0.500 16.747 1.00 0.00
C
+HETATM 6 z-ax ZAX 3 52.728 19.562 -0.493 1.00 0.00
C
+HETATM 7 z-ax ZAX 3 54.276 21.468 -2.217 1.00 0.00
N
+CONECT 2 3
+CONECT 3 2
+CONECT 5 6
+CONECT 6 5
+MASTER 0 0 3 0 0 0 0 0 7 0 4 0
+END
Added: 1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.bz2?rev=14902&view=auto
==============================================================================
Binary file - no diff available.
Propchange: 1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.bz2
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added: 1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.log.bz2?rev=14902&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.log.bz2
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Copied: 1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.py
(from r14894, 1.3/test_suite/shared_data/frame_order/rigid/frame_order.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.py?p2=1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.py&p1=1.3/test_suite/shared_data/frame_order/rigid/frame_order.py&r1=14894&r2=14902&rev=14902&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/frame_order/rigid/frame_order.py (original)
+++ 1.3/test_suite/shared_data/frame_order/free_rotor/frame_order.py Mon Oct
24 15:44:36 2011
@@ -1,4 +1,4 @@
-# Script for optimising the rigid frame order test model of CaM.
+# Script for optimising the free rotor frame order test model of CaM.
# Python module imports.
from numpy import array, float64, transpose, zeros
@@ -61,13 +61,13 @@
align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
# Select the model.
- frame_order.select_model('rigid')
+ frame_order.select_model('free rotor')
# Set the reference domain.
frame_order.ref_domain('N')
# Optimise.
- grid_search(inc=3)
+ grid_search(inc=11)
minimise('simplex', constraints=False)
@@ -95,7 +95,7 @@
frame_order.pivot(pivot)
# Create the cone PDB file.
- #frame_order.cone_pdb(file='cone.pdb', force=True)
+ frame_order.cone_pdb(file='cone.pdb', force=True)
# Set the domains.
frame_order.domain_to_pdb(domain='N', pdb='1J7O_1st_NH.pdb')
r14902 - /1.3/test_suite/shared_data/frame_order/free_rotor/