Hi,
The following are the problems I have found in the version 2.1 (and
2.1.1) files. This continues from
https://mail.gna.org/public/relax-devel/2011-02/msg00013.html. At the
end is the diff of the original files verses the files I have
modified. The modifications were essential to allow these files to be
parsable. As you will see below, most of the problems arise from the
fact that the entity saveframe data does not match the sequence data
in the relaxation data or model-free saveframes. The second major
problem is inconsistency in the tag names. A third is that there is
zero consistency in the _Order_parameter.Model_fit tag making parsing
quite difficult (though doable). So, one by one:
bmr15910.str: The S2_parameters saveframe is missing the residue numbers.
bmr4245.str: _Tau_e_value_error should be _Tau_e_value_fit_error.
bmr4267.str: A residue number is wrong - probably need to check with
the authors for this.
bmr4390.str: _T2_relaxation_value should be _T2_value.
bmr5548.str: Looks to be a few residues misnamed.
bmr5808.str, bmr6243.str, bmr6577.str: _S2_value_error should be
_S2_value_fit_error.
bmr5841.str: _S2_error should be _S2_value_fit_error.
bmr6474.str: Some numbers are not numbers (0.0006.99), and _S2_error
should be _S2_value_fit_error.
None of these files have a corresponding v3.1 version. This shouldn't
be too hard to fix, unless they need to be manually ported to v3.1.
Next will be the v3.1 problems.
Cheers,
Edward
[edau@localhost bmr2.1_files_orig]$ cat diff
diff -ur ./bmr15910.str ../bmr2.1_files/bmr15910.str
--- ./bmr15910.str 2011-01-28 07:51:08.000000000 +0100
+++ ../bmr2.1_files/bmr15910.str 2011-02-01 14:20:26.000000000 +0100
@@ -1706,124 +1706,124 @@
_S2N_value
_S2N_value_fit_error
- . MET N 5 0.218 0.016 . . 0.762 0.013 0.286 0.021
925.50 33.63 . . . .
- . GLY N 5 0.453 0.010 . . 0.779 0.008 0.582 0.015
1367.45 66.47 . . . .
- . ARG N 6 0.556 0.028 . . 0.752 0.017 0.740 0.029
8222.98 2489.86 . . . .
- . PHE N 4 0.739 0.011 22.80 5.12 . . . . .
. . . . .
- . THR N 3 0.808 0.011 . . . . . . .
. . . . .
- . GLU N 1 0.879 0.007 . . . . . . .
. . . . .
- . ARG N 3 0.869 0.013 . . . . . . .
. . . . .
- . ALA N 3 0.863 0.011 . . . . . . .
. . . . .
- . GLN N 3 0.848 0.014 . . . . . . .
. . . . .
- . LYS N 1 0.894 0.017 . . . . . . .
. . . . .
- . VAL N 3 0.858 0.012 . . . . . . .
. . . . .
- . LEU N 3 0.887 0.014 . . . . . . .
. . . . .
- . ALA N 1 0.878 0.008 . . . . . . .
. . . . .
- . LEU N 1 0.875 0.009 . . . . . . .
. . . . .
- . ALA N 1 0.879 0.005 . . . . . . .
. . . . .
- . GLN N 3 0.826 0.009 . . . . . . .
. . . . .
- . GLU N 1 0.876 0.009 . . . . . . .
. . . . .
- . GLU N 3 0.868 0.012 . . . . . . .
. . . . .
- . ALA N 3 0.848 0.008 . . . . . . .
. . . . .
- . LEU N 3 0.840 0.011 . . . . . . .
. . . . .
- . ARG N 3 0.872 0.009 . . . . . . .
. . . . .
- . LEU N 3 0.851 0.011 . . . . . . .
. . . . .
- . GLY N 3 0.823 0.010 . . . . . . .
. . . . .
- . HIS N 3 0.844 0.010 . . . . . . .
. . . . .
- . ASN N 2 0.826 0.014 24.99 12.31 . . . . .
. . . . .
- . ASN N 7 0.577 0.168 . . 0.730 0.073 0.789 0.196
2553.48 2011.96 . . . .
- . ILE N 3 0.782 0.013 . . . . . . .
. . . . .
- . GLY N 3 0.803 0.019 . . . . . . .
. . . . .
- . GLU N 3 0.832 0.012 . . . . . . .
. . . . .
- . HIS N 3 0.863 0.014 . . . . . . .
. . . . .
- . LEU N 3 0.848 0.013 . . . . . . .
. . . . .
- . LEU N 3 0.840 0.011 . . . . . . .
. . . . .
- . GLY N 3 0.850 0.010 . . . . . . .
. . . . .
- . LEU N 3 0.844 0.010 . . . . . . .
. . . . .
- . VAL N 3 0.836 0.012 . . . . . . .
. . . . .
- . ARG N 1 0.830 0.006 . . . . . . .
. . . . .
- . GLU N 3 0.827 0.010 . . . . . . .
. . . . .
- . GLY N 3 0.793 0.020 . . . . . . .
. . . . .
- . GLY N 3 0.853 0.025 . . . . . . .
. . . . .
- . ILE N 3 0.843 0.018 . . . . . . .
. . . . .
- . ALA N 3 0.854 0.012 . . . . . . .
. . . . .
- . ALA N 3 0.782 0.009 . . . . . . .
. . . . .
- . ALA N 3 0.833 0.010 . . . . . . .
. . . . .
- . ALA N 4 0.805 0.011 13.45 6.85 . . . . .
. . . . .
- . LEU N 4 0.768 0.013 10.06 6.12 . . . . .
. . . . .
- . GLY N 3 0.815 0.010 . . . . . . .
. . . . .
- . GLY N 4 0.523 0.007 32.28 1.74 . . . . .
. . . . .
- . SER N 4 0.804 0.009 19.67 7.16 . . . . .
. . . . .
- . GLU N 3 0.823 0.009 . . . . . . .
. . . . .
- . LYS N 1 0.821 0.009 . . . . . . .
. . . . .
- . ILE N 3 0.834 0.011 . . . . . . .
. . . . .
- . GLN N 3 0.855 0.011 . . . . . . .
. . . . .
- . GLU N 1 0.871 0.010 . . . . . . .
. . . . .
- . VAL N 3 0.842 0.010 . . . . . . .
. . . . .
- . GLU N 3 0.845 0.011 . . . . . . .
. . . . .
- . SER N 4 0.828 0.009 18.21 6.33 . . . . .
. . . . .
- . LEU N 3 0.818 0.011 . . . . . . .
. . . . .
- . ILE N 4 0.768 0.012 24.35 9.48 . . . . .
. . . . .
- . GLY N 5 0.698 0.015 . . 0.799 0.007 0.874 0.019
1137.56 184.49 . . . .
- . ARG N 8 0.469 0.103 . . 0.630 0.038 0.744 0.123
6335.33 2296.42 . . . .
- . GLY N 5 0.644 0.015 . . 0.791 0.008 0.814 0.015
624.91 102.95 . . . .
- . GLN N 6 0.415 0.013 . . 0.676 0.032 0.614 0.021
2203.72 588.46 . . . .
- . MET N 6 0.338 0.012 . . 0.702 0.024 0.481 0.019
1742.14 209.39 . . . .
- . SER N 8 0.234 0.124 . . 0.558 0.041 0.420 0.196
4730.12 1806.42 . . . .
- . THR N 6 0.591 0.023 . . 0.674 0.024 0.876 0.026
3821.93 2436.56 . . . .
- . ILE N 7 0.543 0.079 . . 0.756 0.023 0.719 0.086
1447.04 455.41 . . . .
- . HIS N 7 0.616 0.136 . . 0.771 0.064 0.800 0.136
2118.46 1385.90 . . . .
- . TYR N 3 0.778 0.015 . . . . . . .
. . . . .
- . THR N 3 0.814 0.015 . . . . . . .
. . . . .
- . ARG N 3 0.862 0.025 . . . . . . .
. . . . .
- . ALA N 1 0.883 0.011 . . . . . . .
. . . . .
- . LYS N 7 0.335 0.227 . . 0.704 0.066 0.476 0.282
6244.59 2226.06 . . . .
- . LYS N 1 0.885 0.018 . . . . . . .
. . . . .
- . VAL N 3 0.866 0.010 . . . . . . .
. . . . .
- . ILE N 1 0.891 0.009 . . . . . . .
. . . . .
- . GLU N 1 0.891 0.007 . . . . . . .
. . . . .
- . LEU N 1 0.884 0.013 . . . . . . .
. . . . .
- . SER N 4 0.881 0.015 24.67 13.66 . . . . .
. . . . .
- . MET N 1 0.882 0.009 . . . . . . .
. . . . .
- . ASP N 3 0.848 0.010 . . . . . . .
. . . . .
- . GLU N 3 0.831 0.013 . . . . . . .
. . . . .
- . ALA N 1 0.872 0.008 . . . . . . .
. . . . .
- . ARG N 3 0.849 0.012 . . . . . . .
. . . . .
- . GLY N 3 0.817 0.012 . . . . . . .
. . . . .
- . HIS N 4 0.781 0.011 15.80 6.15 . . . . .
. . . . .
- . SER N 3 0.743 0.044 . . . . . . .
. . . . .
- . TYR N 7 0.640 0.076 . . 0.756 0.027 0.847 0.077
2423.54 767.23 . . . .
- . VAL N 4 0.800 0.017 18.48 12.66 . . . . .
. . . . .
- . GLY N 3 0.808 0.024 . . . . . . .
. . . . .
- . GLU N 3 0.815 0.013 . . . . . . .
. . . . .
- . HIS N 3 0.876 0.015 . . . . . . .
. . . . .
- . ILE N 3 0.841 0.014 . . . . . . .
. . . . .
- . LEU N 3 0.859 0.012 . . . . . . .
. . . . .
- . LEU N 3 0.845 0.020 . . . . . . .
. . . . .
- . GLY N 3 0.860 0.011 . . . . . . .
. . . . .
- . LEU N 3 0.860 0.017 . . . . . . .
. . . . .
- . GLU N 3 0.872 0.015 . . . . . . .
. . . . .
- . GLY N 3 0.830 0.011 . . . . . . .
. . . . .
- . GLY N 3 0.870 0.050 . . . . . . .
. . . . .
- . VAL N 3 0.830 0.023 . . . . . . .
. . . . .
- . ALA N 3 0.837 0.013 . . . . . . .
. . . . .
- . ARG N 3 0.828 0.011 . . . . . . .
. . . . .
- . ASN N 3 0.831 0.010 . . . . . . .
. . . . .
- . ASN N 3 0.813 0.010 . . . . . . .
. . . . .
- . LEU N 3 0.791 0.013 . . . . . . .
. . . . .
- . VAL N 3 0.814 0.009 . . . . . . .
. . . . .
- . SER N 7 0.487 0.149 . . 0.654 0.084 0.745 0.184
2963.99 1765.98 . . . .
- . LEU N 1 0.868 0.009 . . . . . . .
. . . . .
- . ASN N 3 0.830 0.011 . . . . . . .
. . . . .
- . LYS N 1 0.864 0.013 . . . . . . .
. . . . .
- . ARG N 3 0.848 0.011 . . . . . . .
. . . . .
- . GLN N 3 0.861 0.012 . . . . . . .
. . . . .
- . VAL N 4 0.840 0.010 21.23 11.35 . . . . .
. . . . .
- . LEU N 3 0.838 0.013 . . . . . . .
. . . . .
- . LEU N 4 0.810 0.014 13.64 6.81 . . . . .
. . . . .
- . LEU N 4 0.751 0.011 27.27 5.72 . . . . .
. . . . .
- . SER N 6 0.103 0.026 . . 0.483 0.006 0.213 0.053
6366.45 941.85 . . . .
- . ASN N 6 0.037 0.006 . . 0.282 0.011 0.130 0.018
1532.60 97.50 . . . .
+ 3 MET N 5 0.218 0.016 . . 0.762 0.013 0.286 0.021
925.50 33.63 . . . .
+ 5 GLY N 5 0.453 0.010 . . 0.779 0.008 0.582 0.015
1367.45 66.47 . . . .
+ 6 ARG N 6 0.556 0.028 . . 0.752 0.017 0.740 0.029
8222.98 2489.86 . . . .
+ 7 PHE N 4 0.739 0.011 22.80 5.12 . . . .
. . . . . .
+ 8 THR N 3 0.808 0.011 . . . . . .
. . . . . .
+ 9 GLU N 1 0.879 0.007 . . . . . .
. . . . . .
+ 10 ARG N 3 0.869 0.013 . . . . . .
. . . . . .
+ 11 ALA N 3 0.863 0.011 . . . . . .
. . . . . .
+ 12 GLN N 3 0.848 0.014 . . . . . .
. . . . . .
+ 13 LYS N 1 0.894 0.017 . . . . . .
. . . . . .
+ 14 VAL N 3 0.858 0.012 . . . . . .
. . . . . .
+ 15 LEU N 3 0.887 0.014 . . . . . .
. . . . . .
+ 16 ALA N 1 0.878 0.008 . . . . . .
. . . . . .
+ 17 LEU N 1 0.875 0.009 . . . . . .
. . . . . .
+ 18 ALA N 1 0.879 0.005 . . . . . .
. . . . . .
+ 19 GLN N 3 0.826 0.009 . . . . . .
. . . . . .
+ 20 GLU N 1 0.876 0.009 . . . . . .
. . . . . .
+ 21 GLU N 3 0.868 0.012 . . . . . .
. . . . . .
+ 22 ALA N 3 0.848 0.008 . . . . . .
. . . . . .
+ 23 LEU N 3 0.840 0.011 . . . . . .
. . . . . .
+ 24 ARG N 3 0.872 0.009 . . . . . .
. . . . . .
+ 25 LEU N 3 0.851 0.011 . . . . . .
. . . . . .
+ 26 GLY N 3 0.823 0.010 . . . . . .
. . . . . .
+ 27 HIS N 3 0.844 0.010 . . . . . .
. . . . . .
+ 28 ASN N 2 0.826 0.014 24.99 12.31 . . . .
. . . . . .
+ 29 ASN N 7 0.577 0.168 . . 0.730 0.073 0.789 0.196
2553.48 2011.96 . . . .
+ 30 ILE N 3 0.782 0.013 . . . . . .
. . . . . .
+ 31 GLY N 3 0.803 0.019 . . . . . .
. . . . . .
+ 33 GLU N 3 0.832 0.012 . . . . . .
. . . . . .
+ 34 HIS N 3 0.863 0.014 . . . . . .
. . . . . .
+ 36 LEU N 3 0.848 0.013 . . . . . .
. . . . . .
+ 37 LEU N 3 0.840 0.011 . . . . . .
. . . . . .
+ 38 GLY N 3 0.850 0.010 . . . . . .
. . . . . .
+ 39 LEU N 3 0.844 0.010 . . . . . .
. . . . . .
+ 40 VAL N 3 0.836 0.012 . . . . . .
. . . . . .
+ 41 ARG N 1 0.830 0.006 . . . . . .
. . . . . .
+ 42 GLU N 3 0.827 0.010 . . . . . .
. . . . . .
+ 43 GLY N 3 0.793 0.020 . . . . . .
. . . . . .
+ 45 GLY N 3 0.853 0.025 . . . . . .
. . . . . .
+ 46 ILE N 3 0.843 0.018 . . . . . .
. . . . . .
+ 47 ALA N 3 0.854 0.012 . . . . . .
. . . . . .
+ 48 ALA N 3 0.782 0.009 . . . . . .
. . . . . .
+ 50 ALA N 3 0.833 0.010 . . . . . .
. . . . . .
+ 53 ALA N 4 0.805 0.011 13.45 6.85 . . . .
. . . . . .
+ 54 LEU N 4 0.768 0.013 10.06 6.12 . . . .
. . . . . .
+ 55 GLY N 3 0.815 0.010 . . . . . .
. . . . . .
+ 57 GLY N 4 0.523 0.007 32.28 1.74 . . . .
. . . . . .
+ 58 SER N 4 0.804 0.009 19.67 7.16 . . . .
. . . . . .
+ 59 GLU N 3 0.823 0.009 . . . . . .
. . . . . .
+ 60 LYS N 1 0.821 0.009 . . . . . .
. . . . . .
+ 61 ILE N 3 0.834 0.011 . . . . . .
. . . . . .
+ 62 GLN N 3 0.855 0.011 . . . . . .
. . . . . .
+ 64 GLU N 1 0.871 0.010 . . . . . .
. . . . . .
+ 65 VAL N 3 0.842 0.010 . . . . . .
. . . . . .
+ 66 GLU N 3 0.845 0.011 . . . . . .
. . . . . .
+ 67 SER N 4 0.828 0.009 18.21 6.33 . . . .
. . . . . .
+ 68 LEU N 3 0.818 0.011 . . . . . .
. . . . . .
+ 69 ILE N 4 0.768 0.012 24.35 9.48 . . . .
. . . . . .
+ 70 GLY N 5 0.698 0.015 . . 0.799 0.007 0.874 0.019
1137.56 184.49 . . . .
+ 71 ARG N 8 0.469 0.103 . . 0.630 0.038 0.744 0.123
6335.33 2296.42 . . . .
+ 72 GLY N 5 0.644 0.015 . . 0.791 0.008 0.814 0.015
624.91 102.95 . . . .
+ 73 GLN N 6 0.415 0.013 . . 0.676 0.032 0.614 0.021
2203.72 588.46 . . . .
+ 75 MET N 6 0.338 0.012 . . 0.702 0.024 0.481 0.019
1742.14 209.39 . . . .
+ 76 SER N 8 0.234 0.124 . . 0.558 0.041 0.420 0.196
4730.12 1806.42 . . . .
+ 78 THR N 6 0.591 0.023 . . 0.674 0.024 0.876 0.026
3821.93 2436.56 . . . .
+ 79 ILE N 7 0.543 0.079 . . 0.756 0.023 0.719 0.086
1447.04 455.41 . . . .
+ 80 HIS N 7 0.616 0.136 . . 0.771 0.064 0.800 0.136
2118.46 1385.90 . . . .
+ 81 TYR N 3 0.778 0.015 . . . . . .
. . . . . .
+ 82 THR N 3 0.814 0.015 . . . . . .
. . . . . .
+ 84 ARG N 3 0.862 0.025 . . . . . .
. . . . . .
+ 85 ALA N 1 0.883 0.011 . . . . . .
. . . . . .
+ 86 LYS N 7 0.335 0.227 . . 0.704 0.066 0.476 0.282
6244.59 2226.06 . . . .
+ 87 LYS N 1 0.885 0.018 . . . . . .
. . . . . .
+ 88 VAL N 3 0.866 0.010 . . . . . .
. . . . . .
+ 89 ILE N 1 0.891 0.009 . . . . . .
. . . . . .
+ 90 GLU N 1 0.891 0.007 . . . . . .
. . . . . .
+ 91 LEU N 1 0.884 0.013 . . . . . .
. . . . . .
+ 92 SER N 4 0.881 0.015 24.67 13.66 . . . .
. . . . . .
+ 93 MET N 1 0.882 0.009 . . . . . .
. . . . . .
+ 94 ASP N 3 0.848 0.010 . . . . . .
. . . . . .
+ 95 GLU N 3 0.831 0.013 . . . . . .
. . . . . .
+ 96 ALA N 1 0.872 0.008 . . . . . .
. . . . . .
+ 97 ARG N 3 0.849 0.012 . . . . . .
. . . . . .
+ 100 GLY N 3 0.817 0.012 . . . . . .
. . . . . .
+ 101 HIS N 4 0.781 0.011 15.80 6.15 . . . .
. . . . . .
+ 102 SER N 3 0.743 0.044 . . . . . .
. . . . . .
+ 103 TYR N 7 0.640 0.076 . . 0.756 0.027 0.847 0.077
2423.54 767.23 . . . .
+ 104 VAL N 4 0.800 0.017 18.48 12.66 . . . .
. . . . . .
+ 105 GLY N 3 0.808 0.024 . . . . . .
. . . . . .
+ 107 GLU N 3 0.815 0.013 . . . . . .
. . . . . .
+ 108 HIS N 3 0.876 0.015 . . . . . .
. . . . . .
+ 109 ILE N 3 0.841 0.014 . . . . . .
. . . . . .
+ 110 LEU N 3 0.859 0.012 . . . . . .
. . . . . .
+ 111 LEU N 3 0.845 0.020 . . . . . .
. . . . . .
+ 112 GLY N 3 0.860 0.011 . . . . . .
. . . . . .
+ 113 LEU N 3 0.860 0.017 . . . . . .
. . . . . .
+ 116 GLU N 3 0.872 0.015 . . . . . .
. . . . . .
+ 117 GLY N 3 0.830 0.011 . . . . . .
. . . . . .
+ 119 GLY N 3 0.870 0.050 . . . . . .
. . . . . .
+ 120 VAL N 3 0.830 0.023 . . . . . .
. . . . . .
+ 121 ALA N 3 0.837 0.013 . . . . . .
. . . . . .
+ 123 ARG N 3 0.828 0.011 . . . . . .
. . . . . .
+ 126 ASN N 3 0.831 0.010 . . . . . .
. . . . . .
+ 127 ASN N 3 0.813 0.010 . . . . . .
. . . . . .
+ 128 LEU N 3 0.791 0.013 . . . . . .
. . . . . .
+ 130 VAL N 3 0.814 0.009 . . . . . .
. . . . . .
+ 131 SER N 7 0.487 0.149 . . 0.654 0.084 0.745 0.184
2963.99 1765.98 . . . .
+ 132 LEU N 1 0.868 0.009 . . . . . .
. . . . . .
+ 133 ASN N 3 0.830 0.011 . . . . . .
. . . . . .
+ 134 LYS N 1 0.864 0.013 . . . . . .
. . . . . .
+ 136 ARG N 3 0.848 0.011 . . . . . .
. . . . . .
+ 138 GLN N 3 0.861 0.012 . . . . . .
. . . . . .
+ 139 VAL N 4 0.840 0.010 21.23 11.35 . . . .
. . . . . .
+ 140 LEU N 3 0.838 0.013 . . . . . .
. . . . . .
+ 142 LEU N 4 0.810 0.014 13.64 6.81 . . . .
. . . . . .
+ 143 LEU N 4 0.751 0.011 27.27 5.72 . . . .
. . . . . .
+ 145 SER N 6 0.103 0.026 . . 0.483 0.006 0.213 0.053
6366.45 941.85 . . . .
+ 146 ASN N 6 0.037 0.006 . . 0.282 0.011 0.130 0.018
1532.60 97.50 . . . .
stop_
diff -ur ./bmr4245.str ../bmr2.1_files/bmr4245.str
--- ./bmr4245.str 2011-01-28 05:56:31.000000000 +0100
+++ ../bmr2.1_files/bmr4245.str 2011-02-01 20:47:35.000000000 +0100
@@ -1324,7 +1324,7 @@
_Order_parameter_value
_Order_parameter_value_error
_Tau_e_value
- _Tau_e_value_error
+ _Tau_e_value_fit_error
_Chemical_shift_anisotropy_value
_Chemical_shift_anisotropy_value_error
_Normalized_chi_squared_fit
diff -ur ./bmr4267.str ../bmr2.1_files/bmr4267.str
--- ./bmr4267.str 2011-01-28 05:56:57.000000000 +0100
+++ ../bmr2.1_files/bmr4267.str 2011-02-01 19:00:17.000000000 +0100
@@ -3105,8 +3105,8 @@
99 LYS N 0.993 0.020
100 SER N 1.018 0.027
101 TYR N 1.047 0.023
- 102 GLY N 1.016 0.051
- 103 LEU N 1.013 0.020
+ 103 GLY N 1.016 0.051
+ 104 LEU N 1.013 0.020
105 THR N 1.103 0.032
106 SER N 1.043 0.025
107 TYR N 1.059 0.031
@@ -4604,7 +4604,7 @@
175 GLN 0.534 0.063
176 CYS 0.703 0.145
178 ASP 0.708 0.050
- 79 GLY -0.224 0.050
+ 179 GLY -0.224 0.050
stop_
diff -ur ./bmr4390.str ../bmr2.1_files/bmr4390.str
--- ./bmr4390.str 2011-02-01 21:01:34.000000000 +0100
+++ ../bmr2.1_files/bmr4390.str 2011-02-01 21:00:58.000000000 +0100
@@ -493,7 +493,7 @@
_Residue_seq_code
_Residue_label
_Atom_name
- _T2_relaxation_value
+ _T2_value
_T2_value_error
1 3 ALA N 1.922 0.013
Only in ../bmr2.1_files: .bmr4689.str.swp
Only in ../bmr2.1_files: .bmr4970.str.swp
diff -ur ./bmr5548.str ../bmr2.1_files/bmr5548.str
--- ./bmr5548.str 2011-01-28 06:01:18.000000000 +0100
+++ ../bmr2.1_files/bmr5548.str 2011-01-31 16:48:00.000000000 +0100
@@ -1405,11 +1405,11 @@
_Tau_e_value_fit_error
4 GLU N . 0.08 0.01 595.9 37.04
- 6 ASP N . 0.12 0.01 864.25 56.54
+ 6 GLU N . 0.12 0.01 864.25 56.54
7 TYR N . 0.11 0.02 849.24 55.81
9 GLY N . 0.12 0.02 939.6 67.63
10 ASP N . 0.2 0.02 920.89 75.43
- 11 ARG N . 0.21 0.03 1050.46 98.67
+ 11 ASN N . 0.21 0.03 1050.46 98.67
12 ALA N . 0.21 0.02 1088.9 101.6
13 THR N . 0.35 0.02 1162.35 150.12
15 GLU N . 0.58 0.03 992.57 218.99
@@ -1470,7 +1470,7 @@
6 GLU N . 0.72 0.02 63.39 14.12
7 TYR N . 0.86 0.01 . .
10 ASP N . 0.76 0.01 . .
- 11 ARG N . 0.76 0.01 . .
+ 11 ASN N . 0.76 0.01 . .
12 ALA N . 0.77 0.01 . .
13 THR N . 0.84 0.02 . .
15 GLU N . 0.78 0.02 . .
diff -ur ./bmr5808.str ../bmr2.1_files/bmr5808.str
--- ./bmr5808.str 2011-01-28 06:02:30.000000000 +0100
+++ ../bmr2.1_files/bmr5808.str 2011-01-31 15:53:40.000000000 +0100
@@ -1792,7 +1792,7 @@
_Residue_label
_Atom_name
_S2_value
- _S2_value_error
+ _S2_value_fit_error
1 1 GLU N 0.136 0.025
2 2 SER N 0.212 0.020
diff -ur ./bmr5841.str ../bmr2.1_files/bmr5841.str
--- ./bmr5841.str 2011-01-28 06:02:33.000000000 +0100
+++ ../bmr2.1_files/bmr5841.str 2011-02-01 21:12:30.000000000 +0100
@@ -1340,7 +1340,7 @@
_Residue_label
_Atom_name
_S2_value
- _S2_error
+ _S2_value_fit_error
_Rex_value
_Rex_error
_Tau_e_value
diff -ur ./bmr6243.str ../bmr2.1_files/bmr6243.str
--- ./bmr6243.str 2011-01-28 06:05:35.000000000 +0100
+++ ../bmr2.1_files/bmr6243.str 2011-01-31 15:54:03.000000000 +0100
@@ -3533,7 +3533,7 @@
_Residue_label
_Atom_name
_S2_value
- _S2_value_error
+ _S2_value_fit_error
1 2 GLU N 0.3941 0.0156
2 3 CYS N 0.7177 0.0121
@@ -3677,7 +3677,7 @@
_Residue_label
_Atom_name
_S2_value
- _S2_value_error
+ _S2_value_fit_error
1 2 GLU N 0.3692 0.0312
2 4 SER N 0.8487 0.0085
diff -ur ./bmr6474.str ../bmr2.1_files/bmr6474.str
--- ./bmr6474.str 2011-01-28 06:06:43.000000000 +0100
+++ ../bmr2.1_files/bmr6474.str 2011-02-01 21:17:38.000000000 +0100
@@ -1016,8 +1016,8 @@
23 ALA N 0.0484 0.0015
24 VAL N 0.0547 0.000478
25 ASN N 0.0612 0.0024
- 26 SER N 0.0519 0.0006.99
- 27 THR N 0.0559 0.0007.42
+ 26 SER N 0.0519 0.000699
+ 27 THR N 0.0559 0.000742
28 SER N 0.0613 0.000281
29 SER N 0.0591 0.000163
31 LYS N 0.0561 0.000418
@@ -1261,7 +1261,7 @@
_Residue_label
_Atom_name
_S2_value
- _S2_error
+ _S2_value_fit_error
_Rex_value
_Rex_error
_Tau_e_value
diff -ur ./bmr6577.str ../bmr2.1_files/bmr6577.str
--- ./bmr6577.str 2011-01-28 06:07:14.000000000 +0100
+++ ../bmr2.1_files/bmr6577.str 2011-01-31 15:53:47.000000000 +0100
@@ -2277,7 +2277,7 @@
_Residue_label
_Atom_name
_S2_value
- _S2_value_error
+ _S2_value_fit_error
7 THR N 0.086 0.010
10 SER N 0.106 0.013
On 2 February 2011 14:35, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
Hi Eldon,
I don't know if this is the best channel for this information. Is
there a BMRB mailing list where it would be better for this
information?
Ok, this is how I have found these inconsistencies. I have used relax
to read in the BMRB NMR-STAR formatted files. This uses bmrblib which
I wrote (http://gna.org/projects/bmrblib/). This library is pretty
close to complete for relaxation data and model-free data, and would
be very easy to extend to handle the entirety of the NMR-STAR
dictionary. It can both read and write valid NMR-STAR formatted files
in versions 2.1, 3.0, and 3.1 (a little debugging might be still
required, and expansion to different revisions such as 2.1.1 is also
possible). This Python library is an abstraction of the underlying
file format. The very low level reading and writing of the STAR
format is handled by Jurgen F. Doreleijers' pystarlib (jurgenfd att
gmail dott com, http://code.google.com/p/pystarlib/).
For reading the entire BMRB model-free data content, I have performed
the following. I have downloaded all of the files from
http://www.bmrb.wisc.edu/search/query_grid/query_1_46.html using the
link http://www.bmrb.wisc.edu/ftp/pub/bmrb/compress/query_1_46.tar.gz.
These are all in the version 2.1 or 2.1.1 format. Then using the
file names, I have downloaded all of the corresponding v3.1 files from
http://www.bmrb.wisc.edu/ftp/pub/bmrb/entry_lists/nmr-star3.1/. It
looks like maybe 30% of the old formatted files have been converted to
the newer format so far. I will write 2 subsequent emails with
explanations of the problems with the version 2.1 files and the 3.1
files separately.
In this mail, I would like to describe general problems. The first is
that pystarlib cannot handle the semi-colon notation in non-free
looping tag categories, e.g.:
loop_
_Vendor.Name
_Vendor.Address
_Vendor.Electronic_address
_Vendor.Entry_ID
_Vendor.Software_ID
'J. Patrick Loria' .
;
http://xbeams.chem.yale.edu/~loria/
patrick.loria@xxxxxxxx
; 15097 1
This is in the v3.1 file bmr15097.str. The basic pystarlib
functionality probably needs to be fixed, assuming this construct is a
valid STAR format. The second is that the bmr4970.str entry is not
parsable. This file has multiple 15N S2_parameters saveframes:
save_S2_parameters_15N_22C
save_S2_parameters_15N_35C
save_S2_parameters_15N_47C
save_S2_parameters_15N_60C
save_S2_parameters_15N_73C
But these all have:
loop_
_Sample_label
$sample_one
stop_
_Sample_conditions_label $sample_conditions_one
They might be the same sample, but the sample conditions are different
as the temperature is changing. By eye, this is obvious, but for the
automatic parsing of this data, the file has to be blacklisted and
skipped.
Cheers,
Edward
Re: Inconsistencies in the v2.1 (or v2.1.1) BMRB model-free entries.