[BioPython] Alternate Conformations in PDB
Michael Sierk
mls5w at virginia.edu
Fri Apr 15 13:39:03 EDT 2005
How does the PDB module deal with alternate conformations? It appears
to me that it is completely ignoring them, at least in the polypeptide
builder.
Thanks,
Mike Sierk
Here's the snippet of code:
> print "id: ", id
> pdb_file = '/rd0/users/mls5w/cathdoms/' + id + '.pdb'
> p = PDBParser()
> s = p.get_structure('1', pdb_file) # The structure
> ppb=CaPPBuilder()
> for pp in ppb.build_peptides(s):
> print pp.get_sequence()
>
Here's the output:
> id: 11baA0
> Seq('KESAAAKFERQHMDS', <class Bio.Alphabet.ProteinAlphabet at
> 0x62f300>)
> Seq('SNYCNLMMCCRKMTQGKCKPVNTFVHESLADVKAVCSQKKVTCKNGQTNCYQSKSTMRIT
> ...', <class Bio.Alphabet.ProteinAlphabet at 0x62f300>)
And here's the relevant section of the PDB file:
> ATOM 89 N HIS A 12 7.245 -5.906 13.618 1.00 13.83
> N
> ATOM 90 CA HIS A 12 7.227 -6.425 14.964 1.00 13.71
> C
> ATOM 91 C HIS A 12 7.373 -5.379 16.042 1.00 14.43
> C
> ATOM 92 O HIS A 12 7.253 -5.726 17.224 1.00 14.41
> O
> ATOM 93 CB HIS A 12 8.405 -7.418 15.156 1.00 11.77
> C
> ATOM 94 CG HIS A 12 8.257 -8.620 14.267 1.00 9.61
> C
> ATOM 95 ND1 HIS A 12 7.438 -9.677 14.614 1.00 8.63
> N
> ATOM 96 CD2 HIS A 12 8.761 -8.909 13.054 1.00 9.08
> C
> ATOM 97 CE1 HIS A 12 7.469 -10.573 13.653 1.00 8.45
> C
> ATOM 98 NE2 HIS A 12 8.244 -10.136 12.692 1.00 9.30
> N
> ATOM 99 N MET A 13 7.676 -4.145 15.632 1.00 15.20
> N
> ATOM 100 CA MET A 13 7.908 -3.151 16.679 1.00 16.58
> C
> ATOM 101 C MET A 13 6.710 -2.207 16.806 1.00 18.05
> C
> ATOM 102 O MET A 13 6.222 -1.682 15.802 1.00 18.98
> O
> ATOM 103 CB MET A 13 9.150 -2.336 16.326 1.00 16.39
> C
> ATOM 104 CG MET A 13 10.462 -3.110 16.502 1.00 14.43
> C
> ATOM 105 SD MET A 13 10.738 -3.774 18.125 1.00 14.79
> S
> ATOM 106 CE MET A 13 10.504 -2.444 19.253 1.00 13.41
> C
> ATOM 107 N ASP A 14 6.232 -2.054 18.027 1.00 18.73
> N
> ATOM 108 CA ASP A 14 5.248 -1.020 18.349 1.00 20.36
> C
> ATOM 109 C ASP A 14 5.471 -0.573 19.800 1.00 21.48
> C
> ATOM 110 O ASP A 14 4.799 -0.915 20.761 1.00 19.90
> O
> ATOM 111 CB ASP A 14 3.850 -1.536 18.122 1.00 20.82
> C
> ATOM 112 CG ASP A 14 2.763 -0.518 18.409 1.00 20.73
> C
> ATOM 113 OD1 ASP A 14 3.013 0.679 18.204 1.00 21.16
> O
> ATOM 114 OD2 ASP A 14 1.676 -0.922 18.878 1.00 20.89
> O
> ATOM 115 N SER A 15 6.531 0.266 19.929 1.00 22.96
> N
> ATOM 116 CA SER A 15 7.021 0.672 21.236 1.00 25.33
> C
> ATOM 117 C SER A 15 6.142 1.732 21.895 1.00 25.92
> C
> ATOM 118 O SER A 15 5.631 2.643 21.240 1.00 26.33
> O
> ATOM 119 CB SER A 15 8.431 1.278 21.165 1.00 25.96
> C
> ATOM 120 OG SER A 15 9.224 0.674 20.169 1.00 28.77
> O
> ATOM 121 N AGLY A 16 5.838 1.525 23.178 0.50 26.35
> N
> ATOM 122 N BGLY A 16 6.124 1.705 23.225 0.50 25.97
> N
> ATOM 123 CA AGLY A 16 4.936 2.410 23.894 0.50 27.02
> C
> ATOM 124 CA BGLY A 16 5.414 2.708 24.008 0.50 26.33
> C
> ATOM 125 C AGLY A 16 4.234 1.754 25.072 0.50 27.16
> C
> ATOM 126 C BGLY A 16 3.966 2.816 23.527 0.50 26.37
> C
> ATOM 127 O AGLY A 16 4.212 0.540 25.212 0.50 27.16
> O
> ATOM 128 O BGLY A 16 3.341 3.874 23.573 0.50 26.73
> O
> ATOM 129 N AASN A 17 3.636 2.582 25.913 0.50 27.76
> N
> ATOM 130 N BASN A 17 3.485 1.689 23.016 0.50 26.24
> N
> ATOM 131 CA AASN A 17 2.987 2.195 27.145 0.50 28.39
> C
> ATOM 132 CA BASN A 17 2.127 1.580 22.548 0.50 25.85
> C
> ATOM 133 C AASN A 17 1.661 1.467 26.992 0.50 28.38
> C
> ATOM 134 C BASN A 17 1.516 0.294 23.105 0.50 25.52
> C
> ATOM 135 O AASN A 17 1.453 0.474 27.719 0.50 28.66
> O
> ATOM 136 O BASN A 17 2.210 -0.697 23.262 0.50 25.46
> O
> ATOM 137 CB AASN A 17 2.763 3.460 27.988 0.50 29.72
> C
> ATOM 138 CB BASN A 17 1.985 1.538 21.029 0.50 26.31
> C
> ATOM 139 CG AASN A 17 2.781 3.204 29.473 0.50 30.83
> C
> ATOM 140 CG BASN A 17 0.521 1.841 20.683 0.50 26.41
> C
> ATOM 145 N ASER A 18 0.750 1.899 26.127 0.50 28.07
> N
> ATOM 146 N BSER A 18 0.240 0.382 23.399 0.50 25.45
> N
> ATOM 147 CA ASER A 18 -0.539 1.242 25.929 0.50 27.72
> C
> ATOM 148 CA BSER A 18 -0.525 -0.705 23.998 0.50 25.06
> C
> ATOM 149 C ASER A 18 -1.045 1.350 24.492 0.50 27.14
> C
> ATOM 150 C BSER A 18 -1.777 -1.015 23.183 0.50 24.72
> C
> ATOM 151 O ASER A 18 -1.950 2.120 24.156 0.50 26.94
> O
> ATOM 152 O BSER A 18 -2.368 -0.143 22.535 0.50 24.51
> O
> ATOM 153 CB ASER A 18 -1.621 1.834 26.845 0.50 28.33
> C
> ATOM 154 CB BSER A 18 -0.997 -0.266 25.397 0.50 24.82
> C
> ATOM 155 OG ASER A 18 -1.392 1.513 28.209 0.50 29.30
> O
> ATOM 156 OG BSER A 18 -2.132 -1.021 25.794 0.50 25.79
> O
> ATOM 157 N APRO A 19 -0.468 0.545 23.598 0.50 26.85
> N
> ATOM 158 N BPRO A 19 -2.203 -2.267 23.241 0.50 24.66
> N
> ATOM 159 CA APRO A 19 -0.783 0.550 22.177 0.50 26.33
> C
> ATOM 160 CA BPRO A 19 -3.401 -2.682 22.525 0.50 24.80
> C
> ATOM 161 C APRO A 19 -2.171 0.081 21.778 0.50 25.90
> C
> ATOM 162 C BPRO A 19 -4.683 -2.125 23.129 0.50 25.11
> C
> ATOM 163 O APRO A 19 -2.629 0.411 20.667 0.50 25.39
> O
> ATOM 164 O BPRO A 19 -5.696 -2.031 22.426 0.50 25.01
> O
> ATOM 165 CB APRO A 19 0.313 -0.344 21.569 0.50 26.13
> C
> ATOM 166 CB BPRO A 19 -3.325 -4.213 22.567 0.50 24.85
> C
> ATOM 167 CG APRO A 19 0.703 -1.221 22.715 0.50 26.33
> C
> ATOM 168 CG BPRO A 19 -1.877 -4.499 22.849 0.50 24.41
> C
> ATOM 169 CD APRO A 19 0.728 -0.284 23.894 0.50 26.61
> C
> ATOM 170 CD BPRO A 19 -1.454 -3.407 23.797 0.50 24.40
> C
> ATOM 171 N ASER A 20 -2.876 -0.674 22.618 0.50 25.65
> N
> ATOM 172 N BSER A 20 -4.653 -1.682 24.379 0.50 25.23
> N
> ATOM 173 CA ASER A 20 -4.230 -1.118 22.259 0.50 25.89
> C
> ATOM 174 CA BSER A 20 -5.848 -1.272 25.101 0.50 25.72
> C
> ATOM 175 C ASER A 20 -5.291 -0.139 22.750 0.50 25.73
> C
> ATOM 176 C BSER A 20 -6.254 0.166 24.944 0.50 26.25
> C
> ATOM 177 O ASER A 20 -6.480 -0.463 22.793 0.50 26.21
> O
> ATOM 178 O BSER A 20 -7.348 0.525 25.439 0.50 27.13
> O
> ATOM 179 CB ASER A 20 -4.540 -2.530 22.712 0.50 25.71
> C
> ATOM 180 CB BSER A 20 -5.570 -1.510 26.607 0.50 24.71
> C
> ATOM 181 OG ASER A 20 -4.728 -2.715 24.098 0.50 25.54
> O
> ATOM 182 OG BSER A 20 -4.669 -0.508 27.054 0.50 24.26
> O
> ATOM 183 N ASER A 21 -4.886 1.088 23.074 0.50 25.75
> N
> ATOM 184 N BSER A 21 -5.466 1.026 24.306 0.50 26.72
> N
> ATOM 185 CA ASER A 21 -5.768 2.144 23.524 0.50 25.75
> C
> ATOM 186 CA BSER A 21 -5.907 2.416 24.149 0.50 27.32
> C
> ATOM 187 C ASER A 21 -6.611 2.788 22.422 0.50 26.28
> C
> ATOM 188 C BSER A 21 -6.794 2.644 22.931 0.50 27.72
> C
> ATOM 189 O ASER A 21 -6.206 3.117 21.302 0.50 26.12
> O
> ATOM 190 O BSER A 21 -6.464 2.331 21.778 0.50 28.30
> O
> ATOM 191 CB ASER A 21 -4.993 3.250 24.251 0.50 24.73
> C
> ATOM 192 CB BSER A 21 -4.704 3.354 24.068 0.50 26.81
> C
> ATOM 193 OG ASER A 21 -5.885 4.221 24.785 0.50 24.45
> O
> ATOM 194 OG BSER A 21 -5.089 4.561 23.427 0.50 27.93
> O
> ATOM 195 N ASER A 22 -7.889 2.965 22.778 0.50 26.48
> N
> ATOM 196 N BSER A 22 -7.965 3.250 23.169 0.50 27.84
> N
> ATOM 197 CA ASER A 22 -8.920 3.579 21.976 0.50 26.69
> C
> ATOM 198 CA BSER A 22 -8.918 3.570 22.113 0.50 27.56
> C
> ATOM 199 C ASER A 22 -8.428 4.801 21.209 0.50 26.80
> C
> ATOM 200 C BSER A 22 -8.537 4.831 21.343 0.50 27.43
> C
> ATOM 201 O ASER A 22 -8.764 4.977 20.033 0.50 26.70
> O
> ATOM 202 O BSER A 22 -9.053 5.066 20.240 0.50 27.39
> O
> ATOM 203 CB ASER A 22 -10.060 4.097 22.893 0.50 26.60
> C
> ATOM 204 CB BSER A 22 -10.326 3.759 22.688 0.50 27.51
> C
> ATOM 205 OG ASER A 22 -9.541 4.989 23.880 0.50 26.51
> O
> ATOM 206 OG BSER A 22 -10.313 4.024 24.085 0.50 26.99
> O
> ATOM 207 N SER A 23 -7.640 5.631 21.902 1.00 27.00
> N
> ATOM 208 CA SER A 23 -7.169 6.864 21.294 1.00 26.84
> C
> ATOM 209 C SER A 23 -6.336 6.629 20.054 1.00 26.48
> C
> ATOM 210 O SER A 23 -6.133 7.548 19.242 1.00 26.87
> O
> ATOM 211 CB SER A 23 -6.294 7.609 22.306 1.00 28.70
> C
> ATOM 212 OG SER A 23 -6.859 7.488 23.616 1.00 32.19
> O
> ATOM 213 N ASN A 24 -5.845 5.405 19.860 1.00 25.76
> N
> ATOM 214 CA ASN A 24 -5.059 5.083 18.679 1.00 25.09
> C
> ATOM 215 C ASN A 24 -5.839 4.660 17.454 1.00 23.88
> C
> ATOM 216 O ASN A 24 -5.270 4.417 16.381 1.00 23.10
> O
> ATOM 217 CB ASN A 24 -4.125 3.903 19.074 1.00 28.98
> C
> ATOM 218 CG ASN A 24 -2.816 4.508 19.592 1.00 31.51
> C
> ATOM 219 OD1 ASN A 24 -2.010 4.982 18.768 1.00 33.38
> O
> ATOM 220 ND2 ASN A 24 -2.623 4.518 20.908 1.00 32.55
> N
> ATOM 221 N TYR A 25 -7.172 4.572 17.571 1.00 21.77
> N
> ATOM 222 CA TYR A 25 -8.002 4.106 16.460 1.00 19.42
> C
> ATOM 223 C TYR A 25 -7.721 4.816 15.163 1.00 18.30
> C
> ATOM 224 O TYR A 25 -7.485 4.187 14.119 1.00 18.39
> O
> ATOM 225 CB TYR A 25 -9.493 4.208 16.852 1.00 17.65
> C
> ATOM 226 CG TYR A 25 -10.419 3.819 15.695 1.00 16.80
> C
> ATOM 227 CD1 TYR A 25 -10.770 2.507 15.449 1.00 15.58
> C
> ATOM 228 CD2 TYR A 25 -10.926 4.825 14.879 1.00 15.90
> C
> ATOM 229 CE1 TYR A 25 -11.574 2.188 14.353 1.00 16.54
> C
> ATOM 230 CE2 TYR A 25 -11.738 4.520 13.803 1.00 16.61
> C
> ATOM 231 CZ TYR A 25 -12.059 3.198 13.561 1.00 15.96
> C
> ATOM 232 OH TYR A 25 -12.862 2.927 12.478 1.00 17.88
> O
> ATOM 233 N CYS A 26 -7.720 6.149 15.146 1.00 17.44
> N
> ATOM 234 CA CYS A 26 -7.559 6.858 13.875 1.00 16.90
> C
> ATOM 235 C CYS A 26 -6.186 6.627 13.271 1.00 17.07
> C
> ATOM 236 O CYS A 26 -5.981 6.456 12.073 1.00 16.96
> O
> ATOM 237 CB CYS A 26 -7.769 8.356 14.136 1.00 16.94
> C
> ATOM 238 SG CYS A 26 -9.578 8.741 14.286 1.00 15.18
> S
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++
Michael Sierk, Postdoctoral Fellow email:
mls5w<AT>virginia<dot>edu
Biochemistry & Molecular Genetics Dept. Phone (W): (434) 924-2821
University of Virginia (H): (434) 970-2268
------------------------------------------------------------------------
------
"There is something fascinating about science. One gets such wholesome
returns of conjecture out of such a trifling investment of fact."
-- Mark Twain.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++
Michael Sierk, Postdoctoral Fellow email:
mls5w<AT>virginia<dot>edu
Biochemistry & Molecular Genetics Dept. Phone (W): (434) 924-2821
University of Virginia (H): (434) 970-2268
------------------------------------------------------------------------
------
"There is something fascinating about science. One gets such wholesome
returns of conjecture out of such a trifling investment of fact."
-- Mark Twain.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++
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