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add CryoREAD files
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Han Zhu committed May 3, 2024
1 parent c5c31da commit 7383cc9
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1 change: 1 addition & 0 deletions CryoREAD/.gitignore
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.idea/
514 changes: 514 additions & 0 deletions CryoREAD/CryoREAD.ipynb
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Binary file added CryoREAD/CryoREAD_tutorial.pptx
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372 changes: 372 additions & 0 deletions CryoREAD/README.md
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25 changes: 25 additions & 0 deletions CryoREAD/atomic/A.pdb
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ATOM 1 OP3 A A 1 2.890 -0.774 -6.042 0.00 0.00 O
ATOM 2 P A A 1 1.779 0.230 -5.452 0.00 0.00 P
ATOM 3 OP1 A A 1 2.388 1.557 -5.217 0.00 0.00 O
ATOM 4 OP2 A A 1 0.572 0.372 -6.507 0.00 0.00 O
ATOM 5 O5' A A 1 1.211 -0.353 -4.063 0.00 0.00 O
ATOM 6 C5' A A 1 0.235 0.576 -3.592 0.00 0.00 C
ATOM 7 C4' A A 1 -0.346 0.080 -2.267 0.00 0.00 C
ATOM 8 O4' A A 1 0.691 -0.016 -1.267 0.00 0.00 O
ATOM 9 C3' A A 1 -1.350 1.106 -1.698 0.00 0.00 C
ATOM 10 O3' A A 1 -2.690 0.727 -2.016 0.00 0.00 O
ATOM 11 C2' A A 1 -1.119 1.051 -0.171 0.00 0.00 C
ATOM 12 O2' A A 1 -2.310 0.638 0.502 0.00 0.00 O
ATOM 13 C1' A A 1 0.000 -0.000 -0.000 0.00 0.00 C
ATOM 14 N9 A A 1 0.913 0.396 1.074 0.00 0.00 N
ATOM 15 C8 A A 1 2.020 1.180 0.943 0.00 0.00 C
ATOM 16 N7 A A 1 2.598 1.330 2.099 0.00 0.00 N
ATOM 17 C5 A A 1 1.898 0.659 3.044 0.00 0.00 C
ATOM 18 C6 A A 1 2.045 0.458 4.427 0.00 0.00 C
ATOM 19 N6 A A 1 3.099 1.031 5.117 0.00 0.00 N
ATOM 20 N1 A A 1 1.146 -0.289 5.058 0.00 0.00 N
ATOM 21 C2 A A 1 0.138 -0.839 4.407 0.00 0.00 C
ATOM 22 N3 A A 1 -0.037 -0.684 3.112 0.00 0.00 N
ATOM 23 C4 A A 1 0.811 0.047 2.397 0.00 0.00 C
TER 24 A A 1
END
23 changes: 23 additions & 0 deletions CryoREAD/atomic/C.pdb
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ATOM 1 OP3 C A 1 2.890 -0.774 -6.042 0.00 0.00 O
ATOM 2 P C A 1 1.779 0.230 -5.452 0.00 0.00 P
ATOM 3 OP1 C A 1 2.388 1.558 -5.216 0.00 0.00 O
ATOM 4 OP2 C A 1 0.571 0.372 -6.507 0.00 0.00 O
ATOM 5 O5' C A 1 1.211 -0.353 -4.063 0.00 0.00 O
ATOM 6 C5' C A 1 0.235 0.576 -3.592 0.00 0.00 C
ATOM 7 C4' C A 1 -0.347 0.080 -2.268 0.00 0.00 C
ATOM 8 O4' C A 1 0.691 -0.017 -1.268 0.00 0.00 O
ATOM 9 C3' C A 1 -1.350 1.106 -1.698 0.00 0.00 C
ATOM 10 O3' C A 1 -2.690 0.726 -2.017 0.00 0.00 O
ATOM 11 C2' C A 1 -1.118 1.051 -0.170 0.00 0.00 C
ATOM 12 O2' C A 1 -2.310 0.639 0.502 0.00 0.00 O
ATOM 13 C1' C A 1 0.000 -0.000 -0.000 0.00 0.00 C
ATOM 14 N1 C A 1 0.913 0.396 1.074 0.00 0.00 N
ATOM 15 C2 C A 1 1.561 1.571 1.001 0.00 0.00 C
ATOM 16 O2 C A 1 1.381 2.297 0.037 0.00 0.00 O
ATOM 17 N3 C A 1 2.398 1.958 1.963 0.00 0.00 N
ATOM 18 C4 C A 1 2.613 1.188 3.022 0.00 0.00 C
ATOM 19 N4 C A 1 3.479 1.595 4.009 0.00 0.00 N
ATOM 20 C5 C A 1 1.952 -0.053 3.126 0.00 0.00 C
ATOM 21 C6 C A 1 1.100 -0.428 2.143 0.00 0.00 C
TER 22 C A 1
END
24 changes: 24 additions & 0 deletions CryoREAD/atomic/DA.pdb
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ATOM 1 OP3 A A 1 2.890 -0.774 -6.042 0.00 0.00 O
ATOM 2 P A A 1 1.779 0.230 -5.452 0.00 0.00 P
ATOM 3 OP1 A A 1 2.388 1.557 -5.217 0.00 0.00 O
ATOM 4 OP2 A A 1 0.572 0.372 -6.507 0.00 0.00 O
ATOM 5 O5' A A 1 1.211 -0.353 -4.063 0.00 0.00 O
ATOM 6 C5' A A 1 0.235 0.576 -3.592 0.00 0.00 C
ATOM 7 C4' A A 1 -0.346 0.080 -2.267 0.00 0.00 C
ATOM 8 O4' A A 1 0.691 -0.016 -1.267 0.00 0.00 O
ATOM 9 C3' A A 1 -1.350 1.106 -1.698 0.00 0.00 C
ATOM 10 O3' A A 1 -2.690 0.727 -2.016 0.00 0.00 O
ATOM 11 C2' A A 1 -1.119 1.051 -0.171 0.00 0.00 C
ATOM 13 C1' A A 1 0.000 -0.000 -0.000 0.00 0.00 C
ATOM 14 N9 A A 1 0.913 0.396 1.074 0.00 0.00 N
ATOM 15 C8 A A 1 2.020 1.180 0.943 0.00 0.00 C
ATOM 16 N7 A A 1 2.598 1.330 2.099 0.00 0.00 N
ATOM 17 C5 A A 1 1.898 0.659 3.044 0.00 0.00 C
ATOM 18 C6 A A 1 2.045 0.458 4.427 0.00 0.00 C
ATOM 19 N6 A A 1 3.099 1.031 5.117 0.00 0.00 N
ATOM 20 N1 A A 1 1.146 -0.289 5.058 0.00 0.00 N
ATOM 21 C2 A A 1 0.138 -0.839 4.407 0.00 0.00 C
ATOM 22 N3 A A 1 -0.037 -0.684 3.112 0.00 0.00 N
ATOM 23 C4 A A 1 0.811 0.047 2.397 0.00 0.00 C
TER 24 A A 1
END
22 changes: 22 additions & 0 deletions CryoREAD/atomic/DC.pdb
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ATOM 1 OP3 C A 1 2.890 -0.774 -6.042 0.00 0.00 O
ATOM 2 P C A 1 1.779 0.230 -5.452 0.00 0.00 P
ATOM 3 OP1 C A 1 2.388 1.558 -5.216 0.00 0.00 O
ATOM 4 OP2 C A 1 0.571 0.372 -6.507 0.00 0.00 O
ATOM 5 O5' C A 1 1.211 -0.353 -4.063 0.00 0.00 O
ATOM 6 C5' C A 1 0.235 0.576 -3.592 0.00 0.00 C
ATOM 7 C4' C A 1 -0.347 0.080 -2.268 0.00 0.00 C
ATOM 8 O4' C A 1 0.691 -0.017 -1.268 0.00 0.00 O
ATOM 9 C3' C A 1 -1.350 1.106 -1.698 0.00 0.00 C
ATOM 10 O3' C A 1 -2.690 0.726 -2.017 0.00 0.00 O
ATOM 11 C2' C A 1 -1.118 1.051 -0.170 0.00 0.00 C
ATOM 13 C1' C A 1 0.000 -0.000 -0.000 0.00 0.00 C
ATOM 14 N1 C A 1 0.913 0.396 1.074 0.00 0.00 N
ATOM 15 C2 C A 1 1.561 1.571 1.001 0.00 0.00 C
ATOM 16 O2 C A 1 1.381 2.297 0.037 0.00 0.00 O
ATOM 17 N3 C A 1 2.398 1.958 1.963 0.00 0.00 N
ATOM 18 C4 C A 1 2.613 1.188 3.022 0.00 0.00 C
ATOM 19 N4 C A 1 3.479 1.595 4.009 0.00 0.00 N
ATOM 20 C5 C A 1 1.952 -0.053 3.126 0.00 0.00 C
ATOM 21 C6 C A 1 1.100 -0.428 2.143 0.00 0.00 C
TER 22 C A 1
END
25 changes: 25 additions & 0 deletions CryoREAD/atomic/DG.pdb
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ATOM 1 OP3 G A 1 2.890 -0.774 -6.041 0.00 0.00 O
ATOM 2 P G A 1 1.779 0.230 -5.452 0.00 0.00 P
ATOM 3 OP1 G A 1 2.387 1.557 -5.218 0.00 0.00 O
ATOM 4 OP2 G A 1 0.571 0.373 -6.507 0.00 0.00 O
ATOM 5 O5' G A 1 1.211 -0.353 -4.063 0.00 0.00 O
ATOM 6 C5' G A 1 0.235 0.576 -3.592 0.00 0.00 C
ATOM 7 C4' G A 1 -0.346 0.080 -2.267 0.00 0.00 C
ATOM 8 O4' G A 1 0.691 -0.016 -1.267 0.00 0.00 O
ATOM 9 C3' G A 1 -1.349 1.106 -1.698 0.00 0.00 C
ATOM 10 O3' G A 1 -2.690 0.727 -2.017 0.00 0.00 O
ATOM 11 C2' G A 1 -1.118 1.051 -0.170 0.00 0.00 C
ATOM 13 C1' G A 1 0.000 -0.000 -0.000 0.00 0.00 C
ATOM 14 N9 G A 1 0.913 0.396 1.074 0.00 0.00 N
ATOM 15 C8 G A 1 2.021 1.181 0.942 0.00 0.00 C
ATOM 16 N7 G A 1 2.598 1.330 2.099 0.00 0.00 N
ATOM 17 C5 G A 1 1.896 0.651 3.040 0.00 0.00 C
ATOM 18 C6 G A 1 2.047 0.459 4.433 0.00 0.00 C
ATOM 19 O6 G A 1 2.978 0.966 5.036 0.00 0.00 O
ATOM 20 N1 G A 1 1.131 -0.295 5.079 0.00 0.00 N
ATOM 21 C2 G A 1 0.100 -0.862 4.393 0.00 0.00 C
ATOM 22 N2 G A 1 -0.811 -1.629 5.075 0.00 0.00 N
ATOM 23 N3 G A 1 -0.052 -0.691 3.100 0.00 0.00 N
ATOM 24 C4 G A 1 0.812 0.048 2.394 0.00 0.00 C
TER 25 G A 1
END
23 changes: 23 additions & 0 deletions CryoREAD/atomic/DT.pdb
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ATOM 1 OP3 U A 1 -3.912 -2.311 1.636 0.00 0.00 O
ATOM 2 P U A 1 -3.968 -1.665 3.118 0.00 0.00 P
ATOM 3 OP1 U A 1 -4.406 -2.599 4.208 0.00 0.00 O
ATOM 4 OP2 U A 1 -4.901 -0.360 2.920 0.00 0.00 O
ATOM 5 O5' U A 1 -2.493 -1.028 3.315 0.00 0.00 O
ATOM 6 C5' U A 1 -2.005 -0.136 2.327 0.00 0.00 C
ATOM 7 C4' U A 1 -0.611 0.328 2.728 0.00 0.00 C
ATOM 8 O4' U A 1 0.247 -0.829 2.764 0.00 0.00 O
ATOM 9 C3' U A 1 0.008 1.286 1.720 0.00 0.00 C
ATOM 10 O3' U A 1 0.965 2.121 2.368 0.00 0.00 O
ATOM 11 C2' U A 1 0.710 0.360 0.754 0.00 0.00 C
ATOM 13 C1' U A 1 1.157 -0.778 1.657 0.00 0.00 C
ATOM 14 N1 U A 1 1.164 -2.047 0.989 0.00 0.00 N
ATOM 15 C2 U A 1 2.333 -2.544 0.374 0.00 0.00 C
ATOM 16 O2 U A 1 3.410 -1.945 0.363 0.00 0.00 O
ATOM 17 N3 U A 1 2.194 -3.793 -0.240 0.00 0.00 N
ATOM 18 C4 U A 1 1.047 -4.570 -0.300 0.00 0.00 C
ATOM 19 O4 U A 1 0.995 -5.663 -0.857 0.00 0.00 O
ATOM 20 C5 U A 1 -0.143 -3.980 0.369 0.00 0.00 C
ATOM 21 C7 U A 1 -1.420 -4.757 0.347 0.00 0.00 C
ATOM 22 C6 U A 1 -0.013 -2.784 0.958 0.00 0.00 C
TER 23 U A 1
END
26 changes: 26 additions & 0 deletions CryoREAD/atomic/G.pdb
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ATOM 1 OP3 G A 1 2.890 -0.774 -6.041 0.00 0.00 O
ATOM 2 P G A 1 1.779 0.230 -5.452 0.00 0.00 P
ATOM 3 OP1 G A 1 2.387 1.557 -5.218 0.00 0.00 O
ATOM 4 OP2 G A 1 0.571 0.373 -6.507 0.00 0.00 O
ATOM 5 O5' G A 1 1.211 -0.353 -4.063 0.00 0.00 O
ATOM 6 C5' G A 1 0.235 0.576 -3.592 0.00 0.00 C
ATOM 7 C4' G A 1 -0.346 0.080 -2.267 0.00 0.00 C
ATOM 8 O4' G A 1 0.691 -0.016 -1.267 0.00 0.00 O
ATOM 9 C3' G A 1 -1.349 1.106 -1.698 0.00 0.00 C
ATOM 10 O3' G A 1 -2.690 0.727 -2.017 0.00 0.00 O
ATOM 11 C2' G A 1 -1.118 1.051 -0.170 0.00 0.00 C
ATOM 12 O2' G A 1 -2.310 0.638 0.502 0.00 0.00 O
ATOM 13 C1' G A 1 0.000 -0.000 -0.000 0.00 0.00 C
ATOM 14 N9 G A 1 0.913 0.396 1.074 0.00 0.00 N
ATOM 15 C8 G A 1 2.021 1.181 0.942 0.00 0.00 C
ATOM 16 N7 G A 1 2.598 1.330 2.099 0.00 0.00 N
ATOM 17 C5 G A 1 1.896 0.651 3.040 0.00 0.00 C
ATOM 18 C6 G A 1 2.047 0.459 4.433 0.00 0.00 C
ATOM 19 O6 G A 1 2.978 0.966 5.036 0.00 0.00 O
ATOM 20 N1 G A 1 1.131 -0.295 5.079 0.00 0.00 N
ATOM 21 C2 G A 1 0.100 -0.862 4.393 0.00 0.00 C
ATOM 22 N2 G A 1 -0.811 -1.629 5.075 0.00 0.00 N
ATOM 23 N3 G A 1 -0.052 -0.691 3.100 0.00 0.00 N
ATOM 24 C4 G A 1 0.812 0.048 2.394 0.00 0.00 C
TER 25 G A 1
END
23 changes: 23 additions & 0 deletions CryoREAD/atomic/U.pdb
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ATOM 1 OP3 U A 1 2.891 -0.774 -6.042 0.00 0.00 O
ATOM 2 P U A 1 1.779 0.230 -5.452 0.00 0.00 P
ATOM 3 OP1 U A 1 2.389 1.557 -5.217 0.00 0.00 O
ATOM 4 OP2 U A 1 0.573 0.372 -6.508 0.00 0.00 O
ATOM 5 O5' U A 1 1.211 -0.353 -4.063 0.00 0.00 O
ATOM 6 C5' U A 1 0.235 0.577 -3.593 0.00 0.00 C
ATOM 7 C4' U A 1 -0.348 0.080 -2.270 0.00 0.00 C
ATOM 8 O4' U A 1 0.690 -0.016 -1.267 0.00 0.00 O
ATOM 9 C3' U A 1 -1.352 1.104 -1.697 0.00 0.00 C
ATOM 10 O3' U A 1 -2.692 0.721 -2.011 0.00 0.00 O
ATOM 11 C2' U A 1 -1.118 1.052 -0.172 0.00 0.00 C
ATOM 12 O2' U A 1 -2.308 0.639 0.504 0.00 0.00 O
ATOM 13 C1' U A 1 -0.001 -0.001 0.001 0.00 0.00 C
ATOM 14 N1 U A 1 0.913 0.397 1.076 0.00 0.00 N
ATOM 15 C2 U A 1 1.587 1.555 0.981 0.00 0.00 C
ATOM 16 O2 U A 1 1.429 2.264 0.007 0.00 0.00 O
ATOM 17 N3 U A 1 2.429 1.947 1.957 0.00 0.00 N
ATOM 18 C4 U A 1 2.616 1.171 3.045 0.00 0.00 C
ATOM 19 O4 U A 1 3.381 1.523 3.925 0.00 0.00 O
ATOM 20 C5 U A 1 1.915 -0.053 3.153 0.00 0.00 C
ATOM 21 C6 U A 1 1.073 -0.418 2.163 0.00 0.00 C
TER 22 U A 1
END
Empty file added CryoREAD/atomic/__init__.py
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