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0ut0fcontrol/BENZ_BENZ_rep.pdb

Last active February 22, 2020 13:28
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show how to rotation molecules (jupyter notebook + nglview + mdtraj + rotation matrix)
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BENZ_BENZ_rep.pdb
MODEL 1
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 65 2 2 12
ATOM 1 C01 FRG A 43 5.084 3.510 1.252 1.00 0.00 C
ATOM 2 1H01 FRG A 43 5.193 2.605 1.831 1.00 0.00 H
ATOM 3 C02 FRG A 43 6.084 3.888 0.377 1.00 0.00 C
ATOM 4 1H02 FRG A 43 6.980 3.294 0.273 1.00 0.00 H
ATOM 5 C03 FRG A 43 5.903 5.006 -0.405 1.00 0.00 C
ATOM 6 1H03 FRG A 43 6.684 5.293 -1.095 1.00 0.00 H
ATOM 7 C04 FRG A 43 4.799 5.797 -0.291 1.00 0.00 C
ATOM 8 1H04 FRG A 43 4.688 6.684 -0.898 1.00 0.00 H
ATOM 9 C05 FRG A 43 3.806 5.427 0.587 1.00 0.00 C
ATOM 10 1H05 FRG A 43 2.917 6.034 0.673 1.00 0.00 H
ATOM 11 C06 FRG A 43 3.948 4.286 1.388 1.00 0.00 C
ATOM 12 1H06 FRG A 43 3.160 4.010 2.074 1.00 0.00 H
ATOM 13 C01 FRG Z 46 2.398 -0.000 -0.000 1.00 0.00 C
ATOM 14 1H01 FRG Z 46 3.339 -0.529 0.042 1.00 0.00 H
ATOM 15 C02 FRG Z 46 1.212 -0.677 -0.005 1.00 0.00 C
ATOM 16 1H02 FRG Z 46 1.190 -1.756 0.004 1.00 0.00 H
ATOM 17 C03 FRG Z 46 0.000 0.000 0.000 1.00 0.00 C
ATOM 18 1H03 FRG Z 46 -0.921 -0.563 0.028 1.00 0.00 H
ATOM 19 C04 FRG Z 46 -0.045 1.371 -0.016 1.00 0.00 C
ATOM 20 1H04 FRG Z 46 -0.999 1.876 -0.002 1.00 0.00 H
ATOM 21 C05 FRG Z 46 1.137 2.079 -0.000 1.00 0.00 C
ATOM 22 1H05 FRG Z 46 1.129 3.161 -0.000 1.00 0.00 H
ATOM 23 C06 FRG Z 46 2.345 1.385 0.002 1.00 0.00 C
ATOM 24 1H06 FRG Z 46 3.262 1.954 -0.017 1.00 0.00 H
ENDMDL
MODEL 20
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 65 2 2 12
ATOM 1 C01 FRG A 22 0.716 -2.784 -3.677 1.00 0.00 C
ATOM 2 1H01 FRG A 22 -0.258 -2.482 -3.323 1.00 0.00 H
ATOM 3 C02 FRG A 22 1.761 -3.074 -2.809 1.00 0.00 C
ATOM 4 1H02 FRG A 22 1.606 -2.997 -1.744 1.00 0.00 H
ATOM 5 C03 FRG A 22 3.003 -3.480 -3.263 1.00 0.00 C
ATOM 6 1H03 FRG A 22 3.791 -3.706 -2.557 1.00 0.00 H
ATOM 7 C04 FRG A 22 3.225 -3.623 -4.633 1.00 0.00 C
ATOM 8 1H04 FRG A 22 4.184 -3.956 -5.001 1.00 0.00 H
ATOM 9 C05 FRG A 22 2.184 -3.333 -5.515 1.00 0.00 C
ATOM 10 1H05 FRG A 22 2.338 -3.435 -6.579 1.00 0.00 H
ATOM 11 C06 FRG A 22 0.952 -2.924 -5.040 1.00 0.00 C
ATOM 12 1H06 FRG A 22 0.166 -2.705 -5.748 1.00 0.00 H
ATOM 13 C01 FRG Z 33 2.395 -0.000 0.000 1.00 0.00 C
ATOM 14 1H01 FRG Z 33 3.335 -0.531 -0.033 1.00 0.00 H
ATOM 15 C02 FRG Z 33 1.199 -0.688 0.006 1.00 0.00 C
ATOM 16 1H02 FRG Z 33 1.189 -1.767 0.023 1.00 0.00 H
ATOM 17 C03 FRG Z 33 0.000 0.000 0.000 1.00 0.00 C
ATOM 18 1H03 FRG Z 33 -0.927 -0.555 -0.006 1.00 0.00 H
ATOM 19 C04 FRG Z 33 -0.037 1.365 -0.029 1.00 0.00 C
ATOM 20 1H04 FRG Z 33 -0.977 1.894 -0.054 1.00 0.00 H
ATOM 21 C05 FRG Z 33 1.151 2.048 0.000 1.00 0.00 C
ATOM 22 1H05 FRG Z 33 1.141 3.127 0.007 1.00 0.00 H
ATOM 23 C06 FRG Z 33 2.358 1.389 0.017 1.00 0.00 C
ATOM 24 1H06 FRG Z 33 3.272 1.966 0.028 1.00 0.00 H
ENDMDL
MODEL 22
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 65 2 2 12
ATOM 1 C01 FRG A 164 -0.672 -3.623 -2.355 1.00 0.00 C
ATOM 2 1H01 FRG A 164 -0.307 -3.221 -3.288 1.00 0.00 H
ATOM 3 C02 FRG A 164 -0.047 -4.685 -1.720 1.00 0.00 C
ATOM 4 1H02 FRG A 164 0.827 -5.145 -2.156 1.00 0.00 H
ATOM 5 C03 FRG A 164 -0.562 -5.188 -0.510 1.00 0.00 C
ATOM 6 1H03 FRG A 164 -0.110 -6.035 -0.016 1.00 0.00 H
ATOM 7 C04 FRG A 164 -1.672 -4.541 0.050 1.00 0.00 C
ATOM 8 1H04 FRG A 164 -2.061 -4.898 0.991 1.00 0.00 H
ATOM 9 C05 FRG A 164 -2.296 -3.512 -0.582 1.00 0.00 C
ATOM 10 1H05 FRG A 164 -3.169 -3.055 -0.142 1.00 0.00 H
ATOM 11 C06 FRG A 164 -1.811 -3.050 -1.804 1.00 0.00 C
ATOM 12 1H06 FRG A 164 -2.312 -2.233 -2.300 1.00 0.00 H
ATOM 13 C01 FRG Z 154 2.407 0.000 0.000 1.00 0.00 C
ATOM 14 1H01 FRG Z 154 3.348 -0.530 -0.020 1.00 0.00 H
ATOM 15 C02 FRG Z 154 1.188 -0.678 -0.009 1.00 0.00 C
ATOM 16 1H02 FRG Z 154 1.158 -1.757 -0.028 1.00 0.00 H
ATOM 17 C03 FRG Z 154 0.000 0.000 0.000 1.00 0.00 C
ATOM 18 1H03 FRG Z 154 -0.925 -0.558 -0.003 1.00 0.00 H
ATOM 19 C04 FRG Z 154 -0.053 1.366 -0.042 1.00 0.00 C
ATOM 20 1H04 FRG Z 154 -0.993 1.898 -0.054 1.00 0.00 H
ATOM 21 C05 FRG Z 154 1.154 2.039 0.000 1.00 0.00 C
ATOM 22 1H05 FRG Z 154 1.152 3.119 0.016 1.00 0.00 H
ATOM 23 C06 FRG Z 154 2.371 1.371 0.010 1.00 0.00 C
ATOM 24 1H06 FRG Z 154 3.285 1.947 0.013 1.00 0.00 H
ENDMDL
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