show how to rotation molecules (jupyter notebook + nglview + mdtraj + rotation matrix)

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

test.ipynb