``````

In [2]:

%autosave 0
from __future__ import print_function

``````
``````

IPython.notebook.set_autosave_interval(0)

Autosave disabled

``````

# RMSD/eRMSD calculation

We here show how to calculate distances between three-dimensional structures. eRMSD can be calculated using the function

```ermsd = bb.ermsd(reference_file,target_file)
```

`reference_file` and `target_file` can be e.g. PDB files. eRMSD between reference and all frames in a simulation can be calculated by specifying the trajectory and topology files:

```ermsd = bb.ermsd(reference_file,target_traj_file,topology=topology_file)
```

All trajectory formats accepted by MDTRAJ (e.g. pdb, xtc, trr, dcd, binpos, netcdf, mdcrd, prmtop) can be used. Let us see a practical example:

``````

In [3]:

# import barnaba
import barnaba as bb

# define trajectory and topology files
native="uucg2.pdb"
traj = "../test/data/UUCG.xtc"
top = "../test/data/UUCG.pdb"

# calculate eRMSD between native and all frames in trajectory
ermsd = bb.ermsd(native,traj,topology=top)

``````
``````

``````

We plot the eRMSD over time (every 50 frames to make the plot nicer) and make an histogram

``````

In [15]:

import matplotlib.pyplot as plt
plt.xlabel("Frame")
plt.ylabel("eRMSD from native")
plt.plot(ermsd[::50])
plt.show()

plt.hist(ermsd,density=True,bins=50)
plt.xlabel("eRMSD from native")
plt.show()

``````
``````

``````

As a rule of thumb, eRMSD below 0.7-0.8 can be considered low, as such the peak around 0.4 eRMSD corresponds to structures that are very similar to the native.

Nota Bene

• eRMSD is a dimensionless number.
• Remember to remove periodic boundary conditions before performing the analysis.

We can also calculate the root mean squared deviation (RMSD) after optimal superposition by using

```rmsd = bb.rmsd(reference_file,target_file)
```

or

```rmsd = bb.rmsd(reference_file,target_traj_file,topology=topology_file)
```

for trajectories. By default RMSD is calculated using backbone atoms only (`heavy_atom=False`): this makes it possible to calculate RMSD between structures with different sequences. If `heavy_atom=True`, RMSD is calculated using all heavy atoms. Values are expressed in nanometers.

``````

In [5]:

# calculate RMSD
rmsd = bb.rmsd(native,traj,topology=top,heavy_atom=False)

# plot time series
plt.xlabel("Frame")
plt.ylabel("RMSD from native (nm)")
plt.plot(rmsd[::50])
plt.show()

# make histogram
plt.hist(rmsd,density=True,bins=50)
plt.ylabel("RMSD from native (nm)")
plt.show()

``````
``````

# found  93 atoms in common

``````

Structures with eRMSD lower than 0.7 are typically significantly similar to the reference. Note that structures with low RMSD (less than 0.4 nm) may be very different from native. We can check if this is true by comparing RMSD and eRMSD

``````

In [6]:

plt.xlabel("eRMSD from native")
plt.ylabel("RMSD from native (nm)")
plt.axhline(0.4,ls = "--", c= 'k')
plt.axvline(0.7,ls = "--", c= 'k')
plt.scatter(ermsd,rmsd,s=2.5)
plt.show()

``````
``````

``````

We can clearly see that the two measures are correlated, but several structures with low RMSD have very large eRMSD. We cherry-pick a structure with RMSD from native \$\approx\$ 0.3 nm, but high eRMSD.

``````

In [7]:

import numpy as np
low_rmsd = np.where(rmsd<0.3)
idx_a = np.argsort(ermsd[low_rmsd])[-1]
low_e = low_rmsd[0][idx_a]
print("Highest eRMSD for structures with  RMSD ~ 0.3nm")
print("eRMSD:%5.3f; RMSD: %5.3f nm" % (ermsd[low_e],rmsd[low_e]))

plt.xlabel("eRMSD from native")
plt.ylabel("RMSD from native (nm)")
plt.axhline(0.4,ls = "--", c= 'k')
plt.axvline(0.7,ls = "--", c= 'k')

plt.scatter(ermsd,rmsd,s=2.5)
plt.scatter(ermsd[low_e],rmsd[low_e],s=50,c='r')
plt.show()

``````
``````

Highest eRMSD for structures with  RMSD ~ 0.3nm
eRMSD:2.149; RMSD: 0.257 nm

``````

We can extract a frame from the simulation using the save function from MDTraj. Aligned structures are written to disk by passing a string `out` to the `rmsd` function.

``````

In [8]:

import mdtraj as md

# save low ermsd
tt[low_e].save("low_rmsd.pdb")

# align to native and write aligned PDB to disk
rmsd1 = bb.rmsd(native,'low_rmsd.pdb',out='low_rmsd_align.pdb')

``````
``````

# found  93 atoms in common

``````

Finally, we use py3Dmol module to visualize the native and the low-RMSD/high-eRMSD structure.

``````

In [14]:

import py3Dmol

p = py3Dmol.view(width=900,height=600,viewergrid=(1,2))

p.setStyle({'stick':{}})
p.setBackgroundColor('0xeeeeee')
p.zoomTo()

``````
``````

Out[14]:

if(typeof \$3Dmolpromise === 'undefined') \$3Dmolpromise = \$.when(\$.getScript('https://3dmol.csb.pitt.edu/build/3Dmol.js'))
var viewer_153752110091 = null;
\$3Dmolpromise.done(function() {
var viewergrid_153752110091 = null;
viewergrid_153752110091 = \$3Dmol.createViewerGrid(\$("#3dmolviewer_153752110091"),{rows: 1, cols: 2, control_all: true},{backgroundColor:"white"});
viewer_153752110091 = viewergrid_153752110091[0][0];
viewergrid_153752110091[0][0].addModel("MODEL        0\nATOM      1  P     C A1448       3.240  11.055   1.258  1.00  0.00          P   \nATOM      2  OP1   C A1448       3.203  11.712   2.589  1.00  0.00          O   \nATOM      3  OP2   C A1448       3.911   9.741   1.110  1.00  0.00          O   \nATOM      4  O5'   C A1448       1.745  10.919   0.725  1.00  0.00          O   \nATOM      5  C5'   C A1448       0.794  11.990   0.884  1.00  0.00          C   \nATOM      6  C4'   C A1448      -0.612  11.510   0.596  1.00  0.00          C   \nATOM      7  O4'   C A1448      -0.800  11.384  -0.840  1.00  0.00          O   \nATOM      8  C3'   C A1448      -0.996  10.152   1.167  1.00  0.00          C   \nATOM      9  O3'   C A1448      -1.468  10.295   2.506  1.00  0.00          O   \nATOM     10  C2'   C A1448      -2.088   9.707   0.205  1.00  0.00          C   \nATOM     11  O2'   C A1448      -3.348  10.292   0.469  1.00  0.00          O   \nATOM     12  C1'   C A1448      -1.530  10.203  -1.130  1.00  0.00          C   \nATOM     13  N1    C A1448      -0.619   9.259  -1.813  1.00  0.00          N   \nATOM     14  C2    C A1448      -1.136   8.075  -2.355  1.00  0.00          C   \nATOM     15  O2    C A1448      -2.345   7.830  -2.227  1.00  0.00          O   \nATOM     16  N3    C A1448      -0.299   7.218  -2.986  1.00  0.00          N   \nATOM     17  C4    C A1448       0.997   7.518  -3.107  1.00  0.00          C   \nATOM     18  N4    C A1448       1.786   6.647  -3.738  1.00  0.00          N   \nATOM     19  C5    C A1448       1.546   8.718  -2.571  1.00  0.00          C   \nATOM     20  C6    C A1448       0.710   9.554  -1.943  1.00  0.00          C   \nATOM     21  P     C A1449      -1.042   9.242   3.643  1.00  0.00          P   \nATOM     22  OP1   C A1449      -1.586   9.726   4.938  1.00  0.00          O   \nATOM     23  OP2   C A1449       0.416   8.972   3.511  1.00  0.00          O   \nATOM     24  O5'   C A1449      -1.857   7.933   3.245  1.00  0.00          O   \nATOM     25  C5'   C A1449      -3.295   7.929   3.280  1.00  0.00          C   \nATOM     26  C4'   C A1449      -3.845   6.681   2.628  1.00  0.00          C   \nATOM     27  O4'   C A1449      -3.464   6.641   1.226  1.00  0.00          O   \nATOM     28  C3'   C A1449      -3.348   5.355   3.181  1.00  0.00          C   \nATOM     29  O3'   C A1449      -4.022   4.981   4.381  1.00  0.00          O   \nATOM     30  C2'   C A1449      -3.637   4.412   2.020  1.00  0.00          C   \nATOM     31  O2'   C A1449      -4.983   3.987   1.935  1.00  0.00          O   \nATOM     32  C1'   C A1449      -3.290   5.292   0.818  1.00  0.00          C   \nATOM     33  N1    C A1449      -1.910   5.111   0.327  1.00  0.00          N   \nATOM     34  C2    C A1449      -1.588   3.927  -0.345  1.00  0.00          C   \nATOM     35  O2    C A1449      -2.466   3.065  -0.501  1.00  0.00          O   \nATOM     36  N3    C A1449      -0.326   3.749  -0.801  1.00  0.00          N   \nATOM     37  C4    C A1449       0.592   4.699  -0.616  1.00  0.00          C   \nATOM     38  N4    C A1449       1.822   4.479  -1.085  1.00  0.00          N   \nATOM     39  C5    C A1449       0.291   5.914   0.064  1.00  0.00          C   \nATOM     40  C6    C A1449      -0.960   6.077   0.516  1.00  0.00          C   \nATOM     41  P     U A1450      -3.241   4.169   5.527  1.00  0.00          P   \nATOM     42  OP1   U A1450      -4.229   3.777   6.565  1.00  0.00          O   \nATOM     43  OP2   U A1450      -2.041   4.955   5.916  1.00  0.00          O   \nATOM     44  O5'   U A1450      -2.750   2.855   4.769  1.00  0.00          O   \nATOM     45  C5'   U A1450      -3.673   1.799   4.441  1.00  0.00          C   \nATOM     46  C4'   U A1450      -2.982   0.700   3.668  1.00  0.00          C   \nATOM     47  O4'   U A1450      -2.338   1.242   2.487  1.00  0.00          O   \nATOM     48  C3'   U A1450      -1.859  -0.026   4.389  1.00  0.00          C   \nATOM     49  O3'   U A1450      -2.380  -0.982   5.312  1.00  0.00          O   \nATOM     50  C2'   U A1450      -1.089  -0.645   3.226  1.00  0.00          C   \nATOM     51  O2'   U A1450      -1.618  -1.866   2.749  1.00  0.00          O   \nATOM     52  C1'   U A1450      -1.211   0.446   2.156  1.00  0.00          C   \nATOM     53  N1    U A1450      -0.020   1.305   2.064  1.00  0.00          N   \nATOM     54  C2    U A1450       1.077   0.800   1.387  1.00  0.00          C   \nATOM     55  O2    U A1450       1.084  -0.303   0.865  1.00  0.00          O   \nATOM     56  N3    U A1450       2.164   1.636   1.344  1.00  0.00          N   \nATOM     57  C4    U A1450       2.272   2.895   1.895  1.00  0.00          C   \nATOM     58  O4    U A1450       3.324   3.525   1.769  1.00  0.00          O   \nATOM     59  C5    U A1450       1.100   3.345   2.583  1.00  0.00          C   \nATOM     60  C6    U A1450       0.022   2.554   2.645  1.00  0.00          C   \nATOM     61  P     U A1451      -1.524  -1.450   6.594  1.00  0.00          P   \nATOM     62  OP1   U A1451      -2.478  -1.730   7.698  1.00  0.00          O   \nATOM     63  OP2   U A1451      -0.423  -0.476   6.812  1.00  0.00          O   \nATOM     64  O5'   U A1451      -0.872  -2.819   6.102  1.00  0.00          O   \nATOM     65  C5'   U A1451      -0.400  -3.820   7.027  1.00  0.00          C   \nATOM     66  C4'   U A1451      -0.651  -5.205   6.474  1.00  0.00          C   \nATOM     67  O4'   U A1451      -2.082  -5.459   6.452  1.00  0.00          O   \nATOM     68  C3'   U A1451      -0.150  -5.459   5.055  1.00  0.00          C   \nATOM     69  O3'   U A1451       0.386  -6.771   4.919  1.00  0.00          O   \nATOM     70  C2'   U A1451      -1.400  -5.261   4.203  1.00  0.00          C   \nATOM     71  O2'   U A1451      -1.392  -5.979   2.985  1.00  0.00          O   \nATOM     72  C1'   U A1451      -2.494  -5.775   5.136  1.00  0.00          C   \nATOM     73  N1    U A1451      -3.803  -5.151   4.887  1.00  0.00          N   \nATOM     74  C2    U A1451      -4.518  -5.583   3.784  1.00  0.00          C   \nATOM     75  O2    U A1451      -4.115  -6.453   3.031  1.00  0.00          O   \nATOM     76  N3    U A1451      -5.727  -4.959   3.599  1.00  0.00          N   \nATOM     77  C4    U A1451      -6.284  -3.967   4.380  1.00  0.00          C   \nATOM     78  O4    U A1451      -7.387  -3.505   4.080  1.00  0.00          O   \nATOM     79  C5    U A1451      -5.483  -3.570   5.498  1.00  0.00          C   \nATOM     80  C6    U A1451      -4.298  -4.157   5.707  1.00  0.00          C   \nATOM     81  P     C A1452       1.968  -6.996   4.950  1.00  0.00          P   \nATOM     82  OP1   C A1452       2.221  -8.458   4.995  1.00  0.00          O   \nATOM     83  OP2   C A1452       2.538  -6.119   6.005  1.00  0.00          O   \nATOM     84  O5'   C A1452       2.438  -6.448   3.530  1.00  0.00          O   \nATOM     85  C5'   C A1452       3.606  -6.991   2.887  1.00  0.00          C   \nATOM     86  C4'   C A1452       4.254  -5.971   1.976  1.00  0.00          C   \nATOM     87  O4'   C A1452       3.568  -4.690   2.073  1.00  0.00          O   \nATOM     88  C3'   C A1452       5.732  -5.681   2.235  1.00  0.00          C   \nATOM     89  O3'   C A1452       6.454  -5.537   1.014  1.00  0.00          O   \nATOM     90  C2'   C A1452       5.686  -4.369   3.013  1.00  0.00          C   \nATOM     91  O2'   C A1452       6.868  -3.596   2.933  1.00  0.00          O   \nATOM     92  C1'   C A1452       4.511  -3.670   2.335  1.00  0.00          C   \nATOM     93  N1    C A1452       3.862  -2.616   3.141  1.00  0.00          N   \nATOM     94  C2    C A1452       4.114  -1.272   2.833  1.00  0.00          C   \nATOM     95  O2    C A1452       4.881  -1.003   1.896  1.00  0.00          O   \nATOM     96  N3    C A1452       3.517  -0.303   3.566  1.00  0.00          N   \nATOM     97  C4    C A1452       2.697  -0.632   4.568  1.00  0.00          C   \nATOM     98  N4    C A1452       2.130   0.356   5.264  1.00  0.00          N   \nATOM     99  C5    C A1452       2.423  -1.992   4.901  1.00  0.00          C   \nATOM    100  C6    C A1452       3.020  -2.942   4.169  1.00  0.00          C   \nATOM    101  P     G A1453       7.047  -6.827   0.263  1.00  0.00          P   \nATOM    102  OP1   G A1453       6.177  -7.991   0.574  1.00  0.00          O   \nATOM    103  OP2   G A1453       8.501  -6.899   0.558  1.00  0.00          O   \nATOM    104  O5'   G A1453       6.871  -6.470  -1.281  1.00  0.00          O   \nATOM    105  C5'   G A1453       5.662  -5.872  -1.798  1.00  0.00          C   \nATOM    106  C4'   G A1453       4.735  -6.931  -2.348  1.00  0.00          C   \nATOM    107  O4'   G A1453       3.769  -7.302  -1.334  1.00  0.00          O   \nATOM    108  C3'   G A1453       3.899  -6.506  -3.545  1.00  0.00          C   \nATOM    109  O3'   G A1453       4.654  -6.699  -4.739  1.00  0.00          O   \nATOM    110  C2'   G A1453       2.681  -7.427  -3.459  1.00  0.00          C   \nATOM    111  O2'   G A1453       2.821  -8.658  -4.140  1.00  0.00          O   \nATOM    112  C1'   G A1453       2.540  -7.644  -1.948  1.00  0.00          C   \nATOM    113  N9    G A1453       1.467  -6.879  -1.315  1.00  0.00          N   \nATOM    114  C8    G A1453       0.222  -7.351  -0.976  1.00  0.00          C   \nATOM    115  N7    G A1453      -0.533  -6.447  -0.414  1.00  0.00          N   \nATOM    116  C5    G A1453       0.261  -5.309  -0.376  1.00  0.00          C   \nATOM    117  C6    G A1453      -0.018  -4.007   0.121  1.00  0.00          C   \nATOM    118  O6    G A1453      -1.057  -3.588   0.645  1.00  0.00          O   \nATOM    119  N1    G A1453       1.069  -3.154  -0.041  1.00  0.00          N   \nATOM    120  C2    G A1453       2.271  -3.504  -0.609  1.00  0.00          C   \nATOM    121  N2    G A1453       3.201  -2.539  -0.674  1.00  0.00          N   \nATOM    122  N3    G A1453       2.543  -4.713  -1.076  1.00  0.00          N   \nATOM    123  C4    G A1453       1.501  -5.560  -0.928  1.00  0.00          C   \nATOM    124  P     G A1454       4.480  -5.700  -5.978  1.00  0.00          P   \nATOM    125  OP1   G A1454       5.270  -6.244  -7.113  1.00  0.00          O   \nATOM    126  OP2   G A1454       4.759  -4.323  -5.496  1.00  0.00          O   \nATOM    127  O5'   G A1454       2.937  -5.867  -6.347  1.00  0.00          O   \nATOM    128  C5'   G A1454       2.105  -4.756  -6.743  1.00  0.00          C   \nATOM    129  C4'   G A1454       0.851  -4.732  -5.902  1.00  0.00          C   \nATOM    130  O4'   G A1454       1.214  -4.525  -4.508  1.00  0.00          O   \nATOM    131  C3'   G A1454      -0.138  -3.619  -6.213  1.00  0.00          C   \nATOM    132  O3'   G A1454      -1.010  -3.951  -7.291  1.00  0.00          O   \nATOM    133  C2'   G A1454      -0.859  -3.464  -4.881  1.00  0.00          C   \nATOM    134  O2'   G A1454      -1.840  -4.452  -4.636  1.00  0.00          O   \nATOM    135  C1'   G A1454       0.306  -3.619  -3.904  1.00  0.00          C   \nATOM    136  N9    G A1454       1.011  -2.365  -3.669  1.00  0.00          N   \nATOM    137  C8    G A1454       2.303  -2.060  -4.028  1.00  0.00          C   \nATOM    138  N7    G A1454       2.654  -0.847  -3.697  1.00  0.00          N   \nATOM    139  C5    G A1454       1.526  -0.317  -3.087  1.00  0.00          C   \nATOM    140  C6    G A1454       1.304   0.964  -2.521  1.00  0.00          C   \nATOM    141  O6    G A1454       2.087   1.919  -2.443  1.00  0.00          O   \nATOM    142  N1    G A1454       0.016   1.080  -2.007  1.00  0.00          N   \nATOM    143  C2    G A1454      -0.938   0.093  -2.034  1.00  0.00          C   \nATOM    144  N2    G A1454      -2.124   0.401  -1.488  1.00  0.00          N   \nATOM    145  N3    G A1454      -0.743  -1.108  -2.557  1.00  0.00          N   \nATOM    146  C4    G A1454       0.502  -1.242  -3.062  1.00  0.00          C   \nATOM    147  P     G A1455      -1.462  -2.825  -8.345  1.00  0.00          P   \nATOM    148  OP1   G A1455      -2.239  -3.494  -9.421  1.00  0.00          O   \nATOM    149  OP2   G A1455      -0.267  -2.014  -8.703  1.00  0.00          O   \nATOM    150  O5'   G A1455      -2.471  -1.925  -7.501  1.00  0.00          O   \nATOM    151  C5'   G A1455      -3.691  -2.480  -6.970  1.00  0.00          C   \nATOM    152  C4'   G A1455      -4.476  -1.439  -6.202  1.00  0.00          C   \nATOM    153  O4'   G A1455      -3.757  -1.047  -4.999  1.00  0.00          O   \nATOM    154  C3'   G A1455      -4.734  -0.125  -6.919  1.00  0.00          C   \nATOM    155  O3'   G A1455      -5.789  -0.232  -7.870  1.00  0.00          O   \nATOM    156  C2'   G A1455      -5.018   0.808  -5.749  1.00  0.00          C   \nATOM    157  O2'   G A1455      -6.319   0.705  -5.203  1.00  0.00          O   \nATOM    158  C1'   G A1455      -3.972   0.334  -4.741  1.00  0.00          C   \nATOM    159  N9    G A1455      -2.695   1.032  -4.876  1.00  0.00          N   \nATOM    160  C8    G A1455      -1.541   0.545  -5.442  1.00  0.00          C   \nATOM    161  N7    G A1455      -0.556   1.400  -5.413  1.00  0.00          N   \nATOM    162  C5    G A1455      -1.093   2.522  -4.797  1.00  0.00          C   \nATOM    163  C6    G A1455      -0.500   3.774  -4.496  1.00  0.00          C   \nATOM    164  O6    G A1455       0.657   4.150  -4.715  1.00  0.00          O   \nATOM    165  N1    G A1455      -1.402   4.631  -3.873  1.00  0.00          N   \nATOM    166  C2    G A1455      -2.710   4.327  -3.587  1.00  0.00          C   \nATOM    167  N2    G A1455      -3.421   5.289  -2.979  1.00  0.00          N   \nATOM    168  N3    G A1455      -3.275   3.160  -3.859  1.00  0.00          N   \nATOM    169  C4    G A1455      -2.414   2.311  -4.461  1.00  0.00          C   \nTER     170        G A1455\nENDMDL\nEND\n","pdb");
viewergrid_153752110091[0][1].addModel("REMARK   1 CREATED WITH MDTraj 1.9.1, 2018-09-21\nCRYST1   55.478   55.478   55.478  60.00  60.00  90.00 P 1           1 \nMODEL        0\nATOM      1  O5'   C A   1      -0.130  11.056   5.158  1.00  0.00          O   \nATOM      2  H5T   C A   1       0.796  10.833   5.150  1.00  0.00          H   \nATOM      3  C5'   C A   1      -0.520  11.850   4.031  1.00  0.00          C   \nATOM      4 1H5'   C A   1       0.042  12.765   3.855  1.00  0.00          H   \nATOM      5 2H5'   C A   1      -1.527  12.213   4.272  1.00  0.00          H   \nATOM      6  C4'   C A   1      -0.397  10.940   2.800  1.00  0.00          C   \nATOM      7  H4'   C A   1      -0.558  11.556   1.919  1.00  0.00          H   \nATOM      8  O4'   C A   1       0.901  10.283   2.739  1.00  0.00          O   \nATOM      9  C1'   C A   1       0.755   9.304   1.770  1.00  0.00          C   \nATOM     10  H1'   C A   1       0.946   9.729   0.787  1.00  0.00          H   \nATOM     11  N1    C A   1       1.674   8.173   2.107  1.00  0.00          N   \nATOM     12  C6    C A   1       1.604   7.455   3.262  1.00  0.00          C   \nATOM     13  H6    C A   1       0.874   7.741   4.013  1.00  0.00          H   \nATOM     14  C5    C A   1       2.472   6.400   3.473  1.00  0.00          C   \nATOM     15  H5    C A   1       2.443   5.865   4.412  1.00  0.00          H   \nATOM     16  C4    C A   1       3.349   6.082   2.441  1.00  0.00          C   \nATOM     17  N4    C A   1       4.214   5.155   2.635  1.00  0.00          N   \nATOM     18  H41   C A   1       4.144   4.567   3.453  1.00  0.00          H   \nATOM     19  H42   C A   1       4.757   4.906   1.820  1.00  0.00          H   \nATOM     20  N3    C A   1       3.460   6.784   1.361  1.00  0.00          N   \nATOM     21  C2    C A   1       2.622   7.800   1.167  1.00  0.00          C   \nATOM     22  O2    C A   1       2.825   8.552   0.180  1.00  0.00          O   \nATOM     23  C3'   C A   1      -1.378   9.788   2.805  1.00  0.00          C   \nATOM     24  H3'   C A   1      -1.419   9.416   3.831  1.00  0.00          H   \nATOM     25  C2'   C A   1      -0.669   8.804   1.914  1.00  0.00          C   \nATOM     26 1H2'   C A   1      -0.630   7.809   2.341  1.00  0.00          H   \nATOM     27  O2'   C A   1      -1.266   8.699   0.644  1.00  0.00          O   \nATOM     28 2HO'   C A   1      -1.883   9.426   0.686  1.00  0.00          H   \nATOM     29  O3'   C A   1      -2.604  10.214   2.183  1.00  0.00          O   \nATOM     30  P     C A   2      -3.918   9.866   2.832  1.00  0.00          P   \nATOM     31  OP1   C A   2      -4.840  10.805   2.092  1.00  0.00          O   \nATOM     32  OP2   C A   2      -3.860   9.956   4.283  1.00  0.00          O   \nATOM     33  O5'   C A   2      -4.345   8.418   2.457  1.00  0.00          O   \nATOM     34  C5'   C A   2      -4.601   8.095   1.084  1.00  0.00          C   \nATOM     35 1H5'   C A   2      -3.800   8.306   0.373  1.00  0.00          H   \nATOM     36 2H5'   C A   2      -5.457   8.679   0.760  1.00  0.00          H   \nATOM     37  C4'   C A   2      -4.816   6.601   1.069  1.00  0.00          C   \nATOM     38  H4'   C A   2      -5.500   6.366   1.892  1.00  0.00          H   \nATOM     39  O4'   C A   2      -5.306   6.200  -0.185  1.00  0.00          O   \nATOM     40  C1'   C A   2      -4.718   4.953  -0.610  1.00  0.00          C   \nATOM     41  H1'   C A   2      -5.492   4.187  -0.591  1.00  0.00          H   \nATOM     42  N1    C A   2      -4.109   5.175  -2.010  1.00  0.00          N   \nATOM     43  C6    C A   2      -3.481   6.388  -2.343  1.00  0.00          C   \nATOM     44  H6    C A   2      -3.562   7.250  -1.698  1.00  0.00          H   \nATOM     45  C5    C A   2      -2.848   6.547  -3.519  1.00  0.00          C   \nATOM     46  H5    C A   2      -2.441   7.520  -3.754  1.00  0.00          H   \nATOM     47  C4    C A   2      -2.727   5.353  -4.320  1.00  0.00          C   \nATOM     48  N4    C A   2      -2.021   5.327  -5.437  1.00  0.00          N   \nATOM     49  H41   C A   2      -1.427   6.116  -5.655  1.00  0.00          H   \nATOM     50  H42   C A   2      -1.849   4.413  -5.824  1.00  0.00          H   \nATOM     51  N3    C A   2      -3.373   4.210  -4.084  1.00  0.00          N   \nATOM     52  C2    C A   2      -4.066   4.129  -2.915  1.00  0.00          C   \nATOM     53  O2    C A   2      -4.602   3.058  -2.621  1.00  0.00          O   \nATOM     54  C3'   C A   2      -3.476   5.802   1.297  1.00  0.00          C   \nATOM     55  H3'   C A   2      -2.647   6.319   0.810  1.00  0.00          H   \nATOM     56  C2'   C A   2      -3.765   4.543   0.546  1.00  0.00          C   \nATOM     57 1H2'   C A   2      -2.861   4.241   0.013  1.00  0.00          H   \nATOM     58  O2'   C A   2      -4.356   3.513   1.287  1.00  0.00          O   \nATOM     59 2HO'   C A   2      -3.759   3.384   2.031  1.00  0.00          H   \nATOM     60  O3'   C A   2      -3.117   5.599   2.661  1.00  0.00          O   \nATOM     61  P     U A   3      -1.713   4.898   2.956  1.00  0.00          P   \nATOM     62  OP1   U A   3      -1.186   5.451   4.154  1.00  0.00          O   \nATOM     63  OP2   U A   3      -0.906   4.966   1.706  1.00  0.00          O   \nATOM     64  O5'   U A   3      -2.120   3.374   3.135  1.00  0.00          O   \nATOM     65  C5'   U A   3      -2.914   2.982   4.212  1.00  0.00          C   \nATOM     66 1H5'   U A   3      -3.884   3.485   4.143  1.00  0.00          H   \nATOM     67 2H5'   U A   3      -2.525   3.212   5.200  1.00  0.00          H   \nATOM     68  C4'   U A   3      -3.056   1.456   4.229  1.00  0.00          C   \nATOM     69  H4'   U A   3      -3.606   1.211   5.139  1.00  0.00          H   \nATOM     70  O4'   U A   3      -3.753   0.913   3.122  1.00  0.00          O   \nATOM     71  C1'   U A   3      -2.987  -0.057   2.451  1.00  0.00          C   \nATOM     72  H1'   U A   3      -3.654  -0.882   2.204  1.00  0.00          H   \nATOM     73  N1    U A   3      -2.491   0.632   1.206  1.00  0.00          N   \nATOM     74  C6    U A   3      -1.159   0.995   1.085  1.00  0.00          C   \nATOM     75  H6    U A   3      -0.425   0.777   1.849  1.00  0.00          H   \nATOM     76  C5    U A   3      -0.781   1.618  -0.050  1.00  0.00          C   \nATOM     77  H5    U A   3       0.208   2.028  -0.146  1.00  0.00          H   \nATOM     78  C4    U A   3      -1.731   2.004  -1.027  1.00  0.00          C   \nATOM     79  O4    U A   3      -1.525   2.729  -2.031  1.00  0.00          O   \nATOM     80  N3    U A   3      -2.992   1.443  -0.902  1.00  0.00          N   \nATOM     81  H3    U A   3      -3.688   1.674  -1.590  1.00  0.00          H   \nATOM     82  C2    U A   3      -3.370   0.667   0.112  1.00  0.00          C   \nATOM     83  O2    U A   3      -4.508   0.153   0.117  1.00  0.00          O   \nATOM     84  C3'   U A   3      -1.733   0.730   4.343  1.00  0.00          C   \nATOM     85  H3'   U A   3      -0.897   1.243   3.885  1.00  0.00          H   \nATOM     86  C2'   U A   3      -2.017  -0.598   3.492  1.00  0.00          C   \nATOM     87 1H2'   U A   3      -1.097  -0.888   2.974  1.00  0.00          H   \nATOM     88  O2'   U A   3      -2.607  -1.679   4.185  1.00  0.00          O   \nATOM     89 2HO'   U A   3      -1.986  -2.245   4.652  1.00  0.00          H   \nATOM     90  O3'   U A   3      -1.377   0.457   5.702  1.00  0.00          O   \nATOM     91  P     U A   4      -0.091  -0.314   6.124  1.00  0.00          P   \nATOM     92  OP1   U A   4       0.034  -0.199   7.626  1.00  0.00          O   \nATOM     93  OP2   U A   4       0.994   0.173   5.302  1.00  0.00          O   \nATOM     94  O5'   U A   4      -0.225  -1.857   5.744  1.00  0.00          O   \nATOM     95  C5'   U A   4      -0.487  -2.876   6.664  1.00  0.00          C   \nATOM     96 1H5'   U A   4      -1.435  -2.637   7.150  1.00  0.00          H   \nATOM     97 2H5'   U A   4       0.322  -2.874   7.389  1.00  0.00          H   \nATOM     98  C4'   U A   4      -0.557  -4.203   5.893  1.00  0.00          C   \nATOM     99  H4'   U A   4      -0.782  -5.029   6.576  1.00  0.00          H   \nATOM    100  O4'   U A   4      -1.431  -4.138   4.813  1.00  0.00          O   \nATOM    101  C1'   U A   4      -0.955  -4.771   3.634  1.00  0.00          C   \nATOM    102  H1'   U A   4      -1.653  -5.606   3.479  1.00  0.00          H   \nATOM    103  N1    U A   4      -1.017  -3.937   2.382  1.00  0.00          N   \nATOM    104  C6    U A   4       0.033  -3.168   1.984  1.00  0.00          C   \nATOM    105  H6    U A   4       0.864  -2.964   2.652  1.00  0.00          H   \nATOM    106  C5    U A   4       0.051  -2.367   0.883  1.00  0.00          C   \nATOM    107  H5    U A   4       0.903  -1.835   0.513  1.00  0.00          H   \nATOM    108  C4    U A   4      -1.068  -2.502  -0.037  1.00  0.00          C   \nATOM    109  O4    U A   4      -1.168  -2.076  -1.145  1.00  0.00          O   \nATOM    110  N3    U A   4      -2.097  -3.274   0.415  1.00  0.00          N   \nATOM    111  H3    U A   4      -2.931  -3.145  -0.143  1.00  0.00          H   \nATOM    112  C2    U A   4      -2.147  -3.889   1.637  1.00  0.00          C   \nATOM    113  O2    U A   4      -3.175  -4.465   1.946  1.00  0.00          O   \nATOM    114  C3'   U A   4       0.785  -4.453   5.172  1.00  0.00          C   \nATOM    115  H3'   U A   4       1.196  -3.505   4.813  1.00  0.00          H   \nATOM    116  C2'   U A   4       0.450  -5.315   3.926  1.00  0.00          C   \nATOM    117 1H2'   U A   4       1.177  -5.131   3.128  1.00  0.00          H   \nATOM    118  O2'   U A   4       0.483  -6.646   4.378  1.00  0.00          O   \nATOM    119 2HO'   U A   4       1.079  -6.628   5.128  1.00  0.00          H   \nATOM    120  O3'   U A   4       1.804  -5.066   5.966  1.00  0.00          O   \nATOM    121  P     C A   5       3.329  -5.216   5.627  1.00  0.00          P   \nATOM    122  OP1   C A   5       3.841  -5.704   6.875  1.00  0.00          O   \nATOM    123  OP2   C A   5       3.746  -3.888   5.087  1.00  0.00          O   \nATOM    124  O5'   C A   5       3.455  -6.336   4.577  1.00  0.00          O   \nATOM    125  C5'   C A   5       4.778  -6.939   4.281  1.00  0.00          C   \nATOM    126 1H5'   C A   5       5.232  -7.250   5.224  1.00  0.00          H   \nATOM    127 2H5'   C A   5       5.430  -6.158   3.892  1.00  0.00          H   \nATOM    128  C4'   C A   5       4.709  -7.980   3.211  1.00  0.00          C   \nATOM    129  H4'   C A   5       5.694  -8.438   3.107  1.00  0.00          H   \nATOM    130  O4'   C A   5       3.706  -8.935   3.340  1.00  0.00          O   \nATOM    131  C1'   C A   5       3.384  -9.504   2.106  1.00  0.00          C   \nATOM    132  H1'   C A   5       4.118 -10.277   1.892  1.00  0.00          H   \nATOM    133  N1    C A   5       1.984  -9.951   2.122  1.00  0.00          N   \nATOM    134  C6    C A   5       0.945  -9.022   2.159  1.00  0.00          C   \nATOM    135  H6    C A   5       1.093  -7.982   2.399  1.00  0.00          H   \nATOM    136  C5    C A   5      -0.348  -9.478   1.998  1.00  0.00          C   \nATOM    137  H5    C A   5      -1.184  -8.790   1.979  1.00  0.00          H   \nATOM    138  C4    C A   5      -0.596 -10.905   1.969  1.00  0.00          C   \nATOM    139  N4    C A   5      -1.848 -11.322   1.849  1.00  0.00          N   \nATOM    140  H41   C A   5      -2.440 -10.595   1.452  1.00  0.00          H   \nATOM    141  H42   C A   5      -2.055 -12.305   1.911  1.00  0.00          H   \nATOM    142  N3    C A   5       0.406 -11.776   2.099  1.00  0.00          N   \nATOM    143  C2    C A   5       1.698 -11.341   2.106  1.00  0.00          C   \nATOM    144  O2    C A   5       2.600 -12.213   2.195  1.00  0.00          O   \nATOM    145  C3'   C A   5       4.248  -7.288   1.955  1.00  0.00          C   \nATOM    146  H3'   C A   5       3.480  -6.554   2.207  1.00  0.00          H   \nATOM    147  C2'   C A   5       3.655  -8.380   1.082  1.00  0.00          C   \nATOM    148 1H2'   C A   5       2.746  -8.127   0.533  1.00  0.00          H   \nATOM    149  O2'   C A   5       4.699  -8.824   0.152  1.00  0.00          O   \nATOM    150 2HO'   C A   5       4.661  -8.294  -0.643  1.00  0.00          H   \nATOM    151  O3'   C A   5       5.329  -6.512   1.376  1.00  0.00          O   \nATOM    152  P     G A   6       5.089  -5.416   0.328  1.00  0.00          P   \nATOM    153  OP1   G A   6       6.423  -4.856   0.064  1.00  0.00          O   \nATOM    154  OP2   G A   6       4.083  -4.435   0.819  1.00  0.00          O   \nATOM    155  O5'   G A   6       4.636  -6.160  -0.965  1.00  0.00          O   \nATOM    156  C5'   G A   6       5.552  -6.510  -2.027  1.00  0.00          C   \nATOM    157 1H5'   G A   6       6.469  -6.961  -1.626  1.00  0.00          H   \nATOM    158 2H5'   G A   6       5.887  -5.607  -2.537  1.00  0.00          H   \nATOM    159  C4'   G A   6       4.986  -7.425  -3.082  1.00  0.00          C   \nATOM    160  H4'   G A   6       5.697  -7.597  -3.889  1.00  0.00          H   \nATOM    161  O4'   G A   6       4.688  -8.725  -2.618  1.00  0.00          O   \nATOM    162  C1'   G A   6       3.347  -9.129  -3.030  1.00  0.00          C   \nATOM    163  H1'   G A   6       3.341  -9.628  -3.990  1.00  0.00          H   \nATOM    164  N9    G A   6       2.694 -10.186  -2.179  1.00  0.00          N   \nATOM    165  C8    G A   6       1.465 -10.056  -1.553  1.00  0.00          C   \nATOM    166  H8    G A   6       0.920  -9.132  -1.662  1.00  0.00          H   \nATOM    167  N7    G A   6       1.116 -11.255  -1.038  1.00  0.00          N   \nATOM    168  C5    G A   6       2.270 -12.083  -1.307  1.00  0.00          C   \nATOM    169  C6    G A   6       2.344 -13.551  -1.285  1.00  0.00          C   \nATOM    170  O6    G A   6       1.479 -14.337  -1.025  1.00  0.00          O   \nATOM    171  N1    G A   6       3.478 -14.045  -1.824  1.00  0.00          N   \nATOM    172  H1    G A   6       3.513 -15.048  -1.959  1.00  0.00          H   \nATOM    173  C2    G A   6       4.422 -13.333  -2.479  1.00  0.00          C   \nATOM    174  N2    G A   6       5.512 -13.932  -3.016  1.00  0.00          N   \nATOM    175  H21   G A   6       5.704 -14.862  -2.663  1.00  0.00          H   \nATOM    176  H22   G A   6       6.205 -13.258  -3.305  1.00  0.00          H   \nATOM    177  N3    G A   6       4.231 -11.995  -2.627  1.00  0.00          N   \nATOM    178  C4    G A   6       3.168 -11.404  -2.073  1.00  0.00          C   \nATOM    179  C3'   G A   6       3.731  -6.903  -3.729  1.00  0.00          C   \nATOM    180  H3'   G A   6       3.435  -5.917  -3.379  1.00  0.00          H   \nATOM    181  C2'   G A   6       2.633  -7.748  -3.155  1.00  0.00          C   \nATOM    182 1H2'   G A   6       2.238  -7.311  -2.240  1.00  0.00          H   \nATOM    183  O2'   G A   6       1.558  -7.976  -4.066  1.00  0.00          O   \nATOM    184 2HO'   G A   6       1.344  -7.260  -4.657  1.00  0.00          H   \nATOM    185  O3'   G A   6       3.857  -7.008  -5.123  1.00  0.00          O   \nATOM    186  P     G A   7       4.314  -5.917  -5.968  1.00  0.00          P   \nATOM    187  OP1   G A   7       4.694  -6.530  -7.272  1.00  0.00          O   \nATOM    188  OP2   G A   7       5.287  -5.027  -5.336  1.00  0.00          O   \nATOM    189  O5'   G A   7       2.968  -5.053  -6.079  1.00  0.00          O   \nATOM    190  C5'   G A   7       2.007  -5.188  -7.123  1.00  0.00          C   \nATOM    191 1H5'   G A   7       2.142  -6.162  -7.585  1.00  0.00          H   \nATOM    192 2H5'   G A   7       2.203  -4.527  -7.965  1.00  0.00          H   \nATOM    193  C4'   G A   7       0.488  -5.149  -6.770  1.00  0.00          C   \nATOM    194  H4'   G A   7      -0.107  -5.464  -7.621  1.00  0.00          H   \nATOM    195  O4'   G A   7       0.217  -6.021  -5.685  1.00  0.00          O   \nATOM    196  C1'   G A   7      -0.971  -5.703  -5.053  1.00  0.00          C   \nATOM    197  H1'   G A   7      -1.778  -6.272  -5.517  1.00  0.00          H   \nATOM    198  N9    G A   7      -0.942  -5.908  -3.597  1.00  0.00          N   \nATOM    199  C8    G A   7      -1.705  -6.698  -2.817  1.00  0.00          C   \nATOM    200  H8    G A   7      -2.537  -7.236  -3.251  1.00  0.00          H   \nATOM    201  N7    G A   7      -1.364  -6.834  -1.574  1.00  0.00          N   \nATOM    202  C5    G A   7      -0.314  -5.886  -1.477  1.00  0.00          C   \nATOM    203  C6    G A   7       0.537  -5.565  -0.316  1.00  0.00          C   \nATOM    204  O6    G A   7       0.602  -6.086   0.773  1.00  0.00          O   \nATOM    205  N1    G A   7       1.489  -4.632  -0.685  1.00  0.00          N   \nATOM    206  H1    G A   7       2.297  -4.588  -0.074  1.00  0.00          H   \nATOM    207  C2    G A   7       1.602  -4.069  -1.870  1.00  0.00          C   \nATOM    208  N2    G A   7       2.527  -3.164  -2.027  1.00  0.00          N   \nATOM    209  H21   G A   7       2.981  -2.790  -1.209  1.00  0.00          H   \nATOM    210  H22   G A   7       2.548  -2.724  -2.936  1.00  0.00          H   \nATOM    211  N3    G A   7       0.818  -4.314  -2.932  1.00  0.00          N   \nATOM    212  C4    G A   7      -0.103  -5.286  -2.679  1.00  0.00          C   \nATOM    213  C3'   G A   7       0.002  -3.829  -6.233  1.00  0.00          C   \nATOM    214  H3'   G A   7       0.772  -3.501  -5.532  1.00  0.00          H   \nATOM    215  C2'   G A   7      -1.238  -4.199  -5.349  1.00  0.00          C   \nATOM    216 1H2'   G A   7      -1.345  -3.557  -4.472  1.00  0.00          H   \nATOM    217  O2'   G A   7      -2.477  -4.115  -6.006  1.00  0.00          O   \nATOM    218 2HO'   G A   7      -2.663  -3.177  -6.103  1.00  0.00          H   \nATOM    219  O3'   G A   7      -0.058  -2.871  -7.235  1.00  0.00          O   \nATOM    220  P     G A   8      -0.177  -1.348  -6.889  1.00  0.00          P   \nATOM    221  OP1   G A   8      -0.087  -0.596  -8.154  1.00  0.00          O   \nATOM    222  OP2   G A   8       0.786  -0.992  -5.810  1.00  0.00          O   \nATOM    223  O5'   G A   8      -1.689  -1.198  -6.354  1.00  0.00          O   \nATOM    224  C5'   G A   8      -2.852  -0.837  -7.126  1.00  0.00          C   \nATOM    225 1H5'   G A   8      -2.951  -1.618  -7.872  1.00  0.00          H   \nATOM    226 2H5'   G A   8      -2.606   0.097  -7.626  1.00  0.00          H   \nATOM    227  C4'   G A   8      -4.106  -0.713  -6.306  1.00  0.00          C   \nATOM    228  H4'   G A   8      -4.899  -0.408  -6.981  1.00  0.00          H   \nATOM    229  O4'   G A   8      -4.436  -2.035  -5.874  1.00  0.00          O   \nATOM    230  C1'   G A   8      -4.920  -2.089  -4.541  1.00  0.00          C   \nATOM    231  H1'   G A   8      -5.948  -1.734  -4.476  1.00  0.00          H   \nATOM    232  N9    G A   8      -4.903  -3.425  -3.924  1.00  0.00          N   \nATOM    233  C8    G A   8      -5.038  -4.596  -4.570  1.00  0.00          C   \nATOM    234  H8    G A   8      -5.051  -4.549  -5.641  1.00  0.00          H   \nATOM    235  N7    G A   8      -5.325  -5.595  -3.784  1.00  0.00          N   \nATOM    236  C5    G A   8      -5.298  -5.136  -2.500  1.00  0.00          C   \nATOM    237  C6    G A   8      -5.596  -5.687  -1.225  1.00  0.00          C   \nATOM    238  O6    G A   8      -6.004  -6.816  -0.922  1.00  0.00          O   \nATOM    239  N1    G A   8      -5.626  -4.743  -0.219  1.00  0.00          N   \nATOM    240  H1    G A   8      -5.723  -5.110   0.716  1.00  0.00          H   \nATOM    241  C2    G A   8      -5.225  -3.456  -0.366  1.00  0.00          C   \nATOM    242  N2    G A   8      -5.421  -2.630   0.575  1.00  0.00          N   \nATOM    243  H21   G A   8      -5.866  -2.992   1.401  1.00  0.00          H   \nATOM    244  H22   G A   8      -5.187  -1.657   0.440  1.00  0.00          H   \nATOM    245  N3    G A   8      -4.861  -2.935  -1.491  1.00  0.00          N   \nATOM    246  C4    G A   8      -4.963  -3.808  -2.568  1.00  0.00          C   \nATOM    247  C3'   G A   8      -3.907   0.101  -5.031  1.00  0.00          C   \nATOM    248  H3'   G A   8      -2.891   0.510  -4.970  1.00  0.00          H   \nATOM    249  C2'   G A   8      -4.030  -0.981  -3.889  1.00  0.00          C   \nATOM    250 1H2'   G A   8      -3.026  -1.393  -3.742  1.00  0.00          H   \nATOM    251  O2'   G A   8      -4.427  -0.439  -2.681  1.00  0.00          O   \nATOM    252 2HO'   G A   8      -4.692  -1.211  -2.172  1.00  0.00          H   \nATOM    253  O3'   G A   8      -4.929   1.096  -4.947  1.00  0.00          O   \nATOM    254 HO3'   G A   8      -4.920   1.311  -4.009  1.00  0.00          H   \nTER     255        G A   8\nENDMDL\nEND\n","pdb");
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In [11]:

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Out[11]:

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On the left the native UUCG and on the right the highest eRMSD among all structures with RMSD from native \$\approx\$ 0.3nm.

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In [ ]:

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