Torsion angles from DSSR

By following citations to 3DNA/DSSR, I recently came across the paper "RNAtango: Analysing and comparing RNA 3D structures via torsional angles" in PLOS Computational Biology by Mackowiak M, Adamczyk B, Szachniuk M, and Zok T. This work provides a nice summary of definitions of torsion and pseudo-torsion angles in RNA structure, and an angular metrics (MCQ, Mean of Circular Quantities) to score structure similarity. The RNAtango web application allows user to explore the distribution of torsion angles in a single structure/fragment (Single model), compare RNA models with a native structure (Models vs Target), or perform a comparative analysis in a set of models (Model vs Model).

In the Introduction section, 3DNA/DSSR are mentioned along with other related tools, as below:

Several bioinformatics tools have been designed for analyzing torsion and pseudotorsion angles, each with its own strengths and limitations. 3DNA, an open-source toolkit, provides comprehensive functionality, including torsion and pseudotorsion angle calculations [27], but lacks support for the current standard PDBx/mmCIF file format. DSSR, the successor to 3DNA, overcomes this limitation by supporting both PDB and PDBx/mmCIF files. However, it is a closed-source, commercial application that requires licensing, even for research purposes [28]. Curves+, another tool used for torsion angle analysis, is currently inaccessible due to the unavailability of its webpage and source code hosting [29]. Barnaba, a Python library and toolset for analyzing single structures or trajectories, supports torsion angle calculations but, like 3DNA, does not support the PDBx/mmCIF format [30]. For users seeking amore user friendly option, AMIGOS III offers a PyMOL plugin that calculates pseudotorsion angles and presents them in Ramachandran-like plots [17].

Every bioinformatic software has been developed for a specific purpose, and no two such tools can be identical. It is a good thing that the community has a choice for RNA backbone analysis. Indeed, 3DNA has been superseded by DSSR, which is licensed by Columbia Technology Ventures (CTV) to ensure its continuous development and availability. However, DSSR remain competitive due to its unmatched functionality, usability, and support: it saves users a substantial amount of time and effort when compared to other options.

From the very beginning, it has been my dream to make DSSR stand out for its quality and value, and be widely accessible. The CTV DSSR distribution by no means follow typical commercial license for a software product: specifically, it does not include a license key to limit DSSR's usage to a specific machine and operating system, and there is no expire date for the software either. Moreover, the Basic Academic license was free of charge when DSSR was initially licensed by the CTV in August 2020, and remained so until around end of 2021 when the web-based "Express Licenses" functionality no longer worked. Manually handling the large number of requests for free academic licenses was not sustainable, and that was when the DSSR Basic Academic free license was removed. Upon user requests, we late on re-introduced DSSR Basic Academic license, but with a one-time fee of $200 to cover the running cost. That may be reason for the remark in the RNAtango paper that DSSR "requires licensing, even for research purposes".

With the recent NIH R24 funding support on "X3DNA-DSSR: a resource for structural bioinformatics of nucleic acids", we are providing DSSR Basic free of charge to the academic community. Academic Users may submit a license request for DSSR Basic or DSSR Pro by clicking "Express Licensing". Checking the list of licensees, I am thrilled to see the many new DSSR users from leading institutions around the world, including Stockholm University, Ghent University, Universitaet Heidelberg, University of Palermo, CSSB-Hamburg, Nicolaus Copernicus University, NIH, Harvard, ... Clearly, DSSR fills a niche, and the demands for it remain strong!

Back to torsion angles, it is safe to say that DSSR has unique features not available or easily accessible elsewhere. Here are some use cases using tRNA PDB entry 1ehz as an example:

x3dna-dssr -i=1ehz.cif # generate dssr-torsions.txt among other output files
x3dna-dssr -i=1ehz.cif --torsion-file -o=1ehz-torsions.txt # just the torsion file 1ehz-torsions.txt
x3dna-dssr -i=1ehz.cif --json | jq .nts[54] > 1ehz-PSU55.txt # DSSR-derived features for nucleotide PSU55

Users can easily run the DSSR commands listed above and get the results in human-readable text and machine-friendly JSON formats. For verification, the contents of 1ehz-torsions.txt and 1ehz-PSU55.txt are available by clicking the links.

It is worth noting that DSSR has the --nmr option for the analysis of an ensemble of NMR structures, in .pdb or .cif format, as deposited in the PDB. The combination of --nmr and --json renders DSSR easily accessible to the molecular dynamics (MD) community.

In principle, calculating torsion angles is a straightforward process. In reality, factors such as modified nucleotides (especially pseudouridine), missing atoms, NMR ensembles or MD trajectories, PDB vs mmCIF formats, etc. make the implementation complicated. Without paying great attention to details, it is easy to make subtle mistakes. For example, with RNAtango the chi (χ) torsion angle for A.PSU55 of 1ehz is listed as -152.42°, which is wrong. The correct value should be -147.0° as reported by DSSR (see below and the link 1ehz-PSU55.txt above).

DSSR provides a comprehensive list of backbone parameters (as listed below for 1ehz). The program is efficient and robust, and has been battle tested. I am always quick to fix any bugs once verified, and am willing to add new features once thoroughly studied. In short, DSSR has been designed to be a reliable tool that the community can trust and build upon.


DSSR-derived backbone features for tRNA 1ehz:

         Output of DNA/RNA backbone conformational parameters
             DSSR v2.4.5-2024sep24 by xiangjun@x3dna.org
******************************************************************************************
Main chain conformational parameters:

  alpha:   O3'(i-1)-P-O5'-C5'
  beta:    P-O5'-C5'-C4'
  gamma:   O5'-C5'-C4'-C3'
  delta:   C5'-C4'-C3'-O3'
  epsilon: C4'-C3'-O3'-P(i+1)
  zeta:    C3'-O3'-P(i+1)-O5'(i+1)
  e-z:     epsilon-zeta (BI/BII backbone classification)

  chi for pyrimidines(Y): O4'-C1'-N1-C2; purines(R): O4'-C1'-N9-C4
    Range [170, -50(310)] is assigned to anti, and [50, 90] to syn

  phase-angle: the phase angle of pseudorotation and puckering
  sugar-type: ~C2'-endo for C2'-endo like conformation, or
               ~C3'-endo for C3'-endo like conformation
              Note the ONE column offset (for easy visual distinction)

ssZp: single-stranded Zp, defined as the z-coordinate of the 3' phosphorus atom
      (P) expressed in the standard reference frame of the 5' base; the value is
      POSITIVE when P lies on the +z-axis side (base in anti conformation);
      NEGATIVE if P is on the -z-axis side (base in syn conformation)
  Dp: perpendicular distance of the 3' P atom to the glycosidic bond
      [Ref: Chen et al. (2010): "MolProbity: all-atom structure
            validation for macromolecular crystallography."
            Acta Crystallogr D Biol Crystallogr, 66(1):12-21]
splay: angle between the bridging P to the two base-origins of a dinucleotide.

          nt               alpha    beta   gamma   delta  epsilon   zeta     e-z        chi            phase-angle   sugar-type    ssZp     Dp    splay
 1     G A.G1                ---  -128.1    67.8    82.9  -155.6   -68.6    -87(BI)   -167.8(anti)    16.1(C3'-endo)  ~C3'-endo    4.59    4.57   24.92
 2     C A.C2              -67.4  -178.4    53.8    83.4  -145.1   -76.8    -68(BI)   -163.8(anti)    16.1(C3'-endo)  ~C3'-endo    4.52    4.63   21.15
 3     G A.G3              -74.5   169.7    59.5    80.7  -148.3   -80.0    -68(BI)   -161.9(anti)    14.6(C3'-endo)  ~C3'-endo    4.75    4.69   22.28
 4     G A.G4              -64.4   162.2    60.7    82.2  -157.4   -68.7    -89(BI)   -168.7(anti)    20.8(C3'-endo)  ~C3'-endo    4.68    4.57   25.22
 5     A A.A5              -74.7  -176.5    53.4    84.9  -137.5   -81.7    -56(BI)   -162.9(anti)     4.8(C3'-endo)  ~C3'-endo    4.49    4.76   22.04
 6     U A.U6              -48.8   157.6    55.3    81.3  -151.0   -77.0    -74(BI)   -160.0(anti)    18.2(C3'-endo)  ~C3'-endo    4.31    4.51   22.89
 7     U A.U7              -59.5  -178.7    62.5   137.3  -105.9   -52.0    -54(--)   -133.1(anti)   156.1(C2'-endo) ~C2'-endo     1.55    1.41  126.99
 8     U A.U8              -83.8  -145.6    55.4    78.6  -142.8  -118.6    -24(--)   -161.5(anti)    10.5(C3'-endo)  ~C3'-endo    4.60    4.76   62.37
 9     A A.A9              -69.7  -141.7    52.3   147.8  -106.2   -77.3    -29(--)    -70.5(anti)   149.8(C2'-endo) ~C2'-endo     1.00    1.14   57.38
 10    g A.2MG10           177.8   147.2    60.1    89.3  -126.2   -88.7    -37(--)    169.6(anti)     6.6(C3'-endo)  ~C3'-endo    4.68    4.63   23.87
 11    C A.C11             -56.1   167.9    48.2    87.2  -150.5   -69.9    -81(BI)   -160.9(anti)    16.8(C3'-endo)  ~C3'-endo    4.28    4.46   21.20
 12    U A.U12             -67.8   172.9    51.8    80.7  -158.5   -65.2    -93(BI)   -158.3(anti)    25.2(C3'-endo)  ~C3'-endo    4.29    4.45   21.01
 13    C A.C13             166.6  -169.9   178.6    82.5  -153.1   -97.4    -56(BI)   -168.3(anti)    23.7(C3'-endo)  ~C3'-endo    4.28    4.36   31.59
 14    A A.A14              83.4  -158.3  -114.6    92.0  -125.5   -57.3    -68(--)   -170.7(anti)   358.9(C2'-exo)   ~C3'-endo    4.67    4.74   38.01
 15    G A.G15             -55.1   162.5    51.9    79.8  -136.3  -143.9      8(--)   -164.5(anti)    16.0(C3'-endo)  ~C3'-endo    4.72    4.74   26.17
 16    u A.H2U16            -6.1    91.2    76.8    96.8   -61.8  -131.2     69(--)    -85.8(anti)    18.8(C3'-endo)  ~C3'-endo   -0.71    3.38  145.77
 17    u A.H2U17            27.8   107.7   174.1    94.8   178.0    76.2    102(--)   -142.5(anti)   341.4(C2'-exo)   ~C3'-endo   -0.90    4.20  105.55
 18    G A.G18              45.4  -159.4    59.0   150.6   -95.2  -179.1     84(BII)   -99.5(anti)   154.3(C2'-endo) ~C2'-endo     1.60    1.09   51.64
 19    G A.G19             -71.4  -178.9    53.8   153.8   -91.6   -83.7     -8(--)    -80.3(anti)   167.6(C2'-endo) ~C2'-endo    -1.14    0.48  130.30
 20    G A.G20             -81.3  -150.7    47.8    89.9  -122.3   -54.1    -68(--)    177.8(anti)     8.7(C3'-endo)  ~C3'-endo    4.90    4.76   57.04
 21    A A.A21             -75.6   148.6  -176.6    78.2  -168.9   -75.6    -93(BI)   -160.2(anti)    13.0(C3'-endo)  ~C3'-endo    4.00    4.26   40.66
 22    G A.G22             158.8   153.5   179.3    82.0  -145.0   -80.4    -65(BI)   -175.5(anti)   353.8(C2'-exo)   ~C3'-endo    4.60    4.73   25.62
 23    A A.A23             -53.3   174.8    52.5    82.3  -155.3   -66.4    -89(BI)   -158.0(anti)    12.6(C3'-endo)  ~C3'-endo    4.18    4.61   22.96
 24    G A.G24             -68.8   178.2    46.8    83.6  -144.3   -72.8    -71(BI)   -160.7(anti)    13.4(C3'-endo)  ~C3'-endo    4.63    4.74   20.51
 25    C A.C25             -65.1   168.9    53.9    83.3  -145.1   -68.4    -77(BI)   -160.3(anti)    17.4(C3'-endo)  ~C3'-endo    4.56    4.70   30.70
 26    g A.M2G26           -53.8   170.8    47.7    86.0  -136.3   -76.9    -59(BI)   -163.4(anti)     9.3(C3'-endo)  ~C3'-endo    4.57    4.67   27.36
 27    C A.C27             -53.0   166.9    43.6    83.4  -148.5   -73.4    -75(BI)   -168.2(anti)    18.3(C3'-endo)  ~C3'-endo    4.53    4.62   23.07
 28    C A.C28             -72.4   178.3    49.3    80.1  -152.1   -67.0    -85(BI)   -160.6(anti)     9.2(C3'-endo)  ~C3'-endo    4.55    4.73   21.61
 29    A A.A29             -66.6   174.0    55.6    81.4  -155.5   -78.3    -77(BI)   -165.9(anti)    13.7(C3'-endo)  ~C3'-endo    4.73    4.65   26.96
 30    G A.G30             -54.0   165.9    56.9    83.6  -144.7   -62.3    -82(BI)   -171.7(anti)    14.5(C3'-endo)  ~C3'-endo    4.67    4.65   25.72
 31    A A.A31             -69.9   177.8    52.3    83.7  -137.0   -75.5    -61(BI)   -156.7(anti)    14.6(C3'-endo)  ~C3'-endo    4.24    4.72   21.52
 32    c A.OMC32           -52.7   161.4    49.3    80.1  -145.9   -71.2    -75(BI)   -149.9(anti)    20.4(C3'-endo)  ~C3'-endo    4.16    4.63   25.94
 33    U A.U33             -67.7  -177.0    47.0    82.1  -148.0   -53.7    -94(BI)   -148.2(anti)    13.3(C3'-endo)  ~C3'-endo    4.19    4.64   75.47
 34    g A.OMG34           171.1   148.1    52.5    83.4  -132.5   -71.8    -61(BI)   -171.2(anti)    12.2(C3'-endo)  ~C3'-endo    4.15    4.58   22.09
 35    A A.A35             -47.7   163.7    40.2    80.9  -143.7   -59.5    -84(BI)   -154.4(anti)    21.9(C3'-endo)  ~C3'-endo    4.20    4.54   20.57
 36    A A.A36             -52.4   165.7    51.3    72.2  -160.4   -85.2    -75(BI)   -158.4(anti)    45.8(C4'-exo)   ~C3'-endo    4.49    4.31   24.48
 37    g A.YYG37           -57.5   163.0    47.8    81.1  -148.1   -67.0    -81(BI)   -168.8(anti)    15.4(C3'-endo)  ~C3'-endo    4.63    4.65   32.08
 38    A A.A38             -61.8  -180.0    46.9    82.5  -136.8   -76.4    -60(BI)   -169.4(anti)     2.4(C3'-endo)  ~C3'-endo    4.63    4.78   23.75
 39    P A.PSU39           -47.7   160.4    53.3    79.3  -140.1   -68.6    -72(BI)   -165.6(anti)    15.8(C3'-endo)  ~C3'-endo    4.55    4.68   26.68
 40    c A.5MC40           -67.4   172.0    56.2    83.2  -154.2   -74.9    -79(BI)   -162.6(anti)    17.3(C3'-endo)  ~C3'-endo    4.52    4.60   27.71
 41    U A.U41             -68.2  -179.4    52.4    78.9  -137.3   -84.7    -53(BI)   -169.0(anti)    13.4(C3'-endo)  ~C3'-endo    4.54    4.75   24.14
 42    G A.G42             -47.9   158.7    55.6    79.8  -160.3   -70.3    -90(BI)   -169.0(anti)    20.9(C3'-endo)  ~C3'-endo    4.43    4.51   23.54
 43    G A.G43             -67.0  -178.3    55.6    81.6  -154.9   -76.4    -78(BI)   -160.2(anti)    12.6(C3'-endo)  ~C3'-endo    4.24    4.61   20.95
 44    A A.A44             -59.7   162.1    60.0    85.3  -142.8   -57.2    -86(BI)   -159.4(anti)    16.9(C3'-endo)  ~C3'-endo    4.25    4.61   31.07
 45    G A.G45             -71.9  -176.9    51.0    87.6  -135.1   -78.7    -56(BI)   -149.3(anti)    15.4(C3'-endo)  ~C3'-endo    4.01    4.58   40.27
 46    g A.7MG46           -56.8  -146.5    48.4   141.6  -102.7  -137.9     35(--)    -65.8(anti)   154.5(C2'-endo) ~C2'-endo     0.21    0.96  139.04
 47    U A.U47              62.4  -164.0    44.4   146.1   -93.7   -78.0    -16(--)   -112.0(anti)   164.9(C2'-endo) ~C2'-endo     0.26    0.39  157.37
 48    C A.C48             -73.5  -174.3   161.5   145.6  -143.5    75.6    141(--)   -140.1(anti)   158.2(C2'-endo) ~C2'-endo     1.92    1.80  147.54
 49    c A.5MC49            50.7   168.5    42.2    84.3  -145.0   -82.1    -63(BI)   -173.6(anti)    10.1(C3'-endo)  ~C3'-endo    4.77    4.75   25.83
 50    U A.U50             -51.7   177.2    42.1    80.4  -150.6   -67.8    -83(BI)   -165.3(anti)     5.6(C3'-endo)  ~C3'-endo    4.38    4.75   23.15
 51    G A.G51             -63.9   176.8    52.8    79.4  -150.4   -71.3    -79(BI)   -156.6(anti)    11.5(C3'-endo)  ~C3'-endo    4.44    4.67   21.28
 52    U A.U52             -64.7   173.6    48.5    80.3  -156.5   -69.4    -87(BI)   -164.0(anti)    14.1(C3'-endo)  ~C3'-endo    4.64    4.74   25.47
 53    G A.G53             -56.9   171.5    56.2    83.9  -159.4   -64.9    -95(BI)   -169.2(anti)    19.8(C3'-endo)  ~C3'-endo    4.59    4.57   24.53
 54    t A.5MU54           -79.7  -172.8    57.7    77.6  -128.6   -70.7    -58(BI)   -161.5(anti)    20.6(C3'-endo)  ~C3'-endo    4.56    4.80   30.73
 55    P A.PSU55           -49.7   168.8    44.1    76.6  -140.8   -69.9    -71(BI)   -147.0(anti)    10.1(C3'-endo)  ~C3'-endo    4.15    4.74   71.28
 56    C A.C56             166.4   171.8    53.3    83.4  -132.7   -70.6    -62(BI)   -161.5(anti)    12.6(C3'-endo)  ~C3'-endo    4.37    4.76   28.07
 57    G A.G57             -65.7   167.1    57.5    81.7  -145.2   -67.6    -78(BI)   -159.3(anti)    12.8(C3'-endo)  ~C3'-endo    4.36    4.65   42.47
 58    a A.1MA58           -60.8  -146.1    71.8   156.7   -78.3  -169.3     91(BII)   -86.3(anti)   161.1(C2'-endo) ~C2'-endo     0.48    0.68   73.92
 59    U A.U59              72.6  -158.8    63.7    84.6  -148.8   -53.7    -95(BI)   -165.6(anti)    25.8(C3'-endo)  ~C3'-endo    4.67    4.42   27.88
 60    C A.C60             -72.2   179.5    66.0   148.3   -97.1   -66.4    -31(--)   -117.8(anti)   154.8(C2'-endo) ~C2'-endo     0.99    0.86   90.64
 61    C A.C61             -84.3   179.8    38.2    83.0  -152.3   -74.5    -78(BI)   -166.7(anti)    14.8(C3'-endo)  ~C3'-endo    4.45    4.52   25.80
 62    A A.A62             -60.1   179.6    46.9    80.5  -145.6   -74.1    -71(BI)   -158.7(anti)     9.9(C3'-endo)  ~C3'-endo    4.18    4.66   19.23
 63    C A.C63             -62.0   167.3    50.9    80.7  -152.3   -70.7    -82(BI)   -152.6(anti)    10.7(C3'-endo)  ~C3'-endo    4.32    4.62   23.62
 64    A A.A64             -66.9   180.0    44.1    75.8  -147.5   -76.5    -71(BI)   -161.8(anti)    12.9(C3'-endo)  ~C3'-endo    4.68    4.86   25.64
 65    G A.G65             -44.0   164.2    49.9    79.8  -152.0   -73.3    -79(BI)   -172.8(anti)    16.5(C3'-endo)  ~C3'-endo    4.92    4.76   25.20
 66    A A.A66             -57.9   178.5    52.0    81.7  -151.0   -73.5    -77(BI)   -164.9(anti)    22.5(C3'-endo)  ~C3'-endo    4.56    4.60   22.73
 67    A A.A67             -62.0   164.1    54.2    83.2  -152.2   -78.3    -74(BI)   -162.8(anti)    15.0(C3'-endo)  ~C3'-endo    4.71    4.67   23.30
 68    U A.U68             -59.8   175.3    47.3    82.2  -152.9   -65.4    -88(BI)   -160.1(anti)    11.2(C3'-endo)  ~C3'-endo    4.30    4.60   24.35
 69    U A.U69             -63.8   168.1    55.1    79.1  -155.4   -85.6    -70(BI)   -161.4(anti)    14.7(C3'-endo)  ~C3'-endo    4.55    4.61   19.23
 70    C A.C70             -61.7   164.6    53.1    79.0  -158.5   -64.5    -94(BI)   -152.0(anti)    15.0(C3'-endo)  ~C3'-endo    4.20    4.56   20.96
 71    G A.G71             -78.4   173.6    60.3    80.3  -149.6   -68.4    -81(BI)   -162.8(anti)    13.5(C3'-endo)  ~C3'-endo    4.50    4.71   22.80
 72    C A.C72             -73.2   176.2    62.1    83.0  -152.3   -67.9    -84(BI)   -161.6(anti)    19.5(C3'-endo)  ~C3'-endo    4.56    4.63   26.14
 73    A A.A73             -63.3   177.7    50.4    81.6  -148.2   -66.1    -82(BI)   -167.4(anti)    15.0(C3'-endo)  ~C3'-endo    4.65    4.71   26.33
 74    C A.C74             -66.9  -174.9    50.7    85.9  -145.0   -58.8    -86(BI)   -153.1(anti)    11.8(C3'-endo)  ~C3'-endo    4.22    4.61   33.45
 75    C A.C75             -52.3   175.7    42.3    85.6  -131.9   163.9     64(BII)  -151.7(anti)    15.1(C3'-endo)  ~C3'-endo    3.96    4.60  159.78
 76    A A.A76             -71.0   130.2   164.6   160.9     ---     ---     ---       138.5(anti)   176.1(C2'-endo) ~C2'-endo      ---     ---     ---
******************************************************************************************
Virtual eta/theta torsion angles:

  eta:    C4'(i-1)-P(i)-C4'(i)-P(i+1)
  theta:  P(i)-C4'(i)-P(i+1)-C4'(i+1)
    [Ref: Olson (1980): "Configurational statistics of polynucleotide chains.
          An updated virtual bond model to treat effects of base stacking."
          Macromolecules, 13(3):721-728]

  eta':   C1'(i-1)-P(i)-C1'(i)-P(i+1)
  theta': P(i)-C1'(i)-P(i+1)-C1'(i+1)
    [Ref: Keating et al. (2011): "A new way to see RNA." Quarterly Reviews
          of Biophysics, 44(4):433-466]

  eta":   base(i-1)-P(i)-base(i)-P(i+1)
  theta": P(i)-base(i)-P(i+1)-base(i+1)

          nt                eta   theta     eta'  theta'    eta"  theta"
 1     G A.G1                ---  -139.3     ---  -136.5     ---  -110.8
 2     C A.C2              171.9  -144.6  -175.5  -144.1  -136.1  -118.1
 3     G A.G3              160.2  -151.4   173.9  -153.9  -145.0  -143.7
 4     G A.G4              164.3  -144.6   177.7  -144.1  -154.8   -98.7
 5     A A.A5              166.9  -138.1  -178.3  -135.8  -116.3  -111.6
 6     U A.U6              172.1  -149.7  -170.8  -143.9  -130.1  -126.5
 7     U A.U7             -158.0   -42.7  -138.7   -60.7  -120.5   -31.5
 8     U A.U8              162.7   160.7  -159.9  -163.8  -142.6   176.2
 9     A A.A9             -140.6   -38.9  -159.3  -112.7   157.1  -105.5
 10    g A.2MG10            27.8  -130.3    97.2  -130.1   134.8  -110.3
 11    C A.C11             170.3  -135.8  -175.7  -136.7  -137.8  -119.9
 12    U A.U12             159.9  -121.6   176.5  -130.6  -148.5  -101.4
 13    C A.C13             178.1  -179.1  -166.8   176.7  -118.5   178.4
 14    A A.A14             171.9  -146.5   172.1  -133.4  -179.7   -74.6
 15    G A.G15             164.3  -177.9  -166.6  -161.0   -92.6  -101.8
 16    u A.H2U16          -124.1   -77.5  -114.2  -108.3   -72.5  -127.0
 17    u A.H2U17           -10.5   -64.3     7.7   -94.7    17.3  -125.4
 18    G A.G18             -21.0  -167.4    45.3  -160.9    61.3  -124.2
 19    G A.G19            -127.4   -43.3  -122.0   -72.9  -105.8    -7.8
 20    G A.G20             165.3  -100.4  -160.4  -101.1  -177.9  -115.4
 21    A A.A21             -78.3   152.7   -68.0   155.1   -61.1   154.8
 22    G A.G22             159.5   167.6   156.6   178.8   157.1  -162.6
 23    A A.A23             178.4  -141.8  -173.5  -141.2  -156.1  -112.0
 24    G A.G24             163.7  -139.5   177.7  -137.6  -137.6  -103.8
 25    C A.C25             161.4  -132.6   179.2  -131.0  -128.2   -89.0
 26    g A.M2G26           173.0  -133.0  -167.7  -130.4  -106.9   -93.6
 27    C A.C27             163.5  -142.3  -178.0  -141.5  -123.6  -105.6
 28    C A.C28             157.5  -143.8   171.1  -144.3  -136.3  -125.5
 29    A A.A29             163.5  -152.9   179.0  -150.8  -142.9  -124.7
 30    G A.G30             178.3  -127.8  -167.7  -126.5  -128.2   -72.5
 31    A A.A31             165.4  -133.9  -174.3  -131.0  -101.0   -93.9
 32    c A.OMC32           164.5  -139.2  -175.9  -138.0  -122.3  -108.9
 33    U A.U33             165.1  -114.0   177.8  -158.5  -141.1   138.3
 34    g A.OMG34            27.3  -121.7    50.5  -123.7    22.7   -84.4
 35    A A.A35             162.5  -127.7  -177.7  -128.5  -116.8  -113.4
 36    A A.A36             164.9  -172.7  -174.4  -169.2  -142.3  -115.1
 37    g A.YYG37           163.1  -135.2   174.1  -131.3  -119.8   -79.8
 38    A A.A38             170.2  -133.9  -173.3  -129.0  -104.3  -105.5
 39    P A.PSU39           174.0  -132.6  -168.6  -131.2  -127.5   -89.6
 40    c A.5MC40           163.1  -148.5  -177.6  -149.3  -115.9  -131.7
 41    U A.U41             169.4  -148.8   177.2  -144.0  -152.9  -120.5
 42    G A.G42             171.2  -150.4  -171.5  -151.6  -133.9  -124.5
 43    G A.G43             174.2  -151.6  -174.4  -150.0  -134.0  -124.5
 44    A A.A44             173.2  -120.4  -171.8  -120.0  -133.3   -72.6
 45    G A.G45             168.6  -141.6  -168.3  -128.4  -103.4  -133.4
 46    g A.7MG46          -143.2  -107.3  -133.6  -149.6  -148.2  -162.7
 47    U A.U47             -31.5   -56.8     4.8   -91.0    24.9  -110.7
 48    C A.C48             -82.5    53.9   -29.3    17.5     1.5  -107.6
 49    c A.5MC49           -56.7  -145.3   -36.6  -142.8   103.2  -130.2
 50    U A.U50             174.8  -146.6  -176.9  -142.8  -153.6  -113.8
 51    G A.G51             170.3  -147.3  -175.5  -148.2  -134.2  -122.1
 52    U A.U52             160.3  -145.8   173.9  -144.3  -141.8  -119.6
 53    G A.G53             174.9  -141.5  -167.2  -142.4  -124.7  -111.6
 54    t A.5MU54           171.1  -129.2  -177.4  -122.6  -133.3   -76.4
 55    P A.PSU55           165.3  -115.2  -173.6  -155.4  -112.1   145.1
 56    C A.C56              31.4  -126.9    51.6  -124.1    25.3   -87.4
 57    G A.G57             164.3  -142.5  -174.1  -131.9  -119.2  -113.8
 58    a A.1MA58          -131.5  -108.7  -105.3  -171.2  -104.2   159.8
 59    U A.U59               1.8  -119.4    26.8  -109.9    49.0   -56.9
 60    C A.C60            -171.8   -40.7  -130.1   -68.5   -70.2   -35.8
 61    C A.C61             122.4  -148.3   168.6  -144.1  -158.2  -117.4
 62    A A.A62             173.0  -146.6  -176.9  -144.9  -142.0  -119.6
 63    C A.C63             164.5  -148.3   177.9  -149.6  -143.9  -128.6
 64    A A.A64             158.4  -151.0   168.5  -148.2  -154.8  -122.8
 65    G A.G65             173.6  -147.3  -172.0  -145.4  -130.5  -121.2
 66    A A.A66             177.6  -145.4  -170.1  -142.7  -133.5  -111.9
 67    A A.A67             165.6  -149.3  -176.9  -149.8  -129.8  -126.7
 68    U A.U68             168.9  -138.2   179.4  -136.1  -143.2   -96.5
 69    U A.U69             165.6  -160.5  -176.0  -161.2  -118.8  -156.9
 70    C A.C70             166.7  -146.2   173.6  -149.0  -171.6  -127.0
 71    G A.G71             161.0  -143.0   174.0  -142.3  -146.3  -113.4
 72    C A.C72             166.1  -141.5  -177.5  -141.9  -131.5  -110.2
 73    A A.A73             167.6  -137.8  -177.2  -133.3  -127.1   -89.8
 74    C A.C74             171.2  -122.1  -172.8  -116.5  -116.2   -72.1
 75    C A.C75             174.9   106.5  -161.9   109.8  -102.9  -139.3
 76    A A.A76               ---     ---     ---     ---     ---     ---
******************************************************************************************
Sugar conformational parameters:

  v0: C4'-O4'-C1'-C2'
  v1: O4'-C1'-C2'-C3'
  v2: C1'-C2'-C3'-C4'
  v3: C2'-C3'-C4'-O4'
  v4: C3'-C4'-O4'-C1'

  tm: the amplitude of pucker
  P:  the phase angle of pseudorotation
    [Ref: Altona & Sundaralingam (1972): "Conformational analysis
          of the sugar ring in nucleosides and nucleotides. A new
          description using the concept of pseudorotation."
          J Am Chem Soc, 94(23):8205-8212]

          nt                 v0      v1      v2      v3      v4      tm      P   Puckering
 1     G A.G1                1.7   -23.4    35.1   -35.2    21.1    36.5    16.1  C3'-endo
 2     C A.C2                1.6   -23.2    34.8   -34.8    20.9    36.2    16.1  C3'-endo
 3     G A.G3                2.7   -25.1    36.8   -36.1    21.2    38.1    14.6  C3'-endo
 4     G A.G4               -1.6   -22.3    36.3   -38.2    25.0    38.8    20.8  C3'-endo
 5     A A.A5               10.1   -32.6    41.5   -36.6    16.7    41.7     4.8  C3'-endo
 6     U A.U6                0.3   -24.0    37.3   -38.1    23.9    39.2    18.2  C3'-endo
 7     U A.U7              -24.4    35.4   -32.4    18.9     3.3    35.4   156.1  C2'-endo
 8     U A.U8                5.8   -28.7    39.7   -37.2    19.7    40.4    10.5  C3'-endo
 9     A A.A9              -31.7    41.8   -35.6    18.1     8.4    41.2   149.8  C2'-endo
 10    g A.2MG10             7.8   -28.0    36.7   -33.0    15.9    37.0     6.6  C3'-endo
 11    C A.C11               1.2   -21.2    32.1   -32.5    19.8    33.5    16.8  C3'-endo
 12    U A.U12              -4.6   -19.3    34.5   -37.9    26.7    38.1    25.2  C3'-endo
 13    C A.C13              -3.4   -19.4    33.8   -36.4    25.1    36.9    23.7  C3'-endo
 14    A A.A14              12.6   -30.8    36.8   -30.2    11.0    36.8   358.9   C2'-exo
 15    G A.G15               1.9   -24.6    36.8   -36.8    22.2    38.3    16.0  C3'-endo
 16    u A.H2U16             0.0   -18.7    29.2   -30.2    19.2    30.9    18.8  C3'-endo
 17    u A.H2U17            23.0   -36.7    35.1   -23.2     0.2    37.0   341.4   C2'-exo
 18    G A.G18             -27.9    39.5   -35.0    20.2     4.8    38.9   154.3  C2'-endo
 19    G A.G19             -17.6    31.0   -31.9    23.1    -3.8    32.7   167.6  C2'-endo
 20    G A.G20               6.6   -27.8    36.6   -34.2    17.5    37.0     8.7  C3'-endo
 21    A A.A21               3.8   -25.0    35.1   -34.4    19.4    36.0    13.0  C3'-endo
 22    G A.G22              16.4   -34.1    38.1   -29.5     8.3    38.3   353.8   C2'-exo
 23    A A.A23               4.2   -26.6    37.4   -36.5    20.1    38.3    12.6  C3'-endo
 24    G A.G24               3.9   -28.4    40.3   -39.3    22.4    41.5    13.4  C3'-endo
 25    C A.C25               0.6   -24.5    37.8   -38.0    23.6    39.6    17.4  C3'-endo
 26    g A.M2G26             6.3   -27.5    37.1   -34.7    17.9    37.6     9.3  C3'-endo
 27    C A.C27               0.2   -23.5    36.5   -37.2    23.6    38.4    18.3  C3'-endo
 28    C A.C28               6.6   -29.0    39.1   -36.3    18.8    39.6     9.2  C3'-endo
 29    A A.A29               3.4   -26.6    38.4   -37.4    21.4    39.5    13.7  C3'-endo
 30    G A.G30               2.6   -24.2    35.7   -34.9    20.4    36.9    14.5  C3'-endo
 31    A A.A31               2.6   -24.0    35.0   -34.6    20.2    36.2    14.6  C3'-endo
 32    c A.OMC32            -1.2   -21.7    35.1   -36.7    23.9    37.4    20.4  C3'-endo
 33    U A.U33               3.5   -25.4    36.5   -35.3    20.1    37.5    13.3  C3'-endo
 34    g A.OMG34             3.9   -22.7    32.2   -30.8    17.1    32.9    12.2  C3'-endo
 35    A A.A35              -2.0   -19.9    32.7   -34.9    23.4    35.2    21.9  C3'-endo
 36    A A.A36             -20.6    -7.3    30.6   -43.2    40.5    43.9    45.8   C4'-exo
 37    g A.YYG37             2.1   -24.1    36.0   -35.6    21.0    37.4    15.4  C3'-endo
 38    A A.A38              10.9   -30.3    37.6   -32.5    13.6    37.7     2.4  C3'-endo
 39    P A.PSU39             2.1   -25.6    38.5   -38.4    22.8    40.0    15.8  C3'-endo
 40    c A.5MC40             0.8   -22.5    34.6   -35.0    21.5    36.3    17.3  C3'-endo
 41    U A.U41               3.8   -27.7    39.9   -38.6    22.0    41.0    13.4  C3'-endo
 42    G A.G42              -1.7   -22.4    36.8   -38.6    25.4    39.4    20.9  C3'-endo
 43    G A.G43               4.3   -27.6    39.1   -37.6    21.1    40.1    12.6  C3'-endo
 44    A A.A44               1.0   -23.0    35.2   -35.4    21.6    36.8    16.9  C3'-endo
 45    G A.G45               2.1   -24.3    35.7   -35.4    21.2    37.0    15.4  C3'-endo
 46    g A.7MG46           -27.4    38.6   -34.7    19.7     4.7    38.5   154.5  C2'-endo
 47    U A.U47             -20.9    34.8   -35.1    24.3    -2.2    36.4   164.9  C2'-endo
 48    C A.C48             -25.6    38.4   -35.6    22.1     2.1    38.4   158.2  C2'-endo
 49    c A.5MC49             5.8   -28.1    38.7   -36.0    19.1    39.3    10.1  C3'-endo
 50    U A.U50               9.4   -32.2    41.0   -36.4    17.6    41.2     5.6  C3'-endo
 51    G A.G51               4.9   -27.9    38.9   -36.8    20.3    39.7    11.5  C3'-endo
 52    U A.U52               3.2   -28.5    41.4   -40.1    23.6    42.7    14.1  C3'-endo
 53    G A.G53              -1.0   -23.1    37.0   -38.3    24.9    39.4    19.8  C3'-endo
 54    t A.5MU54            -1.4   -22.2    35.9   -37.7    24.8    38.3    20.6  C3'-endo
 55    P A.PSU55             6.2   -29.9    40.9   -38.3    20.4    41.5    10.1  C3'-endo
 56    C A.C56               3.8   -25.3    35.7   -34.5    19.2    36.6    12.6  C3'-endo
 57    G A.G57               4.0   -26.7    37.9   -36.5    20.6    38.9    12.8  C3'-endo
 58    a A.1MA58           -24.3    38.4   -36.9    23.9     0.2    39.0   161.1  C2'-endo
 59    U A.U59              -4.4   -18.3    31.8   -35.7    25.4    35.3    25.8  C3'-endo
 60    C A.C60             -28.8    40.5   -36.4    21.2     4.7    40.3   154.8  C2'-endo
 61    C A.C61               2.6   -25.5    36.8   -36.6    21.5    38.1    14.8  C3'-endo
 62    A A.A62               5.9   -27.8    38.1   -35.4    18.8    38.7     9.9  C3'-endo
 63    C A.C63               5.4   -27.3    37.5   -35.5    19.1    38.1    10.7  C3'-endo
 64    A A.A64               4.1   -28.6    40.2   -38.8    22.2    41.2    12.9  C3'-endo
 65    G A.G65               1.5   -26.6    39.5   -39.9    24.3    41.2    16.5  C3'-endo
 66    A A.A66              -2.9   -21.6    36.5   -38.8    26.5    39.5    22.5  C3'-endo
 67    A A.A67               2.4   -24.9    36.5   -36.1    21.4    37.8    15.0  C3'-endo
 68    U A.U68               5.3   -28.4    39.5   -37.5    20.3    40.3    11.2  C3'-endo
 69    U A.U69               2.9   -26.3    38.3   -37.9    22.3    39.6    14.7  C3'-endo
 70    C A.C70               2.4   -25.9    38.7   -37.9    22.4    40.1    15.0  C3'-endo
 71    G A.G71               3.7   -27.4    39.2   -38.3    21.8    40.3    13.5  C3'-endo
 72    C A.C72              -0.6   -21.9    34.9   -36.2    23.1    37.0    19.5  C3'-endo
 73    A A.A73               2.4   -25.4    37.3   -36.9    21.8    38.6    15.0  C3'-endo
 74    C A.C74               4.4   -25.4    35.6   -34.0    18.6    36.4    11.8  C3'-endo
 75    C A.C75               2.3   -22.5    33.1   -33.0    19.2    34.3    15.1  C3'-endo
 76    A A.A76             -13.6    30.5   -34.8    27.7    -9.1    34.8   176.1  C2'-endo
******************************************************************************************
Assignment of sugar-phosphate backbone suites

  bin: name of the 12 bins based on [delta(i-1), delta, gamma], where
       delta(i-1) and delta can be either 3 (for C3'-endo sugar) or 2
       (for C2'-endo) and gamma can be p/t/m (for gauche+/trans/gauche-
       conformations, respectively) (2x2x3=12 combinations: 33p, 33t,
       ... 22m); 'inc' refers to incomplete cases (i.e., with missing
       torsions), and 'trig' to triages (i.e., with torsion angle
       outliers)
  cluster: 2-char suite name, for one of 53 reported clusters (46
           certain and 7 wannabes), '__' for incomplete cases, and
           '!!' for outliers
  suiteness: measure of conformer-match quality (low to high in range 0 to 1)

    [Ref: Richardson et al. (2008): "RNA backbone: consensus all-angle
          conformers and modular string nomenclature (an RNA Ontology
          Consortium contribution)." RNA, 14(3):465-481]

          nt             bin    cluster   suiteness
 1     G A.G1            inc      __       0
 2     C A.C2            33p      1a       0.935
 3     G A.G3            33p      1a       0.868
 4     G A.G4            33p      1a       0.842
 5     A A.A5            33p      1a       0.847
 6     U A.U6            33p      1a       0.664
 7     U A.U7            32p      1b       0.803
 8     U A.U8            23p      2a       0.509
 9     A A.A9            32p      1[       0.046
 10    g A.2MG10         23p      2g       0.640
 11    C A.C11           33p      1a       0.507
 12    U A.U12           33p      1a       0.898
 13    C A.C13           33t      1c       0.824
 14    A A.A14           trig     !!       0
 15    G A.G15           33p      1a       0.484
 16    u A.H2U16         trig     !!       0
 17    u A.H2U17         33t      !!       0
 18    G A.G18           32p      5p       0.026
 19    G A.G19           22p      4b       0.512
 20    G A.G20           23p      2a       0.623
 21    A A.A21           33t      !!       0
 22    G A.G22           33t      1f       0.714
 23    A A.A23           33p      1a       0.840
 24    G A.G24           33p      1a       0.881
 25    C A.C25           33p      1a       0.967
 26    g A.M2G26         33p      1a       0.819
 27    C A.C27           33p      1a       0.698
 28    C A.C28           33p      1a       0.923
 29    A A.A29           33p      1a       0.973
 30    G A.G30           33p      1a       0.838
 31    A A.A31           33p      1a       0.914
 32    c A.OMC32         33p      1a       0.782
 33    U A.U33           33p      1a       0.897
 34    g A.OMG34         33p      1g       0.784
 35    A A.A35           33p      1a       0.517
 36    A A.A36           33p      1a       0.670
 37    g A.YYG37         33p      1a       0.625
 38    A A.A38           33p      1a       0.903
 39    P A.PSU39         33p      1a       0.680
 40    c A.5MC40         33p      1a       0.942
 41    U A.U41           33p      1a       0.945
 42    G A.G42           33p      1a       0.630
 43    G A.G43           33p      1a       0.882
 44    A A.A44           33p      1a       0.837
 45    G A.G45           33p      1a       0.749
 46    g A.7MG46         32p      1[       0.849
 47    U A.U47           22p      4p       0.589
 48    C A.C48           22t      2u       0.283
 49    c A.5MC49         23p      6d       0.520
 50    U A.U50           33p      1a       0.656
 51    G A.G51           33p      1a       0.981
 52    U A.U52           33p      1a       0.945
 53    G A.G53           33p      1a       0.896
 54    t A.5MU54         33p      1a       0.720
 55    P A.PSU55         33p      1a       0.586
 56    C A.C56           33p      1g       0.894
 57    G A.G57           33p      1a       0.837
 58    a A.1MA58         32p      1[       0.332
 59    U A.U59           23p      4d       0.411
 60    C A.C60           32p      1b       0.662
 61    C A.C61           23p      2a       0.553
 62    A A.A62           33p      1a       0.895
 63    C A.C63           33p      1a       0.964
 64    A A.A64           33p      1a       0.791
 65    G A.G65           33p      1a       0.586
 66    A A.A66           33p      1a       0.940
 67    A A.A67           33p      1a       0.941
 68    U A.U68           33p      1a       0.891
 69    U A.U69           33p      1a       0.951
 70    C A.C70           33p      1a       0.809
 71    G A.G71           33p      1a       0.761
 72    C A.C72           33p      1a       0.832
 73    A A.A73           33p      1a       0.965
 74    C A.C74           33p      1a       0.886
 75    C A.C75           33p      1a       0.639
 76    A A.A76           32t      !!       0

Concatenated suite string per chain. To avoid confusion of lower case
modified nucleotide name (e.g., 'a') with suite cluster (e.g., '1a'),
use --suite-delimiter to add delimiters (matched '()' by default).

1   A RNA nts=76  G1aC1aG1aG1aA1aU1bU2aU1[A2gg1aC1aU1cC!!A1aG!!u!!u5pG4bG2aG!!A1fG1aA1aG1aC1ag1aC1aC1aA1aG1aA1ac1aU1gg1aA1aA1ag1aA1aP1ac1aU1aG1aG1aA1aG1[g4pU2uC6dc1aU1aG1aU1aG1at1aP1gC1aG1[a4dU1bC2aC1aA1aC1aA1aG1aA1aA1aU1aU1aC1aG1aC1aA1aC1aC!!A
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