![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 weeks ago
Closed 8 weeks ago
#18652 closed defect (can't reproduce)
Crash in chain_trace_atoms
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002d4c7f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f35b0140 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1687 in chain_trace_atoms
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 479 in _update_chain_trace_graphics
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 385 in _update_graphics
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 369 in update_graphics_if_needed
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1899 in _update_graphics_if_needed
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 295 in check_for_drawing_change
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 76 in draw_new_frame
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, cython.cimports.libc.math, Cython.Utils, Cython.Plex.Actions, Cython.Plex.Transitions, Cython.Plex.Machines, Cython.Plex.DFA, Cython.Plex.Scanners, Cython.Compiler.Scanning, Cython.StringIOTree, Cython.Compiler.Code, lxml._elementpath, lxml.etree, Cython.Tempita._tempita, Cython.Compiler.Visitor, Cython.Compiler.Parsing, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, markupsafe._speedups, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 109)
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{
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"captureTime" : "2025-08-28 12:04:58.7889 +0200",
"incident" : "9B2E9DB1-D9E5-4A0C-A531-69554AF53421",
"pid" : 65026,
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"procLaunch" : "2025-08-28 12:03:06.6868 +0200",
"procStartAbsTime" : 5488458050002,
"procExitAbsTime" : 5491147847084,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> devel build /Users/luca.genz/Nextcloud/PhD/NucleoSpot/tool
running build
running build_py
copying src/run_DSSR.py -> build/lib/chimerax/NucleoSpot
copying src/methods.py -> build/lib/chimerax/NucleoSpot
copying src/interface_identification.py -> build/lib/chimerax/NucleoSpot
copying src/two_d_representation.py -> build/lib/chimerax/NucleoSpot
copying src/tool.py -> build/lib/chimerax/NucleoSpot
copying src/template.html -> build/lib/chimerax/NucleoSpot
running bdist_wheel
installing to build/bdist.macosx-10.9-universal2/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-universal2/wheel
creating build/bdist.macosx-10.9-universal2/wheel/chimerax
creating build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/run_DSSR.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/rna_structure_utils.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/parsing.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/html_clusters.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/simple_rnaview.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/methods.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/specific_interactions.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/rna_demo.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/rnascape.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/integration_example.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/debug_tool.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/get_helix_coords.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/__init__.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/view.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/interface_identification.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/template.html ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/two_d_representation.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/rnaview_window.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/tool.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/2d_representation.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/.DS_Store -> build/bdist.macosx-10.9-universal2/wheel
running install_egg_info
running egg_info
writing ChimeraX_NucleoSpot.egg-info/PKG-INFO
writing dependency_links to ChimeraX_NucleoSpot.egg-info/dependency_links.txt
writing requirements to ChimeraX_NucleoSpot.egg-info/requires.txt
writing top-level names to ChimeraX_NucleoSpot.egg-info/top_level.txt
writing manifest file 'ChimeraX_NucleoSpot.egg-info/SOURCES.txt'
Copying ChimeraX_NucleoSpot.egg-info to
build/bdist.macosx-10.9-universal2/wheel/ChimeraX_NucleoSpot-0.1-py3.11.egg-
info
running install_scripts
creating
build/bdist.macosx-10.9-universal2/wheel/ChimeraX_NucleoSpot-0.1.dist-
info/WHEEL
creating 'dist/ChimeraX_NucleoSpot-0.1-py3-none-any.whl' and adding
'build/bdist.macosx-10.9-universal2/wheel' to it
adding '.DS_Store'
adding 'chimerax/NucleoSpot/2d_representation.py'
adding 'chimerax/NucleoSpot/__init__.py'
adding 'chimerax/NucleoSpot/debug_tool.py'
adding 'chimerax/NucleoSpot/get_helix_coords.py'
adding 'chimerax/NucleoSpot/html_clusters.py'
adding 'chimerax/NucleoSpot/integration_example.py'
adding 'chimerax/NucleoSpot/interface_identification.py'
adding 'chimerax/NucleoSpot/methods.py'
adding 'chimerax/NucleoSpot/parsing.py'
adding 'chimerax/NucleoSpot/rna_demo.py'
adding 'chimerax/NucleoSpot/rna_structure_utils.py'
adding 'chimerax/NucleoSpot/rnascape.py'
adding 'chimerax/NucleoSpot/rnaview_window.py'
adding 'chimerax/NucleoSpot/run_DSSR.py'
adding 'chimerax/NucleoSpot/simple_rnaview.py'
adding 'chimerax/NucleoSpot/specific_interactions.py'
adding 'chimerax/NucleoSpot/template.html'
adding 'chimerax/NucleoSpot/tool.py'
adding 'chimerax/NucleoSpot/two_d_representation.py'
adding 'chimerax/NucleoSpot/view.py'
adding 'ChimeraX_NucleoSpot-0.1.dist-info/METADATA'
adding 'ChimeraX_NucleoSpot-0.1.dist-info/WHEEL'
adding 'ChimeraX_NucleoSpot-0.1.dist-info/top_level.txt'
adding 'ChimeraX_NucleoSpot-0.1.dist-info/RECORD'
removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in
/Users/luca.genz/Nextcloud/PhD/NucleoSpot/tool/dist/ChimeraX_NucleoSpot-0.1-py3-none-
any.whl
> devel install /Users/luca.genz/Nextcloud/PhD/NucleoSpot/tool
running build
running build_py
copying src/run_DSSR.py -> build/lib/chimerax/NucleoSpot
copying src/methods.py -> build/lib/chimerax/NucleoSpot
copying src/interface_identification.py -> build/lib/chimerax/NucleoSpot
copying src/two_d_representation.py -> build/lib/chimerax/NucleoSpot
copying src/tool.py -> build/lib/chimerax/NucleoSpot
copying src/template.html -> build/lib/chimerax/NucleoSpot
running bdist_wheel
installing to build/bdist.macosx-10.9-universal2/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-universal2/wheel
creating build/bdist.macosx-10.9-universal2/wheel/chimerax
creating build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/run_DSSR.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/rna_structure_utils.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/parsing.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/html_clusters.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/simple_rnaview.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/methods.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/specific_interactions.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/rna_demo.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/rnascape.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/integration_example.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/debug_tool.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/get_helix_coords.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/__init__.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/view.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/interface_identification.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/template.html ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/two_d_representation.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/rnaview_window.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/tool.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/chimerax/NucleoSpot/2d_representation.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/NucleoSpot
copying build/lib/.DS_Store -> build/bdist.macosx-10.9-universal2/wheel
running install_egg_info
running egg_info
writing ChimeraX_NucleoSpot.egg-info/PKG-INFO
writing dependency_links to ChimeraX_NucleoSpot.egg-info/dependency_links.txt
writing requirements to ChimeraX_NucleoSpot.egg-info/requires.txt
writing top-level names to ChimeraX_NucleoSpot.egg-info/top_level.txt
writing manifest file 'ChimeraX_NucleoSpot.egg-info/SOURCES.txt'
Copying ChimeraX_NucleoSpot.egg-info to
build/bdist.macosx-10.9-universal2/wheel/ChimeraX_NucleoSpot-0.1-py3.11.egg-
info
running install_scripts
creating
build/bdist.macosx-10.9-universal2/wheel/ChimeraX_NucleoSpot-0.1.dist-
info/WHEEL
creating 'dist/ChimeraX_NucleoSpot-0.1-py3-none-any.whl' and adding
'build/bdist.macosx-10.9-universal2/wheel' to it
adding '.DS_Store'
adding 'chimerax/NucleoSpot/2d_representation.py'
adding 'chimerax/NucleoSpot/__init__.py'
adding 'chimerax/NucleoSpot/debug_tool.py'
adding 'chimerax/NucleoSpot/get_helix_coords.py'
adding 'chimerax/NucleoSpot/html_clusters.py'
adding 'chimerax/NucleoSpot/integration_example.py'
adding 'chimerax/NucleoSpot/interface_identification.py'
adding 'chimerax/NucleoSpot/methods.py'
adding 'chimerax/NucleoSpot/parsing.py'
adding 'chimerax/NucleoSpot/rna_demo.py'
adding 'chimerax/NucleoSpot/rna_structure_utils.py'
adding 'chimerax/NucleoSpot/rnascape.py'
adding 'chimerax/NucleoSpot/rnaview_window.py'
adding 'chimerax/NucleoSpot/run_DSSR.py'
adding 'chimerax/NucleoSpot/simple_rnaview.py'
adding 'chimerax/NucleoSpot/specific_interactions.py'
adding 'chimerax/NucleoSpot/template.html'
adding 'chimerax/NucleoSpot/tool.py'
adding 'chimerax/NucleoSpot/two_d_representation.py'
adding 'chimerax/NucleoSpot/view.py'
adding 'ChimeraX_NucleoSpot-0.1.dist-info/METADATA'
adding 'ChimeraX_NucleoSpot-0.1.dist-info/WHEEL'
adding 'ChimeraX_NucleoSpot-0.1.dist-info/top_level.txt'
adding 'ChimeraX_NucleoSpot-0.1.dist-info/RECORD'
removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in
/Users/luca.genz/Nextcloud/PhD/NucleoSpot/tool/dist/ChimeraX_NucleoSpot-0.1-py3-none-
any.whl
[toolshed install](help:user/commands/toolshed.html#install)
/Users/luca.genz/Nextcloud/PhD/NucleoSpot/tool/dist/ChimeraX_NucleoSpot-0.1-py3-none-
any.whl reinstall true
[toolshed install
/Users/luca.genz/Nextcloud/PhD/NucleoSpot/tool/dist/ChimeraX_NucleoSpot-0.1-py3-none-
any.whl reinstall true](cxcmd:toolshed install
/Users/luca.genz/Nextcloud/PhD/NucleoSpot/tool/dist/ChimeraX_NucleoSpot-0.1-py3-none-
any.whl reinstall true)
Installed ChimeraX-NucleoSpot (0.1)
> open
> /var/folders/98/5tp430816j7gbtk22tfkw_380000gq/T/tmp8mgdceir/7sot.pdb.pdb
> format pdb
Chain information for 7sot.pdb.pdb #1
---
Chain | Description
A | No description available
B | No description available
> ui tool show NucleoSpot
Please register the custom scheme 'nucleospot' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.
Calculation of interface was successful
> save
> /var/folders/98/5tp430816j7gbtk22tfkw_380000gq/T/tmp9gwkqi2u/7sot.pdb.pdb.pdb
> format pdb models #1
{'num_stacks': 2, 'stacks': [{'index': 1, 'num_nts': 2, 'nts_short': 'YA',
'nts_long': '..A.TYR.336.,..B.A.-2.'}, {'index': 2, 'num_nts': 4, 'nts_short':
'FAAH', 'nts_long': '..A.PHE.348.,..B.A.-1.,..B.A.-4.,..A.HIS.368.'}],
'num_ssSegments': 1, 'ssSegments': [{'index': 1, 'is_broken': True, 'num_nts':
3, 'nts_short': 'AAA', 'nts_long': '..B.A.-4.,..B.A.-2.,..B.A.-1.'}],
'num_splayUnits': 1, 'splayUnits': [{'index': 1, 'num_nts': 2, 'nts_short':
'AA', 'nts_long': '..B.A.-2.,..B.A.-1.'}], 'dbn': {'all_chains': {'num_nts':
3, 'num_chars': 4, 'bseq': 'A&AA', 'sstr': '.&..', 'form': '-&.-'}, 'chain_B':
{'num_nts': 3, 'num_chars': 4, 'bseq': 'A&AA', 'sstr': '.&..', 'form':
'-&.-'}}, 'chains': {'chain_B': {'num_nts': 3, 'bseq': 'A&AA', 'sstr': '.&..',
'form': '-&.-', 'helical_rise': 1.815, 'helical_rise_std': 0.237,
'helical_axis': [-0.879, 0.426, 0.215], 'point1': [14.694, 20.846, 19.073],
'point2': [11.151, 22.563, 19.938], 'num_chars': 7, 'suite': 'A..A2uA'}},
'num_nts': 3, 'nts': [{'index': 1, 'index_chain': 1, 'chain_name': 'B',
'nt_resnum': -4, 'nt_name': 'A', 'nt_code': 'A', 'nt_id': '..B.A.-4.',
'linked_nts': [None, None], 'nt_type': 'RNA', 'dbn': '.', 'is_broken': True,
'summary': "break,syn,~C2'-endo,non-pair-contact,ss-non-loop", 'alpha': None,
'beta': -122.413, 'gamma': 50.682, 'delta': 145.781, 'epsilon': None, 'zeta':
None, 'epsilon_zeta': None, 'bb_type': '--', 'chi': 48.719, 'glyco_bond':
'syn', 'C5prime_xyz': [-5.406, 3.611, 0.799], 'P_xyz': [-6.023, 2.06, -1.245],
'form': '-', 'ssZp': None, 'Dp': None, 'splay_angle': None, 'splay_distance':
None, 'splay_ratio': None, 'eta': None, 'theta': None, 'eta_prime': None,
'theta_prime': None, 'eta_base': None, 'theta_base': None, 'v0': -21.668,
'v1': 35.843, 'v2': -35.739, 'v3': 24.132, 'v4': -1.82, 'amplitude': 37.181,
'phase_angle': 163.991, 'puckering': "C2'-endo", 'sugar_class': "~C2'-endo",
'bin': 'inc', 'cluster': '__', 'suiteness': 0.0, 'filter_rmsd': 0.04, 'frame':
{'rmsd': 0.015, 'origin': [8.873, 14.504, 14.217], 'x_axis': [-0.55, -0.383,
0.742], 'y_axis': [0.484, 0.578, 0.658], 'z_axis': [-0.68, 0.721, -0.132],
'quaternion': [-0.473, 0.033, 0.752, 0.458]}}, {'index': 2, 'index_chain': 2,
'chain_name': 'B', 'nt_resnum': -2, 'nt_name': 'A', 'nt_code': 'A', 'nt_id':
'..B.A.-2.', 'linked_nts': [None, '..B.A.-1.'], 'nt_type': 'RNA', 'dbn': '.',
'summary': "anti,~C2'-endo,ss-non-loop,splayed-apart", 'alpha': None, 'beta':
155.382, 'gamma': -36.019, 'delta': 156.539, 'epsilon': -87.553, 'zeta':
-60.093, 'epsilon_zeta': -27.46, 'bb_type': '--', 'chi': -112.168,
'glyco_bond': 'anti', 'C5prime_xyz': [-2.141, 8.327, -1.537], 'P_xyz':
[-1.077, 10.58, -0.796], 'form': '.', 'ssZp': 0.369, 'Dp': 0.545,
'splay_angle': 144.865, 'splay_distance': 19.405, 'splay_ratio': 0.953, 'eta':
None, 'theta': -45.341, 'eta_prime': None, 'theta_prime': -61.462, 'eta_base':
None, 'theta_base': -62.56, 'v0': -22.286, 'v1': 38.932, 'v2': -39.669, 'v3':
27.801, 'v4': -3.692, 'amplitude': 40.828, 'phase_angle': 166.316,
'puckering': "C2'-endo", 'sugar_class': "~C2'-endo", 'bin': 'inc', 'cluster':
'__', 'suiteness': 0.0, 'filter_rmsd': 0.042, 'frame': {'rmsd': 0.016,
'origin': [14.149, 24.253, 28.9], 'x_axis': [0.53, 0.846, 0.06], 'y_axis':
[0.22, -0.069, -0.973], 'z_axis': [-0.819, 0.529, -0.223], 'quaternion':
[0.556, -0.675, -0.395, 0.281]}}, {'index': 3, 'index_chain': 3, 'chain_name':
'B', 'nt_resnum': -1, 'nt_name': 'A', 'nt_code': 'A', 'nt_id': '..B.A.-1.',
'linked_nts': ['..B.A.-2.', None], 'nt_type': 'RNA', 'dbn': '.', 'summary':
"anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart",
'alpha': -72.627, 'beta': 145.76, 'gamma': -173.345, 'delta': 123.179,
'epsilon': None, 'zeta': None, 'epsilon_zeta': None, 'bb_type': '--', 'chi':
-124.896, 'glyco_bond': 'anti', 'C5prime_xyz': [-1.707, 8.555, -1.511],
'P_xyz': [-1.73, 9.682, -3.873], 'form': '-', 'ssZp': None, 'Dp': None,
'splay_angle': None, 'splay_distance': None, 'splay_ratio': None, 'eta': None,
'theta': None, 'eta_prime': None, 'theta_prime': None, 'eta_base': None,
'theta_base': None, 'v0': -29.083, 'v1': 29.345, 'v2': -18.742, 'v3': 2.333,
'v4': 17.196, 'amplitude': 30.304, 'phase_angle': 128.203, 'puckering':
"C1'-exo", 'sugar_class': "~C2'-endo", 'bin': '22t', 'cluster': '2u',
'suiteness': 0.021, 'filter_rmsd': 0.036, 'frame': {'rmsd': 0.017, 'origin':
[8.684, 18.659, 11.141], 'x_axis': [-0.554, -0.832, 0.023], 'y_axis': [-0.067,
0.072, 0.995], 'z_axis': [-0.83, 0.55, -0.096], 'quaternion': [-0.325, -0.343,
0.656, 0.589]}}], 'num_hbonds': 109, 'hbonds': [{'index': 1, 'atom1_serNum':
4, 'atom2_serNum': 31, 'donAcc_type': 'standard', 'distance': 3.016,
'atom1_id': 'O@..A.HIS.320.', 'atom2_id': 'N@..A.GLU.324.', 'atom_pair':
'O:N', 'residue_pair': 'aa:aa'}, {'index': 2, 'atom1_serNum': 9,
'atom2_serNum': 40, 'donAcc_type': 'standard', 'distance': 2.899, 'atom1_id':
'O@..A.HIS.321.', 'atom2_id': 'N@..A.LEU.325.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 3, 'atom1_serNum': 19, 'atom2_serNum': 48,
'donAcc_type': 'standard', 'distance': 2.929, 'atom1_id': 'O@..A.SER.322.',
'atom2_id': 'N@..A.LEU.326.', 'atom_pair': 'O:N', 'residue_pair': 'aa:aa'},
{'index': 4, 'atom1_serNum': 25, 'atom2_serNum': 56, 'donAcc_type':
'standard', 'distance': 2.912, 'atom1_id': 'O@..A.GLN.323.', 'atom2_id':
'N@..A.LYS.327.', 'atom_pair': 'O:N', 'residue_pair': 'aa:aa'}, {'index': 5,
'atom1_serNum': 34, 'atom2_serNum': 65, 'donAcc_type': 'standard', 'distance':
3.067, 'atom1_id': 'O@..A.GLU.324.', 'atom2_id': 'N@..A.ASP.328.',
'atom_pair': 'O:N', 'residue_pair': 'aa:aa'}, {'index': 6, 'atom1_serNum': 38,
'atom2_serNum': 64, 'donAcc_type': 'standard', 'distance': 3.28, 'atom1_id':
'OE1@..A.GLU.324.', 'atom2_id': 'NZ@..A.LYS.327.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 7, 'atom1_serNum': 39, 'atom2_serNum': 64,
'donAcc_type': 'standard', 'distance': 2.828, 'atom1_id': 'OE2@..A.GLU.324.',
'atom2_id': 'NZ@..A.LYS.327.', 'atom_pair': 'O:N', 'residue_pair': 'aa:aa'},
{'index': 8, 'atom1_serNum': 43, 'atom2_serNum': 73, 'donAcc_type':
'standard', 'distance': 3.11, 'atom1_id': 'O@..A.LEU.325.', 'atom2_id':
'N@..A.TYR.329.', 'atom_pair': 'O:N', 'residue_pair': 'aa:aa'}, {'index': 9,
'atom1_serNum': 51, 'atom2_serNum': 85, 'donAcc_type': 'standard', 'distance':
2.96, 'atom1_id': 'O@..A.LEU.326.', 'atom2_id': 'N@..A.ILE.330.', 'atom_pair':
'O:N', 'residue_pair': 'aa:aa'}, {'index': 10, 'atom1_serNum': 59,
'atom2_serNum': 93, 'donAcc_type': 'standard', 'distance': 2.833, 'atom1_id':
'O@..A.LYS.327.', 'atom2_id': 'N@..A.LYS.331.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 11, 'atom1_serNum': 68, 'atom2_serNum':
102, 'donAcc_type': 'standard', 'distance': 3.018, 'atom1_id':
'O@..A.ASP.328.', 'atom2_id': 'N@..A.ARG.332.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 12, 'atom1_serNum': 72, 'atom2_serNum':
109, 'donAcc_type': 'standard', 'distance': 3.232, 'atom1_id':
'OD2@..A.ASP.328.', 'atom2_id': 'NE@..A.ARG.332.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 13, 'atom1_serNum': 76, 'atom2_serNum':
113, 'donAcc_type': 'standard', 'distance': 3.017, 'atom1_id':
'O@..A.TYR.329.', 'atom2_id': 'N@..A.GLN.333.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 14, 'atom1_serNum': 88, 'atom2_serNum':
122, 'donAcc_type': 'standard', 'distance': 3.006, 'atom1_id':
'O@..A.ILE.330.', 'atom2_id': 'N@..A.ILE.334.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 15, 'atom1_serNum': 96, 'atom2_serNum':
130, 'donAcc_type': 'standard', 'distance': 2.856, 'atom1_id':
'O@..A.LYS.331.', 'atom2_id': 'N@..A.GLU.335.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 16, 'atom1_serNum': 105, 'atom2_serNum':
139, 'donAcc_type': 'standard', 'distance': 3.047, 'atom1_id':
'O@..A.ARG.332.', 'atom2_id': 'N@..A.TYR.336.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 17, 'atom1_serNum': 116, 'atom2_serNum':
121, 'donAcc_type': 'standard', 'distance': 3.191, 'atom1_id':
'O@..A.GLN.333.', 'atom2_id': 'NE2@..A.GLN.333.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 18, 'atom1_serNum': 116, 'atom2_serNum':
151, 'donAcc_type': 'standard', 'distance': 3.35, 'atom1_id':
'O@..A.GLN.333.', 'atom2_id': 'N@..A.TYR.337.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 19, 'atom1_serNum': 120, 'atom2_serNum':
429, 'donAcc_type': 'standard', 'distance': 2.824, 'atom1_id':
'OE1@..A.GLN.333.', 'atom2_id': 'NE@..A.ARG.369.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 20, 'atom1_serNum': 121, 'atom2_serNum':
793, 'donAcc_type': 'standard', 'distance': 3.006, 'atom1_id':
'NE2@..A.GLN.333.', 'atom2_id': 'N3@..B.A.-2.', 'atom_pair': 'N:N',
'residue_pair': 'nt:aa'}, {'index': 21, 'atom1_serNum': 125, 'atom2_serNum':
163, 'donAcc_type': 'standard', 'distance': 3.241, 'atom1_id':
'O@..A.ILE.334.', 'atom2_id': 'N@..A.PHE.338.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 22, 'atom1_serNum': 133, 'atom2_serNum':
174, 'donAcc_type': 'standard', 'distance': 3.111, 'atom1_id':
'O@..A.GLU.335.', 'atom2_id': 'N@..A.SER.339.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 23, 'atom1_serNum': 138, 'atom2_serNum':
562, 'donAcc_type': 'acceptable', 'distance': 2.559, 'atom1_id':
'OE2@..A.GLU.335.', 'atom2_id': 'OG@..A.SER.387.', 'atom_pair': 'O:O',
'residue_pair': 'aa:aa'}, {'index': 24, 'atom1_serNum': 142, 'atom2_serNum':
174, 'donAcc_type': 'standard', 'distance': 2.992, 'atom1_id':
'O@..A.TYR.336.', 'atom2_id': 'N@..A.SER.339.', 'atom_pair': 'O:N',
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'NH2@..A.ARG.399.', 'atom2_id': 'OE2@..A.GLU.401.', 'atom_pair': 'N:O',
'residue_pair': 'aa:aa'}, {'index': 107, 'atom1_serNum': 657, 'atom2_serNum':
826, 'donAcc_type': 'acceptable', 'distance': 2.97, 'atom1_id':
'NH2@..A.ARG.399.', 'atom2_id': 'O3@..A.SO4.502.', 'atom_pair': 'N:O',
'residue_pair': 'aa:ligand'}, {'index': 108, 'atom1_serNum': 681,
'atom2_serNum': 699, 'donAcc_type': 'standard', 'distance': 3.373, 'atom1_id':
'O@..A.GLU.402.', 'atom2_id': 'N@..A.LYS.405.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}, {'index': 109, 'atom1_serNum': 690, 'atom2_serNum':
706, 'donAcc_type': 'standard', 'distance': 3.255, 'atom1_id':
'O@..A.PRO.403.', 'atom2_id': 'N@..A.TRP.406.', 'atom_pair': 'O:N',
'residue_pair': 'aa:aa'}], 'refCoords': {'purine': [' 12 ATOMS, 12 BONDS', ' 1
N -2.2500 5.0000 0.4000', ' 2 N -2.2500 0.5000 0.4000', ' 3 N -2.2500 0.5000
-0.4000', ' 4 N -2.2500 5.0000 -0.4000', ' 5 C 2.2500 5.0000 0.4000', ' 6 C
2.2500 0.5000 0.4000', ' 7 C 2.2500 0.5000 -0.4000', ' 8 C 2.2500 5.0000
-0.4000', ' 9 C -2.2500 5.0000 0.4000', ' 10 C -2.2500 0.5000 0.4000', ' 11 C
-2.2500 0.5000 -0.4000', ' 12 C -2.2500 5.0000 -0.4000', ' 1 1 2', ' 2 2 3', '
3 3 4', ' 4 4 1', ' 5 5 6', ' 6 6 7', ' 7 7 8', ' 8 5 8', ' 9 9 5', ' 10 10
6', ' 11 11 7', ' 12 12 8'], 'pyrimidine': [' 12 ATOMS, 12 BONDS', ' 1 N
-2.2500 5.0000 0.4000', ' 2 N -2.2500 2.0000 0.4000', ' 3 N -2.2500 2.0000
-0.4000', ' 4 N -2.2500 5.0000 -0.4000', ' 5 C 2.2500 5.0000 0.4000', ' 6 C
2.2500 2.0000 0.4000', ' 7 C 2.2500 2.0000 -0.4000', ' 8 C 2.2500 5.0000
-0.4000', ' 9 C -2.2500 5.0000 0.4000', ' 10 C -2.2500 2.0000 0.4000', ' 11 C
-2.2500 2.0000 -0.4000', ' 12 C -2.2500 5.0000 -0.4000', ' 1 1 2', ' 2 2 3', '
3 3 4', ' 4 4 1', ' 5 5 6', ' 6 6 7', ' 7 7 8', ' 8 5 8', ' 9 9 5', ' 10 10
6', ' 11 11 7', ' 12 12 8'], 'wc_pair': [' 12 ATOMS, 12 BONDS', ' 1 N -2.2500
5.0000 0.4000', ' 2 N -2.2500 -5.0000 0.4000', ' 3 N -2.2500 -5.0000 -0.4000',
' 4 N -2.2500 5.0000 -0.4000', ' 5 C 2.2500 5.0000 0.4000', ' 6 C 2.2500
-5.0000 0.4000', ' 7 C 2.2500 -5.0000 -0.4000', ' 8 C 2.2500 5.0000 -0.4000',
' 9 C -2.2500 5.0000 0.4000', ' 10 C -2.2500 -5.0000 0.4000', ' 11 C -2.2500
-5.0000 -0.4000', ' 12 C -2.2500 5.0000 -0.4000', ' 1 1 2', ' 2 2 3', ' 3 3
4', ' 4 4 1', ' 5 5 6', ' 6 6 7', ' 7 7 8', ' 8 5 8', ' 9 9 5', ' 10 10 6', '
11 11 7', ' 12 12 8']}, 'metadata': {'version': 'DSSR v2.6.0-2025jul24 by
xiangjun@x3dna.org', 'license':
'http://innovation.columbia.edu/technologies/CU20391', 'url':
'http://x3dna.org/', 'url_alt': 'http://home.x3dna.org/', 'forum':
'http://forum.x3dna.org/', 'citation': "Lu et al. (2015). 'DSSR: an integrated
software tool for dissecting the spatial structure of RNA.' Nucleic Acids
Res., 43(21):e142 [doi:10.1093/nar/gkv716].", 'command': 'x3dna-dssr
-i=/var/folders/98/5tp430816j7gbtk22tfkw_380000gq/T/tmp9gwkqi2u/7sot.pdb.pdb.pdb
--json --prefix=7sot.pdb.pdb', 'input_file':
'/var/folders/98/5tp430816j7gbtk22tfkw_380000gq/T/tmp9gwkqi2u/7sot.pdb.pdb.pdb',
'str_id': '7sot.pdb.pdb', 'num_aaChains': 1, 'aaChains': 'A=91',
'num_naChains': 1, 'naChains': 'B=3', 'num_atoms': 894, 'num_waters': 69,
'num_notes': 52, 'notes': [{'Aminors': 'A-minor interactions (including types
I and II)'}, {'Cstem_index': "stem index of the 'Canonical' helix in k-turn"},
{'Cstem_pair': 'Cstem bp delineating the k-turn internal loop'}, {'Dp':
"perpendicular distance of the 3' P atom to the glycosidic bond"}, {'GA_pair':
'sheared G-A pair in k-turn'}, {'HtypePknot': 'H-type pseudoknot'}, {'Kturn':
'kink-turn (k-turn)'}, {'LW': 'Leontis-Westhof'}, {'NCstem_index': "stem index
of the 'Non-Canonical' helix in k-turn"}, {'NCstem_pair': 'NCstem bp
delineating the k-turn internal loop'}, {'Uturn': 'U-turn of the UNR- or GNRA-
type'}, {'aa': 'amino acid'}, {'atom_pair': 'symbols of the two atoms involved
in an H-bond'}, {'auxfiles': 'auxiliary files'}, {'glyco_bond': 'conformation
of base related to sugar (syn or anti)'}, {'bb_type': 'backbone conformation,
BI or BII'}, {'bending_angle': 'angle between two helical axes'}, {'bp': 'base
pair'}, {'bseq': 'base sequence in one-letter code'}, {'bulge': 'bulge loop'},
{'coaxStacks': 'coaxial stacking of stems within a helix'}, {'dbn': 'dot
bracket notation'}, {'desc': 'description'}, {'donAcc_type': 'donor/acceptor
type of the atom pair in an H-bond'}, {'epsilon_zeta': 'difference between
epsilon and zeta torsion angles'}, {'hairpin': 'hairpin loop'}, {'hbond':
'hydrogen bond (H-bond)'}, {'helix': 'defined by base-stacking interactions,
regardless of bp type and backbone connectivity'}, {'id': 'identifier'},
{'iloop': 'internal loop'}, {'index': 'serial number'}, {'isoCanonPairs':
'isolated canonical pairs'}, {'junction': '(multi-branched) junction loop'},
{'kissingLoop': 'kissing loop'}, {'multiplet': '3+ bases in a coplanar
geometry'}, {'na': 'nucleic acid'}, {'nonPair': 'two nts not forming a pair,
but with H-bonding/stacking interactions'}, {'nonStack': 'nucleotide not
involved in stacking interactions'}, {'nt': 'nucleotide'}, {'num': 'number'},
{'oArea': 'overlap areas between two bases, including exocyclic atoms'},
{'oArea_ring': 'overlap areas between two bases, including only ring atoms'},
{'phosContacts': 'H-bonding and atom-capping interactions involving a
phosphate'}, {'residue_pair': 'types of the two residues involved in an
H-bond'}, {'rmsd': 'root-mean-squares deviation'}, {'serNum': 'serial
number'}, {'ssSegments': 'single-stranded segments not involved in loops'},
{'ssZp': "Z-coordinate of the 3' phosphorus atom with reference to the 5' base
plane"}, {'sstr': 'secondary structure in dbn'}, {'stem': 'helix consisting of
only canonical pairs, with a continuous backbone'}, {'str_id': 'structure
identifier, derived from inpfile with extension removed'}, {'vert_dist':
'vertical distance from an atom to a base plane'}], 'num_auxfiles': 6,
'auxfiles': [{'index': 1, 'name': '7sot.pdb.pdb-2ndstrs.bpseq', 'desc':
'secondary structure in bpseq format'}, {'index': 2, 'name':
'7sot.pdb.pdb-2ndstrs.ct', 'desc': 'secondary structure in connectivity table
format'}, {'index': 3, 'name': '7sot.pdb.pdb-2ndstrs.dbn', 'desc': 'secondary
structure in dot-bracket notation'}, {'index': 4, 'name': '7sot.pdb.pdb-
torsions.txt', 'desc': 'backbone torsion angles and suite names'}, {'index':
5, 'name': '7sot.pdb.pdb-splays.pdb', 'desc': 'an ensemble of splayed-apart
units'}, {'index': 6, 'name': '7sot.pdb.pdb-stacks.pdb', 'desc': 'an ensemble
of base stacks'}], 'start_at': '2025-08-28 12:03:57', 'finish_at': '2025-08-28
12:03:57', 'time_used': '00:00:00:00'}}
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File "/Users/luca.genz/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/NucleoSpot/tool.py",
line 280, in handle_scheme
DSSR_Object(self.session, model, self.dssr_path).draw_2d_structure()
File "/Users/luca.genz/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/NucleoSpot/run_DSSR.py", line 54, in draw_2d_structure
pairs = [(p['nt1'], p['nt2']) for p in self.dssr_data['pairs']]
~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'pairs'
KeyError: 'pairs'
File "/Users/luca.genz/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/NucleoSpot/run_DSSR.py", line 54, in draw_2d_structure
pairs = [(p['nt1'], p['nt2']) for p in self.dssr_data['pairs']]
~~~~~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
> close
> open 3zp8 format mmcif fromDatabase pdb
3zp8 title:
High-resolution full-length hammerhead ribozyme [more info...]
Chain information for 3zp8 #1
---
Chain | Description
A | HAMMERHEAD RIBOZYME, ENZYME STRAND
B | HAMMERHEAD RIBOZYME, SUBSTRATE STRAND
Non-standard residues in 3zp8 #1
---
GDP — guanosine-5'-diphosphate
NA — sodium ion
OMC — O2'-methylycytidine-5'-monophosphate
Calculation of interface was successful
> save /var/folders/98/5tp430816j7gbtk22tfkw_380000gq/T/tmp6ei_grby/3zp8.pdb
> format pdb models #1
{'num_pairs': 30, 'pairs': [{'index': 1, 'nt1': '..A.GDP.1.', 'nt2':
'..B.DC.20.', 'bp': 'g-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW',
'DSSR': 'cW-W'}, {'index': 2, 'nt1': '..A.G.2.', 'nt2': '..B.C.19.', 'bp':
'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 3, 'nt1': '..A.A.3.', 'nt2': '..B.U.18.', 'bp': 'A-U', 'name': 'WC',
'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 4, 'nt1':
'..A.U.4.', 'nt2': '..B.C.15.', 'bp': 'U-C', 'name': '--', 'Saenger': '--',
'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 5, 'nt1': '..A.U.4.', 'nt2':
'..B.A.17.', 'bp': 'U-A', 'name': '--', 'Saenger': '--', 'LW': 'cWW', 'DSSR':
'cW-W'}, {'index': 6, 'nt1': '..A.G.5.', 'nt2': '..B.C.14.', 'bp': 'G-C',
'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 7,
'nt1': '..A.U.6.', 'nt2': '..A.A.28.', 'bp': 'U-A', 'name': 'rHoogsteen',
'Saenger': '24-XXIV', 'LW': 'tWH', 'DSSR': 'tW-M'}, {'index': 8, 'nt1':
'..A.C.8.', 'nt2': '..A.C.26.', 'bp': 'C+C', 'name': '--', 'Saenger': '15-XV',
'LW': 'tWW', 'DSSR': 'tW+W'}, {'index': 9, 'nt1': '..A.U.9.', 'nt2':
'..B.A.12.', 'bp': 'U-A', 'name': 'WC', 'Saenger': '20-XX', 'LW': 'cWW',
'DSSR': 'cW-W'}, {'index': 10, 'nt1': '..A.A.10.', 'nt2': '..B.U.11.', 'bp':
'A-U', 'name': 'WC', 'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 11, 'nt1': '..A.C.11.', 'nt2': '..B.G.10.', 'bp': 'C-G', 'name':
'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 12, 'nt1':
'..A.C.12.', 'nt2': '..B.G.9.', 'bp': 'C-G', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 13, 'nt1': '..A.A.13.',
'nt2': '..B.U.8.', 'bp': 'A-U', 'name': 'WC', 'Saenger': '20-XX', 'LW': 'cWW',
'DSSR': 'cW-W'}, {'index': 14, 'nt1': '..A.G.14.', 'nt2': '..B.C.7.', 'bp':
'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 15, 'nt1': '..A.C.15.', 'nt2': '..A.G.20.', 'bp': 'C-G', 'name':
'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 16, 'nt1':
'..A.G.17.', 'nt2': '..A.A.38.', 'bp': 'G-A', 'name': '--', 'Saenger': '--',
'LW': 'cSW', 'DSSR': 'cm-W'}, {'index': 17, 'nt1': '..A.A.21.', 'nt2':
'..A.G.36.', 'bp': 'A-G', 'name': 'Sheared', 'Saenger': '11-XI', 'LW': 'tHS',
'DSSR': 'tM-m'}, {'index': 18, 'nt1': '..A.G.22.', 'nt2': '..A.C.35.', 'bp':
'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 19, 'nt1': '..A.U.23.', 'nt2': '..A.A.34.', 'bp': 'U-A', 'name':
'WC', 'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 20, 'nt1':
'..A.C.24.', 'nt2': '..A.G.33.', 'bp': 'C-G', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 21, 'nt1': '..A.C.25.',
'nt2': '..A.G.32.', 'bp': 'C-G', 'name': 'WC', 'Saenger': '19-XIX', 'LW':
'cWW', 'DSSR': 'cW-W'}, {'index': 22, 'nt1': '..A.A.28.', 'nt2': '..A.U.30.',
'bp': 'A-U', 'name': '--', 'Saenger': '--', 'LW': '.SW', 'DSSR': '.m-W'},
{'index': 23, 'nt1': '..A.A.31.', 'nt2': '..B.U.13.', 'bp': 'A-U', 'name':
'rHoogsteen', 'Saenger': '24-XXIV', 'LW': 'tHW', 'DSSR': 'tM-W'}, {'index':
24, 'nt1': '..A.A.37.', 'nt2': '..B.OMC.6.', 'bp': 'A-c', 'name': '--',
'Saenger': '--', 'LW': 'tHW', 'DSSR': 'tM-W'}, {'index': 25, 'nt1':
'..A.A.38.', 'nt2': '..B.OMC.6.', 'bp': 'A-c', 'name': '--', 'Saenger': '--',
'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 26, 'nt1': '..A.A.39.', 'nt2':
'..B.U.5.', 'bp': 'A-U', 'name': 'WC', 'Saenger': '20-XX', 'LW': 'cWW',
'DSSR': 'cW-W'}, {'index': 27, 'nt1': '..A.C.40.', 'nt2': '..B.G.4.', 'bp':
'C-G', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 28, 'nt1': '..A.G.41.', 'nt2': '..B.C.3.', 'bp': 'G-C', 'name':
'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 29, 'nt1':
'..A.C.42.', 'nt2': '..B.G.2.', 'bp': 'C-G', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 30, 'nt1': '..A.C.43.',
'nt2': '..B.G.1.', 'bp': 'C-G', 'name': 'WC', 'Saenger': '19-XIX', 'LW':
'cWW', 'DSSR': 'cW-W'}], 'num_multiplets': 3, 'multiplets': [{'index': 1,
'num_nts': 3, 'nts_short': 'UCA', 'nts_long': '..A.U.4.,..B.C.15.,..B.A.17.',
'planarity': 0.37}, {'index': 2, 'num_nts': 3, 'nts_short': 'UAU', 'nts_long':
'..A.U.6.,..A.A.28.,..A.U.30.', 'planarity': 0.997}, {'index': 3, 'num_nts':
3, 'nts_short': 'GAc', 'nts_long': '..A.G.17.,..A.A.38.,..B.OMC.6.',
'planarity': 0.957}], 'num_helices': 4, 'helices': [{'index': 1, 'num_stems':
1, 'strand1': 'gGAUGU', 'strand2': 'CCUCCA', 'bp_type': '|||.|.',
'helix_form': 'AAxAx', 'num_pairs': 6, 'pairs': [{'index': 1, 'nt1':
'..A.GDP.1.', 'nt2': '..B.DC.20.', 'bp': 'g-C', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 2, 'nt1': '..A.G.2.', 'nt2':
'..B.C.19.', 'bp': 'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW',
'DSSR': 'cW-W'}, {'index': 3, 'nt1': '..A.A.3.', 'nt2': '..B.U.18.', 'bp':
'A-U', 'name': 'WC', 'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 4, 'nt1': '..A.U.4.', 'nt2': '..B.C.15.', 'bp': 'U-C', 'name': '--',
'Saenger': '--', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 5, 'nt1': '..A.G.5.',
'nt2': '..B.C.14.', 'bp': 'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW':
'cWW', 'DSSR': 'cW-W'}, {'index': 6, 'nt1': '..A.U.6.', 'nt2': '..A.A.28.',
'bp': 'U-A', 'name': 'rHoogsteen', 'Saenger': '24-XXIV', 'LW': 'tWH', 'DSSR':
'tW-M'}]}, {'index': 2, 'num_stems': 1, 'strand1': 'CGGACG', 'strand2':
'CCCUGA', 'bp_type': '.||||.', 'helix_form': 'xAAA.', 'num_pairs': 6, 'pairs':
[{'index': 1, 'nt1': '..A.C.8.', 'nt2': '..A.C.26.', 'bp': 'C+C', 'name':
'--', 'Saenger': '15-XV', 'LW': 'tWW', 'DSSR': 'tW+W'}, {'index': 2, 'nt1':
'..A.G.32.', 'nt2': '..A.C.25.', 'bp': 'G-C', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 3, 'nt1': '..A.G.33.',
'nt2': '..A.C.24.', 'bp': 'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW':
'cWW', 'DSSR': 'cW-W'}, {'index': 4, 'nt1': '..A.A.34.', 'nt2': '..A.U.23.',
'bp': 'A-U', 'name': 'WC', 'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 5, 'nt1': '..A.C.35.', 'nt2': '..A.G.22.', 'bp': 'C-G', 'name':
'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 6, 'nt1':
'..A.G.36.', 'nt2': '..A.A.21.', 'bp': 'G-A', 'name': 'Sheared', 'Saenger':
'11-XI', 'LW': 'tSH', 'DSSR': 'tm-M'}]}, {'index': 3, 'num_stems': 1,
'strand1': 'GCUGGUAU', 'strand2': 'CGACCAUA', 'bp_type': '|||||||.',
'helix_form': 'x.AAAAx', 'num_pairs': 8, 'pairs': [{'index': 1, 'nt1':
'..A.G.20.', 'nt2': '..A.C.15.', 'bp': 'G-C', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 2, 'nt1': '..B.C.7.', 'nt2':
'..A.G.14.', 'bp': 'C-G', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW',
'DSSR': 'cW-W'}, {'index': 3, 'nt1': '..B.U.8.', 'nt2': '..A.A.13.', 'bp':
'U-A', 'name': 'WC', 'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 4, 'nt1': '..B.G.9.', 'nt2': '..A.C.12.', 'bp': 'G-C', 'name': 'WC',
'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 5, 'nt1':
'..B.G.10.', 'nt2': '..A.C.11.', 'bp': 'G-C', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 6, 'nt1': '..B.U.11.',
'nt2': '..A.A.10.', 'bp': 'U-A', 'name': 'WC', 'Saenger': '20-XX', 'LW':
'cWW', 'DSSR': 'cW-W'}, {'index': 7, 'nt1': '..B.A.12.', 'nt2': '..A.U.9.',
'bp': 'A-U', 'name': 'WC', 'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 8, 'nt1': '..B.U.13.', 'nt2': '..A.A.31.', 'bp': 'U-A', 'name':
'rHoogsteen', 'Saenger': '24-XXIV', 'LW': 'tWH', 'DSSR': 'tW-M'}]}, {'index':
4, 'num_stems': 1, 'strand1': 'AACGCC', 'strand2': 'cUGCGG', 'bp_type':
'.|||||', 'helix_form': '.AAA.', 'num_pairs': 6, 'pairs': [{'index': 1, 'nt1':
'..A.A.38.', 'nt2': '..B.OMC.6.', 'bp': 'A-c', 'name': '--', 'Saenger': '--',
'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 2, 'nt1': '..A.A.39.', 'nt2':
'..B.U.5.', 'bp': 'A-U', 'name': 'WC', 'Saenger': '20-XX', 'LW': 'cWW',
'DSSR': 'cW-W'}, {'index': 3, 'nt1': '..A.C.40.', 'nt2': '..B.G.4.', 'bp':
'C-G', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 4, 'nt1': '..A.G.41.', 'nt2': '..B.C.3.', 'bp': 'G-C', 'name': 'WC',
'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 5, 'nt1':
'..A.C.42.', 'nt2': '..B.G.2.', 'bp': 'C-G', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 6, 'nt1': '..A.C.43.',
'nt2': '..B.G.1.', 'bp': 'C-G', 'name': 'WC', 'Saenger': '19-XIX', 'LW':
'cWW', 'DSSR': 'cW-W'}]}], 'num_stems': 4, 'stems': [{'index': 1,
'helix_index': 1, 'strand1': 'gGA', 'strand2': 'CCU', 'bp_type': '|||',
'helix_form': 'AA', 'num_pairs': 3, 'pairs': [{'index': 1, 'nt1':
'..A.GDP.1.', 'nt2': '..B.DC.20.', 'bp': 'g-C', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 2, 'nt1': '..A.G.2.', 'nt2':
'..B.C.19.', 'bp': 'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW',
'DSSR': 'cW-W'}, {'index': 3, 'nt1': '..A.A.3.', 'nt2': '..B.U.18.', 'bp':
'A-U', 'name': 'WC', 'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'}]},
{'index': 2, 'helix_index': 3, 'strand1': 'UACCAG', 'strand2': 'AUGGUC',
'bp_type': '||||||', 'helix_form': 'AAAA.', 'num_pairs': 6, 'pairs':
[{'index': 1, 'nt1': '..A.U.9.', 'nt2': '..B.A.12.', 'bp': 'U-A', 'name':
'WC', 'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 2, 'nt1':
'..A.A.10.', 'nt2': '..B.U.11.', 'bp': 'A-U', 'name': 'WC', 'Saenger':
'20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 3, 'nt1': '..A.C.11.', 'nt2':
'..B.G.10.', 'bp': 'C-G', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW',
'DSSR': 'cW-W'}, {'index': 4, 'nt1': '..A.C.12.', 'nt2': '..B.G.9.', 'bp':
'C-G', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 5, 'nt1': '..A.A.13.', 'nt2': '..B.U.8.', 'bp': 'A-U', 'name': 'WC',
'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 6, 'nt1':
'..A.G.14.', 'nt2': '..B.C.7.', 'bp': 'G-C', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}]}, {'index': 3, 'helix_index': 2,
'strand1': 'GUCC', 'strand2': 'CAGG', 'bp_type': '||||', 'helix_form': 'AAA',
'num_pairs': 4, 'pairs': [{'index': 1, 'nt1': '..A.G.22.', 'nt2': '..A.C.35.',
'bp': 'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 2, 'nt1': '..A.U.23.', 'nt2': '..A.A.34.', 'bp': 'U-A', 'name':
'WC', 'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 3, 'nt1':
'..A.C.24.', 'nt2': '..A.G.33.', 'bp': 'C-G', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 4, 'nt1': '..A.C.25.',
'nt2': '..A.G.32.', 'bp': 'C-G', 'name': 'WC', 'Saenger': '19-XIX', 'LW':
'cWW', 'DSSR': 'cW-W'}]}, {'index': 4, 'helix_index': 4, 'strand1': 'ACGCC',
'strand2': 'UGCGG', 'bp_type': '|||||', 'helix_form': 'AAA.', 'num_pairs': 5,
'pairs': [{'index': 1, 'nt1': '..A.A.39.', 'nt2': '..B.U.5.', 'bp': 'A-U',
'name': 'WC', 'Saenger': '20-XX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 2,
'nt1': '..A.C.40.', 'nt2': '..B.G.4.', 'bp': 'C-G', 'name': 'WC', 'Saenger':
'19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}, {'index': 3, 'nt1': '..A.G.41.',
'nt2': '..B.C.3.', 'bp': 'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW':
'cWW', 'DSSR': 'cW-W'}, {'index': 4, 'nt1': '..A.C.42.', 'nt2': '..B.G.2.',
'bp': 'C-G', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'},
{'index': 5, 'nt1': '..A.C.43.', 'nt2': '..B.G.1.', 'bp': 'C-G', 'name': 'WC',
'Saenger': '19-XIX', 'LW': 'cWW', 'DSSR': 'cW-W'}]}], 'num_isoCanonPairs': 2,
'isoCanonPairs': [{'index': -1, 'helix_index': 1, 'nt1': '..A.G.5.', 'nt2':
'..B.C.14.', 'bp': 'G-C', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW',
'DSSR': 'cW-W'}, {'index': -2, 'helix_index': 3, 'nt1': '..A.C.15.', 'nt2':
'..A.G.20.', 'bp': 'C-G', 'name': 'WC', 'Saenger': '19-XIX', 'LW': 'cWW',
'DSSR': 'cW-W'}], 'num_stacks': 11, 'stacks': [{'index': 1, 'num_nts': 2,
'nts_short': 'CG', 'nts_long': '..A.C.8.,..A.G.32.'}, {'index': 2, 'num_nts':
2, 'nts_short': 'GA', 'nts_long': '..A.G.17.,..A.A.18.'}, {'index': 3,
'num_nts': 2, 'nts_short': 'GC', 'nts_long': '..A.G.20.,..B.C.7.'}, {'index':
4, 'num_nts': 2, 'nts_short': 'AU', 'nts_long': '..B.A.12.,..B.U.13.'},
{'index': 5, 'num_nts': 3, 'nts_short': 'UAU', 'nts_long':
'..A.U.9.,..A.A.31.,..A.U.30.'}, {'index': 6, 'num_nts': 3, 'nts_short':
'GCU', 'nts_long': '..A.G.14.,..A.C.15.,..A.U.19.'}, {'index': 7, 'num_nts':
3, 'nts_short': 'ACC', 'nts_long': '..A.A.28.,..B.C.14.,..B.C.15.'}, {'index':
8, 'num_nts': 3, 'nts_short': 'AAU', 'nts_long':
'..B.A.16.,..B.A.17.,..B.U.18.'}, {'index': 9, 'num_nts': 4, 'nts_short':
'CGcU', 'nts_long': '..A.C.35.,..A.G.36.,..B.OMC.6.,..B.U.5.'}, {'index': 10,
'num_nts': 5, 'nts_short': 'GAAAA', 'nts_long':
'..A.G.22.,..A.A.21.,..A.A.37.,..A.A.38.,..A.A.39.'}, {'index': 11, 'num_nts':
8, 'nts_short': 'AUGUAACC', 'nts_long':
'..A.A.3.,..A.U.4.,..A.G.5.,..A.U.6.,..A.A.7.,..A.A.27.,..A.C.26.,..A.C.25.'}],
'nonStack': {'num_nts': 2, 'nts_short': 'UA', 'nts_long':
'..A.U.16.,..A.A.29.'}, 'num_atom2bases': 3, 'atom2bases': [{'index': 1,
'type': 'phosphate', 'atom': 'OP2@..A.A.18.', 'nt': '..A.U.16.', 'vert_dist':
2.91}, {'index': 2, 'type': 'sugar', 'atom': "O4'@..A.U.19.", 'nt':
'..A.G.20.', 'vert_dist': 2.907}, {'index': 3, 'type': 'sugar', 'atom':
"O4'@..A.A.28.", 'nt': '..A.U.30.', 'vert_dist': 3.345}], 'num_hairpins': 2,
'hairpins': [{'index': 1, 'type': 'hairpin loop', 'bridging_nts': [4],
'stem_indices': [-2], 'summary': '[1] 4 [A.15 A.20] 1', 'num_nts': 6,
'nts_short': 'CUGAUG', 'nts_long':
'..A.C.15.,..A.U.16.,..A.G.17.,..A.A.18.,..A.U.19.,..A.G.20.', 'num_stems': 1,
'bridges': [{'index': 1, 'num_nts': 4, 'nts_short': 'UGAU', 'nts_long':
'..A.U.16.,..A.G.17.,..A.A.18.,..A.U.19.'}]}, {'index': 2, 'type': 'hairpin
loop', 'bridging_nts': [6], 'stem_indices': [3], 'summary': '[1] 6 [A.25 A.32]
4', 'num_nts': 8, 'nts_short': 'CCAAAUAG', 'nts_long':
'..A.C.25.,..A.C.26.,..A.A.27.,..A.A.28.,..A.A.29.,..A.U.30.,..A.A.31.,..A.G.32.',
'num_stems': 1, 'bridges': [{'index': 1, 'num_nts': 6, 'nts_short': 'CAAAUA',
'nts_long': '..A.C.26.,..A.A.27.,..A.A.28.,..A.A.29.,..A.U.30.,..A.A.31.'}]}],
'num_iloops': 2, 'iloops': [{'index': 1, 'type': 'asymmetric internal loop',
'bridging_nts': [1, 3], 'stem_indices': [1, -1], 'summary': '[2] 1 3 [A.3 B.18
A.5 B.14] 3 1', 'num_nts': 8, 'nts_short': 'AUGCCAAU', 'nts_long':
'..A.A.3.,..A.U.4.,..A.G.5.,..B.C.14.,..B.C.15.,..B.A.16.,..B.A.17.,..B.U.18.',
'num_stems': 2, 'bridges': [{'index': 1, 'num_nts': 1, 'nts_short': 'U',
'nts_long': '..A.U.4.'}, {'index': 2, 'num_nts': 3, 'nts_short': 'CAA',
'nts_long': '..B.C.15.,..B.A.16.,..B.A.17.'}]}, {'index': 2, 'type':
'asymmetric internal loop', 'bridging_nts': [3, 1], 'stem_indices': [-1, 2],
'summary': '[2] 3 1 [A.5 B.14 A.9 B.12] 1 6', 'num_nts': 8, 'nts_short':
'GUACUAUC', 'nts_long':
'..A.G.5.,..A.U.6.,..A.A.7.,..A.C.8.,..A.U.9.,..B.A.12.,..B.U.13.,..B.C.14.',
'num_stems': 2, 'bridges': [{'index': 1, 'num_nts': 3, 'nts_short': 'UAC',
'nts_long': '..A.U.6.,..A.A.7.,..A.C.8.'}, {'index': 2, 'num_nts': 1,
'nts_short': 'U', 'nts_long': '..B.U.13.'}]}], 'num_junctions': 1,
'junctions': [{'index': 1, 'type': '4-way junction', 'bridging_nts': [0, 1, 3,
1], 'stem_indices': [2, -2, 3, 4], 'summary': '[4] 0 1 3 1 [A.14 B.7 A.15 A.20
A.22 A.35 A.39 B.5] 6 1 4 5', 'num_nts': 13, 'nts_short': 'GCGAGCGAAAUcC',
'nts_long':
'..A.G.14.,..A.C.15.,..A.G.20.,..A.A.21.,..A.G.22.,..A.C.35.,..A.G.36.,..A.A.37.,..A.A.38.,..A.A.39.,..B.U.5.,..B.OMC.6.,..B.C.7.',
'num_stems': 4, 'bridges': [{'index': 1, 'num_nts': 0, 'nts_short': '',
'nts_long': ''}, {'index': 2, 'num_nts': 1, 'nts_short': 'A', 'nts_long':
'..A.A.21.'}, {'index': 3, 'num_nts': 3, 'nts_short': 'GAA', 'nts_long':
'..A.G.36.,..A.A.37.,..A.A.38.'}, {'index': 4, 'num_nts': 1, 'nts_short': 'c',
'nts_long': '..B.OMC.6.'}]}], 'num_Aminors': 2, 'Aminors': [{'index': 1,
'type': 'X', 'desc_short': 'A vs A-c (--)', 'desc_long': '..A.A.37. vs
..A.A.38.,..B.OMC.6.', 'A_nt1': {'desc': '..A.A.37. vs ..A.A.38.',
'face_type': '+', 'hbonds_num': 0, 'hbonds_desc': ''}, 'A_nt2': {'desc':
'..A.A.37. vs ..B.OMC.6.', 'face_type': '-', 'hbonds_num': 1, 'hbonds_desc':
'N6(amino)-O2(carbonyl)[3.01]'}}, {'index': 2, 'type': 'X', 'desc_short': 'A
vs U-C (--)', 'desc_long': '..B.A.17. vs ..A.U.4.,..B.C.15.', 'A_nt1':
{'desc': '..B.A.17. vs ..A.U.4.', 'face_type': '-', 'hbonds_num': 1,
'hbonds_desc': 'N6(amino)-O2(carbonyl)[2.86]'}, 'A_nt2': {'desc': '..B.A.17.
vs ..B.C.15.', 'face_type': '+', 'hbonds_num': 0, 'hbonds_desc': ''}}],
'num_splayUnits': 6, 'splayUnits': [{'index': 1, 'num_nts': 2, 'nts_short':
'CU', 'nts_long': '..A.C.8.,..A.U.9.'}, {'index': 2, 'num_nts': 2,
'nts_short': 'AU', 'nts_long': '..A.A.18.,..A.U.19.'}, {'index': 3, 'num_nts':
2, 'nts_short': 'GA', 'nts_long': '..A.G.20.,..A.A.21.'}, {'index': 4,
'num_nts': 3, 'nts_short': 'AAU', 'nts_long':
'..A.A.28.,..A.A.29.,..A.U.30.'}, {'index': 5, 'num_nts': 2, 'nts_short':
'cC', 'nts_long': '..B.OMC.6.,..B.C.7.'}, {'index': 6, 'num_nts': 2,
'nts_short': 'UC', 'nts_long': '..B.U.13.,..B.C.14.'}], 'dbn': {'all_chains':
{'num_nts': 63, 'num_chars': 64, 'bseq':
'gGAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACGAAACGCC&GGCGUcCUGGUAUCCAAUCC', 'bseqUP':
'GGAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACGAAACGCC&GGCGUCCUGGUAUCCAAUCC', 'sstr':
'(((.(...(((((((....).((((......))))...(((((&))))).)))))).)...)))', 'form':
'AA..AA..AAAA.........AAAA......AAA...AAAA.-&AAAA..AAAAA.....AAA-'},
'chain_A': {'num_nts': 43, 'num_chars': 43, 'bseq':
'gGAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACGAAACGCC', 'bseqUP':
'GGAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACGAAACGCC', 'sstr':
'(((.(...(((((((....).((((......))))...(((((', 'form':
'AA..AA..AAAA.........AAAA......AAA...AAAA.-'}, 'chain_B': {'num_nts': 20,
'num_chars': 20, 'bseq': 'GGCGUcCUGGUAUCCAAUCC', 'bseqUP':
'GGCGUCCUGGUAUCCAAUCC', 'sstr': '))))).)))))).)...)))', 'form':
'AAAA..AAAAA.....AAA-'}}, 'chains': {'chain_A': {'num_nts': 43, 'bseq':
'gGAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACGAAACGCC', 'sstr':
'(((.(...(((((((....).((((......))))...(((((', 'form':
'AA..AA..AAAA.........AAAA......AAA...AAAA.-', 'helical_rise': 0.794,
'helical_rise_std': 2.778, 'helical_axis': [-0.75, -0.638, -0.174], 'point1':
[-9.049, 19.054, -7.514], 'point2': [-33.99, -2.153, -13.3], 'num_chars': 127,
'suite':
'g1aG1aA1aU1aG1aU1aA7rC0aU1aA1aC1aC1aA!!G1bC4aU1gG1aA1[U6gG9aA1aG1aU1aC1aC1aC1aA1[A!!A2aU1bA!!G1aG1aA1aC1aG&aA1aA1aA1aC1aG1aC1cC'},
'chain_B': {'num_nts': 20, 'bseq': 'GGCGUcCUGGUAUCCAAUCC', 'sstr':
'))))).)))))).)...)))', 'form': 'AAAA..AAAAA.....AAA-', 'helical_rise': 3.047,
'helical_rise_std': 1.1, 'helical_axis': [0.291, 0.149, 0.945], 'point1':
[-23.369, 5.83, -36.548], 'point2': [-6.503, 14.454, 18.154], 'num_chars': 58,
'suite': 'G1aG1aC1aG1aU1bc!!C1aU1aG1aG1aU1aA1bU4aC1bC!!A1aA1aU1aC1aC'}},
'num_nts': 63, 'nts': [{'index': 1, 'index_chain': 1, 'chain_name': 'A',
'nt_resnum': 1, 'nt_name': 'GDP', 'nt_code': 'g', 'is_modified': True,
'nt_id': '..A.GDP.1.', 'linked_nts': [None, '..A.G.2.'], 'nt_type': 'RNA',
'dbn': '(', 'summary': "modified,anti,~C3'-endo,BI,canonical,non-pair-
contact,helix-end,stem-end", 'alpha': None, 'beta': None, 'gamma': 61.162,
'delta': 84.934, 'epsilon': -150.559, 'zeta': -75.537, 'epsilon_zeta':
-75.022, 'bb_type': 'BI', 'chi': -178.315, 'glyco_bond': 'anti',
'C5prime_xyz': [-1.17, 8.324, 1.629], 'P_xyz': [None, None, None], 'form':
'A', 'ssZp': 4.748, 'Dp': 4.741, 'splay_angle': 26.162, 'splay_distance':
4.081, 'splay_ratio': 0.235, 'eta': None, 'theta': None, 'eta_prime': None,
'theta_prime': None, 'eta_base': None, 'theta_base': None, 'v0': 9.199, 'v1':
-30.85, 'v2': 38.89, 'v3': -34.764, 'v4': 16.366, 'amplitude': 39.056,
'phase_angle': 5.289, 'puckering': "C3'-endo", 'sugar_class': "~C3'-endo",
'bin': 'inc', 'cluster': '__', 'suiteness': 0.0, 'filter_rmsd': 0.065,
'frame': {'rmsd': 0.065, 'origin': [-5.978, 18.088, 15.226], 'x_axis': [0.878,
-0.288, -0.382], 'y_axis': [-0.321, -0.947, -0.025], 'z_axis': [-0.354, 0.145,
-0.924], 'quaternion': [-0.044, 0.968, -0.157, -0.19]}}, {'index': 2,
'index_chain': 2, 'chain_name': 'A', 'nt_resnum': 2, 'nt_name': 'G',
'nt_code': 'G', 'nt_id': '..A.G.2.', 'linked_nts': ['..A.GDP.1.', '..A.A.3.'],
'nt_type': 'RNA', 'dbn': '(', 'summary': "anti,~C3'-endo,BI,canonical,non-
pair-contact,helix,stem", 'alpha': -55.175, 'beta': 167.809, 'gamma': 56.086,
'delta': 77.853, 'epsilon': -151.763, 'zeta': -72.051, 'epsilon_zeta':
-79.713, 'bb_type': 'BI', 'chi': -167.395, 'glyco_bond': 'anti',
'C5prime_xyz': [-1.539, 8.672, 0.966], 'P_xyz': [1.022, 9.118, 1.158], 'form':
'A', 'ssZp': 4.537, 'Dp': 4.642, 'splay_angle': 22.737, 'splay_distance':
3.531, 'splay_ratio': 0.2, 'eta': 174.675, 'theta': -148.387, 'eta_prime':
-170.793, 'theta_prime': -148.301, 'eta_base': -136.255, 'theta_base':
-121.616, 'v0': 3.488, 'v1': -27.348, 'v2': 39.621, 'v3': -38.691, 'v4':
22.099, 'amplitude': 40.799, 'phase_angle': 13.801, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.872,
'filter_rmsd': 0.01, 'frame': {'rmsd': 0.01, 'origin': [-5.656, 20.621,
12.043], 'x_axis': [0.572, -0.717, -0.399], 'y_axis': [-0.735, -0.664, 0.138],
'z_axis': [-0.364, 0.214, -0.906], 'quaternion': [-0.022, 0.886, -0.409,
-0.215]}}, {'index': 3, 'index_chain': 3, 'chain_name': 'A', 'nt_resnum': 3,
'nt_name': 'A', 'nt_code': 'A', 'nt_id': '..A.A.3.', 'linked_nts':
['..A.G.2.', '..A.U.4.'], 'nt_type': 'RNA', 'dbn': '(', 'summary':
"anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,internal-loop",
'alpha': -64.831, 'beta': 179.58, 'gamma': 48.917, 'delta': 78.781, 'epsilon':
-140.007, 'zeta': -65.919, 'epsilon_zeta': -74.088, 'bb_type': 'BI', 'chi':
-160.835, 'glyco_bond': 'anti', 'C5prime_xyz': [-1.136, 8.653, 0.533],
'P_xyz': [1.451, 8.986, 0.68], 'form': '.', 'ssZp': 4.486, 'Dp': 4.798,
'splay_angle': 31.462, 'splay_distance': 4.797, 'splay_ratio': 0.272, 'eta':
168.82, 'theta': -133.082, 'eta_prime': 177.405, 'theta_prime': -126.49,
'eta_base': -142.998, 'theta_base': -82.987, 'v0': 6.149, 'v1': -29.137, 'v2':
39.914, 'v3': -37.279, 'v4': 19.669, 'amplitude': 40.529, 'phase_angle':
10.001, 'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p',
'cluster': '1a', 'suiteness': 0.922, 'filter_rmsd': 0.038, 'frame': {'rmsd':
0.01, 'origin': [-5.155, 21.682, 8.713], 'x_axis': [0.055, -0.974, -0.218],
'y_axis': [-0.96, -0.111, 0.256], 'z_axis': [-0.273, 0.196, -0.942],
'quaternion': [0.021, 0.726, -0.666, -0.169]}}, {'index': 4, 'index_chain': 4,
'chain_name': 'A', 'nt_resnum': 4, 'nt_name': 'U', 'nt_code': 'U', 'nt_id':
'..A.U.4.', 'linked_nts': ['..A.A.3.', '..A.G.5.'], 'nt_type': 'RNA', 'dbn':
'.', 'summary': "anti,~C3'-endo,BI,non-canonical,non-pair-
contact,helix,multiplet,internal-loop,A-minor", 'alpha': -55.197, 'beta':
165.926, 'gamma': 54.802, 'delta': 79.387, 'epsilon': -144.522, 'zeta':
-63.578, 'epsilon_zeta': -80.943, 'bb_type': 'BI', 'chi': -165.154,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.253, 8.623, 0.883], 'P_xyz': [1.35,
8.818, 0.919], 'form': '.', 'ssZp': 4.612, 'Dp': 4.731, 'splay_angle': 31.21,
'splay_distance': 4.743, 'splay_ratio': 0.269, 'eta': 170.064, 'theta':
-132.084, 'eta_prime': -167.079, 'theta_prime': -129.11, 'eta_base': -104.301,
'theta_base': -89.583, 'v0': 5.475, 'v1': -27.707, 'v2': 38.255, 'v3':
-36.007, 'v4': 19.312, 'amplitude': 38.926, 'phase_angle': 10.648,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.868, 'filter_rmsd': 0.11, 'frame': {'rmsd': 0.011,
'origin': [-6.145, 18.634, 5.144], 'x_axis': [-0.648, -0.732, 0.208],
'y_axis': [-0.689, 0.681, 0.249], 'z_axis': [-0.324, 0.018, -0.946],
'quaternion': [-0.147, -0.393, 0.905, 0.074]}}, {'index': 5, 'index_chain': 5,
'chain_name': 'A', 'nt_resnum': 5, 'nt_name': 'G', 'nt_code': 'G', 'nt_id':
'..A.G.5.', 'linked_nts': ['..A.U.4.', '..A.U.6.'], 'nt_type': 'RNA', 'dbn':
'(', 'summary': "anti,~C3'-endo,BI,isolated-canonical,non-pair-
contact,helix,internal-loop", 'alpha': -67.654, 'beta': 173.751, 'gamma':
59.025, 'delta': 81.784, 'epsilon': -138.557, 'zeta': -74.75, 'epsilon_zeta':
-63.807, 'bb_type': 'BI', 'chi': -170.327, 'glyco_bond': 'anti',
'C5prime_xyz': [-1.352, 8.557, 1.157], 'P_xyz': [1.238, 8.694, 1.498], 'form':
'A', 'ssZp': 4.607, 'Dp': 4.717, 'splay_angle': 23.016, 'splay_distance':
3.645, 'splay_ratio': 0.202, 'eta': 170.653, 'theta': -136.66, 'eta_prime':
-169.223, 'theta_prime': -136.125, 'eta_base': -109.672, 'theta_base':
-109.394, 'v0': 4.885, 'v1': -27.277, 'v2': 38.158, 'v3': -36.379, 'v4':
19.799, 'amplitude': 38.947, 'phase_angle': 11.558, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.911,
'filter_rmsd': 0.011, 'frame': {'rmsd': 0.011, 'origin': [-9.309, 16.556,
2.286], 'x_axis': [-0.875, 0.023, 0.483], 'y_axis': [0.05, 0.998, 0.043],
'z_axis': [-0.481, 0.062, -0.875], 'quaternion': [-0.249, 0.019, 0.968,
0.027]}}, {'index': 6, 'index_chain': 6, 'chain_name': 'A', 'nt_resnum': 6,
'nt_name': 'U', 'nt_code': 'U', 'nt_id': '..A.U.6.', 'linked_nts':
['..A.G.5.', '..A.A.7.'], 'nt_type': 'RNA', 'dbn': '.', 'summary':
"anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-
end,multiplet,internal-loop", 'alpha': -59.474, 'beta': 168.146, 'gamma':
51.985, 'delta': 76.491, 'epsilon': -143.903, 'zeta': -71.31, 'epsilon_zeta':
-72.592, 'bb_type': 'BI', 'chi': -160.981, 'glyco_bond': 'anti',
'C5prime_xyz': [-1.474, 8.686, 0.58], 'P_xyz': [1.081, 9.232, 0.571], 'form':
'A', 'ssZp': 4.465, 'Dp': 4.715, 'splay_angle': 21.301, 'splay_distance':
3.399, 'splay_ratio': 0.188, 'eta': 165.281, 'theta': -144.893, 'eta_prime':
-179.678, 'theta_prime': -143.323, 'eta_base': -134.547, 'theta_base':
-112.537, 'v0': 3.612, 'v1': -27.271, 'v2': 39.248, 'v3': -38.299, 'v4':
21.807, 'amplitude': 40.38, 'phase_angle': 13.6, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.888,
'filter_rmsd': 0.098, 'frame': {'rmsd': 0.011, 'origin': [-12.013, 15.444,
0.109], 'x_axis': [-0.68, 0.592, 0.433], 'y_axis': [0.493, 0.806, -0.328],
'z_axis': [-0.543, -0.009, -0.84], 'quaternion': [-0.268, 0.297, 0.912,
-0.092]}}, {'index': 7, 'index_chain': 7, 'chain_name': 'A', 'nt_resnum': 7,
'nt_name': 'A', 'nt_code': 'A', 'nt_id': '..A.A.7.', 'linked_nts':
['..A.U.6.', '..A.C.8.'], 'nt_type': 'RNA', 'dbn': '.', 'summary':
"anti,~C3'-endo,non-pair-contact,internal-loop", 'alpha': -66.24, 'beta':
169.917, 'gamma': 60.167, 'delta': 78.087, 'epsilon': -126.289, 'zeta':
-111.475, 'epsilon_zeta': -14.813, 'bb_type': '--', 'chi': -158.768,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.496, 8.742, 0.366], 'P_xyz': [1.019,
9.301, 0.07], 'form': '.', 'ssZp': 4.276, 'Dp': 4.792, 'splay_angle': 48.996,
'splay_distance': 7.386, 'splay_ratio': 0.416, 'eta': 173.171, 'theta':
-148.925, 'eta_prime': -175.193, 'theta_prime': -155.792, 'eta_base':
-132.909, 'theta_base': -126.918, 'v0': 1.035, 'v1': -24.523, 'v2': 37.267,
'v3': -37.804, 'v4': 23.225, 'amplitude': 39.008, 'phase_angle': 17.185,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.863, 'filter_rmsd': 0.038, 'frame': {'rmsd': 0.01,
'origin': [-15.211, 15.472, -1.042], 'x_axis': [-0.228, 0.938, 0.261],
'y_axis': [0.663, 0.346, -0.663], 'z_axis': [-0.713, 0.022, -0.701],
'quaternion': [-0.323, 0.531, 0.754, -0.213]}}, {'index': 8, 'index_chain': 8,
'chain_name': 'A', 'nt_resnum': 8, 'nt_name': 'C', 'nt_code': 'C', 'nt_id':
'..A.C.8.', 'linked_nts': ['..A.A.7.', '..A.U.9.'], 'nt_type': 'RNA', 'dbn':
'.', 'summary': "turn,syn,~C2'-endo,non-canonical,non-pair-contact,helix-
end,internal-loop,phosphate,splayed-apart", 'alpha': 68.935, 'beta': -128.21,
'gamma': -67.911, 'delta': 154.968, 'epsilon': -114.385, 'zeta': 115.193,
'epsilon_zeta': 130.422, 'bb_type': '--', 'chi': 59.938, 'glyco_bond': 'syn',
'C5prime_xyz': [-5.191, 3.949, 1.201], 'P_xyz': [-7.509, 3.387, 2.277],
'form': '.', 'ssZp': -0.795, 'Dp': 0.921, 'splay_angle': 91.839,
'splay_distance': 13.738, 'splay_ratio': 0.72, 'eta': -105.214, 'theta':
70.43, 'eta_prime': -110.621, 'theta_prime': 84.573, 'eta_base': -101.729,
'theta_base': 116.204, 'v0': -16.931, 'v1': 34.334, 'v2': -37.638, 'v3':
28.981, 'v4': -7.694, 'amplitude': 37.936, 'phase_angle': 172.822,
'puckering': "C2'-endo", 'sugar_class': "~C2'-endo", 'bin': '32m', 'cluster':
'7r', 'suiteness': 0.174, 'filter_rmsd': 0.074, 'frame': {'rmsd': 0.015,
'origin': [-20.265, 16.913, -6.232], 'x_axis': [-0.691, -0.287, 0.663],
'y_axis': [0.307, -0.948, -0.09], 'z_axis': [0.654, 0.141, 0.743],
'quaternion': [-0.161, 0.358, 0.014, 0.919]}}, {'index': 9, 'index_chain': 9,
'chain_name': 'A', 'nt_resnum': 9, 'nt_name': 'U', 'nt_code': 'U', 'nt_id':
'..A.U.9.', 'linked_nts': ['..A.C.8.', '..A.A.10.'], 'nt_type': 'RNA', 'dbn':
'(', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-
end,internal-loop,splayed-apart", 'alpha': -70.111, 'beta': 156.927, 'gamma':
40.85, 'delta': 81.262, 'epsilon': -148.944, 'zeta': -74.523, 'epsilon_zeta':
-74.421, 'bb_type': 'BI', 'chi': -159.95, 'glyco_bond': 'anti', 'C5prime_xyz':
[-1.389, 8.672, 0.548], 'P_xyz': [1.224, 8.849, 0.844], 'form': 'A', 'ssZp':
4.391, 'Dp': 4.637, 'splay_angle': 21.015, 'splay_distance': 3.3,
'splay_ratio': 0.183, 'eta': -174.963, 'theta': -142.879, 'eta_prime':
-178.089, 'theta_prime': -143.279, 'eta_base': -148.468, 'theta_base':
-117.739, 'v0': 3.851, 'v1': -26.038, 'v2': 37.134, 'v3': -35.95, 'v4':
20.182, 'amplitude': 38.1, 'phase_angle': 12.932, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '23p', 'cluster': '0a', 'suiteness': 0.438,
'filter_rmsd': 0.107, 'frame': {'rmsd': 0.011, 'origin': [-13.92, 4.816,
-4.775], 'x_axis': [-0.924, -0.203, -0.325], 'y_axis': [0.062, 0.759, -0.648],
'z_axis': [0.378, -0.619, -0.689], 'quaternion': [0.191, -0.038, 0.918,
-0.345]}}, {'index': 10, 'index_chain': 10, 'chain_name': 'A', 'nt_resnum':
10, 'nt_name': 'A', 'nt_code': 'A', 'nt_id': '..A.A.10.', 'linked_nts':
['..A.U.9.', '..A.C.11.'], 'nt_type': 'RNA', 'dbn': '(', 'summary':
"anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", 'alpha': -66.901,
'beta': 171.68, 'gamma': 52.041, 'delta': 80.39, 'epsilon': -142.749, 'zeta':
-76.969, 'epsilon_zeta': -65.78, 'bb_type': 'BI', 'chi': -159.313,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.361, 8.687, 0.477], 'P_xyz': [1.242,
9.049, 0.564], 'form': 'A', 'ssZp': 4.399, 'Dp': 4.696, 'splay_angle': 20.459,
'splay_distance': 3.245, 'splay_ratio': 0.179, 'eta': 164.179, 'theta':
-144.227, 'eta_prime': 176.044, 'theta_prime': -143.372, 'eta_base': -143.07,
'theta_base': -113.808, 'v0': 4.265, 'v1': -26.156, 'v2': 36.991, 'v3':
-35.57, 'v4': 19.729, 'amplitude': 37.864, 'phase_angle': 12.326, 'puckering':
"C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a',
'suiteness': 0.986, 'filter_rmsd': 0.035, 'frame': {'rmsd': 0.007, 'origin':
[-13.64, 1.979, -6.438], 'x_axis': [-0.783, 0.357, -0.51], 'y_axis': [0.594,
0.671, -0.443], 'z_axis': [0.184, -0.65, -0.737], 'quaternion': [0.194, 0.266,
0.893, -0.306]}}, {'index': 11, 'index_chain': 11, 'chain_name': 'A',
'nt_resnum': 11, 'nt_name': 'C', 'nt_code': 'C', 'nt_id': '..A.C.11.',
'linked_nts': ['..A.A.10.', '..A.C.12.'], 'nt_type': 'RNA', 'dbn': '(',
'summary': "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", 'alpha':
-62.822, 'beta': 160.461, 'gamma': 61.217, 'delta': 78.202, 'epsilon':
-149.305, 'zeta': -74.877, 'epsilon_zeta': -74.427, 'bb_type': 'BI', 'chi':
-159.044, 'glyco_bond': 'anti', 'C5prime_xyz': [-1.372, 8.795, 0.426],
'P_xyz': [1.175, 9.193, -0.051], 'form': 'A', 'ssZp': 4.417, 'Dp': 4.673,
'splay_angle': 26.958, 'splay_distance': 4.305, 'splay_ratio': 0.235, 'eta':
164.978, 'theta': -148.414, 'eta_prime': -179.011, 'theta_prime': -149.861,
'eta_base': -132.724, 'theta_base': -132.042, 'v0': 2.598, 'v1': -26.105,
'v2': 38.391, 'v3': -37.907, 'v4': 22.286, 'amplitude': 39.732, 'phase_angle':
14.923, 'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p',
'cluster': '1a', 'suiteness': 0.825, 'filter_rmsd': 0.061, 'frame': {'rmsd':
0.004, 'origin': [-14.763, -0.02, -8.734], 'x_axis': [-0.343, 0.701, -0.625],
'y_axis': [0.939, 0.247, -0.239], 'z_axis': [-0.013, -0.669, -0.743],
'quaternion': [0.2, 0.537, 0.764, -0.297]}}, {'index': 12, 'index_chain': 12,
'chain_name': 'A', 'nt_resnum': 12, 'nt_name': 'C', 'nt_code': 'C', 'nt_id':
'..A.C.12.', 'linked_nts': ['..A.C.11.', '..A.A.13.'], 'nt_type': 'RNA',
'dbn': '(', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem", 'alpha': -60.504, 'beta': -179.551, 'gamma': 46.499,
'delta': 78.108, 'epsilon': -149.89, 'zeta': -70.597, 'epsilon_zeta': -79.292,
'bb_type': 'BI', 'chi': -162.776, 'glyco_bond': 'anti', 'C5prime_xyz':
[-1.367, 8.758, 0.696], 'P_xyz': [1.117, 9.284, 1.335], 'form': 'A', 'ssZp':
4.467, 'Dp': 4.653, 'splay_angle': 21.935, 'splay_distance': 3.454,
'splay_ratio': 0.192, 'eta': 169.719, 'theta': -148.22, 'eta_prime': 178.198,
'theta_prime': -144.008, 'eta_base': -151.291, 'theta_base': -113.969, 'v0':
3.169, 'v1': -26.644, 'v2': 38.785, 'v3': -38.021, 'v4': 22.004, 'amplitude':
40.008, 'phase_angle': 14.203, 'puckering': "C3'-endo", 'sugar_class':
"~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.871, 'filter_rmsd':
0.065, 'frame': {'rmsd': 0.005, 'origin': [-16.566, -2.451, -11.796],
'x_axis': [0.15, 0.927, -0.343], 'y_axis': [0.985, -0.11, 0.131], 'z_axis':
[0.084, -0.358, -0.93], 'quaternion': [0.165, 0.74, 0.646, -0.088]}},
{'index': 13, 'index_chain': 13, 'chain_name': 'A', 'nt_resnum': 13,
'nt_name': 'A', 'nt_code': 'A', 'nt_id': '..A.A.13.', 'linked_nts':
['..A.C.12.', '..A.G.14.'], 'nt_type': 'RNA', 'dbn': '(', 'summary':
"anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", 'alpha': -64.26,
'beta': -179.036, 'gamma': 47.229, 'delta': 79.964, 'epsilon': -148.142,
'zeta': -51.956, 'epsilon_zeta': -96.186, 'bb_type': 'BI', 'chi': -155.907,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.306, 8.707, 0.298], 'P_xyz': [1.243,
9.11, 0.719], 'form': '.', 'ssZp': 4.305, 'Dp': 4.662, 'splay_angle': 21.549,
'splay_distance': 3.798, 'splay_ratio': 0.198, 'eta': 167.136, 'theta':
-126.737, 'eta_prime': 178.438, 'theta_prime': -128.178, 'eta_base': -141.299,
'theta_base': -107.066, 'v0': 2.761, 'v1': -25.589, 'v2': 37.574, 'v3':
-37.062, 'v4': 21.568, 'amplitude': 38.841, 'phase_angle': 14.673,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.899, 'filter_rmsd': 0.034, 'frame': {'rmsd': 0.009,
'origin': [-17.312, -2.4, -15.168], 'x_axis': [0.664, 0.748, -0.008],
'y_axis': [0.734, -0.649, 0.202], 'z_axis': [0.146, -0.14, -0.979],
'quaternion': [0.094, 0.907, 0.408, 0.038]}}, {'index': 14, 'index_chain': 14,
'chain_name': 'A', 'nt_resnum': 14, 'nt_name': 'G', 'nt_code': 'G', 'nt_id':
'..A.G.14.', 'linked_nts': ['..A.A.13.', '..A.C.15.'], 'nt_type': 'RNA',
'dbn': '(', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem-end,junction-loop", 'alpha': -126.255, 'beta': 159.678,
'gamma': 130.472, 'delta': 85.401, 'epsilon': -139.86, 'zeta': -85.893,
'epsilon_zeta': -53.967, 'bb_type': 'BI', 'chi': -162.993, 'glyco_bond':
'anti', 'C5prime_xyz': [-1.982, 8.823, 0.637], 'P_xyz': [-0.225, 10.2,
-0.753], 'form': '.', 'ssZp': 4.068, 'Dp': 4.305, 'splay_angle': 19.069,
'splay_distance': 3.161, 'splay_ratio': 0.166, 'eta': 179.375, 'theta':
-166.856, 'eta_prime': -162.452, 'theta_prime': -157.346, 'eta_base': -126.71,
'theta_base': -148.479, 'v0': -5.443, 'v1': -15.214, 'v2': 28.742, 'v3':
-32.776, 'v4': 24.138, 'amplitude': 32.569, 'phase_angle': 28.055,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': 'trig', 'cluster':
'!!', 'suiteness': 0.0, 'filter_rmsd': 0.015, 'frame': {'rmsd': 0.015,
'origin': [-16.733, -0.243, -18.24], 'x_axis': [0.896, 0.394, 0.204],
'y_axis': [0.408, -0.912, -0.031], 'z_axis': [0.174, 0.111, -0.979],
'quaternion': [-0.036, 0.973, 0.206, 0.097]}}, {'index': 15, 'index_chain':
15, 'chain_name': 'A', 'nt_resnum': 15, 'nt_name': 'C', 'nt_code': 'C',
'nt_id': '..A.C.15.', 'linked_nts': ['..A.G.14.', '..A.U.16.'], 'nt_type':
'RNA', 'dbn': '(', 'summary': "anti,~C2'-endo,BII,isolated-canonical,non-pair-
contact,helix-end,hairpin-loop,junction-loop", 'alpha': -55.324, 'beta':
172.935, 'gamma': 51.703, 'delta': 153.075, 'epsilon': -87.252, 'zeta':
153.802, 'epsilon_zeta': 118.946, 'bb_type': 'BII', 'chi': -106.89,
'glyco_bond': 'anti', 'C5prime_xyz': [-2.491, 8.342, -1.746], 'P_xyz':
[-0.123, 9.467, -1.669], 'form': '.', 'ssZp': 0.797, 'Dp': 0.815,
'splay_angle': 46.983, 'splay_distance': 7.539, 'splay_ratio': 0.4, 'eta':
-167.733, 'theta': -173.227, 'eta_prime': -139.432, 'theta_prime': 172.984,
'eta_base': -133.884, 'theta_base': -132.357, 'v0': -26.828, 'v1': 41.596,
'v2': -39.315, 'v3': 25.0, 'v4': 1.012, 'amplitude': 41.882, 'phase_angle':
159.834, 'puckering': "C2'-endo", 'sugar_class': "~C2'-endo", 'bin': '32p',
'cluster': '1b', 'suiteness': 0.693, 'filter_rmsd': 0.066, 'frame': {'rmsd':
0.008, 'origin': [-16.938, 1.134, -21.079], 'x_axis': [0.932, -0.05, 0.36],
'y_axis': [0.097, -0.92, -0.38], 'z_axis': [0.35, 0.389, -0.852],
'quaternion': [-0.2, 0.962, 0.012, 0.185]}}, {'index': 16, 'index_chain': 16,
'chain_name': 'A', 'nt_resnum': 16, 'nt_name': 'U', 'nt_code': 'U', 'nt_id':
'..A.U.16.', 'linked_nts': ['..A.C.15.', '..A.G.17.'], 'nt_type': 'RNA',
'dbn': '.', 'summary': "u-turn,anti,~C3'-endo,BI,non-stack,non-pair-
contact,hairpin-loop,cap-acceptor", 'alpha': -63.285, 'beta': 126.377,
'gamma': 50.664, 'delta': 75.796, 'epsilon': -144.114, 'zeta': -71.429,
'epsilon_zeta': -72.685, 'bb_type': 'BI', 'chi': -159.368, 'glyco_bond':
'anti', 'C5prime_xyz': [-1.781, 8.849, 0.443], 'P_xyz': [0.741, 9.034,
-0.226], 'form': '.', 'ssZp': 4.409, 'Dp': 4.653, 'splay_angle': 69.534,
'splay_distance': 10.508, 'splay_ratio': 0.571, 'eta': -172.401, 'theta':
-113.705, 'eta_prime': -164.795, 'theta_prime': -160.661, 'eta_base':
-105.243, 'theta_base': 135.669, 'v0': -2.183, 'v1': -21.897, 'v2': 36.377,
'v3': -38.661, 'v4': 25.75, 'amplitude': 39.169, 'phase_angle': 21.763,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '23p', 'cluster':
'4a', 'suiteness': 0.237, 'filter_rmsd': 0.104, 'frame': {'rmsd': 0.005,
'origin': [-18.133, 3.03, -28.276], 'x_axis': [0.451, -0.419, -0.788],
'y_axis': [-0.445, -0.871, 0.209], 'z_axis': [-0.774, 0.256, -0.579],
'quaternion': [-0.014, 0.852, -0.254, -0.459]}}, {'index': 17, 'index_chain':
17, 'chain_name': 'A', 'nt_resnum': 17, 'nt_name': 'G', 'nt_code': 'G',
'nt_id': '..A.G.17.', 'linked_nts': ['..A.U.16.', '..A.A.18.'], 'nt_type':
'RNA', 'dbn': '.', 'summary': "turn,u-turn,anti,~C3'-endo,BI,non-
canonical,non-pair-contact,multiplet,hairpin-loop", 'alpha': 164.433, 'beta':
170.848, 'gamma': 56.691, 'delta': 83.708, 'epsilon': -135.224, 'zeta':
-68.445, 'epsilon_zeta': -66.779, 'bb_type': 'BI', 'chi': -168.218,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.829, 8.728, 1.005], 'P_xyz': [0.6,
9.208, 1.856], 'form': '.', 'ssZp': 4.142, 'Dp': 4.428, 'splay_angle': 23.44,
'splay_distance': 3.753, 'splay_ratio': 0.203, 'eta': 33.046, 'theta':
-128.508, 'eta_prime': 51.469, 'theta_prime': -129.01, 'eta_base': 22.719,
'theta_base': -76.727, 'v0': -1.614, 'v1': -19.698, 'v2': 32.32, 'v3':
-34.324, 'v4': 22.543, 'amplitude': 34.69, 'phase_angle': 21.301, 'puckering':
"C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1g',
'suiteness': 0.861, 'filter_rmsd': 0.01, 'frame': {'rmsd': 0.01, 'origin':
[-25.805, 6.781, -22.153], 'x_axis': [-0.262, -0.565, 0.783], 'y_axis':
[-0.198, -0.763, -0.616], 'z_axis': [0.945, -0.316, 0.088], 'quaternion':
[-0.126, 0.594, -0.321, 0.727]}}, {'index': 18, 'index_chain': 18,
'chain_name': 'A', 'nt_resnum': 18, 'nt_name': 'A', 'nt_code': 'A', 'nt_id':
'..A.A.18.', 'linked_nts': ['..A.G.17.', '..A.U.19.'], 'nt_type': 'RNA',
'dbn': '.', 'summary': "u-turn,anti,~C3'-endo,non-pair-contact,hairpin-
loop,cap-donor,phosphate,splayed-apart", 'alpha': -70.749, 'beta': 163.651,
'gamma': 53.535, 'delta': 79.26, 'epsilon': -115.867, 'zeta': -52.813,
'epsilon_zeta': -63.054, 'bb_type': '--', 'chi': -160.424, 'glyco_bond':
'anti', 'C5prime_xyz': [-1.482, 8.719, 0.476], 'P_xyz': [1.051, 9.218, 0.093],
'form': '.', 'ssZp': 4.328, 'Dp': 4.857, 'splay_angle': 98.432,
'splay_distance': 13.829, 'splay_ratio': 0.757, 'eta': 157.81, 'theta':
-115.576, 'eta_prime': 176.061, 'theta_prime': -117.631, 'eta_base': -113.856,
'theta_base': -102.263, 'v0': 4.706, 'v1': -28.422, 'v2': 40.057, 'v3':
-38.327, 'v4': 21.247, 'amplitude': 40.969, 'phase_angle': 12.107,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.859, 'filter_rmsd': 0.036, 'frame': {'rmsd': 0.016,
'origin': [-23.518, 4.373, -20.406], 'x_axis': [-0.263, -0.963, 0.063],
'y_axis': [0.16, -0.108, -0.981], 'z_axis': [0.952, -0.248, 0.182],
'quaternion': [-0.45, 0.407, -0.493, 0.623]}}, {'index': 19, 'index_chain':
19, 'chain_name': 'A', 'nt_resnum': 19, 'nt_name': 'U', 'nt_code': 'U',
'nt_id': '..A.U.19.', 'linked_nts': ['..A.A.18.', '..A.G.20.'], 'nt_type':
'RNA', 'dbn': '.', 'summary': "turn,u-turn,anti,~C2'-endo,non-pair-
contact,hairpin-loop,cap-donor,phosphate,splayed-apart", 'alpha': -39.44,
'beta': -113.36, 'gamma': 59.452, 'delta': 144.392, 'epsilon': -95.973,
'zeta': 64.141, 'epsilon_zeta': 199.886, 'bb_type': '--', 'chi': -145.559,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.674, 8.691, 0.175], 'P_xyz': [-0.492,
8.771, 2.563], 'form': '.', 'ssZp': 0.968, 'Dp': 1.003, 'splay_angle': 44.752,
'splay_distance': 7.13, 'splay_ratio': 0.42, 'eta': -100.907, 'theta': 84.578,
'eta_prime': -75.922, 'theta_prime': 77.069, 'eta_base': -77.264,
'theta_base': 86.541, 'v0': -19.514, 'v1': 33.292, 'v2': -33.574, 'v3':
23.155, 'v4': -2.459, 'amplitude': 34.717, 'phase_angle': 165.256,
'puckering': "C2'-endo", 'sugar_class': "~C2'-endo", 'bin': '32p', 'cluster':
'1[', 'suiteness': 0.295, 'filter_rmsd': 0.109, 'frame': {'rmsd': 0.011,
'origin': [-12.747, -2.972, -25.017], 'x_axis': [-0.601, -0.624, -0.5],
'y_axis': [-0.702, 0.711, -0.043], 'z_axis': [0.382, 0.326, -0.865],
'quaternion': [0.248, -0.372, 0.891, 0.079]}}, {'index': 20, 'index_chain':
20, 'chain_name': 'A', 'nt_resnum': 20, 'nt_name': 'G', 'nt_code': 'G',
'nt_id': '..A.G.20.', 'linked_nts': ['..A.U.19.', '..A.A.21.'], 'nt_type':
'RNA', 'dbn': ')', 'summary': "~C3'-endo,isolated-canonical,non-pair-
contact,helix-end,hairpin-loop,junction-loop,cap-acceptor,splayed-apart",
'alpha': -112.38, 'beta': -175.94, 'gamma': 52.34, 'delta': 91.502, 'epsilon':
-144.939, 'zeta': 117.35, 'epsilon_zeta': 97.711, 'bb_type': '--', 'chi':
-74.748, 'glyco_bond': '--', 'C5prime_xyz': [-1.877, 6.218, -3.389], 'P_xyz':
[0.508, 5.421, -4.201], 'form': '.', 'ssZp': -1.101, 'Dp': 4.697,
'splay_angle': 136.259, 'splay_distance': 17.59, 'splay_ratio': 0.928, 'eta':
157.217, 'theta': 57.769, 'eta_prime': 173.502, 'theta_prime': 62.979,
'eta_base': 177.952, 'theta_base': 76.079, 'v0': 15.847, 'v1': -30.689, 'v2':
33.293, 'v3': -25.029, 'v4': 5.983, 'amplitude': 33.673, 'phase_angle':
351.385, 'puckering': "C2'-exo", 'sugar_class': "~C3'-endo", 'bin': '23p',
'cluster': '6g', 'suiteness': 0.028, 'filter_rmsd': 0.014, 'frame': {'rmsd':
0.014, 'origin': [-17.217, 0.906, -21.04], 'x_axis': [0.867, -0.139, 0.478],
'y_axis': [0.038, 0.976, 0.214], 'z_axis': [-0.496, -0.168, 0.852],
'quaternion': [0.961, 0.099, -0.254, -0.046]}}, {'index': 21, 'index_chain':
21, 'chain_name': 'A', 'nt_resnum': 21, 'nt_name': 'A', 'nt_code': 'A',
'nt_id': '..A.A.21.', 'linked_nts': ['..A.G.20.', '..A.G.22.'], 'nt_type':
'RNA', 'dbn': '.', 'summary': "anti,~C3'-endo,non-canonical,non-pair-
contact,helix-end,junction-loop,phosphate,splayed-apart", 'alpha': -65.395,
'beta': 150.382, 'gamma': 56.063, 'delta': 80.902, 'epsilon': -119.875,
'zeta': -61.052, 'epsilon_zeta': -58.823, 'bb_type': '--', 'chi': -179.017,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.69, 8.42, 1.597], 'P_xyz': [0.898,
8.683, 1.819], 'form': '.', 'ssZp': 4.646, 'Dp': 4.715, 'splay_angle': 34.495,
'splay_distance': 5.456, 'splay_ratio': 0.299, 'eta': -163.708, 'theta':
-108.722, 'eta_prime': -144.147, 'theta_prime': -107.479, 'eta_base':
-120.957, 'theta_base': -57.255, 'v0': 2.036, 'v1': -24.757, 'v2': 36.791,
'v3': -36.708, 'v4': 21.842, 'amplitude': 38.21, 'phase_angle': 15.667,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'9a', 'suiteness': 0.75, 'filter_rmsd': 0.038, 'frame': {'rmsd': 0.015,
'origin': [-20.292, 17.666, -25.405], 'x_axis': [-0.795, -0.039, 0.605],
'y_axis': [0.32, -0.875, 0.365], 'z_axis': [0.515, 0.483, 0.708],
'quaternion': [-0.098, 0.305, 0.231, 0.919]}}, {'index': 22, 'index_chain':
22, 'chain_name': 'A', 'nt_resnum': 22, 'nt_name': 'G', 'nt_code': 'G',
'nt_id': '..A.G.22.', 'linked_nts': ['..A.A.21.', '..A.U.23.'], 'nt_type':
'RNA', 'dbn': '(', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem-end,junction-loop", 'alpha': -63.437, 'beta': 162.465,
'gamma': 57.94, 'delta': 76.436, 'epsilon': -155.041, 'zeta': -74.079,
'epsilon_zeta': -80.962, 'bb_type': 'BI', 'chi': -164.143, 'glyco_bond':
'anti', 'C5prime_xyz': [-1.551, 8.835, 0.72], 'P_xyz': [0.993, 9.421, 0.654],
'form': 'A', 'ssZp': 4.505, 'Dp': 4.606, 'splay_angle': 24.063,
'splay_distance': 3.779, 'splay_ratio': 0.209, 'eta': 153.514, 'theta':
-153.884, 'eta_prime': -175.163, 'theta_prime': -154.004, 'eta_base': -94.337,
'theta_base': -133.385, 'v0': -0.599, 'v1': -22.986, 'v2': 36.582, 'v3':
-37.947, 'v4': 24.326, 'amplitude': 38.81, 'phase_angle': 19.507, 'puckering':
"C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a',
'suiteness': 0.516, 'filter_rmsd': 0.007, 'frame': {'rmsd': 0.007, 'origin':
[-21.822, 17.58, -20.168], 'x_axis': [-0.093, -0.829, 0.551], 'y_axis':
[0.912, -0.293, -0.287], 'z_axis': [0.399, 0.476, 0.783], 'quaternion':
[0.591, -0.323, -0.064, -0.737]}}, {'index': 23, 'index_chain': 23,
'chain_name': 'A', 'nt_resnum': 23, 'nt_name': 'U', 'nt_code': 'U', 'nt_id':
'..A.U.23.', 'linked_nts': ['..A.G.22.', '..A.C.24.'], 'nt_type': 'RNA',
'dbn': '(', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem", 'alpha': -72.25, 'beta': -177.281, 'gamma': 53.145,
'delta': 80.399, 'epsilon': -144.516, 'zeta': -59.781, 'epsilon_zeta':
-84.735, 'bb_type': 'BI', 'chi': -162.55, 'glyco_bond': 'anti', 'C5prime_xyz':
[-1.289, 8.688, 0.658], 'P_xyz': [1.29, 9.064, 1.025], 'form': 'A', 'ssZp':
4.508, 'Dp': 4.695, 'splay_angle': 22.29, 'splay_distance': 3.832,
'splay_ratio': 0.204, 'eta': 167.621, 'theta': -131.75, 'eta_prime': 174.986,
'theta_prime': -130.822, 'eta_base': -153.387, 'theta_base': -102.76, 'v0':
4.127, 'v1': -26.459, 'v2': 37.534, 'v3': -36.081, 'v4': 20.172, 'amplitude':
38.449, 'phase_angle': 12.527, 'puckering': "C3'-endo", 'sugar_class':
"~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.871, 'filter_rmsd':
0.108, 'frame': {'rmsd': 0.006, 'origin': [-21.902, 19.416, -16.866],
'x_axis': [0.296, -0.943, 0.155], 'y_axis': [0.848, 0.185, -0.496], 'z_axis':
[0.439, 0.278, 0.854], 'quaternion': [0.764, -0.253, 0.093, -0.586]}},
{'index': 24, 'index_chain': 24, 'chain_name': 'A', 'nt_resnum': 24,
'nt_name': 'C', 'nt_code': 'C', 'nt_id': '..A.C.24.', 'linked_nts':
['..A.U.23.', '..A.C.25.'], 'nt_type': 'RNA', 'dbn': '(', 'summary':
"anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", 'alpha': -71.628,
'beta': 170.158, 'gamma': 67.165, 'delta': 73.697, 'epsilon': -162.567,
'zeta': -73.449, 'epsilon_zeta': -89.118, 'bb_type': 'BI', 'chi': -160.581,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.919, 8.94, 0.474], 'P_xyz': [0.442,
10.005, 0.166], 'form': 'A', 'ssZp': 4.446, 'Dp': 4.544, 'splay_angle':
24.436, 'splay_distance': 3.882, 'splay_ratio': 0.214, 'eta': 165.079,
'theta': -162.933, 'eta_prime': -173.612, 'theta_prime': -163.062, 'eta_base':
-125.64, 'theta_base': -137.972, 'v0': -2.843, 'v1': -22.512, 'v2': 37.722,
'v3': -40.515, 'v4': 27.353, 'amplitude': 40.844, 'phase_angle': 22.546,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.585, 'filter_rmsd': 0.064, 'frame': {'rmsd': 0.004,
'origin': [-21.351, 17.782, -13.444], 'x_axis': [0.672, -0.714, -0.197],
'y_axis': [0.63, 0.691, -0.354], 'z_axis': [0.389, 0.114, 0.914],
'quaternion': [0.905, -0.129, 0.162, -0.371]}}, {'index': 25, 'index_chain':
25, 'chain_name': 'A', 'nt_resnum': 25, 'nt_name': 'C', 'nt_code': 'C',
'nt_id': '..A.C.25.', 'linked_nts': ['..A.C.24.', '..A.C.26.'], 'nt_type':
'RNA', 'dbn': '(', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem-end,hairpin-loop", 'alpha': -64.675, 'beta': 175.443,
'gamma': 56.24, 'delta': 79.813, 'epsilon': -149.952, 'zeta': -72.476,
'epsilon_zeta': -77.476, 'bb_type': 'BI', 'chi': -166.46, 'glyco_bond':
'anti', 'C5prime_xyz': [-1.411, 8.759, 0.891], 'P_xyz': [1.142, 9.192, 1.327],
'form': 'A', 'ssZp': 4.503, 'Dp': 4.614, 'splay_angle': 21.907,
'splay_distance': 3.456, 'splay_ratio': 0.191, 'eta': 172.746, 'theta':
-146.247, 'eta_prime': -178.471, 'theta_prime': -145.65, 'eta_base': -143.14,
'theta_base': -115.104, 'v0': 1.613, 'v1': -24.626, 'v2': 36.962, 'v3':
-37.015, 'v4': 22.313, 'amplitude': 38.494, 'phase_angle': 16.218,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.749, 'filter_rmsd': 0.066, 'frame': {'rmsd': 0.007,
'origin': [-20.701, 16.702, -9.772], 'x_axis': [0.826, -0.281, -0.489],
'y_axis': [0.194, 0.956, -0.222], 'z_axis': [0.53, 0.088, 0.844],
'quaternion': [0.952, -0.081, 0.268, -0.125]}}, {'index': 26, 'index_chain':
26, 'chain_name': 'A', 'nt_resnum': 26, 'nt_name': 'C', 'nt_code': 'C',
'nt_id': '..A.C.26.', 'linked_nts': ['..A.C.25.', '..A.A.27.'], 'nt_type':
'RNA', 'dbn': '.', 'summary': "anti,~C3'-endo,BI,non-canonical,non-pair-
contact,helix-end,hairpin-loop", 'alpha': -67.093, 'beta': 169.694, 'gamma':
55.614, 'delta': 78.016, 'epsilon': -143.786, 'zeta': -63.286, 'epsilon_zeta':
-80.499, 'bb_type': 'BI', 'chi': -164.368, 'glyco_bond': 'anti',
'C5prime_xyz': [-1.314, 8.733, 0.766], 'P_xyz': [1.292, 9.117, 0.733], 'form':
'.', 'ssZp': 4.596, 'Dp': 4.743, 'splay_angle': 27.732, 'splay_distance':
4.32, 'splay_ratio': 0.241, 'eta': 163.96, 'theta': -133.501, 'eta_prime':
177.716, 'theta_prime': -130.464, 'eta_base': -135.408, 'theta_base': -89.725,
'v0': 4.877, 'v1': -28.367, 'v2': 39.807, 'v3': -37.953, 'v4': 20.875,
'amplitude': 40.666, 'phase_angle': 11.796, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.961,
'filter_rmsd': 0.069, 'frame': {'rmsd': 0.008, 'origin': [-18.542, 15.51,
-7.351], 'x_axis': [0.794, 0.316, -0.52], 'y_axis': [-0.273, 0.949, 0.16],
'z_axis': [0.544, 0.015, 0.839], 'quaternion': [0.946, 0.039, 0.281, 0.156]}},
{'index': 27, 'index_chain': 27, 'chain_name': 'A', 'nt_resnum': 27,
'nt_name': 'A', 'nt_code': 'A', 'nt_id': '..A.A.27.', 'linked_nts':
['..A.C.26.', '..A.A.28.'], 'nt_type': 'RNA', 'dbn': '.', 'summary':
"anti,~C3'-endo,BI,non-pair-contact,hairpin-loop", 'alpha': -61.692, 'beta':
168.71, 'gamma': 61.552, 'delta': 80.92, 'epsilon': -154.612, 'zeta': -82.198,
'epsilon_zeta': -72.414, 'bb_type': 'BI', 'chi': -160.337, 'glyco_bond':
'anti', 'C5prime_xyz': [-1.4, 8.71, 0.56], 'P_xyz': [1.187, 9.128, 0.435],
'form': '.', 'ssZp': 4.403, 'Dp': 4.584, 'splay_angle': 50.558,
'splay_distance': 7.945, 'splay_ratio': 0.429, 'eta': 171.98, 'theta':
-169.848, 'eta_prime': -165.017, 'theta_prime': -156.13, 'eta_base': -103.593,
'theta_base': -164.834, 'v0': 2.778, 'v1': -24.749, 'v2': 36.168, 'v3':
-35.584, 'v4': 20.679, 'amplitude': 37.354, 'phase_angle': 14.475,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.841, 'filter_rmsd': 0.033, 'frame': {'rmsd': 0.009,
'origin': [-14.387, 16.294, -6.468], 'x_axis': [0.36, 0.896, -0.259],
'y_axis': [-0.68, 0.442, 0.585], 'z_axis': [0.639, -0.034, 0.769],
'quaternion': [0.802, 0.193, 0.28, 0.492]}}, {'index': 28, 'index_chain': 28,
'chain_name': 'A', 'nt_resnum': 28, 'nt_name': 'A', 'nt_code': 'A', 'nt_id':
'..A.A.28.', 'linked_nts': ['..A.A.27.', '..A.A.29.'], 'nt_type': 'RNA',
'dbn': '.', 'summary': "turn,anti,~C2'-endo,non-canonical,non-pair-
contact,helix-end,multiplet,hairpin-loop,cap-donor,phosphate,splayed-apart",
'alpha': -58.224, 'beta': -131.281, 'gamma': 50.984, 'delta': 146.029,
'epsilon': -120.489, 'zeta': 95.864, 'epsilon_zeta': 143.647, 'bb_type': '--',
'chi': -80.606, 'glyco_bond': 'anti', 'C5prime_xyz': [-3.001, 7.321, -2.738],
'P_xyz': [-1.145, 9.162, -2.82], 'form': '.', 'ssZp': 1.014, 'Dp': 1.384,
'splay_angle': 131.267, 'splay_distance': 18.427, 'splay_ratio': 0.911, 'eta':
-134.98, 'theta': 87.897, 'eta_prime': -137.088, 'theta_prime': 36.956,
'eta_base': -163.559, 'theta_base': 11.005, 'v0': -23.987, 'v1': 37.341, 'v2':
-35.651, 'v3': 22.748, 'v4': 0.563, 'amplitude': 37.851, 'phase_angle':
160.366, 'puckering': "C2'-endo", 'sugar_class': "~C2'-endo", 'bin': '32p',
'cluster': '1[', 'suiteness': 0.794, 'filter_rmsd': 0.036, 'frame': {'rmsd':
0.007, 'origin': [-10.094, 11.568, -1.74], 'x_axis': [0.479, 0.77, -0.422],
'y_axis': [-0.531, 0.637, 0.559], 'z_axis': [0.698, -0.044, 0.714],
'quaternion': [0.841, 0.179, 0.333, 0.387]}}, {'index': 29, 'index_chain': 29,
'chain_name': 'A', 'nt_resnum': 29, 'nt_name': 'A', 'nt_code': 'A', 'nt_id':
'..A.A.29.', 'linked_nts': ['..A.A.28.', '..A.U.30.'], 'nt_type': 'RNA',
'dbn': '.', 'summary': "turn,anti,~C2'-endo,non-stack,hairpin-loop,splayed-
apart", 'alpha': -178.936, 'beta': 146.945, 'gamma': -2.717, 'delta': 146.421,
'epsilon': -109.728, 'zeta': -66.511, 'epsilon_zeta': -43.217, 'bb_type':
'--', 'chi': -114.833, 'glyco_bond': 'anti', 'C5prime_xyz': [-2.264, 8.442,
-1.433], 'P_xyz': [-0.546, 10.04, -0.246], 'form': '.', 'ssZp': 1.084, 'Dp':
1.127, 'splay_angle': 120.67, 'splay_distance': 16.804, 'splay_ratio': 0.869,
'eta': 35.187, 'theta': -56.246, 'eta_prime': 66.983, 'theta_prime': -66.55,
'eta_base': 79.646, 'theta_base': -37.572, 'v0': -23.107, 'v1': 37.074, 'v2':
-36.086, 'v3': 23.668, 'v4': -0.613, 'amplitude': 37.925, 'phase_angle':
162.087, 'puckering': "C2'-endo", 'sugar_class': "~C2'-endo", 'bin': 'trig',
'cluster': '!!', 'suiteness': 0.0, 'filter_rmsd': 0.035, 'frame': {'rmsd':
0.008, 'origin': [-24.856, 18.217, 7.059], 'x_axis': [0.509, 0.801, 0.316],
'y_axis': [0.858, -0.503, -0.106], 'z_axis': [0.074, 0.325, -0.943],
'quaternion': [-0.125, 0.86, 0.482, 0.113]}}, {'index': 30, 'index_chain': 30,
'chain_name': 'A', 'nt_resnum': 30, 'nt_name': 'U', 'nt_code': 'U', 'nt_id':
'..A.U.30.', 'linked_nts': ['..A.A.29.', '..A.A.31.'], 'nt_type': 'RNA',
'dbn': '.', 'summary': "anti,~C3'-endo,BI,non-canonical,non-pair-
contact,multiplet,hairpin-loop,cap-acceptor,splayed-apart", 'alpha': -53.561,
'beta': -163.528, 'gamma': 54.963, 'delta': 82.178, 'epsilon': -152.073,
'zeta': -99.593, 'epsilon_zeta': -52.481, 'bb_type': 'BI', 'chi': -127.864,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.646, 8.516, -1.337], 'P_xyz': [0.911,
9.107, -1.536], 'form': '.', 'ssZp': 3.042, 'Dp': 4.543, 'splay_angle':
26.142, 'splay_distance': 4.293, 'splay_ratio': 0.228, 'eta': -174.961,
'theta': -168.379, 'eta_prime': -134.605, 'theta_prime': -160.797, 'eta_base':
-118.693, 'theta_base': 154.347, 'v0': 1.58, 'v1': -22.455, 'v2': 33.707,
'v3': -33.719, 'v4': 20.309, 'amplitude': 35.088, 'phase_angle': 16.125,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '23p', 'cluster':
'2a', 'suiteness': 0.692, 'filter_rmsd': 0.102, 'frame': {'rmsd': 0.003,
'origin': [-12.54, 9.535, -0.379], 'x_axis': [0.188, -0.667, 0.721], 'y_axis':
[-0.975, -0.04, 0.218], 'z_axis': [-0.117, -0.744, -0.658], 'quaternion':
[0.35, 0.687, -0.598, 0.22]}}, {'index': 31, 'index_chain': 31, 'chain_name':
'A', 'nt_resnum': 31, 'nt_name': 'A', 'nt_code': 'A', 'nt_id': '..A.A.31.',
'linked_nts': ['..A.U.30.', '..A.G.32.'], 'nt_type': 'RNA', 'dbn': '.',
'summary': "turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-
end,hairpin-loop", 'alpha': -43.979, 'beta': 161.817, 'gamma': 46.454,
'delta': 146.735, 'epsilon': -102.491, 'zeta': 83.252, 'epsilon_zeta':
174.257, 'bb_type': '--', 'chi': -75.85, 'glyco_bond': 'anti', 'C5prime_xyz':
[-3.498, 7.26, -2.628], 'P_xyz': [-1.342, 8.174, -3.816], 'form': '.', 'ssZp':
1.208, 'Dp': 1.145, 'splay_angle': 68.008, 'splay_distance': 11.255,
'splay_ratio': 0.559, 'eta': -171.474, 'theta': 89.095, 'eta_prime': -154.399,
'theta_prime': 68.47, 'eta_base': 157.902, 'theta_base': 97.767, 'v0':
-28.167, 'v1': 41.422, 'v2': -37.903, 'v3': 22.628, 'v4': 3.187, 'amplitude':
41.257, 'phase_angle': 156.737, 'puckering': "C2'-endo", 'sugar_class':
"~C2'-endo", 'bin': '32p', 'cluster': '1b', 'suiteness': 0.342, 'filter_rmsd':
0.035, 'frame': {'rmsd': 0.009, 'origin': [-13.51, 10.176, -4.512], 'x_axis':
[0.488, -0.452, 0.747], 'y_axis': [-0.78, -0.61, 0.14], 'z_axis': [0.393,
-0.651, -0.65], 'quaternion': [0.238, 0.829, -0.372, 0.344]}}, {'index': 32,
'index_chain': 32, 'chain_name': 'A', 'nt_resnum': 32, 'nt_name': 'G',
'nt_code': 'G', 'nt_id': '..A.G.32.', 'linked_nts': ['..A.A.31.',
'..A.G.33.'], 'nt_type': 'RNA', 'dbn': ')', 'summary':
"anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,hairpin-loop",
'alpha': -118.671, 'beta': 152.042, 'gamma': 88.198, 'delta': 70.394,
'epsilon': -146.475, 'zeta': -79.385, 'epsilon_zeta': -67.089, 'bb_type':
'BI', 'chi': -175.888, 'glyco_bond': 'anti', 'C5prime_xyz': [-1.888, 8.74,
1.344], 'P_xyz': [0.222, 10.02, 0.464], 'form': 'A', 'ssZp': 4.788, 'Dp':
4.751, 'splay_angle': 24.237, 'splay_distance': 3.79, 'splay_ratio': 0.216,
'eta': 162.008, 'theta': -160.039, 'eta_prime': 174.246, 'theta_prime':
-159.379, 'eta_base': -170.359, 'theta_base': -128.613, 'v0': -1.224, 'v1':
-24.992, 'v2': 40.269, 'v3': -42.098, 'v4': 27.268, 'amplitude': 42.908,
'phase_angle': 20.2, 'puckering': "C3'-endo", 'sugar_class': "~C3'-endo",
'bin': '23p', 'cluster': '!!', 'suiteness': 0.0, 'filter_rmsd': 0.009,
'frame': {'rmsd': 0.009, 'origin': [-20.906, 16.832, -9.771], 'x_axis': [0.77,
-0.208, -0.604], 'y_axis': [-0.121, -0.976, 0.182], 'z_axis': [-0.627, -0.067,
-0.776], 'quaternion': [0.066, 0.938, -0.088, -0.328]}}, {'index': 33,
'index_chain': 33, 'chain_name': 'A', 'nt_resnum': 33, 'nt_name': 'G',
'nt_code': 'G', 'nt_id': '..A.G.33.', 'linked_nts': ['..A.G.32.',
'..A.A.34.'], 'nt_type': 'RNA', 'dbn': ')', 'summary':
"anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", 'alpha': -56.82,
'beta': 170.968, 'gamma': 52.973, 'delta': 78.322, 'epsilon': -155.01, 'zeta':
-73.59, 'epsilon_zeta': -81.42, 'bb_type': 'BI', 'chi': -165.658,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.476, 8.685, 0.834], 'P_xyz': [1.091,
9.109, 1.004], 'form': 'A', 'ssZp': 4.554, 'Dp': 4.634, 'splay_angle': 23.806,
'splay_distance': 3.741, 'splay_ratio': 0.21, 'eta': 171.554, 'theta':
-153.063, 'eta_prime': -176.756, 'theta_prime': -153.042, 'eta_base':
-132.713, 'theta_base': -137.579, 'v0': 3.625, 'v1': -27.309, 'v2': 39.374,
'v3': -38.374, 'v4': 21.852, 'amplitude': 40.508, 'phase_angle': 13.589,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.633, 'filter_rmsd': 0.011, 'frame': {'rmsd': 0.011,
'origin': [-21.433, 18.06, -13.318], 'x_axis': [0.583, -0.736, -0.346],
'y_axis': [-0.601, -0.676, 0.425], 'z_axis': [-0.547, -0.04, -0.836],
'quaternion': [0.132, 0.88, -0.38, -0.254]}}, {'index': 34, 'index_chain': 34,
'chain_name': 'A', 'nt_resnum': 34, 'nt_name': 'A', 'nt_code': 'A', 'nt_id':
'..A.A.34.', 'linked_nts': ['..A.G.33.', '..A.C.35.'], 'nt_type': 'RNA',
'dbn': ')', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem", 'alpha': -68.785, 'beta': 179.712, 'gamma': 54.963,
'delta': 78.401, 'epsilon': -145.538, 'zeta': -69.885, 'epsilon_zeta':
-75.653, 'bb_type': 'BI', 'chi': -163.113, 'glyco_bond': 'anti',
'C5prime_xyz': [-1.336, 8.654, 0.694], 'P_xyz': [1.222, 9.143, 0.874], 'form':
'A', 'ssZp': 4.542, 'Dp': 4.727, 'splay_angle': 23.051, 'splay_distance':
3.646, 'splay_ratio': 0.203, 'eta': 170.401, 'theta': -143.168, 'eta_prime':
177.391, 'theta_prime': -139.985, 'eta_base': -156.047, 'theta_base':
-105.422, 'v0': 4.712, 'v1': -27.365, 'v2': 38.496, 'v3': -36.798, 'v4':
20.274, 'amplitude': 39.343, 'phase_angle': 11.913, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.928,
'filter_rmsd': 0.035, 'frame': {'rmsd': 0.009, 'origin': [-21.889, 19.231,
-16.841], 'x_axis': [0.306, -0.952, -0.012], 'y_axis': [-0.838, -0.275,
0.471], 'z_axis': [-0.452, -0.135, -0.882], 'quaternion': [0.193, 0.785,
-0.57, -0.148]}}, {'index': 35, 'index_chain': 35, 'chain_name': 'A',
'nt_resnum': 35, 'nt_name': 'C', 'nt_code': 'C', 'nt_id': '..A.C.35.',
'linked_nts': ['..A.A.34.', '..A.G.36.'], 'nt_type': 'RNA', 'dbn': ')',
'summary': "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-
end,junction-loop", 'alpha': -63.929, 'beta': 164.722, 'gamma': 61.644,
'delta': 78.108, 'epsilon': -141.051, 'zeta': -57.287, 'epsilon_zeta':
-83.764, 'bb_type': 'BI', 'chi': -164.541, 'glyco_bond': 'anti',
'C5prime_xyz': [-1.496, 8.753, 0.784], 'P_xyz': [1.076, 9.224, 0.643], 'form':
'.', 'ssZp': 4.521, 'Dp': 4.702, 'splay_angle': 33.468, 'splay_distance':
5.166, 'splay_ratio': 0.288, 'eta': 168.455, 'theta': -123.695, 'eta_prime':
-174.161, 'theta_prime': -120.501, 'eta_base': -123.222, 'theta_base':
-69.626, 'v0': 2.461, 'v1': -26.299, 'v2': 38.865, 'v3': -38.412, 'v4':
22.667, 'amplitude': 40.259, 'phase_angle': 15.12, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.844,
'filter_rmsd': 0.064, 'frame': {'rmsd': 0.004, 'origin': [-21.697, 17.23,
-19.883], 'x_axis': [-0.215, -0.912, 0.349], 'y_axis': [-0.906, 0.32, 0.276],
'z_axis': [-0.363, -0.257, -0.896], 'quaternion': [-0.228, -0.583, 0.78,
0.006]}}, {'index': 36, 'index_chain': 36, 'chain_name': 'A', 'nt_resnum': 36,
'nt_name': 'G', 'nt_code': 'G', 'nt_id': '..A.G.36.', 'linked_nts':
['..A.C.35.', '..A.A.37.'], 'nt_type': 'RNA', 'dbn': '.', 'summary':
"anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,junction-loop",
'alpha': -68.023, 'beta': 172.368, 'gamma': 61.409, 'delta': 81.86, 'epsilon':
-169.69, 'zeta': -104.578, 'epsilon_zeta': -65.111, 'bb_type': 'BI', 'chi':
-154.327, 'glyco_bond': 'anti', 'C5prime_xyz': [-1.322, 8.76, 0.21], 'P_xyz':
[1.3, 9.019, 0.096], 'form': '.', 'ssZp': 4.228, 'Dp': 4.459, 'splay_angle':
45.007, 'splay_distance': 6.952, 'splay_ratio': 0.383, 'eta': 164.704,
'theta': 172.815, 'eta_prime': -165.433, 'theta_prime': 171.4, 'eta_base':
-90.401, 'theta_base': 169.254, 'v0': 2.49, 'v1': -23.941, 'v2': 35.045, 'v3':
-34.633, 'v4': 20.32, 'amplitude': 36.25, 'phase_angle': 14.813, 'puckering':
"C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a',
'suiteness': 0.776, 'filter_rmsd': 0.007, 'frame': {'rmsd': 0.007, 'origin':
[-24.825, 13.168, -20.52], 'x_axis': [-0.87, -0.17, 0.463], 'y_axis': [-0.347,
0.879, -0.328], 'z_axis': [-0.351, -0.446, -0.823], 'quaternion': [-0.215,
-0.137, 0.945, -0.205]}}, {'index': 37, 'index_chain': 37, 'chain_name': 'A',
'nt_resnum': 37, 'nt_name': 'A', 'nt_code': 'A', 'nt_id': '..A.A.37.',
'linked_nts': ['..A.G.36.', '..A.A.38.'], 'nt_type': 'RNA', 'dbn': '.',
'summary': "anti,~C3'-endo,BI,non-canonical,non-pair-contact,junction-
loop,A-minor", 'alpha': -52.451, 'beta': 174.704, 'gamma': 44.498, 'delta':
83.465, 'epsilon': -141.672, 'zeta': -66.066, 'epsilon_zeta': -75.606,
'bb_type': 'BI', 'chi': -160.121, 'glyco_bond': 'anti', 'C5prime_xyz':
[-1.312, 8.656, 0.599], 'P_xyz': [1.227, 8.963, 1.202], 'form': '.', 'ssZp':
4.359, 'Dp': 4.639, 'splay_angle': 26.032, 'splay_distance': 4.049,
'splay_ratio': 0.225, 'eta': -178.902, 'theta': -131.583, 'eta_prime':
173.458, 'theta_prime': -127.788, 'eta_base': 166.595, 'theta_base': -77.239,
'v0': 4.617, 'v1': -25.448, 'v2': 35.529, 'v3': -33.885, 'v4': 18.48,
'amplitude': 36.261, 'phase_angle': 11.527, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '&a', 'suiteness': 0.794,
'filter_rmsd': 0.038, 'frame': {'rmsd': 0.006, 'origin': [-20.69, 11.25,
-25.769], 'x_axis': [-0.738, -0.206, 0.642], 'y_axis': [-0.437, 0.871,
-0.223], 'z_axis': [-0.513, -0.445, -0.733], 'quaternion': [-0.316, -0.176,
0.914, -0.183]}}, {'index': 38, 'index_chain': 38, 'chain_name': 'A',
'nt_resnum': 38, 'nt_name': 'A', 'nt_code': 'A', 'nt_id': '..A.A.38.',
'linked_nts': ['..A.A.37.', '..A.A.39.'], 'nt_type': 'RNA', 'dbn': '.',
'summary': "anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-
end,multiplet,junction-loop,A-minor,phosphate", 'alpha': -67.427, 'beta':
165.847, 'gamma': 57.268, 'delta': 83.172, 'epsilon': -148.908, 'zeta':
-65.756, 'epsilon_zeta': -83.152, 'bb_type': 'BI', 'chi': -159.467,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.178, 8.642, 0.568], 'P_xyz': [1.436,
8.792, 0.555], 'form': 'A', 'ssZp': 4.379, 'Dp': 4.634, 'splay_angle': 23.638,
'splay_distance': 3.67, 'splay_ratio': 0.205, 'eta': 161.646, 'theta':
-133.687, 'eta_prime': -175.242, 'theta_prime': -133.101, 'eta_base':
-105.521, 'theta_base': -90.984, 'v0': 5.873, 'v1': -27.171, 'v2': 36.951,
'v3': -34.556, 'v4': 18.117, 'amplitude': 37.497, 'phase_angle': 9.793,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.925, 'filter_rmsd': 0.037, 'frame': {'rmsd': 0.008,
'origin': [-24.464, 9.894, -26.33], 'x_axis': [-0.724, 0.602, 0.336],
'y_axis': [0.216, 0.661, -0.718], 'z_axis': [-0.655, -0.447, -0.609],
'quaternion': [-0.286, 0.236, 0.865, -0.337]}}, {'index': 39, 'index_chain':
39, 'chain_name': 'A', 'nt_resnum': 39, 'nt_name': 'A', 'nt_code': 'A',
'nt_id': '..A.A.39.', 'linked_nts': ['..A.A.38.', '..A.C.40.'], 'nt_type':
'RNA', 'dbn': '(', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem-end,junction-loop", 'alpha': -61.268, 'beta': 170.159,
'gamma': 50.25, 'delta': 83.191, 'epsilon': -145.393, 'zeta': -79.219,
'epsilon_zeta': -66.174, 'bb_type': 'BI', 'chi': -152.43, 'glyco_bond':
'anti', 'C5prime_xyz': [-1.225, 8.671, 0.141], 'P_xyz': [1.403, 8.857, 0.171],
'form': 'A', 'ssZp': 4.208, 'Dp': 4.673, 'splay_angle': 20.427,
'splay_distance': 3.237, 'splay_ratio': 0.177, 'eta': 166.11, 'theta':
-145.689, 'eta_prime': -173.691, 'theta_prime': -146.613, 'eta_base':
-112.432, 'theta_base': -125.664, 'v0': 6.072, 'v1': -27.114, 'v2': 36.739,
'v3': -34.163, 'v4': 17.729, 'amplitude': 37.238, 'phase_angle': 9.393,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.949, 'filter_rmsd': 0.04, 'frame': {'rmsd': 0.008,
'origin': [-27.977, 9.879, -27.39], 'x_axis': [-0.333, 0.913, -0.237],
'y_axis': [0.555, -0.014, -0.832], 'z_axis': [-0.762, -0.408, -0.502],
'quaternion': [-0.195, 0.544, 0.675, -0.46]}}, {'index': 40, 'index_chain':
40, 'chain_name': 'A', 'nt_resnum': 40, 'nt_name': 'C', 'nt_code': 'C',
'nt_id': '..A.C.40.', 'linked_nts': ['..A.A.39.', '..A.G.41.'], 'nt_type':
'RNA', 'dbn': '(', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem", 'alpha': -63.616, 'beta': 164.286, 'gamma': 54.323,
'delta': 78.469, 'epsilon': -150.438, 'zeta': -71.737, 'epsilon_zeta': -78.7,
'bb_type': 'BI', 'chi': -155.677, 'glyco_bond': 'anti', 'C5prime_xyz':
[-1.197, 8.768, 0.24], 'P_xyz': [1.39, 9.063, -0.067], 'form': 'A', 'ssZp':
4.317, 'Dp': 4.681, 'splay_angle': 24.424, 'splay_distance': 3.835,
'splay_ratio': 0.212, 'eta': 162.446, 'theta': -146.08, 'eta_prime': 175.033,
'theta_prime': -145.578, 'eta_base': -148.278, 'theta_base': -121.243, 'v0':
5.223, 'v1': -27.795, 'v2': 38.641, 'v3': -36.596, 'v4': 19.793, 'amplitude':
39.38, 'phase_angle': 11.118, 'puckering': "C3'-endo", 'sugar_class':
"~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.913, 'filter_rmsd':
0.06, 'frame': {'rmsd': 0.006, 'origin': [-31.005, 9.207, -28.317], 'x_axis':
[0.115, 0.839, -0.531], 'y_axis': [0.516, -0.507, -0.69], 'z_axis': [-0.849,
-0.195, -0.491], 'quaternion': [-0.17, 0.727, 0.466, -0.475]}}, {'index': 41,
'index_chain': 41, 'chain_name': 'A', 'nt_resnum': 41, 'nt_name': 'G',
'nt_code': 'G', 'nt_id': '..A.G.41.', 'linked_nts': ['..A.C.40.',
'..A.C.42.'], 'nt_type': 'RNA', 'dbn': '(', 'summary':
"anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", 'alpha': -66.826,
'beta': 177.22, 'gamma': 51.206, 'delta': 79.57, 'epsilon': -151.44, 'zeta':
-65.631, 'epsilon_zeta': -85.809, 'bb_type': 'BI', 'chi': -163.574,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.382, 8.71, 0.729], 'P_xyz': [1.18,
9.039, 1.09], 'form': 'A', 'ssZp': 4.521, 'Dp': 4.675, 'splay_angle': 24.038,
'splay_distance': 3.838, 'splay_ratio': 0.212, 'eta': 165.428, 'theta':
-140.409, 'eta_prime': 177.581, 'theta_prime': -138.465, 'eta_base': -143.354,
'theta_base': -108.452, 'v0': 3.535, 'v1': -26.979, 'v2': 38.875, 'v3':
-37.84, 'v4': 21.595, 'amplitude': 39.994, 'phase_angle': 13.59, 'puckering':
"C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a',
'suiteness': 0.962, 'filter_rmsd': 0.009, 'frame': {'rmsd': 0.009, 'origin':
[-34.312, 10.104, -30.039], 'x_axis': [0.647, 0.473, -0.599], 'y_axis':
[0.354, -0.881, -0.313], 'z_axis': [-0.675, -0.009, -0.737], 'quaternion':
[-0.084, 0.904, 0.229, -0.353]}}, {'index': 42, 'index_chain': 42,
'chain_name': 'A', 'nt_resnum': 42, 'nt_name': 'C', 'nt_code': 'C', 'nt_id':
'..A.C.42.', 'linked_nts': ['..A.G.41.', '..A.C.43.'], 'nt_type': 'RNA',
'dbn': '(', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem", 'alpha': -60.485, 'beta': -179.031, 'gamma': 47.305,
'delta': 79.413, 'epsilon': -155.365, 'zeta': -59.78, 'epsilon_zeta': -95.585,
'bb_type': 'BI', 'chi': -156.401, 'glyco_bond': 'anti', 'C5prime_xyz':
[-1.389, 8.787, 0.303], 'P_xyz': [1.156, 9.322, 0.684], 'form': '.', 'ssZp':
4.327, 'Dp': 4.605, 'splay_angle': 18.318, 'splay_distance': 3.626,
'splay_ratio': 0.184, 'eta': 169.664, 'theta': -115.901, 'eta_prime':
-175.936, 'theta_prime': -127.626, 'eta_base': -130.721, 'theta_base':
-110.145, 'v0': 2.882, 'v1': -25.452, 'v2': 37.244, 'v3': -36.563, 'v4':
21.256, 'amplitude': 38.457, 'phase_angle': 14.426, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.896,
'filter_rmsd': 0.065, 'frame': {'rmsd': 0.006, 'origin': [-35.795, 11.998,
-33.029], 'x_axis': [0.812, -0.152, -0.563], 'y_axis': [-0.157, -0.987,
0.039], 'z_axis': [-0.562, 0.057, -0.825], 'quaternion': [-0.005, 0.952,
-0.081, -0.295]}}, {'index': 43, 'index_chain': 43, 'chain_name': 'A',
'nt_resnum': 43, 'nt_name': 'C', 'nt_code': 'C', 'nt_id': '..A.C.43.',
'linked_nts': ['..A.C.42.', None], 'nt_type': 'RNA', 'dbn': '(', 'summary':
"anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end", 'alpha':
152.767, 'beta': -178.524, 'gamma': -179.421, 'delta': 78.553, 'epsilon':
None, 'zeta': None, 'epsilon_zeta': None, 'bb_type': '--', 'chi': -160.441,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.4, 8.752, 0.533], 'P_xyz': [-0.692,
10.687, -1.084], 'form': '-', 'ssZp': None, 'Dp': None, 'splay_angle': None,
'splay_distance': None, 'splay_ratio': None, 'eta': None, 'theta': None,
'eta_prime': None, 'theta_prime': None, 'eta_base': None, 'theta_base': None,
'v0': 2.311, 'v1': -25.662, 'v2': 38.001, 'v3': -37.726, 'v4': 22.355,
'amplitude': 39.407, 'phase_angle': 15.351, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33t', 'cluster': '1c', 'suiteness': 0.834,
'filter_rmsd': 0.06, 'frame': {'rmsd': 0.008, 'origin': [-35.08, 13.955,
-35.997], 'x_axis': [0.734, -0.53, -0.424], 'y_axis': [-0.589, -0.808, -0.01],
'z_axis': [-0.337, 0.258, -0.905], 'quaternion': [-0.072, 0.928, -0.301,
-0.205]}}, {'index': 44, 'index_chain': 1, 'chain_name': 'B', 'nt_resnum': 1,
'nt_name': 'G', 'nt_code': 'G', 'nt_id': '..B.G.1.', 'linked_nts': [None,
'..B.G.2.'], 'nt_type': 'RNA', 'dbn': ')', 'summary':
"anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end", 'alpha':
None, 'beta': None, 'gamma': 48.703, 'delta': 80.686, 'epsilon': -153.026,
'zeta': -79.121, 'epsilon_zeta': -73.905, 'bb_type': 'BI', 'chi': -170.997,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.142, 8.51, 1.192], 'P_xyz': [None,
None, None], 'form': 'A', 'ssZp': 4.663, 'Dp': 4.694, 'splay_angle': 25.025,
'splay_distance': 3.884, 'splay_ratio': 0.22, 'eta': None, 'theta': None,
'eta_prime': None, 'theta_prime': None, 'eta_base': None, 'theta_base': None,
'v0': 7.181, 'v1': -28.919, 'v2': 38.427, 'v3': -35.282, 'v4': 17.78,
'amplitude': 38.821, 'phase_angle': 8.162, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': 'inc', 'cluster': '__', 'suiteness': 0.0,
'filter_rmsd': 0.008, 'frame': {'rmsd': 0.008, 'origin': [-35.279, 13.978,
-35.917], 'x_axis': [0.763, -0.56, -0.324], 'y_axis': [0.573, 0.817, -0.062],
'z_axis': [0.3, -0.139, 0.944], 'quaternion': [0.939, 0.02, 0.166, -0.302]}},
{'index': 45, 'index_chain': 2, 'chain_name': 'B', 'nt_resnum': 2, 'nt_name':
'G', 'nt_code': 'G', 'nt_id': '..B.G.2.', 'linked_nts': ['..B.G.1.',
'..B.C.3.'], 'nt_type': 'RNA', 'dbn': ')', 'summary':
"anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", 'alpha': -54.711,
'beta': 171.758, 'gamma': 52.968, 'delta': 79.694, 'epsilon': -142.652,
'zeta': -70.742, 'epsilon_zeta': -71.909, 'bb_type': 'BI', 'chi': -161.367,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.458, 8.731, 0.704], 'P_xyz': [1.106,
9.034, 1.172], 'form': 'A', 'ssZp': 4.356, 'Dp': 4.639, 'splay_angle': 22.747,
'splay_distance': 3.642, 'splay_ratio': 0.198, 'eta': 178.779, 'theta':
-139.061, 'eta_prime': -171.559, 'theta_prime': -139.185, 'eta_base':
-150.578, 'theta_base': -109.414, 'v0': 5.224, 'v1': -26.853, 'v2': 37.314,
'v3': -35.286, 'v4': 18.934, 'amplitude': 38.002, 'phase_angle': 10.913,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.872, 'filter_rmsd': 0.012, 'frame': {'rmsd': 0.012,
'origin': [-35.935, 11.9, -32.702], 'x_axis': [0.913, -0.168, -0.373],
'y_axis': [0.227, 0.967, 0.12], 'z_axis': [0.34, -0.194, 0.92], 'quaternion':
[0.975, 0.081, 0.183, -0.101]}}, {'index': 46, 'index_chain': 3, 'chain_name':
'B', 'nt_resnum': 3, 'nt_name': 'C', 'nt_code': 'C', 'nt_id': '..B.C.3.',
'linked_nts': ['..B.G.2.', '..B.G.4.'], 'nt_type': 'RNA', 'dbn': ')',
'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem,phosphate", 'alpha': -66.588, 'beta': 174.139, 'gamma':
48.668, 'delta': 77.581, 'epsilon': -153.107, 'zeta': -73.209, 'epsilon_zeta':
-79.898, 'bb_type': 'BI', 'chi': -161.499, 'glyco_bond': 'anti',
'C5prime_xyz': [-1.323, 8.773, 0.591], 'P_xyz': [1.223, 9.254, 0.742], 'form':
'A', 'ssZp': 4.518, 'Dp': 4.672, 'splay_angle': 23.24, 'splay_distance':
3.638, 'splay_ratio': 0.203, 'eta': 159.685, 'theta': -151.885, 'eta_prime':
173.143, 'theta_prime': -148.442, 'eta_base': -140.092, 'theta_base':
-123.885, 'v0': 1.307, 'v1': -25.026, 'v2': 37.954, 'v3': -38.399, 'v4':
23.245, 'amplitude': 39.65, 'phase_angle': 16.82, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.925,
'filter_rmsd': 0.069, 'frame': {'rmsd': 0.009, 'origin': [-33.939, 10.122,
-30.228], 'x_axis': [0.802, 0.469, -0.371], 'y_axis': [-0.336, 0.867, 0.368],
'z_axis': [0.494, -0.17, 0.852], 'quaternion': [0.938, 0.144, 0.231, 0.215]}},
{'index': 47, 'index_chain': 4, 'chain_name': 'B', 'nt_resnum': 4, 'nt_name':
'G', 'nt_code': 'G', 'nt_id': '..B.G.4.', 'linked_nts': ['..B.C.3.',
'..B.U.5.'], 'nt_type': 'RNA', 'dbn': ')', 'summary':
"anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", 'alpha': -69.263,
'beta': 179.469, 'gamma': 54.56, 'delta': 78.921, 'epsilon': -140.734, 'zeta':
-72.171, 'epsilon_zeta': -68.563, 'bb_type': 'BI', 'chi': -158.752,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.326, 8.754, 0.491], 'P_xyz': [1.265,
9.08, 0.69], 'form': 'A', 'ssZp': 4.382, 'Dp': 4.714, 'splay_angle': 24.509,
'splay_distance': 3.94, 'splay_ratio': 0.214, 'eta': 170.337, 'theta':
-139.654, 'eta_prime': 179.203, 'theta_prime': -136.024, 'eta_base': -147.192,
'theta_base': -109.32, 'v0': 3.2, 'v1': -26.508, 'v2': 38.574, 'v3': -37.809,
'v4': 21.848, 'amplitude': 39.782, 'phase_angle': 14.158, 'puckering':
"C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a',
'suiteness': 0.929, 'filter_rmsd': 0.009, 'frame': {'rmsd': 0.009, 'origin':
[-31.083, 8.857, -28.363], 'x_axis': [0.36, 0.874, -0.327], 'y_axis': [-0.642,
0.486, 0.593], 'z_axis': [0.677, -0.003, 0.736], 'quaternion': [0.803, 0.185,
0.312, 0.472]}}, {'index': 48, 'index_chain': 5, 'chain_name': 'B',
'nt_resnum': 5, 'nt_name': 'U', 'nt_code': 'U', 'nt_id': '..B.U.5.',
'linked_nts': ['..B.G.4.', '..B.OMC.6.'], 'nt_type': 'RNA', 'dbn': ')',
'summary': "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-
end,junction-loop", 'alpha': -63.655, 'beta': 175.13, 'gamma': 53.967,
'delta': 79.993, 'epsilon': -132.818, 'zeta': -75.117, 'epsilon_zeta':
-57.701, 'bb_type': 'BI', 'chi': -157.2, 'glyco_bond': 'anti', 'C5prime_xyz':
[-1.714, 8.785, 0.332], 'P_xyz': [0.794, 9.421, 0.448], 'form': '.', 'ssZp':
4.256, 'Dp': 4.68, 'splay_angle': 25.634, 'splay_distance': 4.077,
'splay_ratio': 0.222, 'eta': 171.772, 'theta': -134.473, 'eta_prime':
-175.533, 'theta_prime': -123.431, 'eta_base': -137.807, 'theta_base':
-84.009, 'v0': -0.445, 'v1': -23.281, 'v2': 36.725, 'v3': -37.988, 'v4':
24.232, 'amplitude': 38.89, 'phase_angle': 19.211, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.956,
'filter_rmsd': 0.1, 'frame': {'rmsd': 0.008, 'origin': [-27.525, 9.982,
-27.097], 'x_axis': [-0.247, 0.956, -0.16], 'y_axis': [-0.671, -0.05, 0.739],
'z_axis': [0.699, 0.29, 0.654], 'quaternion': [0.583, 0.193, 0.368, 0.698]}},
{'index': 49, 'index_chain': 6, 'chain_name': 'B', 'nt_resnum': 6, 'nt_name':
'OMC', 'nt_code': 'c', 'is_modified': True, 'nt_id': '..B.OMC.6.',
'linked_nts': ['..B.U.5.', '..B.C.7.'], 'nt_type': 'RNA', 'dbn': '.',
'summary': "modified,anti,~C2'-endo,non-canonical,non-pair-contact,helix-
end,multiplet,junction-loop,A-minor,splayed-apart", 'alpha': -61.059, 'beta':
179.86, 'gamma': 61.162, 'delta': 147.973, 'epsilon': -151.135, 'zeta':
131.581, 'epsilon_zeta': 77.284, 'bb_type': '--', 'chi': -116.236,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.782, 8.521, -1.367], 'P_xyz': [0.787,
9.025, -1.179], 'form': '.', 'ssZp': 2.171, 'Dp': 1.968, 'splay_angle':
129.091, 'splay_distance': 18.794, 'splay_ratio': 0.903, 'eta': 171.969,
'theta': 109.327, 'eta_prime': -149.995, 'theta_prime': 83.344, 'eta_base':
-105.169, 'theta_base': 99.383, 'v0': -21.336, 'v1': 35.26, 'v2': -34.89,
'v3': 23.52, 'v4': -1.572, 'amplitude': 36.36, 'phase_angle': 163.649,
'puckering': "C2'-endo", 'sugar_class': "~C2'-endo", 'bin': '32p', 'cluster':
'1b', 'suiteness': 0.863, 'filter_rmsd': 0.067, 'frame': {'rmsd': 0.022,
'origin': [-26.79, 13.546, -25.259], 'x_axis': [-0.92, 0.381, 0.094],
'y_axis': [-0.127, -0.516, 0.847], 'z_axis': [0.372, 0.767, 0.523],
'quaternion': [0.148, 0.135, 0.469, 0.86]}}, {'index': 50, 'index_chain': 7,
'chain_name': 'B', 'nt_resnum': 7, 'nt_name': 'C', 'nt_code': 'C', 'nt_id':
'..B.C.7.', 'linked_nts': ['..B.OMC.6.', '..B.U.8.'], 'nt_type': 'RNA', 'dbn':
')', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-
end,junction-loop,phosphate,splayed-apart", 'alpha': -90.487, 'beta': 110.479,
'gamma': 177.24, 'delta': 84.359, 'epsilon': -138.838, 'zeta': -81.766,
'epsilon_zeta': -57.072, 'bb_type': 'BI', 'chi': -162.03, 'glyco_bond':
'anti', 'C5prime_xyz': [-1.215, 8.645, 0.727], 'P_xyz': [-1.4, 10.919,
-0.537], 'form': 'A', 'ssZp': 4.408, 'Dp': 4.663, 'splay_angle': 20.973,
'splay_distance': 3.37, 'splay_ratio': 0.183, 'eta': -85.307, 'theta':
157.776, 'eta_prime': -101.846, 'theta_prime': 175.053, 'eta_base': -116.073,
'theta_base': -161.58, 'v0': 5.9, 'v1': -25.892, 'v2': 34.883, 'v3': -32.602,
'v4': 16.778, 'amplitude': 35.348, 'phase_angle': 9.303, 'puckering':
"C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '23t', 'cluster': '!!',
'suiteness': 0.0, 'filter_rmsd': 0.07, 'frame': {'rmsd': 0.01, 'origin':
[-16.708, -0.447, -17.791], 'x_axis': [0.821, 0.329, 0.466], 'y_axis':
[-0.418, 0.903, 0.099], 'z_axis': [-0.389, -0.276, 0.879], 'quaternion':
[0.949, 0.099, -0.225, 0.197]}}, {'index': 51, 'index_chain': 8, 'chain_name':
'B', 'nt_resnum': 8, 'nt_name': 'U', 'nt_code': 'U', 'nt_id': '..B.U.8.',
'linked_nts': ['..B.C.7.', '..B.G.9.'], 'nt_type': 'RNA', 'dbn': ')',
'summary': "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", 'alpha':
-62.597, 'beta': 170.732, 'gamma': 46.609, 'delta': 79.352, 'epsilon':
-144.018, 'zeta': -78.962, 'epsilon_zeta': -65.056, 'bb_type': 'BI', 'chi':
-152.638, 'glyco_bond': 'anti', 'C5prime_xyz': [-1.583, 8.745, 0.088],
'P_xyz': [0.968, 9.313, 0.241], 'form': 'A', 'ssZp': 4.147, 'Dp': 4.652,
'splay_angle': 22.295, 'splay_distance': 3.536, 'splay_ratio': 0.193, 'eta':
162.329, 'theta': -148.03, 'eta_prime': 173.233, 'theta_prime': -147.257,
'eta_base': -161.66, 'theta_base': -118.605, 'v0': 2.128, 'v1': -25.033, 'v2':
37.181, 'v3': -37.027, 'v4': 21.931, 'amplitude': 38.589, 'phase_angle':
15.529, 'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p',
'cluster': '1a', 'suiteness': 0.83, 'filter_rmsd': 0.102, 'frame': {'rmsd':
0.005, 'origin': [-17.257, -2.506, -15.18], 'x_axis': [0.619, 0.754, 0.221],
'y_axis': [-0.776, 0.631, 0.019], 'z_axis': [-0.125, -0.184, 0.975],
'quaternion': [0.898, 0.057, -0.096, 0.426]}}, {'index': 52, 'index_chain': 9,
'chain_name': 'B', 'nt_resnum': 9, 'nt_name': 'G', 'nt_code': 'G', 'nt_id':
'..B.G.9.', 'linked_nts': ['..B.U.8.', '..B.G.10.'], 'nt_type': 'RNA', 'dbn':
')', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem",
'alpha': -69.864, 'beta': 169.62, 'gamma': 50.759, 'delta': 79.114, 'epsilon':
-145.57, 'zeta': -66.753, 'epsilon_zeta': -78.817, 'bb_type': 'BI', 'chi':
-162.828, 'glyco_bond': 'anti', 'C5prime_xyz': [-1.36, 8.72, 0.633], 'P_xyz':
[1.233, 9.071, 0.54], 'form': 'A', 'ssZp': 4.558, 'Dp': 4.741, 'splay_angle':
25.011, 'splay_distance': 4.131, 'splay_ratio': 0.225, 'eta': 156.514,
'theta': -137.047, 'eta_prime': 167.276, 'theta_prime': -136.135, 'eta_base':
-149.886, 'theta_base': -112.868, 'v0': 4.465, 'v1': -28.117, 'v2': 39.797,
'v3': -38.213, 'v4': 21.197, 'amplitude': 40.74, 'phase_angle': 12.354,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.925, 'filter_rmsd': 0.01, 'frame': {'rmsd': 0.01,
'origin': [-16.464, -2.648, -11.737], 'x_axis': [0.112, 0.984, -0.138],
'y_axis': [-0.994, 0.11, -0.021], 'z_axis': [-0.005, 0.139, 0.99],
'quaternion': [0.744, -0.054, 0.045, 0.665]}}, {'index': 53, 'index_chain':
10, 'chain_name': 'B', 'nt_resnum': 10, 'nt_name': 'G', 'nt_code': 'G',
'nt_id': '..B.G.10.', 'linked_nts': ['..B.G.9.', '..B.U.11.'], 'nt_type':
'RNA', 'dbn': ')', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem", 'alpha': -65.526, 'beta': 163.095, 'gamma': 71.85,
'delta': 76.53, 'epsilon': -146.536, 'zeta': -76.952, 'epsilon_zeta': -69.584,
'bb_type': 'BI', 'chi': -171.632, 'glyco_bond': 'anti', 'C5prime_xyz':
[-1.997, 8.741, 1.108], 'P_xyz': [0.433, 9.697, 0.984], 'form': 'A', 'ssZp':
4.557, 'Dp': 4.606, 'splay_angle': 23.482, 'splay_distance': 3.757,
'splay_ratio': 0.207, 'eta': 173.957, 'theta': -151.54, 'eta_prime': -167.336,
'theta_prime': -151.845, 'eta_base': -124.768, 'theta_base': -124.239, 'v0':
-2.341, 'v1': -22.735, 'v2': 37.761, 'v3': -40.221, 'v4': 26.734, 'amplitude':
40.679, 'phase_angle': 21.833, 'puckering': "C3'-endo", 'sugar_class':
"~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.447, 'filter_rmsd':
0.011, 'frame': {'rmsd': 0.011, 'origin': [-14.604, -0.269, -8.918], 'x_axis':
[-0.405, 0.876, -0.26], 'y_axis': [-0.914, -0.391, 0.105], 'z_axis': [-0.01,
0.281, 0.96], 'quaternion': [0.539, -0.081, 0.116, 0.83]}}, {'index': 54,
'index_chain': 11, 'chain_name': 'B', 'nt_resnum': 11, 'nt_name': 'U',
'nt_code': 'U', 'nt_id': '..B.U.11.', 'linked_nts': ['..B.G.10.',
'..B.A.12.'], 'nt_type': 'RNA', 'dbn': ')', 'summary':
"anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", 'alpha': -65.788,
'beta': 173.472, 'gamma': 52.034, 'delta': 77.516, 'epsilon': -147.972,
'zeta': -71.971, 'epsilon_zeta': -76.001, 'bb_type': 'BI', 'chi': -163.374,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.619, 8.717, 0.693], 'P_xyz': [0.918,
9.337, 0.923], 'form': 'A', 'ssZp': 4.504, 'Dp': 4.665, 'splay_angle': 20.554,
'splay_distance': 3.366, 'splay_ratio': 0.185, 'eta': 164.78, 'theta':
-145.319, 'eta_prime': 175.54, 'theta_prime': -143.002, 'eta_base': -142.983,
'theta_base': -114.07, 'v0': 0.82, 'v1': -24.682, 'v2': 38.011, 'v3': -38.549,
'v4': 23.715, 'amplitude': 39.843, 'phase_angle': 17.445, 'puckering':
"C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a',
'suiteness': 0.898, 'filter_rmsd': 0.106, 'frame': {'rmsd': 0.004, 'origin':
[-13.517, 2.148, -6.254], 'x_axis': [-0.852, 0.466, -0.239], 'y_axis': [-0.52,
-0.805, 0.286], 'z_axis': [-0.059, 0.368, 0.928], 'quaternion': [0.26, -0.079,
0.173, 0.947]}}, {'index': 55, 'index_chain': 12, 'chain_name': 'B',
'nt_resnum': 12, 'nt_name': 'A', 'nt_code': 'A', 'nt_id': '..B.A.12.',
'linked_nts': ['..B.U.11.', '..B.U.13.'], 'nt_type': 'RNA', 'dbn': ')',
'summary': "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-
end,internal-loop", 'alpha': -59.074, 'beta': 170.717, 'gamma': 56.046,
'delta': 81.156, 'epsilon': -147.754, 'zeta': -69.831, 'epsilon_zeta':
-77.924, 'bb_type': 'BI', 'chi': -155.679, 'glyco_bond': 'anti',
'C5prime_xyz': [-1.741, 8.811, 0.24], 'P_xyz': [0.789, 9.519, 0.325], 'form':
'.', 'ssZp': 4.215, 'Dp': 4.534, 'splay_angle': 17.325, 'splay_distance':
2.846, 'splay_ratio': 0.152, 'eta': 172.724, 'theta': -139.506, 'eta_prime':
-173.157, 'theta_prime': -131.635, 'eta_base': -131.914, 'theta_base':
-101.873, 'v0': -1.87, 'v1': -20.585, 'v2': 33.864, 'v3': -35.843, 'v4':
23.815, 'amplitude': 36.384, 'phase_angle': 21.447, 'puckering': "C3'-endo",
'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a', 'suiteness': 0.929,
'filter_rmsd': 0.032, 'frame': {'rmsd': 0.011, 'origin': [-14.232, 4.992,
-4.602], 'x_axis': [-0.979, -0.108, -0.172], 'y_axis': [0.001, -0.85, 0.527],
'z_axis': [-0.203, 0.515, 0.833], 'quaternion': [-0.029, -0.098, 0.272,
0.957]}}, {'index': 56, 'index_chain': 13, 'chain_name': 'B', 'nt_resnum': 13,
'nt_name': 'U', 'nt_code': 'U', 'nt_id': '..B.U.13.', 'linked_nts':
['..B.A.12.', '..B.C.14.'], 'nt_type': 'RNA', 'dbn': '.', 'summary':
"anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,internal-
loop,splayed-apart", 'alpha': -59.89, 'beta': 173.032, 'gamma': 61.294,
'delta': 148.604, 'epsilon': -100.447, 'zeta': 142.982, 'epsilon_zeta':
116.572, 'bb_type': 'BII', 'chi': -111.633, 'glyco_bond': 'anti',
'C5prime_xyz': [-2.622, 8.396, -1.501], 'P_xyz': [-0.192, 9.414, -1.618],
'form': '.', 'ssZp': 1.363, 'Dp': 1.118, 'splay_angle': 91.363,
'splay_distance': 13.735, 'splay_ratio': 0.716, 'eta': -168.277, 'theta':
156.416, 'eta_prime': -135.57, 'theta_prime': 145.254, 'eta_base': -103.601,
'theta_base': 179.851, 'v0': -25.687, 'v1': 39.785, 'v2': -37.738, 'v3':
23.871, 'v4': 0.923, 'amplitude': 40.188, 'phase_angle': 159.891, 'puckering':
"C2'-endo", 'sugar_class': "~C2'-endo", 'bin': '32p', 'cluster': '1b',
'suiteness': 0.932, 'filter_rmsd': 0.104, 'frame': {'rmsd': 0.009, 'origin':
[-16.282, 6.414, -3.232], 'x_axis': [-0.751, -0.657, -0.069], 'y_axis':
[0.345, -0.479, 0.807], 'z_axis': [-0.563, 0.582, 0.587], 'quaternion':
[-0.299, -0.188, 0.414, 0.839]}}, {'index': 57, 'index_chain': 14,
'chain_name': 'B', 'nt_resnum': 14, 'nt_name': 'C', 'nt_code': 'C', 'nt_id':
'..B.C.14.', 'linked_nts': ['..B.U.13.', '..B.C.15.'], 'nt_type': 'RNA',
'dbn': ')', 'summary': "anti,~C3'-endo,BI,isolated-canonical,non-pair-
contact,helix,internal-loop,splayed-apart", 'alpha': -43.166, 'beta': 177.391,
'gamma': 42.539, 'delta': 82.162, 'epsilon': -140.988, 'zeta': -74.394,
'epsilon_zeta': -66.595, 'bb_type': 'BI', 'chi': -162.901, 'glyco_bond':
'anti', 'C5prime_xyz': [-1.241, 8.723, 0.722], 'P_xyz': [1.237, 9.123, 1.444],
'form': '.', 'ssZp': 4.435, 'Dp': 4.647, 'splay_angle': 17.947,
'splay_distance': 3.04, 'splay_ratio': 0.16, 'eta': -120.848, 'theta':
-141.235, 'eta_prime': -135.346, 'theta_prime': -130.954, 'eta_base':
-127.631, 'theta_base': -131.212, 'v0': 2.929, 'v1': -24.065, 'v2': 34.907,
'v3': -34.244, 'v4': 19.85, 'amplitude': 36.001, 'phase_angle': 14.157,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '23p', 'cluster':
'4a', 'suiteness': 0.393, 'filter_rmsd': 0.066, 'frame': {'rmsd': 0.006,
'origin': [-9.103, 16.659, 2.44], 'x_axis': [-0.742, 0.051, 0.668], 'y_axis':
[-0.086, -0.996, -0.019], 'z_axis': [0.665, -0.071, 0.744], 'quaternion':
[0.037, 0.357, -0.024, 0.933]}}, {'index': 58, 'index_chain': 15,
'chain_name': 'B', 'nt_resnum': 15, 'nt_name': 'C', 'nt_code': 'C', 'nt_id':
'..B.C.15.', 'linked_nts': ['..B.C.14.', '..B.A.16.'], 'nt_type': 'RNA',
'dbn': '.', 'summary': "anti,~C2'-endo,BII,non-canonical,non-pair-
contact,helix,multiplet,internal-loop,A-minor", 'alpha': -53.383, 'beta':
-177.719, 'gamma': 47.506, 'delta': 144.764, 'epsilon': -105.706, 'zeta':
171.747, 'epsilon_zeta': 82.548, 'bb_type': 'BII', 'chi': -110.845,
'glyco_bond': 'anti', 'C5prime_xyz': [-2.457, 8.423, -1.642], 'P_xyz':
[-0.219, 9.746, -1.333], 'form': '.', 'ssZp': 1.311, 'Dp': 1.192,
'splay_angle': 46.046, 'splay_distance': 8.212, 'splay_ratio': 0.392, 'eta':
-168.723, 'theta': 174.421, 'eta_prime': -144.07, 'theta_prime': 151.297,
'eta_base': -143.761, 'theta_base': 152.712, 'v0': -25.766, 'v1': 37.904,
'v2': -34.796, 'v3': 20.899, 'v4': 2.883, 'amplitude': 37.826, 'phase_angle':
156.911, 'puckering': "C2'-endo", 'sugar_class': "~C2'-endo", 'bin': '32p',
'cluster': '1b', 'suiteness': 0.769, 'filter_rmsd': 0.064, 'frame': {'rmsd':
0.003, 'origin': [-7.356, 18.219, 4.378], 'x_axis': [-0.915, -0.266, 0.303],
'y_axis': [0.297, -0.953, 0.062], 'z_axis': [0.273, 0.147, 0.951],
'quaternion': [-0.144, 0.147, 0.053, 0.977]}}, {'index': 59, 'index_chain':
16, 'chain_name': 'B', 'nt_resnum': 16, 'nt_name': 'A', 'nt_code': 'A',
'nt_id': '..B.A.16.', 'linked_nts': ['..B.C.15.', '..B.A.17.'], 'nt_type':
'RNA', 'dbn': '.', 'summary': "anti,~C3'-endo,BI,non-pair-contact,internal-
loop", 'alpha': -44.492, 'beta': 177.964, 'gamma': -65.699, 'delta': 85.188,
'epsilon': -151.735, 'zeta': -61.767, 'epsilon_zeta': -89.967, 'bb_type':
'BI', 'chi': -169.039, 'glyco_bond': 'anti', 'C5prime_xyz': [-1.361, 8.51,
1.039], 'P_xyz': [-0.521, 10.546, 2.407], 'form': '.', 'ssZp': 4.625, 'Dp':
4.648, 'splay_angle': 28.135, 'splay_distance': 4.305, 'splay_ratio': 0.244,
'eta': 126.407, 'theta': -171.185, 'eta_prime': 106.491, 'theta_prime':
-155.749, 'eta_base': 118.56, 'theta_base': -100.624, 'v0': 4.695, 'v1':
-25.6, 'v2': 35.467, 'v3': -33.759, 'v4': 18.368, 'amplitude': 36.17,
'phase_angle': 11.31, 'puckering': "C3'-endo", 'sugar_class': "~C3'-endo",
'bin': '23m', 'cluster': '!!', 'suiteness': 0.0, 'filter_rmsd': 0.035,
'frame': {'rmsd': 0.009, 'origin': [-0.986, 22.603, 1.616], 'x_axis': [-0.993,
-0.122, -0.001], 'y_axis': [0.122, -0.992, 0.029], 'z_axis': [-0.005, 0.029,
1.0], 'quaternion': [-0.061, -0.002, 0.015, 0.998]}}, {'index': 60,
'index_chain': 17, 'chain_name': 'B', 'nt_resnum': 17, 'nt_name': 'A',
'nt_code': 'A', 'nt_id': '..B.A.17.', 'linked_nts': ['..B.A.16.',
'..B.U.18.'], 'nt_type': 'RNA', 'dbn': '.', 'summary': "anti,~C3'-endo,BI,non-
canonical,non-pair-contact,multiplet,internal-loop,A-minor", 'alpha': -70.234,
'beta': 166.859, 'gamma': 64.67, 'delta': 81.259, 'epsilon': -143.244, 'zeta':
-68.327, 'epsilon_zeta': -74.917, 'bb_type': 'BI', 'chi': -169.353,
'glyco_bond': 'anti', 'C5prime_xyz': [-1.296, 8.577, 1.082], 'P_xyz': [1.318,
8.872, 1.016], 'form': 'A', 'ssZp': 4.624, 'Dp': 4.696, 'splay_angle': 25.705,
'splay_distance': 4.021, 'splay_ratio': 0.225, 'eta': 168.912, 'theta':
-133.608, 'eta_prime': -168.729, 'theta_prime': -132.755, 'eta_base':
-106.514, 'theta_base': -95.813, 'v0': 4.787, 'v1': -26.511, 'v2': 36.945,
'v3': -35.088, 'v4': 19.15, 'amplitude': 37.69, 'phase_angle': 11.407,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.731, 'filter_rmsd': 0.037, 'frame': {'rmsd': 0.006,
'origin': [-3.428, 22.918, 5.147], 'x_axis': [-0.596, -0.793, 0.122],
'y_axis': [0.8, -0.599, 0.013], 'z_axis': [0.063, 0.106, 0.992], 'quaternion':
[-0.446, 0.052, 0.033, 0.893]}}, {'index': 61, 'index_chain': 18,
'chain_name': 'B', 'nt_resnum': 18, 'nt_name': 'U', 'nt_code': 'U', 'nt_id':
'..B.U.18.', 'linked_nts': ['..B.A.17.', '..B.C.19.'], 'nt_type': 'RNA',
'dbn': ')', 'summary': "anti,~C3'-endo,BI,canonical,non-pair-
contact,helix,stem-end,internal-loop", 'alpha': -53.291, 'beta': 172.12,
'gamma': 48.03, 'delta': 80.685, 'epsilon': -131.761, 'zeta': -83.825,
'epsilon_zeta': -47.935, 'bb_type': 'BI', 'chi': -160.848, 'glyco_bond':
'anti', 'C5prime_xyz': [-1.31, 8.731, 0.627], 'P_xyz': [1.247, 9.081, 1.163],
'form': 'A', 'ssZp': 4.312, 'Dp': 4.655, 'splay_angle': 23.326,
'splay_distance': 3.747, 'splay_ratio': 0.202, 'eta': 174.925, 'theta':
-141.711, 'eta_prime': -168.093, 'theta_prime': -137.905, 'eta_base':
-114.555, 'theta_base': -106.775, 'v0': 1.737, 'v1': -23.214, 'v2': 34.822,
'v3': -34.778, 'v4': 20.882, 'amplitude': 36.224, 'phase_angle': 15.989,
'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster':
'1a', 'suiteness': 0.843, 'filter_rmsd': 0.108, 'frame': {'rmsd': 0.007,
'origin': [-5.217, 21.81, 8.574], 'x_axis': [0.13, -0.991, -0.014], 'y_axis':
[0.991, 0.131, -0.028], 'z_axis': [0.03, -0.01, 1.0], 'quaternion': [0.752,
-0.006, 0.014, -0.659]}}, {'index': 62, 'index_chain': 19, 'chain_name': 'B',
'nt_resnum': 19, 'nt_name': 'C', 'nt_code': 'C', 'nt_id': '..B.C.19.',
'linked_nts': ['..B.U.18.', '..B.DC.20.'], 'nt_type': 'RNA', 'dbn': ')',
'summary': "anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem", 'alpha':
-54.739, 'beta': 152.924, 'gamma': 54.016, 'delta': 76.752, 'epsilon':
-147.65, 'zeta': -75.537, 'epsilon_zeta': -72.113, 'bb_type': 'BI', 'chi':
-162.315, 'glyco_bond': 'anti', 'C5prime_xyz': [-1.576, 8.805, 0.643],
'P_xyz': [0.982, 9.238, 0.385], 'form': 'A', 'ssZp': 4.472, 'Dp': 4.666,
'splay_angle': 24.369, 'splay_distance': 3.949, 'splay_ratio': 0.215, 'eta':
161.003, 'theta': -145.511, 'eta_prime': 178.736, 'theta_prime': -146.922,
'eta_base': -134.547, 'theta_base': -124.757, 'v0': 1.598, 'v1': -26.299,
'v2': 39.654, 'v3': -39.699, 'v4': 23.969, 'amplitude': 41.322, 'phase_angle':
16.336, 'puckering': "C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p',
'cluster': '1a', 'suiteness': 0.634, 'filter_rmsd': 0.06, 'frame': {'rmsd':
0.003, 'origin': [-5.567, 20.402, 12.029], 'x_axis': [0.642, -0.75, -0.16],
'y_axis': [0.764, 0.644, 0.049], 'z_axis': [0.066, -0.154, 0.986],
'quaternion': [0.904, 0.056, 0.063, -0.418]}}, {'index': 63, 'index_chain':
20, 'chain_name': 'B', 'nt_resnum': 20, 'nt_name': 'DC', 'nt_code': 'C',
'nt_id': '..B.DC.20.', 'linked_nts': ['..B.C.19.', None], 'nt_type': 'DNA',
'dbn': ')', 'summary': "anti,~C3'-endo,canonical,non-pair-contact,helix-
end,stem-end", 'alpha': -51.445, 'beta': 170.632, 'gamma': 43.982, 'delta':
78.643, 'epsilon': None, 'zeta': None, 'epsilon_zeta': None, 'bb_type': '--',
'chi': -160.158, 'glyco_bond': 'anti', 'C5prime_xyz': [-1.636, 8.845, 0.635],
'P_xyz': [0.852, 9.475, 1.039], 'form': '-', 'ssZp': None, 'Dp': None,
'splay_angle': None, 'splay_distance': None, 'splay_ratio': None, 'eta': None,
'theta': None, 'eta_prime': None, 'theta_prime': None, 'eta_base': None,
'theta_base': None, 'v0': 2.677, 'v1': -28.704, 'v2': 41.91, 'v3': -42.067,
'v4': 24.885, 'amplitude': 43.474, 'phase_angle': 15.418, 'puckering':
"C3'-endo", 'sugar_class': "~C3'-endo", 'bin': '33p', 'cluster': '1a',
'suiteness': 0.713, 'filter_rmsd': 0.067, 'frame': {'rmsd': 0.006, 'origin':
[-5.805, 17.957, 15.121], 'x_axis': [0.914, -0.283, -0.29], 'y_axis': [0.335,
0.931, 0.144], 'z_axis': [0.229, -0.229, 0.946], 'quaternion': [0.974, 0.096,
0.133, -0.159]}}], 'num_hbonds': 99, 'hbonds': [{'index': 1, 'atom1_serNum':
2, 'atom2_serNum': 7, 'donAcc_type': 'acceptable', 'distance': 3.01,
'atom1_id': 'O1B@..A.GDP.1.', 'atom2_id': 'O1A@..A.GDP.1.', 'atom_pair':
'O:O', 'residue_pair': 'nt:nt'}, {'index': 2, 'atom1_serNum': 23,
'atom2_serNum': 1343, 'donAcc_type': 'standard', 'distance': 2.959,
'atom1_id': 'O6@..A.GDP.1.', 'atom2_id': 'N4@..B.DC.20.', 'atom_pair': 'O:N',
'residue_pair': 'nt:nt'}, {'index': 3, 'atom1_serNum': 24, 'atom2_serNum':
1341, 'donAcc_type': 'standard', 'distance': 2.883, 'atom1_id':
'N1@..A.GDP.1.', 'atom2_id': 'N3@..B.DC.20.', 'atom_pair': 'N:N',
'residue_pair': 'nt:nt'}, {'index': 4, 'atom1_serNum': 26, 'atom2_serNum':
1340, 'donAcc_type': 'standard', 'distance': 2.764, 'atom1_id':
'N2@..A.GDP.1.', 'atom2_id': 'O2@..B.DC.20.', 'atom_pair': 'N:O',
'residue_pair': 'nt:nt'}, {'index': 5, 'atom1_serNum': 46, 'atom2_serNum':
1324, 'donAcc_type': 'standard', 'distance': 3.058, 'atom1_id': 'O6@..A.G.2.',
'atom2_id': 'N4@..B.C.19.', 'atom_pair': 'O:N', 'residue_pair': 'nt:nt'},
{'index': 6, 'atom1_serNum': 47, 'atom2_serNum': 1322, 'donAcc_type':
'standard', 'distance': 2.927, 'atom1_id': 'N1@..A.G.2.', 'atom2_id':
'N3@..B.C.19.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'}, {'index': 7,
'atom1_serNum': 49, 'atom2_serNum': 1321, 'donAcc_type': 'standard',
'distance': 2.817, 'atom1_id': 'N2@..A.G.2.', 'atom2_id': 'O2@..B.C.19.',
'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 8, 'atom1_serNum': 69,
'atom2_serNum': 1304, 'donAcc_type': 'standard', 'distance': 3.041,
'atom1_id': 'N6@..A.A.3.', 'atom2_id': 'O4@..B.U.18.', 'atom_pair': 'N:O',
'residue_pair': 'nt:nt'}, {'index': 9, 'atom1_serNum': 70, 'atom2_serNum':
1302, 'donAcc_type': 'standard', 'distance': 2.861, 'atom1_id': 'N1@..A.A.3.',
'atom2_id': 'N3@..B.U.18.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'},
{'index': 10, 'atom1_serNum': 88, 'atom2_serNum': 1282, 'donAcc_type':
'standard', 'distance': 2.857, 'atom1_id': 'O2@..A.U.4.', 'atom2_id':
'N6@..B.A.17.', 'atom_pair': 'O:N', 'residue_pair': 'nt:nt'}, {'index': 11,
'atom1_serNum': 91, 'atom2_serNum': 1240, 'donAcc_type': 'standard',
'distance': 3.045, 'atom1_id': 'O4@..A.U.4.', 'atom2_id': 'N4@..B.C.15.',
'atom_pair': 'O:N', 'residue_pair': 'nt:nt'}, {'index': 12, 'atom1_serNum':
111, 'atom2_serNum': 1220, 'donAcc_type': 'standard', 'distance': 2.877,
'atom1_id': 'O6@..A.G.5.', 'atom2_id': 'N4@..B.C.14.', 'atom_pair': 'O:N',
'residue_pair': 'nt:nt'}, {'index': 13, 'atom1_serNum': 112, 'atom2_serNum':
1218, 'donAcc_type': 'standard', 'distance': 2.919, 'atom1_id': 'N1@..A.G.5.',
'atom2_id': 'N3@..B.C.14.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'},
{'index': 14, 'atom1_serNum': 114, 'atom2_serNum': 1217, 'donAcc_type':
'standard', 'distance': 2.891, 'atom1_id': 'N2@..A.G.5.', 'atom2_id':
'O2@..B.C.14.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 15,
'atom1_serNum': 131, 'atom2_serNum': 598, 'donAcc_type': 'standard',
'distance': 2.8, 'atom1_id': 'O2@..A.U.6.', 'atom2_id': 'N6@..A.A.28.',
'atom_pair': 'O:N', 'residue_pair': 'nt:nt'}, {'index': 16, 'atom1_serNum':
132, 'atom2_serNum': 595, 'donAcc_type': 'standard', 'distance': 2.849,
'atom1_id': 'N3@..A.U.6.', 'atom2_id': 'N7@..A.A.28.', 'atom_pair': 'N:N',
'residue_pair': 'nt:nt'}, {'index': 17, 'atom1_serNum': 147, 'atom2_serNum':
185, 'donAcc_type': 'acceptable', 'distance': 2.953, 'atom1_id':
"O2'@..A.A.7.", 'atom2_id': "O4'@..A.U.9.", 'atom_pair': 'O:O',
'residue_pair': 'nt:nt'}, {'index': 18, 'atom1_serNum': 154, 'atom2_serNum':
583, 'donAcc_type': 'standard', 'distance': 3.111, 'atom1_id': 'N6@..A.A.7.',
'atom2_id': 'OP2@..A.A.28.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'},
{'index': 19, 'atom1_serNum': 161, 'atom2_serNum': 576, 'donAcc_type':
'standard', 'distance': 3.156, 'atom1_id': 'OP2@..A.C.8.', 'atom2_id':
'N6@..A.A.27.', 'atom_pair': 'O:N', 'residue_pair': 'nt:nt'}, {'index': 20,
'atom1_serNum': 169, 'atom2_serNum': 681, 'donAcc_type': 'acceptable',
'distance': 3.257, 'atom1_id': "O2'@..A.C.8.", 'atom2_id': 'N7@..A.G.32.',
'atom_pair': 'O:N', 'residue_pair': 'nt:nt'}, {'index': 21, 'atom1_serNum':
173, 'atom2_serNum': 556, 'donAcc_type': 'standard', 'distance': 2.882,
'atom1_id': 'O2@..A.C.8.', 'atom2_id': 'N4@..A.C.26.', 'atom_pair': 'O:N',
'residue_pair': 'nt:nt'}, {'index': 22, 'atom1_serNum': 174, 'atom2_serNum':
554, 'donAcc_type': 'questionable', 'distance': 2.84, 'atom1_id':
'N3@..A.C.8.', 'atom2_id': 'N3@..A.C.26.', 'atom_pair': 'N:N', 'residue_pair':
'nt:nt'}, {'index': 23, 'atom1_serNum': 176, 'atom2_serNum': 553,
'donAcc_type': 'standard', 'distance': 2.803, 'atom1_id': 'N4@..A.C.8.',
'atom2_id': 'O2@..A.C.26.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'},
{'index': 24, 'atom1_serNum': 194, 'atom2_serNum': 1179, 'donAcc_type':
'standard', 'distance': 2.92, 'atom1_id': 'N3@..A.U.9.', 'atom2_id':
'N1@..B.A.12.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'}, {'index': 25,
'atom1_serNum': 196, 'atom2_serNum': 655, 'donAcc_type': 'acceptable',
'distance': 3.726, 'atom1_id': 'O4@..A.U.9.', 'atom2_id': "O2'@..A.A.31.",
'atom_pair': 'O:O', 'residue_pair': 'nt:nt'}, {'index': 26, 'atom1_serNum':
196, 'atom2_serNum': 1178, 'donAcc_type': 'standard', 'distance': 3.058,
'atom1_id': 'O4@..A.U.9.', 'atom2_id': 'N6@..B.A.12.', 'atom_pair': 'O:N',
'residue_pair': 'nt:nt'}, {'index': 27, 'atom1_serNum': 216, 'atom2_serNum':
1158, 'donAcc_type': 'standard', 'distance': 3.03, 'atom1_id': 'N6@..A.A.10.',
'atom2_id': 'O4@..B.U.11.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'},
{'index': 28, 'atom1_serNum': 217, 'atom2_serNum': 1156, 'donAcc_type':
'standard', 'distance': 2.78, 'atom1_id': 'N1@..A.A.10.', 'atom2_id':
'N3@..B.U.11.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'}, {'index': 29,
'atom1_serNum': 235, 'atom2_serNum': 1138, 'donAcc_type': 'standard',
'distance': 2.839, 'atom1_id': 'O2@..A.C.11.', 'atom2_id': 'N2@..B.G.10.',
'atom_pair': 'O:N', 'residue_pair': 'nt:nt'}, {'index': 30, 'atom1_serNum':
236, 'atom2_serNum': 1136, 'donAcc_type': 'standard', 'distance': 2.889,
'atom1_id': 'N3@..A.C.11.', 'atom2_id': 'N1@..B.G.10.', 'atom_pair': 'N:N',
'residue_pair': 'nt:nt'}, {'index': 31, 'atom1_serNum': 238, 'atom2_serNum':
1135, 'donAcc_type': 'standard', 'distance': 3.014, 'atom1_id':
'N4@..A.C.11.', 'atom2_id': 'O6@..B.G.10.', 'atom_pair': 'N:O',
'residue_pair': 'nt:nt'}, {'index': 32, 'atom1_serNum': 255, 'atom2_serNum':
1115, 'donAcc_type': 'standard', 'distance': 2.819, 'atom1_id':
'O2@..A.C.12.', 'atom2_id': 'N2@..B.G.9.', 'atom_pair': 'O:N', 'residue_pair':
'nt:nt'}, {'index': 33, 'atom1_serNum': 256, 'atom2_serNum': 1113,
'donAcc_type': 'standard', 'distance': 2.879, 'atom1_id': 'N3@..A.C.12.',
'atom2_id': 'N1@..B.G.9.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'},
{'index': 34, 'atom1_serNum': 258, 'atom2_serNum': 1112, 'donAcc_type':
'standard', 'distance': 2.957, 'atom1_id': 'N4@..A.C.12.', 'atom2_id':
'O6@..B.G.9.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 35,
'atom1_serNum': 278, 'atom2_serNum': 1092, 'donAcc_type': 'standard',
'distance': 2.926, 'atom1_id': 'N6@..A.A.13.', 'atom2_id': 'O4@..B.U.8.',
'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 36, 'atom1_serNum':
279, 'atom2_serNum': 1090, 'donAcc_type': 'standard', 'distance': 2.809,
'atom1_id': 'N1@..A.A.13.', 'atom2_id': 'N3@..B.U.8.', 'atom_pair': 'N:N',
'residue_pair': 'nt:nt'}, {'index': 37, 'atom1_serNum': 300, 'atom2_serNum':
1072, 'donAcc_type': 'standard', 'distance': 2.986, 'atom1_id':
'O6@..A.G.14.', 'atom2_id': 'N4@..B.C.7.', 'atom_pair': 'O:N', 'residue_pair':
'nt:nt'}, {'index': 38, 'atom1_serNum': 301, 'atom2_serNum': 1070,
'donAcc_type': 'standard', 'distance': 2.909, 'atom1_id': 'N1@..A.G.14.',
'atom2_id': 'N3@..B.C.7.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'},
{'index': 39, 'atom1_serNum': 303, 'atom2_serNum': 1069, 'donAcc_type':
'standard', 'distance': 2.771, 'atom1_id': 'N2@..A.G.14.', 'atom2_id':
'O2@..B.C.7.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 40,
'atom1_serNum': 316, 'atom2_serNum': 408, 'donAcc_type': 'acceptable',
'distance': 2.706, 'atom1_id': "O2'@..A.C.15.", 'atom2_id': 'O4@..A.U.19.',
'atom_pair': 'O:O', 'residue_pair': 'nt:nt'}, {'index': 41, 'atom1_serNum':
320, 'atom2_serNum': 431, 'donAcc_type': 'standard', 'distance': 2.794,
'atom1_id': 'O2@..A.C.15.', 'atom2_id': 'N2@..A.G.20.', 'atom_pair': 'O:N',
'residue_pair': 'nt:nt'}, {'index': 42, 'atom1_serNum': 321, 'atom2_serNum':
429, 'donAcc_type': 'standard', 'distance': 2.888, 'atom1_id': 'N3@..A.C.15.',
'atom2_id': 'N1@..A.G.20.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'},
{'index': 43, 'atom1_serNum': 323, 'atom2_serNum': 428, 'donAcc_type':
'standard', 'distance': 2.848, 'atom1_id': 'N4@..A.C.15.', 'atom2_id':
'O6@..A.G.20.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 44,
'atom1_serNum': 336, 'atom2_serNum': 383, 'donAcc_type': 'acceptable',
'distance': 2.651, 'atom1_id': "O2'@..A.U.16.", 'atom2_id': 'N7@..A.A.18.',
'atom_pair': 'O:N', 'residue_pair': 'nt:nt'}, {'index': 45, 'atom1_serNum':
340, 'atom2_serNum': 394, 'donAcc_type': 'questionable', 'distance': 3.338,
'atom1_id': 'O2@..A.U.16.', 'atom2_id': "O5'@..A.U.19.", 'atom_pair': 'O:O',
'residue_pair': 'nt:nt'}, {'index': 46, 'atom1_serNum': 341, 'atom2_serNum':
393, 'donAcc_type': 'standard', 'distance': 2.771, 'atom1_id': 'N3@..A.U.16.',
'atom2_id': 'OP2@..A.U.19.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'},
{'index': 47, 'atom1_serNum': 356, 'atom2_serNum': 832, 'donAcc_type':
'acceptable', 'distance': 2.823, 'atom1_id': "O2'@..A.G.17.", 'atom2_id':
"O2'@..A.A.39.", 'atom_pair': 'O:O', 'residue_pair': 'nt:nt'}, {'index': 48,
'atom1_serNum': 356, 'atom2_serNum': 842, 'donAcc_type': 'acceptable',
'distance': 2.716, 'atom1_id': "O2'@..A.G.17.", 'atom2_id': 'N3@..A.A.39.',
'atom_pair': 'O:N', 'residue_pair': 'nt:nt'}, {'index': 49, 'atom1_serNum':
356, 'atom2_serNum': 850, 'donAcc_type': 'acceptable', 'distance': 3.438,
'atom1_id': "O2'@..A.G.17.", 'atom2_id': "O4'@..A.C.40.", 'atom_pair': 'O:O',
'residue_pair': 'nt:nt'}, {'index': 50, 'atom1_serNum': 364, 'atom2_serNum':
1048, 'donAcc_type': 'standard', 'distance': 2.937, 'atom1_id':
'N1@..A.G.17.', 'atom2_id': "O4'@..B.OMC.6.", 'atom_pair': 'N:O',
'residue_pair': 'nt:nt'}, {'index': 51, 'atom1_serNum': 366, 'atom2_serNum':
818, 'donAcc_type': 'standard', 'distance': 3.075, 'atom1_id': 'N2@..A.G.17.',
'atom2_id': 'N1@..A.A.38.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'},
{'index': 52, 'atom1_serNum': 366, 'atom2_serNum': 1040, 'donAcc_type':
'standard', 'distance': 3.123, 'atom1_id': 'N2@..A.G.17.', 'atom2_id':
'O2@..B.OMC.6.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 53,
'atom1_serNum': 386, 'atom2_serNum': 1065, 'donAcc_type': 'acceptable',
'distance': 2.887, 'atom1_id': 'N6@..A.A.18.', 'atom2_id': "O2'@..B.C.7.",
'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 54, 'atom1_serNum':
387, 'atom2_serNum': 1065, 'donAcc_type': 'acceptable', 'distance': 3.318,
'atom1_id': 'N1@..A.A.18.', 'atom2_id': "O2'@..B.C.7.", 'atom_pair': 'N:O',
'residue_pair': 'nt:nt'}, {'index': 55, 'atom1_serNum': 389, 'atom2_serNum':
421, 'donAcc_type': 'acceptable', 'distance': 3.656, 'atom1_id':
'N3@..A.A.18.', 'atom2_id': "O2'@..A.G.20.", 'atom_pair': 'N:O',
'residue_pair': 'nt:nt'}, {'index': 56, 'atom1_serNum': 421, 'atom2_serNum':
1049, 'donAcc_type': 'acceptable', 'distance': 3.426, 'atom1_id':
"O2'@..A.G.20.", 'atom2_id': "O3'@..B.OMC.6.", 'atom_pair': 'O:O',
'residue_pair': 'nt:nt'}, {'index': 57, 'atom1_serNum': 421, 'atom2_serNum':
1057, 'donAcc_type': 'acceptable', 'distance': 3.011, 'atom1_id':
"O2'@..A.G.20.", 'atom2_id': 'OP2@..B.C.7.', 'atom_pair': 'O:O',
'residue_pair': 'nt:nt'}, {'index': 58, 'atom1_serNum': 421, 'atom2_serNum':
1058, 'donAcc_type': 'acceptable', 'distance': 3.16, 'atom1_id':
"O2'@..A.G.20.", 'atom2_id': "O5'@..B.C.7.", 'atom_pair': 'O:O',
'residue_pair': 'nt:nt'}, {'index': 59, 'atom1_serNum': 448, 'atom2_serNum':
775, 'donAcc_type': 'standard', 'distance': 2.993, 'atom1_id': 'N7@..A.A.21.',
'atom2_id': 'N2@..A.G.36.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'},
{'index': 60, 'atom1_serNum': 451, 'atom2_serNum': 765, 'donAcc_type':
'acceptable', 'distance': 2.955, 'atom1_id': 'N6@..A.A.21.', 'atom2_id':
"O2'@..A.G.36.", 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 61,
'atom1_serNum': 451, 'atom2_serNum': 776, 'donAcc_type': 'standard',
'distance': 3.164, 'atom1_id': 'N6@..A.A.21.', 'atom2_id': 'N3@..A.G.36.',
'atom_pair': 'N:N', 'residue_pair': 'nt:nt'}, {'index': 62, 'atom1_serNum':
473, 'atom2_serNum': 752, 'donAcc_type': 'standard', 'distance': 3.02,
'atom1_id': 'O6@..A.G.22.', 'atom2_id': 'N4@..A.C.35.', 'atom_pair': 'O:N',
'residue_pair': 'nt:nt'}, {'index': 63, 'atom1_serNum': 474, 'atom2_serNum':
750, 'donAcc_type': 'standard', 'distance': 2.935, 'atom1_id': 'N1@..A.G.22.',
'atom2_id': 'N3@..A.C.35.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'},
{'index': 64, 'atom1_serNum': 476, 'atom2_serNum': 749, 'donAcc_type':
'standard', 'distance': 2.84, 'atom1_id': 'N2@..A.G.22.', 'atom2_id':
'O2@..A.C.35.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 65,
'atom1_serNum': 494, 'atom2_serNum': 731, 'donAcc_type': 'standard',
'distance': 3.03, 'atom1_id': 'N3@..A.U.23.', 'atom2_id': 'N1@..A.A.34.',
'atom_pair': 'N:N', 'residue_pair': 'nt:nt'}, {'index': 66, 'atom1_serNum':
496, 'atom2_serNum': 730, 'donAcc_type': 'standard', 'distance': 2.889,
'atom1_id': 'O4@..A.U.23.', 'atom2_id': 'N6@..A.A.34.', 'atom_pair': 'O:N',
'residue_pair': 'nt:nt'}, {'index': 67, 'atom1_serNum': 509, 'atom2_serNum':
525, 'donAcc_type': 'acceptable', 'distance': 3.181, 'atom1_id':
"O2'@..A.C.24.", 'atom2_id': "O4'@..A.C.25.", 'atom_pair': 'O:O',
'residue_pair': 'nt:nt'}, {'index': 68, 'atom1_serNum': 513, 'atom2_serNum':
710, 'donAcc_type': 'standard', 'distance': 2.81, 'atom1_id': 'O2@..A.C.24.',
'atom2_id': 'N2@..A.G.33.', 'atom_pair': 'O:N', 'residue_pair': 'nt:nt'},
{'index': 69, 'atom1_serNum': 514, 'atom2_serNum': 708, 'donAcc_type':
'standard', 'distance': 2.966, 'atom1_id': 'N3@..A.C.24.', 'atom2_id':
'N1@..A.G.33.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'}, {'index': 70,
'atom1_serNum': 516, 'atom2_serNum': 707, 'donAcc_type': 'standard',
'distance': 2.965, 'atom1_id': 'N4@..A.C.24.', 'atom2_id': 'O6@..A.G.33.',
'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 71, 'atom1_serNum':
533, 'atom2_serNum': 687, 'donAcc_type': 'standard', 'distance': 3.037,
'atom1_id': 'O2@..A.C.25.', 'atom2_id': 'N2@..A.G.32.', 'atom_pair': 'O:N',
'residue_pair': 'nt:nt'}, {'index': 72, 'atom1_serNum': 534, 'atom2_serNum':
685, 'donAcc_type': 'standard', 'distance': 3.001, 'atom1_id': 'N3@..A.C.25.',
'atom2_id': 'N1@..A.G.32.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'},
{'index': 73, 'atom1_serNum': 536, 'atom2_serNum': 684, 'donAcc_type':
'standard', 'distance': 2.811, 'atom1_id': 'N4@..A.C.25.', 'atom2_id':
'O6@..A.G.32.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 74,
'atom1_serNum': 569, 'atom2_serNum': 631, 'donAcc_type': 'acceptable',
'distance': 3.157, 'atom1_id': "O2'@..A.A.27.", 'atom2_id': "O4'@..A.U.30.",
'atom_pair': 'O:O', 'residue_pair': 'nt:nt'}, {'index': 75, 'atom1_serNum':
591, 'atom2_serNum': 1220, 'donAcc_type': 'acceptable', 'distance': 3.018,
'atom1_id': "O2'@..A.A.28.", 'atom2_id': 'N4@..B.C.14.', 'atom_pair': 'O:N',
'residue_pair': 'nt:nt'}, {'index': 76, 'atom1_serNum': 601, 'atom2_serNum':
640, 'donAcc_type': 'standard', 'distance': 3.036, 'atom1_id': 'N3@..A.A.28.',
'atom2_id': 'N3@..A.U.30.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'},
{'index': 77, 'atom1_serNum': 635, 'atom2_serNum': 651, 'donAcc_type':
'acceptable', 'distance': 2.941, 'atom1_id': "O2'@..A.U.30.", 'atom2_id':
"O4'@..A.A.31.", 'atom_pair': 'O:O', 'residue_pair': 'nt:nt'}, {'index': 78,
'atom1_serNum': 642, 'atom2_serNum': 1193, 'donAcc_type': 'acceptable',
'distance': 2.266, 'atom1_id': 'O4@..A.U.30.', 'atom2_id': "O2'@..B.U.13.",
'atom_pair': 'O:O', 'residue_pair': 'nt:nt'}, {'index': 79, 'atom1_serNum':
659, 'atom2_serNum': 1198, 'donAcc_type': 'standard', 'distance': 2.95,
'atom1_id': 'N7@..A.A.31.', 'atom2_id': 'N3@..B.U.13.', 'atom_pair': 'N:N',
'residue_pair': 'nt:nt'}, {'index': 80, 'atom1_serNum': 662, 'atom2_serNum':
1197, 'donAcc_type': 'standard', 'distance': 3.004, 'atom1_id':
'N6@..A.A.31.', 'atom2_id': 'O2@..B.U.13.', 'atom_pair': 'N:O',
'residue_pair': 'nt:nt'}, {'index': 81, 'atom1_serNum': 765, 'atom2_serNum':
784, 'donAcc_type': 'acceptable', 'distance': 3.279, 'atom1_id':
"O2'@..A.G.36.", 'atom2_id': "O4'@..A.A.37.", 'atom_pair': 'O:O',
'residue_pair': 'nt:nt'}, {'index': 82, 'atom1_serNum': 773, 'atom2_serNum':
1044, 'donAcc_type': 'acceptable', 'distance': 3.138, 'atom1_id':
'N1@..A.G.36.', 'atom2_id': "O2'@..B.OMC.6.", 'atom_pair': 'N:O',
'residue_pair': 'nt:nt'}, {'index': 83, 'atom1_serNum': 795, 'atom2_serNum':
1040, 'donAcc_type': 'standard', 'distance': 3.014, 'atom1_id':
'N6@..A.A.37.', 'atom2_id': 'O2@..B.OMC.6.', 'atom_pair': 'N:O',
'residue_pair': 'nt:nt'}, {'index': 84, 'atom1_serNum': 817, 'atom2_serNum':
1040, 'donAcc_type': 'standard', 'distance': 3.261, 'atom1_id':
'N6@..A.A.38.', 'atom2_id': 'O2@..B.OMC.6.', 'atom_pair': 'N:O',
'residue_pair': 'nt:nt'}, {'index': 85, 'atom1_serNum': 839, 'atom2_serNum':
1008, 'donAcc_type': 'standard', 'distance': 3.221, 'atom1_id':
'N6@..A.A.39.', 'atom2_id': 'O6@..B.G.4.', 'atom_pair': 'N:O', 'residue_pair':
'nt:nt'}, {'index': 86, 'atom1_serNum': 839, 'atom2_serNum': 1031,
'donAcc_type': 'standard', 'distance': 3.021, 'atom1_id': 'N6@..A.A.39.',
'atom2_id': 'O4@..B.U.5.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'},
{'index': 87, 'atom1_serNum': 840, 'atom2_serNum': 1029, 'donAcc_type':
'standard', 'distance': 2.876, 'atom1_id': 'N1@..A.A.39.', 'atom2_id':
'N3@..B.U.5.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'}, {'index': 88,
'atom1_serNum': 858, 'atom2_serNum': 1011, 'donAcc_type': 'standard',
'distance': 2.814, 'atom1_id': 'O2@..A.C.40.', 'atom2_id': 'N2@..B.G.4.',
'atom_pair': 'O:N', 'residue_pair': 'nt:nt'}, {'index': 89, 'atom1_serNum':
859, 'atom2_serNum': 1009, 'donAcc_type': 'standard', 'distance': 2.865,
'atom1_id': 'N3@..A.C.40.', 'atom2_id': 'N1@..B.G.4.', 'atom_pair': 'N:N',
'residue_pair': 'nt:nt'}, {'index': 90, 'atom1_serNum': 861, 'atom2_serNum':
1008, 'donAcc_type': 'standard', 'distance': 2.894, 'atom1_id':
'N4@..A.C.40.', 'atom2_id': 'O6@..B.G.4.', 'atom_pair': 'N:O', 'residue_pair':
'nt:nt'}, {'index': 91, 'atom1_serNum': 881, 'atom2_serNum': 988,
'donAcc_type': 'standard', 'distance': 2.961, 'atom1_id': 'O6@..A.G.41.',
'atom2_id': 'N4@..B.C.3.', 'atom_pair': 'O:N', 'residue_pair': 'nt:nt'},
{'index': 92, 'atom1_serNum': 882, 'atom2_serNum': 986, 'donAcc_type':
'standard', 'distance': 2.868, 'atom1_id': 'N1@..A.G.41.', 'atom2_id':
'N3@..B.C.3.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'}, {'index': 93,
'atom1_serNum': 884, 'atom2_serNum': 985, 'donAcc_type': 'standard',
'distance': 2.756, 'atom1_id': 'N2@..A.G.41.', 'atom2_id': 'O2@..B.C.3.',
'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 94, 'atom1_serNum':
901, 'atom2_serNum': 968, 'donAcc_type': 'standard', 'distance': 2.815,
'atom1_id': 'O2@..A.C.42.', 'atom2_id': 'N2@..B.G.2.', 'atom_pair': 'O:N',
'residue_pair': 'nt:nt'}, {'index': 95, 'atom1_serNum': 902, 'atom2_serNum':
966, 'donAcc_type': 'standard', 'distance': 2.918, 'atom1_id': 'N3@..A.C.42.',
'atom2_id': 'N1@..B.G.2.', 'atom_pair': 'N:N', 'residue_pair': 'nt:nt'},
{'index': 96, 'atom1_serNum': 904, 'atom2_serNum': 965, 'donAcc_type':
'standard', 'distance': 2.964, 'atom1_id': 'N4@..A.C.42.', 'atom2_id':
'O6@..B.G.2.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}, {'index': 97,
'atom1_serNum': 921, 'atom2_serNum': 945, 'donAcc_type': 'standard',
'distance': 2.873, 'atom1_id': 'O2@..A.C.43.', 'atom2_id': 'N2@..B.G.1.',
'atom_pair': 'O:N', 'residue_pair': 'nt:nt'}, {'index': 98, 'atom1_serNum':
922, 'atom2_serNum': 943, 'donAcc_type': 'standard', 'distance': 2.939,
'atom1_id': 'N3@..A.C.43.', 'atom2_id': 'N1@..B.G.1.', 'atom_pair': 'N:N',
'residue_pair': 'nt:nt'}, {'index': 99, 'atom1_serNum': 924, 'atom2_serNum':
942, 'donAcc_type': 'standard', 'distance': 2.945, 'atom1_id': 'N4@..A.C.43.',
'atom2_id': 'O6@..B.G.1.', 'atom_pair': 'N:O', 'residue_pair': 'nt:nt'}],
'refCoords': {'purine': [' 12 ATOMS, 12 BONDS', ' 1 N -2.2500 5.0000 0.4000',
' 2 N -2.2500 0.5000 0.4000', ' 3 N -2.2500 0.5000 -0.4000', ' 4 N -2.2500
5.0000 -0.4000', ' 5 C 2.2500 5.0000 0.4000', ' 6 C 2.2500 0.5000 0.4000', ' 7
C 2.2500 0.5000 -0.4000', ' 8 C 2.2500 5.0000 -0.4000', ' 9 C -2.2500 5.0000
0.4000', ' 10 C -2.2500 0.5000 0.4000', ' 11 C -2.2500 0.5000 -0.4000', ' 12 C
-2.2500 5.0000 -0.4000', ' 1 1 2', ' 2 2 3', ' 3 3 4', ' 4 4 1', ' 5 5 6', ' 6
6 7', ' 7 7 8', ' 8 5 8', ' 9 9 5', ' 10 10 6', ' 11 11 7', ' 12 12 8'],
'pyrimidine': [' 12 ATOMS, 12 BONDS', ' 1 N -2.2500 5.0000 0.4000', ' 2 N
-2.2500 2.0000 0.4000', ' 3 N -2.2500 2.0000 -0.4000', ' 4 N -2.2500 5.0000
-0.4000', ' 5 C 2.2500 5.0000 0.4000', ' 6 C 2.2500 2.0000 0.4000', ' 7 C
2.2500 2.0000 -0.4000', ' 8 C 2.2500 5.0000 -0.4000', ' 9 C -2.2500 5.0000
0.4000', ' 10 C -2.2500 2.0000 0.4000', ' 11 C -2.2500 2.0000 -0.4000', ' 12 C
-2.2500 5.0000 -0.4000', ' 1 1 2', ' 2 2 3', ' 3 3 4', ' 4 4 1', ' 5 5 6', ' 6
6 7', ' 7 7 8', ' 8 5 8', ' 9 9 5', ' 10 10 6', ' 11 11 7', ' 12 12 8'],
'wc_pair': [' 12 ATOMS, 12 BONDS', ' 1 N -2.2500 5.0000 0.4000', ' 2 N -2.2500
-5.0000 0.4000', ' 3 N -2.2500 -5.0000 -0.4000', ' 4 N -2.2500 5.0000
-0.4000', ' 5 C 2.2500 5.0000 0.4000', ' 6 C 2.2500 -5.0000 0.4000', ' 7 C
2.2500 -5.0000 -0.4000', ' 8 C 2.2500 5.0000 -0.4000', ' 9 C -2.2500 5.0000
0.4000', ' 10 C -2.2500 -5.0000 0.4000', ' 11 C -2.2500 -5.0000 -0.4000', ' 12
C -2.2500 5.0000 -0.4000', ' 1 1 2', ' 2 2 3', ' 3 3 4', ' 4 4 1', ' 5 5 6', '
6 6 7', ' 7 7 8', ' 8 5 8', ' 9 9 5', ' 10 10 6', ' 11 11 7', ' 12 12 8']},
'metadata': {'version': 'DSSR v2.6.0-2025jul24 by xiangjun@x3dna.org',
'license': 'http://innovation.columbia.edu/technologies/CU20391', 'url':
'http://x3dna.org/', 'url_alt': 'http://home.x3dna.org/', 'forum':
'http://forum.x3dna.org/', 'citation': "Lu et al. (2015). 'DSSR: an integrated
software tool for dissecting the spatial structure of RNA.' Nucleic Acids
Res., 43(21):e142 [doi:10.1093/nar/gkv716].", 'command': 'x3dna-dssr
-i=/var/folders/98/5tp430816j7gbtk22tfkw_380000gq/T/tmp6ei_grby/3zp8.pdb
--json --prefix=3zp8', 'input_file':
'/var/folders/98/5tp430816j7gbtk22tfkw_380000gq/T/tmp6ei_grby/3zp8.pdb',
'str_id': '3zp8', 'num_naChains': 2, 'naChains': 'A=43,B=20', 'num_atoms':
1649, 'num_waters': 289, 'num_metals': 16, 'metals_desc': 'Na=16',
'num_notes': 52, 'notes': [{'Aminors': 'A-minor interactions (including types
I and II)'}, {'Cstem_index': "stem index of the 'Canonical' helix in k-turn"},
{'Cstem_pair': 'Cstem bp delineating the k-turn internal loop'}, {'Dp':
"perpendicular distance of the 3' P atom to the glycosidic bond"}, {'GA_pair':
'sheared G-A pair in k-turn'}, {'HtypePknot': 'H-type pseudoknot'}, {'Kturn':
'kink-turn (k-turn)'}, {'LW': 'Leontis-Westhof'}, {'NCstem_index': "stem index
of the 'Non-Canonical' helix in k-turn"}, {'NCstem_pair': 'NCstem bp
delineating the k-turn internal loop'}, {'Uturn': 'U-turn of the UNR- or GNRA-
type'}, {'aa': 'amino acid'}, {'atom_pair': 'symbols of the two atoms involved
in an H-bond'}, {'auxfiles': 'auxiliary files'}, {'glyco_bond': 'conformation
of base related to sugar (syn or anti)'}, {'bb_type': 'backbone conformation,
BI or BII'}, {'bending_angle': 'angle between two helical axes'}, {'bp': 'base
pair'}, {'bseq': 'base sequence in one-letter code'}, {'bulge': 'bulge loop'},
{'coaxStacks': 'coaxial stacking of stems within a helix'}, {'dbn': 'dot
bracket notation'}, {'desc': 'description'}, {'donAcc_type': 'donor/acceptor
type of the atom pair in an H-bond'}, {'epsilon_zeta': 'difference between
epsilon and zeta torsion angles'}, {'hairpin': 'hairpin loop'}, {'hbond':
'hydrogen bond (H-bond)'}, {'helix': 'defined by base-stacking interactions,
regardless of bp type and backbone connectivity'}, {'id': 'identifier'},
{'iloop': 'internal loop'}, {'index': 'serial number'}, {'isoCanonPairs':
'isolated canonical pairs'}, {'junction': '(multi-branched) junction loop'},
{'kissingLoop': 'kissing loop'}, {'multiplet': '3+ bases in a coplanar
geometry'}, {'na': 'nucleic acid'}, {'nonPair': 'two nts not forming a pair,
but with H-bonding/stacking interactions'}, {'nonStack': 'nucleotide not
involved in stacking interactions'}, {'nt': 'nucleotide'}, {'num': 'number'},
{'oArea': 'overlap areas between two bases, including exocyclic atoms'},
{'oArea_ring': 'overlap areas between two bases, including only ring atoms'},
{'phosContacts': 'H-bonding and atom-capping interactions involving a
phosphate'}, {'residue_pair': 'types of the two residues involved in an
H-bond'}, {'rmsd': 'root-mean-squares deviation'}, {'serNum': 'serial
number'}, {'ssSegments': 'single-stranded segments not involved in loops'},
{'ssZp': "Z-coordinate of the 3' phosphorus atom with reference to the 5' base
plane"}, {'sstr': 'secondary structure in dbn'}, {'stem': 'helix consisting of
only canonical pairs, with a continuous backbone'}, {'str_id': 'structure
identifier, derived from inpfile with extension removed'}, {'vert_dist':
'vertical distance from an atom to a base plane'}], 'num_auxfiles': 15,
'auxfiles': [{'index': 1, 'name': '3zp8-pairs.pdb', 'desc': 'an ensemble of
base pairs'}, {'index': 2, 'name': '3zp8-multiplets.pdb', 'desc': 'an ensemble
of multiplets'}, {'index': 3, 'name': '3zp8-stems.pdb', 'desc': 'an ensemble
of stems'}, {'index': 4, 'name': '3zp8-helices.pdb', 'desc': 'an ensemble of
helices (coaxial stacking)'}, {'index': 5, 'name': '3zp8-hairpins.pdb',
'desc': 'an ensemble of hairpin loops'}, {'index': 6, 'name':
'3zp8-iloops.pdb', 'desc': 'an ensemble of internal loops'}, {'index': 7,
'name': '3zp8-junctions.pdb', 'desc': 'an ensemble of junctions (multi-
branch)'}, {'index': 8, 'name': '3zp8-2ndstrs.bpseq', 'desc': 'secondary
structure in bpseq format'}, {'index': 9, 'name': '3zp8-2ndstrs.ct', 'desc':
'secondary structure in connectivity table format'}, {'index': 10, 'name':
'3zp8-2ndstrs.dbn', 'desc': 'secondary structure in dot-bracket notation'},
{'index': 11, 'name': '3zp8-torsions.txt', 'desc': 'backbone torsion angles
and suite names'}, {'index': 12, 'name': '3zp8-splays.pdb', 'desc': 'an
ensemble of splayed-apart units'}, {'index': 13, 'name': '3zp8-Aminors.pdb',
'desc': 'an ensemble of A minor motifs (types I and II)'}, {'index': 14,
'name': '3zp8-stacks.pdb', 'desc': 'an ensemble of base stacks'}, {'index':
15, 'name': '3zp8-atom2bases.pdb', 'desc': 'an ensemble of atom-base stacking
interactions'}], 'start_at': '2025-08-28 12:04:58', 'finish_at': '2025-08-28
12:04:58', 'time_used': '00:00:00:00'}}
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate
self.session.ui.thread_safe(self.handle_scheme, url)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe
func(*args, **kw)
File "/Users/luca.genz/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/NucleoSpot/tool.py",
line 280, in handle_scheme
DSSR_Object(self.session, model, self.dssr_path).draw_2d_structure()
File "/Users/luca.genz/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/NucleoSpot/run_DSSR.py", line 96, in draw_2d_structure
ms.new_pseudobond(nt_to_atom[nt1], nt_to_atom[nt2])
^^^^^^^^^^^^^^^^^
AttributeError: 'AtomicStructure' object has no attribute 'new_pseudobond'
AttributeError: 'AtomicStructure' object has no attribute 'new_pseudobond'
File "/Users/luca.genz/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/NucleoSpot/run_DSSR.py", line 96, in draw_2d_structure
ms.new_pseudobond(nt_to_atom[nt1], nt_to_atom[nt2])
^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGQ3D/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 14 days, 2 hours, 17 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LS34A650U:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-clix: 0.1.10
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-NucleoSpot: 0.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-PICKLUSTER: 2.0
ChimeraX-PICKLUSTER-R: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 8 weeks ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in chain_trace_atoms |
comment:2 by , 8 weeks ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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