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Opened 39 hours ago
Closed 37 hours ago
#19314 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-26.0.1-arm64-arm-64bit
ChimeraX Version: 1.10rc202505150242 (2025-05-15 02:42:12 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Bus error
Current thread 0x00000001eeafc800 (most recent call first):
File "/Applications/ChimeraX-1.10-rc2025.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10-rc2025.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10-rc2025.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, chimerax.dssp._dssp, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mmcif.mmcif_write, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, cython.cimports.libc.math, 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._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, chimerax.coulombic._esp, PIL._webp (total: 110)
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{
"uptime" : 190000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 793,
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"build" : "25A362",
"releaseType" : "User"
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"captureTime" : "2025-11-07 12:39:53.3284 -0500",
"codeSigningMonitor" : 2,
"incident" : "F75F7A03-C758-4995-8CB3-0988EAB8F651",
"pid" : 87352,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-11-04 09:02:46.2526 -0500",
"procStartAbsTime" : 1757361711256,
"procExitAbsTime" : 4592998029179,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10-rc2025.05.20.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"crashReporterKey" : "16F0D20E-BF20-76F9-796C-98DD72A4614E",
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 12959,
"sleepWakeUUID" : "DB38B0AE-CC48-466D-8905-1D1CD3EE7487",
"sip" : "enabled",
"vmRegionInfo" : "0x132e31d80 is in 0x132e30000-0x132e34000; bytes after start: 7552 bytes before end: 8831\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n __TEXT 132d0c000-132e30000 [ 1168K] r-x\/rwx SM=COW \/Applications\/ChimeraX-1.10-rc2025.05.20.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/lib\/libatomstruct.dylib\n---> __DATA_CONST 132e30000-132e34000 [ 16K] r--\/rwx SM=COW \/Applications\/ChimeraX-1.10-rc2025.05.20.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/lib\/libatomstruct.dylib\n __DATA 132e34000-132e38000 [ 16K] rw-\/rwx SM=COW \/Applications\/ChimeraX-1.10-rc2025.05.20.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/lib\/libatomstruct.dylib",
"exception" : {"codes":"0x0000000000000002, 0x0000000132e31d80","rawCodes":[2,5148712320],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000132e31d80"},
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UCSF ChimeraX version: 1.10rc202505150242 (2025-05-15)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Refine_52/ADPR-TK2284-NEB7-5_refine_052.pdb
Chain information for ADPR-TK2284-NEB7-5_refine_052.pdb #1
---
Chain | Description
D | No description available
E | No description available
L | No description available
M | No description available
N | No description available
O | No description available
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> set bgColor white
> lighting soft
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Refine_52/ADPR-TK2284-NEB7-5_refine_052 copy.pdb"
Chain information for ADPR-TK2284-NEB7-5_refine_052 copy.pdb #2
---
Chain | Description
D | No description available
E | No description available
L | No description available
M | No description available
N | No description available
O | No description available
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #2 models
> show #2 models
> hide atoms
> show cartoons
Computing secondary structure
> dssp
> set bgColor white
> lighting soft
> graphics silhouettes true
> select #1/M:157
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
63 atoms, 63 bonds, 8 residues, 1 model selected
> select up
994 atoms, 1013 bonds, 130 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #2 models
> select #1/L:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
107 atoms, 106 bonds, 13 residues, 1 model selected
> select up
990 atoms, 1009 bonds, 128 residues, 1 model selected
> delete sel
Drag select of 74 residues
> delete sel
> select clear
> show #2 models
> hide #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #1 models
> show #2 models
> hide #2 models
> show #2 models
> hide #1 models
> select #2/O:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 9 residues, 1 model selected
> select up
1276 atoms, 1301 bonds, 166 residues, 1 model selected
> delete sel
> select #2/N:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
103 atoms, 102 bonds, 13 residues, 1 model selected
> select up
1266 atoms, 1291 bonds, 166 residues, 1 model selected
> delete sel
> show #1 models
> select #1/N
1266 atoms, 1291 bonds, 166 residues, 1 model selected
> select ~sel & ##selected
1738 atoms, 1393 bonds, 540 residues, 1 model selected
> select ~sel & ##selected
1266 atoms, 1291 bonds, 166 residues, 1 model selected
> select #1/N:39-400 #2/L:39-300
1969 atoms, 2007 bonds, 256 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #2 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ADPR-TK2284-NEB7-5_refine_052.pdb, chain N (#1) with ADPR-
TK2284-NEB7-5_refine_052 copy.pdb, chain L (#2), sequence alignment score =
646.4
RMSD between 128 pruned atom pairs is 0.177 angstroms; (across all 128 pairs:
0.177)
> matchmaker #2 & sel to #1 & sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ADPR-TK2284-NEB7-5_refine_052.pdb, chain N (#1) with ADPR-
TK2284-NEB7-5_refine_052 copy.pdb, chain L (#2), sequence alignment score =
646.4
RMSD between 128 pruned atom pairs is 0.177 angstroms; (across all 128 pairs:
0.177)
> color #1 #ff9300ff
> color #2 #008f00ff
> ui mousemode right zoom
> select clear
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/8oxoATP + Ca/DONT USE
> MY MODEL/Ca_8oxoATP_refine_033-FINAL.pdb"
Chain information for Ca_8oxoATP_refine_033-FINAL.pdb #3
---
Chain | Description
A | No description available
B | No description available
> mmaker #1 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#3) with ADPR-
TK2284-NEB7-5_refine_052.pdb, chain O (#1), sequence alignment score = 844.4
RMSD between 156 pruned atom pairs is 0.545 angstroms; (across all 166 pairs:
1.002)
> hide #2 models
Drag select of 14 residues
> select clear
> dssp
> color #3 #0433ffff
> color #3 #0096ffff
> select clear
Drag select of 6 residues
> select rib
Expected an objects specifier or a keyword
> select ::name="RIB"
184 atoms, 184 bonds, 8 residues, 2 models selected
> show sel & #1 atoms
> select clear
> ui tool show "Side View"
> show #2 models
> hide #2 models
> select :60
49 atoms, 40 bonds, 9 residues, 3 models selected
> show sel & #1,3 atoms
> style sel & #1,3 stick
Changed 34 atom styles
> select :134
48 atoms, 39 bonds, 9 residues, 3 models selected
> show sel & #1,3 atoms
> select ~sel & ##selected
8666 atoms, 7979 bonds, 1844 residues, 3 models selected
> select ~sel & ##selected
48 atoms, 39 bonds, 9 residues, 3 models selected
> select up
347 atoms, 338 bonds, 55 residues, 3 models selected
> select :135
47 atoms, 39 bonds, 8 residues, 3 models selected
> show sel & #1,3 atoms
> style sel & #1,3 stick
Changed 30 atom styles
> select #1/N:134@CB
1 atom, 1 residue, 1 model selected
> select #1/N:134@CA
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> select clear
> select :134
48 atoms, 39 bonds, 9 residues, 3 models selected
> hide sel & #1,3 atoms
Drag select of 2 residues, 1 atoms
> select up
95 atoms, 96 bonds, 13 residues, 2 models selected
> select up
2546 atoms, 2595 bonds, 334 residues, 2 models selected
> select up
2582 atoms, 2629 bonds, 339 residues, 2 models selected
> select clear
> show #1,3 atoms
> style #1,3 stick
Changed 5711 atom styles
> select :138
52 atoms, 44 bonds, 8 residues, 3 models selected
> show target m
> hide #2 models
> select clear
> hide #1,3 atoms
> select :138
52 atoms, 44 bonds, 8 residues, 3 models selected
> show sel & #1,3 atoms
Drag select of 75 residues
> select :138
52 atoms, 44 bonds, 8 residues, 3 models selected
> show sel & #1,3 atoms
> select up
368 atoms, 372 bonds, 49 residues, 3 models selected
> select down
52 atoms, 44 bonds, 8 residues, 3 models selected
> select clear
> select :135-140
286 atoms, 275 bonds, 47 residues, 3 models selected
> show sel & #1,3 atoms
> close
> close #
Expected a models specifier or a keyword
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/ADPR-TK2284-NEB7-5_refine_052-coot-0.pdb
Chain information for ADPR-TK2284-NEB7-5_refine_052-coot-0.pdb #1
---
Chain | Description
D | No description available
E | No description available
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Drag select of 158 atoms, 17 bonds
> select clear
> hide cartoons
> hide surfaces
> show cartoons
Computing secondary structure
> hide surfaces
> hide atoms
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/8oxoATP +
> Ca/MyModel/Ca_8oxoATP_refine_033-FINAL.pdb"
Chain information for Ca_8oxoATP_refine_033-FINAL.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide #1 models
> select :137
43 atoms, 36 bonds, 7 residues, 2 models selected
> select :91
56 atoms, 48 bonds, 8 residues, 2 models selected
> show sel & #2 atoms
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Model-Removed-H.pdb
Chain information for Model-Removed-H.pdb #3
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> close
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Refine_61/ADPR-TK2284-NEB7-5_refine_061.pdb
Chain information for ADPR-TK2284-NEB7-5_refine_061.pdb #1
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> dssp
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/Comparison
> of Substrate Binding.cxs"
> view name session-start
opened ChimeraX session
> show #!2 models
> hide #1 models
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Refine_61/ADPR-TK2284-NEB7-5_refine_061.pdb
Chain information for ADPR-TK2284-NEB7-5_refine_061.pdb #5
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> select add #2
2938 atoms, 2874 bonds, 482 residues, 1 model selected
> show sel cartoons
> select #5/N
1273 atoms, 1298 bonds, 166 residues, 1 model selected
> select #5/N #2
4211 atoms, 4172 bonds, 648 residues, 2 models selected
> mmaker sele
> matchmaker sele
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> mmaker select
> matchmaker select
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> ui tool show Matchmaker
> matchmaker #5 & sel to #2 & sel ssFraction 0.7122
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7122
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2qjo(NadM).pdb, chain B (#2) with ADPR-
TK2284-NEB7-5_refine_061.pdb, chain N (#5), sequence alignment score = 380.183
RMSD between 56 pruned atom pairs is 0.836 angstroms; (across all 146 pairs:
13.312)
> select #2/B:219
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> close #1,5#2-4
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Refine_61/ADPR-TK2284-NEB7-5_refine_061.pdb
Chain information for ADPR-TK2284-NEB7-5_refine_061.pdb #1
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB
> Files/2qjo(NadM).pdb"
2qjo(NadM).pdb title:
Crystal structure of A bifunctional NMN adenylyltransferase/adp ribose
pyrophosphatase (nadm) complexed with adprp and nad from synechocystis SP.
[more info...]
Chain information for 2qjo(NadM).pdb #2
---
Chain | Description | UniProt
A B C | bifunctional NMN adenylyltransferase/nudix hydrolase | NADM_SYNY3 1-339
Non-standard residues in 2qjo(NadM).pdb #2
---
APR — adenosine-5-diphosphoribose
NAD — nicotinamide-adenine-dinucleotide
POP — pyrophosphate 2-
SO4 — sulfate ion
26 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #2/C:315
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 7 residues, 1 model selected
> select up
264 atoms, 273 bonds, 30 residues, 1 model selected
> select up
323 atoms, 333 bonds, 39 residues, 1 model selected
> select up
2639 atoms, 2711 bonds, 327 residues, 1 model selected
> delete select
Missing or invalid "atoms" argument: invalid atoms specifier
> delete sel
> select #2/A:243
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
124 atoms, 123 bonds, 15 residues, 1 model selected
> select up
2423 atoms, 2487 bonds, 303 residues, 1 model selected
> delete sel
> select clear
> select #2/B:98
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
139 atoms, 140 bonds, 18 residues, 1 model selected
> select up
2702 atoms, 2775 bonds, 336 residues, 1 model selected
> select clear
Drag select of 125 atoms, 125 bonds
> select clear
Drag select of 93 atoms, 95 bonds
> delete sel
Drag select of 41 atoms, 39 bonds
> delete sel
Drag select of 58 atoms, 56 bonds
> delete sel
Drag select of 6 atoms, 4 bonds
> delete sel
> select #1/N #2
4635 atoms, 4447 bonds, 835 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!2 & sel to #1 & sel ssFraction 0.7122
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7122
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain N (#1) with
2qjo(NadM).pdb, chain B (#2), sequence alignment score = 380.183
RMSD between 56 pruned atom pairs is 0.836 angstroms; (across all 146 pairs:
13.312)
> select clear
> select #2/B:96
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
139 atoms, 140 bonds, 18 residues, 1 model selected
> select up
2702 atoms, 2775 bonds, 336 residues, 1 model selected
> select #1/N #2
4635 atoms, 4447 bonds, 835 residues, 2 models selected
> select clear
> select #2/B:128
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 4 residues, 1 model selected
> select up
2702 atoms, 2775 bonds, 336 residues, 1 model selected
> delete sel
> select clear
> select #2/A:329
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
91 atoms, 94 bonds, 10 residues, 1 model selected
> select up
258 atoms, 267 bonds, 29 residues, 1 model selected
> delete sel
Drag select of 61 atoms, 60 bonds
> delete sel
Drag select of 14 atoms, 8 bonds
> delete sel
> select #1/A:4@C04
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> delete sel
> save /Users/mbanco/Documents/Science/TK2284/Structures/Combined-
> TK2284-NadM.pdb
> save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Combined-TK2284-NadM.pdb displayedOnly true
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Combined-TK2284-NadM.pdb
Summary of feedback from opening /Users/mbanco/Library/CloudStorage/OneDrive-
NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
NEB7-5/Combined-TK2284-NadM.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER L 17 LYS L 29 1 13
Start residue of secondary structure not found: HELIX 2 2 VAL L 81 THR L 93 1
13
Start residue of secondary structure not found: HELIX 3 3 ILE L 144 GLU L 146
1 3
Start residue of secondary structure not found: HELIX 4 4 ALA L 147 ASN L 149
1 3
End residue of secondary structure not found: HELIX 5 5 HIS L 156 ALA L 163 1
8
Start residue of secondary structure not found: HELIX 6 6 ALA M 17 LYS M 29 1
13
Start residue of secondary structure not found: HELIX 7 7 VAL M 81 THR M 93 1
13
Start residue of secondary structure not found: HELIX 8 8 ILE M 144 GLU M 146
1 3
Start residue of secondary structure not found: HELIX 9 9 ALA M 147 ASN M 149
1 3
End residue of secondary structure not found: HELIX 10 10 HIS M 156 ALA M 163
1 8
Start residue of secondary structure not found: HELIX 11 11 SER N 17 LYS N 29
1 13
Start residue of secondary structure not found: HELIX 12 12 VAL N 81 THR N 93
1 13
Start residue of secondary structure not found: HELIX 13 13 ILE N 144 GLU N
146 1 3
Start residue of secondary structure not found: HELIX 14 14 ALA N 147 ASN N
149 1 3
End residue of secondary structure not found: HELIX 15 15 HIS N 156 ALA N 163
1 8
Start residue of secondary structure not found: HELIX 16 16 ALA O 17 ALA O 27
1 11
Start residue of secondary structure not found: HELIX 17 17 GLU O 28 TYR O 30
1 3
Start residue of secondary structure not found: HELIX 18 18 VAL O 81 THR O 93
1 13
Start residue of secondary structure not found: HELIX 19 19 ILE O 144 GLU O
146 1 3
Start residue of secondary structure not found: HELIX 20 20 ALA O 147 ASN O
149 1 3
End residue of secondary structure not found: HELIX 21 21 HIS O 156 ALA O 163
1 8
Start residue of secondary structure not found: SHEET 1 1 1 ASP L 2 LYS L 9 0
Start residue of secondary structure not found: SHEET 2 2 1 GLY L 41 VAL L 49
0
Start residue of secondary structure not found: SHEET 3 3 1 GLY L 53 ARG L 59
0
End residue of secondary structure not found: SHEET 4 4 1 GLY L 72 PHE L 74 0
Start residue of secondary structure not found: SHEET 5 5 1 ASP L 96 LEU L 102
0
Start residue of secondary structure not found: SHEET 6 6 1 GLY L 104 TYR L
106 0
Start residue of secondary structure not found: SHEET 7 7 1 THR L 117 ALA L
121 0
Start residue of secondary structure not found: SHEET 8 8 1 PHE L 122 GLU L
127 0
Start residue of secondary structure not found: SHEET 9 9 1 ALA L 136 PRO L
143 0
4 messages similar to the above omitted
End residue of secondary structure not found: SHEET 14 14 1 GLY M 72 PHE M 74
0
Start residue of secondary structure not found: SHEET 15 15 1 LEU M 95 LEU M
102 0
Start residue of secondary structure not found: SHEET 16 16 1 GLY M 104 TYR M
106 0
Start residue of secondary structure not found: SHEET 17 17 1 THR M 117 ALA M
121 0
Start residue of secondary structure not found: SHEET 18 18 1 PHE M 122 GLY M
128 0
Start residue of secondary structure not found: SHEET 19 19 1 ALA M 136 PHE M
142 0
4 messages similar to the above omitted
End residue of secondary structure not found: SHEET 24 24 1 GLY N 72 PHE N 74
0
Start residue of secondary structure not found: SHEET 25 25 1 LEU N 95 LEU N
102 0
Start residue of secondary structure not found: SHEET 26 26 1 GLY N 104 TYR N
106 0
Start residue of secondary structure not found: SHEET 27 27 1 THR N 117 ALA N
121 0
Start residue of secondary structure not found: SHEET 28 28 1 PHE N 122 GLY N
128 0
Start residue of secondary structure not found: SHEET 29 29 1 ALA N 136 PHE N
142 0
4 messages similar to the above omitted
End residue of secondary structure not found: SHEET 34 34 1 GLY O 72 PHE O 74
0
Start residue of secondary structure not found: SHEET 35 35 1 LEU O 95 LEU O
102 0
Start residue of secondary structure not found: SHEET 36 36 1 GLY O 104 TYR O
106 0
Start residue of secondary structure not found: SHEET 37 37 1 THR O 117 ALA O
121 0
Start residue of secondary structure not found: SHEET 38 38 1 PHE O 122 GLY O
128 0
Start residue of secondary structure not found: SHEET 39 39 1 ALA O 136 PHE O
142 0
Cannot find LINK/SSBOND residue CYS (39 )
Cannot find LINK/SSBOND residue CYS (39 )
Start residue of secondary structure not found: HELIX 1 1 SER L 17 LYS L 29 1
13
Start residue of secondary structure not found: HELIX 2 2 VAL L 81 THR L 93 1
13
Start residue of secondary structure not found: HELIX 3 3 ILE L 144 GLU L 146
1 3
Start residue of secondary structure not found: HELIX 4 4 ALA L 147 ASN L 149
1 3
Start residue of secondary structure not found: HELIX 5 5 HIS L 156 ALA L 163
1 8
55 messages similar to the above omitted
Chain information for Combined-TK2284-NadM.pdb
---
Chain | Description
3.1/L | No description available
3.1/M | No description available
3.1/N | No description available
3.1/O | No description available
Computing secondary structure
> hide #!3.1 models
> hide #1 models
> hide #!2 models
> hide #!3 models
> show #!3.1 models
> hide #!3 models
> show #!3 models
> close #3
> show #1 models
> show #!2 models
> select clear
> save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Combined-TK2284-NadM.pdb
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Combined-TK2284-NadM.pdb
Summary of feedback from opening /Users/mbanco/Library/CloudStorage/OneDrive-
NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
NEB7-5/Combined-TK2284-NadM.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER L 17 LYS L 29 1 13
Start residue of secondary structure not found: HELIX 2 2 VAL L 81 THR L 93 1
13
Start residue of secondary structure not found: HELIX 3 3 ILE L 144 GLU L 146
1 3
Start residue of secondary structure not found: HELIX 4 4 ALA L 147 ASN L 149
1 3
Start residue of secondary structure not found: HELIX 5 5 HIS L 156 ALA L 163
1 8
55 messages similar to the above omitted
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for Combined-TK2284-NadM.pdb
---
Chain | Description
3.1/L | No description available
3.1/M | No description available
3.1/N | No description available
3.1/O | No description available
> hide #1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> close #3
> show #!2 models
Drag select of 5 atoms
> delete sel
> select add #2/B:834@O
1 atom, 1 residue, 1 model selected
> select add #2/B:775@O
2 atoms, 2 residues, 1 model selected
> select add #2/B:786@O
3 atoms, 3 residues, 1 model selected
> select add #2/B:799@O
4 atoms, 4 residues, 1 model selected
> select add #2/B:738@O
5 atoms, 5 residues, 1 model selected
> select #2 HOH
Expected a keyword
> select #2/B:HOH
136 atoms, 136 residues, 1 model selected
> delete sel
> show #1 models
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB
> Files/2qjo(NadM).pdb"
2qjo(NadM).pdb title:
Crystal structure of A bifunctional NMN adenylyltransferase/adp ribose
pyrophosphatase (nadm) complexed with adprp and nad from synechocystis SP.
[more info...]
Chain information for 2qjo(NadM).pdb #3
---
Chain | Description | UniProt
A B C | bifunctional NMN adenylyltransferase/nudix hydrolase | NADM_SYNY3 1-339
Non-standard residues in 2qjo(NadM).pdb #3
---
APR — adenosine-5-diphosphoribose
NAD — nicotinamide-adenine-dinucleotide
POP — pyrophosphate 2-
SO4 — sulfate ion
26 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #3/B:285
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
88 atoms, 90 bonds, 10 residues, 1 model selected
> select up
2702 atoms, 2775 bonds, 336 residues, 1 model selected
> select up
2938 atoms, 2874 bonds, 482 residues, 1 model selected
> select up
8622 atoms, 8541 bonds, 1321 residues, 1 model selected
> select down
2938 atoms, 2874 bonds, 482 residues, 1 model selected
> delete sel
> select #3/A:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
69 atoms, 71 bonds, 8 residues, 1 model selected
> select up
2423 atoms, 2487 bonds, 303 residues, 1 model selected
> select up
2432 atoms, 2495 bonds, 304 residues, 1 model selected
> delete sel
Drag select of 148 atoms, 34 residues, 132 bonds
> delete sel
> select #1/L #3
4080 atoms, 4024 bonds, 3 pseudobonds, 644 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #!3 to #1 ssFraction 0.7122
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7122
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain L (#1) with
2qjo(NadM).pdb, chain C (#3), sequence alignment score = 419.832
RMSD between 91 pruned atom pairs is 0.910 angstroms; (across all 150 pairs:
17.789)
> matchmaker #!3 to #1 ssFraction 0.7122
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7122
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain L (#1) with
2qjo(NadM).pdb, chain C (#3), sequence alignment score = 419.832
RMSD between 91 pruned atom pairs is 0.910 angstroms; (across all 150 pairs:
17.789)
> select clear
> select #3/C:177
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
171 atoms, 174 bonds, 20 residues, 1 model selected
> select up
1560 atoms, 1605 bonds, 190 residues, 1 model selected
> select up
1579 atoms, 1624 bonds, 193 residues, 1 model selected
> select down
1560 atoms, 1605 bonds, 190 residues, 1 model selected
> delete sel
> select #3/B:HOH
Nothing selected
> select #3:HOH
154 atoms, 154 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 52 atoms, 56 bonds
> select up
53 atoms, 56 bonds, 2 residues, 1 model selected
> select down
52 atoms, 56 bonds, 2 residues, 1 model selected
> delete sel
> select clear
> select #3/C:603@O7N
1 atom, 1 residue, 1 model selected
> delete sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
76 atoms, 76 bonds, 10 residues, 1 model selected
> select up
284 atoms, 289 bonds, 39 residues, 1 model selected
> select up
293 atoms, 297 bonds, 40 residues, 1 model selected
> select up
767 atoms, 781 bonds, 101 residues, 1 model selected
> delete sel
> select #3/C:319
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 7 residues, 1 model selected
> select up
264 atoms, 273 bonds, 30 residues, 1 model selected
> select up
300 atoms, 312 bonds, 31 residues, 1 model selected
> select down
264 atoms, 273 bonds, 30 residues, 1 model selected
> delete sel
> select :RIB
42 atoms, 42 bonds, 3 residues, 1 model selected
> delete sel
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB
> Files/2qjo(NadM) copy.pdb"
2qjo(NadM) copy.pdb title:
Crystal structure of A bifunctional NMN adenylyltransferase/adp ribose
pyrophosphatase (nadm) complexed with adprp and nad from synechocystis SP.
[more info...]
Chain information for 2qjo(NadM) copy.pdb #4
---
Chain | Description | UniProt
A B C | bifunctional NMN adenylyltransferase/nudix hydrolase | NADM_SYNY3 1-339
Non-standard residues in 2qjo(NadM) copy.pdb #4
---
APR — adenosine-5-diphosphoribose
NAD — nicotinamide-adenine-dinucleotide
POP — pyrophosphate 2-
SO4 — sulfate ion
26 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #4/C:90
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
139 atoms, 140 bonds, 18 residues, 1 model selected
> select up
2375 atoms, 2438 bonds, 297 residues, 1 model selected
> select up
2384 atoms, 2446 bonds, 298 residues, 1 model selected
> select up
2639 atoms, 2711 bonds, 327 residues, 1 model selected
> select up
2774 atoms, 2806 bonds, 376 residues, 1 model selected
> select up
8622 atoms, 8541 bonds, 1321 residues, 1 model selected
> select down
2774 atoms, 2806 bonds, 376 residues, 1 model selected
> delete sel
> select #4/A:243
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
124 atoms, 123 bonds, 15 residues, 1 model selected
> select up
2423 atoms, 2487 bonds, 303 residues, 1 model selected
> select up
2432 atoms, 2495 bonds, 304 residues, 1 model selected
> select up
2681 atoms, 2754 bonds, 332 residues, 1 model selected
> select up
2910 atoms, 2861 bonds, 463 residues, 1 model selected
> select up
5848 atoms, 5735 bonds, 945 residues, 1 model selected
> select down
2910 atoms, 2861 bonds, 463 residues, 1 model selected
> delete sel
> select #1/O #4
4233 atoms, 4194 bonds, 649 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!2-4 & sel to #1 & sel ssFraction 0.7122
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7122
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain O (#1) with 2qjo(NadM)
copy.pdb, chain B (#4), sequence alignment score = 367.437
RMSD between 65 pruned atom pairs is 0.736 angstroms; (across all 143 pairs:
15.181)
> matchmaker #!2-4 & sel to #1 & sel ssFraction 0.7122
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7122
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain O (#1) with 2qjo(NadM)
copy.pdb, chain B (#4), sequence alignment score = 367.437
RMSD between 65 pruned atom pairs is 0.736 angstroms; (across all 143 pairs:
15.181)
> select clear
> select #4/B:176
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
171 atoms, 174 bonds, 20 residues, 1 model selected
> select up
2702 atoms, 2775 bonds, 336 residues, 1 model selected
> select up
2938 atoms, 2874 bonds, 482 residues, 1 model selected
> select up
8562 atoms, 8106 bonds, 1648 residues, 4 models selected
> select clear
> select #4/B:59
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
87 atoms, 87 bonds, 11 residues, 1 model selected
> select up
2702 atoms, 2775 bonds, 336 residues, 1 model selected
> select up
2938 atoms, 2874 bonds, 482 residues, 1 model selected
> select down
2702 atoms, 2775 bonds, 336 residues, 1 model selected
> select up
2938 atoms, 2874 bonds, 482 residues, 1 model selected
> select down
2702 atoms, 2775 bonds, 336 residues, 1 model selected
> delete sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
44 atoms, 48 bonds, 1 residue, 1 model selected
> delete sel
Drag select of 19 atoms, 12 bonds
> delete sel
> select #4:HOH
137 atoms, 137 residues, 1 model selected
> delete sel
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB
> Files/2qjo(NadM) copy 2.pdb"
2qjo(NadM) copy 2.pdb title:
Crystal structure of A bifunctional NMN adenylyltransferase/adp ribose
pyrophosphatase (nadm) complexed with adprp and nad from synechocystis SP.
[more info...]
Chain information for 2qjo(NadM) copy 2.pdb #5
---
Chain | Description | UniProt
A B C | bifunctional NMN adenylyltransferase/nudix hydrolase | NADM_SYNY3 1-339
Non-standard residues in 2qjo(NadM) copy 2.pdb #5
---
APR — adenosine-5-diphosphoribose
NAD — nicotinamide-adenine-dinucleotide
POP — pyrophosphate 2-
SO4 — sulfate ion
26 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #5/A:206
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
76 atoms, 76 bonds, 10 residues, 1 model selected
> select up
2423 atoms, 2487 bonds, 303 residues, 1 model selected
> select up
2432 atoms, 2495 bonds, 304 residues, 1 model selected
> select up
2681 atoms, 2754 bonds, 332 residues, 1 model selected
> select up
2910 atoms, 2861 bonds, 463 residues, 1 model selected
> select up
8622 atoms, 8541 bonds, 1321 residues, 1 model selected
> select down
2910 atoms, 2861 bonds, 463 residues, 1 model selected
> delete sel
> select #5/B:178
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
171 atoms, 174 bonds, 20 residues, 1 model selected
> select up
2702 atoms, 2775 bonds, 336 residues, 1 model selected
> select up
2938 atoms, 2874 bonds, 482 residues, 1 model selected
> delete sel
> select #1/M #5
4014 atoms, 4070 bonds, 1 pseudobond, 543 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #!5 & sel to #1 & sel ssFraction 0.7122
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7122
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain M (#1) with 2qjo(NadM)
copy 2.pdb, chain C (#5), sequence alignment score = 384.071
RMSD between 83 pruned atom pairs is 0.845 angstroms; (across all 143 pairs:
16.080)
> matchmaker #!5 & sel to #1 & sel ssFraction 0.7122
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7122
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain M (#1) with 2qjo(NadM)
copy 2.pdb, chain C (#5), sequence alignment score = 384.071
RMSD between 83 pruned atom pairs is 0.845 angstroms; (across all 143 pairs:
16.080)
> select clear
> select #5/C:95
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
139 atoms, 140 bonds, 18 residues, 1 model selected
> select up
2375 atoms, 2438 bonds, 297 residues, 1 model selected
> select up
2384 atoms, 2446 bonds, 298 residues, 1 model selected
> select up
2639 atoms, 2711 bonds, 327 residues, 1 model selected
> select up
2774 atoms, 2806 bonds, 376 residues, 1 model selected
> select down
2639 atoms, 2711 bonds, 327 residues, 1 model selected
> select up
2774 atoms, 2806 bonds, 376 residues, 1 model selected
> select down
2639 atoms, 2711 bonds, 327 residues, 1 model selected
> select up
2774 atoms, 2806 bonds, 376 residues, 1 model selected
> select down
2639 atoms, 2711 bonds, 327 residues, 1 model selected
> delete sel
Drag select of 54 atoms, 56 bonds
> delete sel
> select #5:HOH
45 atoms, 45 residues, 1 model selected
> delete sel
> select clear
> save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Combined-TK2284-NadM(1).pdb
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Combined-TK2284-NadM(1).pdb
Summary of feedback from opening /Users/mbanco/Library/CloudStorage/OneDrive-
NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
NEB7-5/Combined-TK2284-NadM(1).pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER L 17 LYS L 29 1 13
Start residue of secondary structure not found: HELIX 2 2 VAL L 81 THR L 93 1
13
Start residue of secondary structure not found: HELIX 3 3 ILE L 144 GLU L 146
1 3
Start residue of secondary structure not found: HELIX 4 4 ALA L 147 ASN L 149
1 3
Start residue of secondary structure not found: HELIX 5 5 HIS L 156 ALA L 163
1 8
235 messages similar to the above omitted
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for Combined-TK2284-NadM(1).pdb
---
Chain | Description
6.1/L | No description available
6.1/M | No description available
6.1/N | No description available
6.1/O | No description available
> hide #1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #6.1 models
> show #6.1 models
> hide #6.2 models
> show #6.2 models
> hide #6.3 models
> show #6.3 models
> hide #6.4 models
> show #6.4 models
> hide #6.2 models
> show #6.2 models
> hide #6.2 models
> show #6.2 models
> hide #6.2 models
> show #6.2 models
> hide #6.2 models
> show #6.2 models
> hide #6.2 models
> show #6.2 models
> close #6
> show #1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2:HOH
150 atoms, 150 residues, 1 model selected
> delete sel
> save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Combined-TK2284-NadM(1).pdb
> combine #1 #2 #3 #4 #5 name New
Remapping chain ID 'B' in 2qjo(NadM).pdb #2 to 'E'
Remapping chain ID 'C' in 2qjo(NadM).pdb #3 to 'F'
Remapping chain ID 'B' in 2qjo(NadM) copy.pdb #4 to 'G'
Remapping chain ID 'C' in 2qjo(NadM) copy 2.pdb #5 to 'H'
> hide #1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> color #6 #7a81ffff
> save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Combined-TK2284-NadM(2).pdb models #6
> close #1,6#2-5
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure
> Manuscript/TK2284-Ribose_Refine_61/ADPR-TK2284-NEB7-5_refine_061.pdb"
Chain information for ADPR-TK2284-NEB7-5_refine_061.pdb #1
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> dssp
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/8oxoATP +
> Ca/MyModel/Ca_8oxoATP_refine_033-FINAL.pdb"
Chain information for Ca_8oxoATP_refine_033-FINAL.pdb #2
---
Chain | Description
A | No description available
B | No description available
> mmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#2) with ADPR-
TK2284-NEB7-5_refine_061.pdb, chain O (#1), sequence alignment score = 842.6
RMSD between 156 pruned atom pairs is 0.544 angstroms; (across all 166 pairs:
1.003)
> dssp
> select add #1
5458 atoms, 5210 bonds, 1018 residues, 1 model selected
> show sel atoms
> hide #1 models
> show #1 models
> select subtract #1
Nothing selected
> undo
> show #1 models
> undo
> select clear
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB
> Files/2qjo(NadM).pdb"
2qjo(NadM).pdb title:
Crystal structure of A bifunctional NMN adenylyltransferase/adp ribose
pyrophosphatase (nadm) complexed with adprp and nad from synechocystis SP.
[more info...]
Chain information for 2qjo(NadM).pdb #3
---
Chain | Description | UniProt
A B C | bifunctional NMN adenylyltransferase/nudix hydrolase | NADM_SYNY3 1-339
Non-standard residues in 2qjo(NadM).pdb #3
---
APR — adenosine-5-diphosphoribose
NAD — nicotinamide-adenine-dinucleotide
POP — pyrophosphate 2-
SO4 — sulfate ion
26 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #3/C:315
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 7 residues, 1 model selected
> select up
264 atoms, 273 bonds, 30 residues, 1 model selected
> select up
323 atoms, 333 bonds, 39 residues, 1 model selected
> select up
2639 atoms, 2711 bonds, 327 residues, 1 model selected
> select up
2774 atoms, 2806 bonds, 376 residues, 1 model selected
> select up
8622 atoms, 8541 bonds, 1321 residues, 1 model selected
> select down
2774 atoms, 2806 bonds, 376 residues, 1 model selected
> delete sel
> select #3/A:208
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
76 atoms, 76 bonds, 10 residues, 1 model selected
> select up
2423 atoms, 2487 bonds, 303 residues, 1 model selected
> select up
2432 atoms, 2495 bonds, 304 residues, 1 model selected
> select up
2681 atoms, 2754 bonds, 332 residues, 1 model selected
> select up
2910 atoms, 2861 bonds, 463 residues, 1 model selected
> select up
5848 atoms, 5735 bonds, 945 residues, 1 model selected
> select down
2910 atoms, 2861 bonds, 463 residues, 1 model selected
> delete sel
> hide #2 models
> select #1/N #3
4211 atoms, 4172 bonds, 648 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!3 & sel to #1 & sel ssFraction 0.7122
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7122
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain N (#1) with
2qjo(NadM).pdb, chain B (#3), sequence alignment score = 380.183
RMSD between 56 pruned atom pairs is 0.836 angstroms; (across all 146 pairs:
13.312)
> matchmaker #!3 & sel to #1 & sel ssFraction 0.7122
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7122
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain N (#1) with
2qjo(NadM).pdb, chain B (#3), sequence alignment score = 380.183
RMSD between 56 pruned atom pairs is 0.836 angstroms; (across all 146 pairs:
13.312)
> show #2 models
> hide #1 models
> select clear
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> hide #2 models
> show #1#!3 atoms
> show #2 models
> hide #2 models
> hide #1 models
> show #2 models
> undo
> hide #!3 models
> hide #1 models
> open /Users/mbanco/Downloads/4JZU.pdb
4JZU.pdb title:
Crystal structure of the bacillus subtilis pyrophosphohydrolase bsrpph bound
to A non-hydrolysable triphosphorylated dinucleotide RNA (PCP- PGPG) - first
guanosine residue In guanosine binding pocket [more info...]
Chain information for 4JZU.pdb #4
---
Chain | Description | UniProt
A B | RNA pyrophosphohydrolase | YTKD_BACSU 1-158
C | RNA (5'-R(*(GCP)P*G)-3') |
Non-standard residues in 4JZU.pdb #4
---
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
GCP — phosphomethylphosphonic acid guanylate ester
> view #4 clip false
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB
> Files/2xsq(NUDT16).pdb"
2xsq(NUDT16).pdb title:
Crystal structure of human nudix motif 16 (NUDT16) In complex with imp and
magnesium [more info...]
Chain information for 2xsq(NUDT16).pdb #5
---
Chain | Description | UniProt
A | U8 snoRNA-decapping enzyme | NUD16_HUMAN 1-195
Non-standard residues in 2xsq(NUDT16).pdb #5
---
CL — chloride ion
IMP — inosinic acid
MG — magnesium ion
27 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #4
> view #5 clip false
> close #5
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB
> Files/5bon(NUDT15).pdb"
5bon(NUDT15).pdb title:
Crystal structure of human NUDT15 (MTH2) [more info...]
Chain information for 5bon(NUDT15).pdb #4
---
Chain | Description | UniProt
A B C D E F G H | probable 8-oxo-DGTP diphosphatase NUDT15 | NUD15_HUMAN 1-164
Non-standard residues in 5bon(NUDT15).pdb #4
---
MG — magnesium ion
58 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> view #4 clip false
> select add #4
11037 atoms, 10194 bonds, 166 pseudobonds, 2370 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> close #4
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB
> Files/3bm4(NUDT5).pdb"
3bm4(NUDT5).pdb title:
Crystal structure of human adp-ribose pyrophosphatase NUDT5 In complex with
magnesium and ampcpr [more info...]
Chain information for 3bm4(NUDT5).pdb #4
---
Chain | Description | UniProt
A B | adp-sugar pyrophosphatase | NUDT5_HUMAN 1-210
Non-standard residues in 3bm4(NUDT5).pdb #4
---
ADV — α-β methylene adp-ribose (ampcpr; {[5-(6-amino-
purin-9-yl)-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxy]-hydroxy-
phosphorylmethyl}-phosphonic acid mono-(3,4,5-trihydroxy-tetrahydro-
furan-2-ylmethyl) ester)
MG — magnesium ion
> view #4 clip false
> hide #!4 models
> show #1 models
> view #1 clip false
> dssp
> select #1/A:4@O09
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 14 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel ignoreHiddenModels true
38 contacts
> contacts sel ignoreHiddenModels true
38 contacts
> close #5
> ui tool show H-Bonds
> hbonds sel restrict cross interModel false intraRes false reveal true
18 hydrogen bonds found
> hbonds sel restrict cross interModel false intraRes false reveal true
18 hydrogen bonds found
> fetch 3X0S
Unknown command: fetch 3X0S
> getcrd 3X0S
Missing or invalid "atoms" argument: invalid atom specifier
> ui tool show "Similar Structures"
You must press the similar structures Search button before you can open
matching structures.
> foldseek #1/N
Not saving entity_poly_seq for non-authoritative sequences
Found 383 similar structures to ADPR-TK2284-NEB7-5_refine_061.pdb #1/N in pdb
database using foldseek, name fs1
> open 3gz8
Summary of feedback from opening 3gz8 fetched from pdb
---
notes | Fetching compressed mmCIF 3gz8 from http://files.rcsb.org/download/3gz8.cif
Fetching CCD APR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/APR/APR.cif
3gz8 title:
Cocrystal structure of NUDIX domain of Shewanella oneidensis NrtR complexed
with ADP ribose [more info...]
Chain information for 3gz8 #5
---
Chain | Description | UniProt
A B C D | MutT/nudix family protein | Q8EFJ3_SHEON 1-159
Non-standard residues in 3gz8 #5
---
APR — adenosine-5-diphosphoribose
3gz8 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Deleted 3 extra chains, 5 C-terminal residues, 2 N-terminal residues, 256 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 3gz8 chain D to query has RMSD 0.874 using 96 of 139 paired
residues within cutoff distance 2.0
> open 3i9x
Summary of feedback from opening 3i9x fetched from pdb
---
note | Fetching compressed mmCIF 3i9x from http://files.rcsb.org/download/3i9x.cif
3i9x title:
Crystal structure of a mutT/nudix family protein from Listeria innocua [more
info...]
Chain information for 3i9x #6
---
Chain | Description | UniProt
A | mutT/nudix family protein | Q92EH0_LISIN 2-177
Non-standard residues in 3i9x #6
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
3i9x mmCIF Assemblies
---
1| author_and_software_defined_assembly
Deleted 11 C-terminal residues, 7 non-polymer residues more than 3.0 Angstroms
away.
Alignment of 3i9x chain A to query has RMSD 0.876 using 85 of 118 paired
residues within cutoff distance 2.0
> hide #5 models
> open 3cng
Summary of feedback from opening 3cng fetched from pdb
---
note | Fetching compressed mmCIF 3cng from http://files.rcsb.org/download/3cng.cif
3cng title:
Crystal structure of NUDIX hydrolase from Nitrosomonas europaea [more info...]
Chain information for 3cng #7
---
Chain | Description | UniProt
A B C D | NUDIX hydrolase | Q82VD6_NITEU 1-185
Non-standard residues in 3cng #7
---
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
GOL — glycerol (glycerin; propane-1,2,3-triol)
NA — sodium ion
ZN — zinc ion
3cng mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
23 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 3 extra chains, 20 C-terminal residues, 29 N-terminal residues, 316
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3cng chain B to query has RMSD 1.02 using 93 of 125 paired
residues within cutoff distance 2.0
> hide #!1 models
> hide #6 models
> close #6
> close #7
> open 2fml
Summary of feedback from opening 2fml fetched from pdb
---
note | Fetching compressed mmCIF 2fml from http://files.rcsb.org/download/2fml.cif
2fml title:
Crystal structure of MutT/nudix family protein from Enterococcus faecalis
[more info...]
Chain information for 2fml #6
---
Chain | Description
A B | MutT/nudix family protein
Non-standard residues in 2fml #6
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 68 C-terminal residues, 13 N-terminal residues, 201
non-polymer residues more than 3.0 Angstroms away.
Alignment of 2fml chain A to query has RMSD 0.614 using 101 of 146 paired
residues within cutoff distance 2.0
> close #6
> open 2yyh
Summary of feedback from opening 2yyh fetched from pdb
---
note | Fetching compressed mmCIF 2yyh from http://files.rcsb.org/download/2yyh.cif
2yyh title:
Crystal structure of Nudix family protein from Aquifex aeolicus [more info...]
Chain information for 2yyh #6
---
Chain | Description | UniProt
A B C D | 8-OXO-dGTPase domain | O67435_AQUAE 1-139
2yyh mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 3 extra chains, 6 C-terminal residues, 452 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 2yyh chain B to query has RMSD 0.759 using 103 of 126 paired
residues within cutoff distance 2.0
> show #!1 models
> close #6
> open 2qjt
Summary of feedback from opening 2qjt fetched from pdb
---
note | Fetching compressed mmCIF 2qjt from http://files.rcsb.org/download/2qjt.cif
2qjt title:
Crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose
pyrophosphatase complexed with AMP and MN ion from Francisella tularensis
[more info...]
Chain information for 2qjt #6
---
Chain | Description | UniProt
A B | Nicotinamide-nucleotide adenylyltransferase | Q5NHR1_FRATT 1-347
Non-standard residues in 2qjt #6
---
AMP — adenosine monophosphate
MN — manganese (II) ion
Deleted 1 extra chains, 7 C-terminal residues, 179 N-terminal residues, 332
non-polymer residues more than 3.0 Angstroms away.
Alignment of 2qjt chain A to query has RMSD 0.728 using 96 of 131 paired
residues within cutoff distance 2.0
> open 2r5w
Summary of feedback from opening 2r5w fetched from pdb
---
note | Fetching compressed mmCIF 2r5w from http://files.rcsb.org/download/2r5w.cif
2r5w title:
Crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose
pyrophosphatase from Francisella tularensis [more info...]
Chain information for 2r5w #7
---
Chain | Description | UniProt
A B | Nicotinamide-nucleotide adenylyltransferase | Q5NHR1_FRATT 1-347
Non-standard residues in 2r5w #7
---
CL — chloride ion
MG — magnesium ion
Deleted 1 extra chains, 7 C-terminal residues, 183 N-terminal residues, 360
non-polymer residues more than 3.0 Angstroms away.
Alignment of 2r5w chain A to query has RMSD 0.744 using 97 of 137 paired
residues within cutoff distance 2.0
> hide #!1 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!1 models
> show #!7 models
> close #7
> open 3i9x
3i9x title:
Crystal structure of a mutT/nudix family protein from Listeria innocua [more
info...]
Chain information for 3i9x #7
---
Chain | Description | UniProt
A | mutT/nudix family protein | Q92EH0_LISIN 2-177
Non-standard residues in 3i9x #7
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
3i9x mmCIF Assemblies
---
1| author_and_software_defined_assembly
Deleted 11 C-terminal residues, 7 non-polymer residues more than 3.0 Angstroms
away.
Alignment of 3i9x chain A to query has RMSD 0.876 using 85 of 118 paired
residues within cutoff distance 2.0
> hide #!6 models
> close #7#6
> open 3cng
3cng title:
Crystal structure of NUDIX hydrolase from Nitrosomonas europaea [more info...]
Chain information for 3cng #6
---
Chain | Description | UniProt
A B C D | NUDIX hydrolase | Q82VD6_NITEU 1-185
Non-standard residues in 3cng #6
---
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
GOL — glycerol (glycerin; propane-1,2,3-triol)
NA — sodium ion
ZN — zinc ion
3cng mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
23 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 3 extra chains, 20 C-terminal residues, 29 N-terminal residues, 316
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3cng chain B to query has RMSD 1.02 using 93 of 125 paired
residues within cutoff distance 2.0
> close #6
> open 3gz5
Summary of feedback from opening 3gz5 fetched from pdb
---
note | Fetching compressed mmCIF 3gz5 from http://files.rcsb.org/download/3gz5.cif
3gz5 title:
Crystal structure of Shewanella oneidensis NrtR [more info...]
Chain information for 3gz5 #6
---
Chain | Description | UniProt
A B | MutT/nudix family protein | Q8EFJ3_SHEON 1-237
Non-standard residues in 3gz5 #6
---
NA — sodium ion
Deleted 1 extra chains, 84 C-terminal residues, 2 N-terminal residues, 188
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3gz5 chain B to query has RMSD 1.02 using 87 of 116 paired
residues within cutoff distance 2.0
> open 2qjo
Summary of feedback from opening 2qjo fetched from pdb
---
notes | Fetching compressed mmCIF 2qjo from http://files.rcsb.org/download/2qjo.cif
Fetching CCD POP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/POP/POP.cif
2qjo title:
crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose
pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.
[more info...]
Chain information for 2qjo #7
---
Chain | Description | UniProt
A B C | Bifunctional NMN adenylyltransferase/Nudix hydrolase | NADM_SYNY3 1-339
Non-standard residues in 2qjo #7
---
APR — adenosine-5-diphosphoribose
NAD — nicotinamide-adenine-dinucleotide
POP — pyrophosphate 2-
SO4 — sulfate ion
2qjo mmCIF Assemblies
---
1| author_and_software_defined_assembly
26 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 2 extra chains, 6 C-terminal residues, 179 N-terminal residues, 266
non-polymer residues more than 3.0 Angstroms away.
Alignment of 2qjo chain B to query has RMSD 0.971 using 94 of 138 paired
residues within cutoff distance 2.0
> close #6-7
> open 3gz5
3gz5 title:
Crystal structure of Shewanella oneidensis NrtR [more info...]
Chain information for 3gz5 #6
---
Chain | Description | UniProt
A B | MutT/nudix family protein | Q8EFJ3_SHEON 1-237
Non-standard residues in 3gz5 #6
---
NA — sodium ion
Deleted 1 extra chains, 84 C-terminal residues, 2 N-terminal residues, 188
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3gz5 chain B to query has RMSD 1.02 using 87 of 116 paired
residues within cutoff distance 2.0
> open 6nci
Summary of feedback from opening 6nci fetched from pdb
---
notes | Fetching compressed mmCIF 6nci from http://files.rcsb.org/download/6nci.cif
Fetching CCD PEG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif
Fetching CCD RB5 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/5/RB5/RB5.cif
6nci title:
Crystal structure of CDP-Chase: Vector data collection [more info...]
Chain information for 6nci #7
---
Chain | Description | UniProt
A B | Phosphohydrolase (MutT/nudix family protein) | Q81EE8_BACCR 1-205
Non-standard residues in 6nci #7
---
PEG — di(hydroxyethyl)ether
PO4 — phosphate ion
RB5 — D-ribose
SO4 — sulfate ion
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 14 C-terminal residues, 31 N-terminal residues, 207
non-polymer residues more than 3.0 Angstroms away.
Alignment of 6nci chain B to query has RMSD 1.1 using 75 of 137 paired
residues within cutoff distance 2.0
> close #6
> hide #!1 models
> open 6nch
Summary of feedback from opening 6nch fetched from pdb
---
note | Fetching compressed mmCIF 6nch from http://files.rcsb.org/download/6nch.cif
6nch title:
Crystal structure of CDP-Chase: Raster data collection [more info...]
Chain information for 6nch #6
---
Chain | Description | UniProt
A B | Phosphohydrolase (MutT/nudix family protein) | Q81EE8_BACCR 1-205
Non-standard residues in 6nch #6
---
PO4 — phosphate ion
RB5 — D-ribose
SO4 — sulfate ion
42 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 14 C-terminal residues, 31 N-terminal residues, 283
non-polymer residues more than 3.0 Angstroms away.
Alignment of 6nch chain B to query has RMSD 1.1 using 74 of 136 paired
residues within cutoff distance 2.0
> open 5bs6
Summary of feedback from opening 5bs6 fetched from pdb
---
note | Fetching compressed mmCIF 5bs6 from http://files.rcsb.org/download/5bs6.cif
5bs6 title:
Apo structure of transcriptional factor AraR from Bacteroides thetaiotaomicron
VPI [more info...]
Chain information for 5bs6 #8
---
Chain | Description | UniProt
A B C D | transcriptional regulator AraR | Q8AAV8_BACTN 1-225
Non-standard residues in 5bs6 #8
---
EDO — 1,2-ethanediol (ethylene glycol)
5bs6 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Deleted 3 extra chains, 86 C-terminal residues, 7 N-terminal residues, 227
non-polymer residues more than 3.0 Angstroms away.
Alignment of 5bs6 chain B to query has RMSD 1.04 using 87 of 117 paired
residues within cutoff distance 2.0
> open 3gg6
Summary of feedback from opening 3gg6 fetched from pdb
---
note | Fetching compressed mmCIF 3gg6 from http://files.rcsb.org/download/3gg6.cif
3gg6 title:
Crystal structure of the NUDIX domain of human NUDT18 [more info...]
Chain information for 3gg6 #9
---
Chain | Description | UniProt
A | Nucleoside diphosphate-linked moiety X motif 18 | NUD18_HUMAN 26-179
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 13 C-terminal residues, 68 non-polymer residues more than 3.0
Angstroms away.
Alignment of 3gg6 chain A to query has RMSD 0.999 using 84 of 124 paired
residues within cutoff distance 2.0
> open 6nci
6nci title:
Crystal structure of CDP-Chase: Vector data collection [more info...]
Chain information for 6nci #10
---
Chain | Description | UniProt
A B | Phosphohydrolase (MutT/nudix family protein) | Q81EE8_BACCR 1-205
Non-standard residues in 6nci #10
---
PEG — di(hydroxyethyl)ether
PO4 — phosphate ion
RB5 — D-ribose
SO4 — sulfate ion
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 14 C-terminal residues, 31 N-terminal residues, 164
non-polymer residues more than 3.0 Angstroms away.
Alignment of 6nci chain A to query has RMSD 0.962 using 66 of 140 paired
residues within cutoff distance 2.0
> close #9#6-8
> open 1vcd
Summary of feedback from opening 1vcd fetched from pdb
---
note | Fetching compressed mmCIF 1vcd from http://files.rcsb.org/download/1vcd.cif
1vcd title:
Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1 [more info...]
Chain information for 1vcd #6
---
Chain | Description | UniProt
A B | Ndx1 | Q75UV1_THETH 1-126
Non-standard residues in 1vcd #6
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
1vcd mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 1 extra chains, 118 non-polymer residues more than 3.0 Angstroms away.
Alignment of 1vcd chain A to query has RMSD 0.947 using 76 of 120 paired
residues within cutoff distance 2.0
> open 1sz3
Summary of feedback from opening 1sz3 fetched from pdb
---
notes | Fetching compressed mmCIF 1sz3 from http://files.rcsb.org/download/1sz3.cif
Fetching CCD GNP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GNP/GNP.cif
1sz3 title:
Crystal structure of nudix hydrolase DR1025 In complexed with GNP and Mg+2
[more info...]
Chain information for 1sz3 #7
---
Chain | Description | UniProt
A B | MutT/nudix family protein | Q9RVK2_DEIRA 1-159
Non-standard residues in 1sz3 #7
---
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 9 C-terminal residues, 4 N-terminal residues, 136 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 1sz3 chain B to query has RMSD 0.912 using 79 of 129 paired
residues within cutoff distance 2.0
> hide #6 models
> close #6
> close #10
> show #!1 models
> open 4dyw
Summary of feedback from opening 4dyw fetched from pdb
---
note | Fetching compressed mmCIF 4dyw from http://files.rcsb.org/download/4dyw.cif
4dyw title:
Crystal structure of MutT NUDIX hydrolase from Burkholderia pseudomallei [more
info...]
Chain information for 4dyw #6
---
Chain | Description | UniProt
A B | MutT/NUDIX family protein | Q3JWU2_BURP1 1-136
4dyw mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| software_defined_assembly
Deleted 1 extra chains, 31 non-polymer residues more than 3.0 Angstroms away.
Alignment of 4dyw chain A to query has RMSD 1.02 using 92 of 126 paired
residues within cutoff distance 2.0
> hide #6 models
> hide #!1 models
> hide #!7 models
> show #6 models
> open 3gz6
Summary of feedback from opening 3gz6 fetched from pdb
---
note | Fetching compressed mmCIF 3gz6 from http://files.rcsb.org/download/3gz6.cif
3gz6 title:
Crystal structure of Shewanella oneidensis NrtR complexed with a 27mer DNA
[more info...]
Chain information for 3gz6 #8
---
Chain | Description | UniProt
A B | MutT/nudix family protein | Q8EFJ3_SHEON 1-237
C | DNA (27-MER) |
D | DNA (27-MER) |
Non-standard residues in 3gz6 #8
---
NA — sodium ion
36 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 3 extra chains, 87 C-terminal residues, 2 N-terminal residues, 66 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 3gz6 chain B to query has RMSD 0.928 using 81 of 116 paired
residues within cutoff distance 2.0
> open 5bs6
5bs6 title:
Apo structure of transcriptional factor AraR from Bacteroides thetaiotaomicron
VPI [more info...]
Chain information for 5bs6 #9
---
Chain | Description | UniProt
A B C D | transcriptional regulator AraR | Q8AAV8_BACTN 1-225
Non-standard residues in 5bs6 #9
---
EDO — 1,2-ethanediol (ethylene glycol)
5bs6 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Deleted 3 extra chains, 87 C-terminal residues, 9 N-terminal residues, 226
non-polymer residues more than 3.0 Angstroms away.
Alignment of 5bs6 chain D to query has RMSD 1.02 using 83 of 118 paired
residues within cutoff distance 2.0
> open 1sjy
Summary of feedback from opening 1sjy fetched from pdb
---
note | Fetching compressed mmCIF 1sjy from http://files.rcsb.org/download/1sjy.cif
1sjy title:
Crystal Structure of NUDIX HYDROLASE DR1025 FROM DEINOCOCCUS RADIODURANS [more
info...]
Chain information for 1sjy #10
---
Chain | Description | UniProt
A | MutT/nudix family protein | Q9RVK2_DEIRA 1-159
1sjy mmCIF Assemblies
---
1| author_defined_assembly
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 32 C-terminal residues, 2 N-terminal residues, 45 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1sjy chain A to query has RMSD 0.902 using 79 of 113 paired
residues within cutoff distance 2.0
> open 3o8s
Summary of feedback from opening 3o8s fetched from pdb
---
notes | Fetching compressed mmCIF 3o8s from http://files.rcsb.org/download/3o8s.cif
Fetching CCD ACT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/ACT/ACT.cif
3o8s title:
Crystal structure of an ADP-ribose pyrophosphatase (SSU98_1448) from
STREPTOCOCCUS SUIS 89-1591 at 2.27 A resolution [more info...]
Chain information for 3o8s #11
---
Chain | Description | UniProt
A | ADP-ribose pyrophosphatase | B9WTJ0_STRSU 1-205
Non-standard residues in 3o8s #11
---
ACT — acetate ion
EDO — 1,2-ethanediol (ethylene glycol)
3o8s mmCIF Assemblies
---
1| author_and_software_defined_assembly
2 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 8 C-terminal residues, 20 non-polymer residues more than 3.0 Angstroms
away.
Alignment of 3o8s chain A to query has RMSD 1.07 using 74 of 118 paired
residues within cutoff distance 2.0
> open 3gz5
3gz5 title:
Crystal structure of Shewanella oneidensis NrtR [more info...]
Chain information for 3gz5 #12
---
Chain | Description | UniProt
A B | MutT/nudix family protein | Q8EFJ3_SHEON 1-237
Non-standard residues in 3gz5 #12
---
NA — sodium ion
Deleted 1 extra chains, 82 C-terminal residues, 1 N-terminal residues, 176
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3gz5 chain A to query has RMSD 0.859 using 81 of 118 paired
residues within cutoff distance 2.0
> open 1su2
Summary of feedback from opening 1su2 fetched from pdb
---
note | Fetching compressed mmCIF 1su2 from http://files.rcsb.org/download/1su2.cif
1su2 title:
Crystal structure of the nudix hydrolase DR1025 In complex with atp [more
info...]
Chain information for 1su2 #13
---
Chain | Description | UniProt
A B | MutT/nudix family protein | Q9RVK2_DEIRA 1-159
Non-standard residues in 1su2 #13
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
35 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 32 C-terminal residues, 3 N-terminal residues, 220
non-polymer residues more than 3.0 Angstroms away.
Alignment of 1su2 chain B to query has RMSD 0.905 using 78 of 113 paired
residues within cutoff distance 2.0
> close #6#7-12
> open 1soi
Summary of feedback from opening 1soi fetched from pdb
---
notes | Fetching compressed mmCIF 1soi from http://files.rcsb.org/download/1soi.cif
Fetching CCD SM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/SM/SM.cif
1soi title:
Crystal structure of nudix hydrolase DR1025 In complex with Sm+3 [more
info...]
Chain information for 1soi #6
---
Chain | Description | UniProt
A | MutT/nudix family protein | Q9RVK2_DEIRA 1-159
Non-standard residues in 1soi #6
---
SM — samarium (III) ion
1soi mmCIF Assemblies
---
1| author_defined_assembly
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 10 C-terminal residues, 2 N-terminal residues, 28 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 1soi chain A to query has RMSD 0.913 using 78 of 130 paired
residues within cutoff distance 2.0
> open 6o3p
Summary of feedback from opening 6o3p fetched from pdb
---
note | Fetching compressed mmCIF 6o3p from http://files.rcsb.org/download/6o3p.cif
6o3p title:
Crystal structure of the catalytic domain of mouse Nudt12 in complex with AMP
and 3 Mg2+ ions [more info...]
Chain information for 6o3p #7
---
Chain | Description | UniProt
A B | Peroxisomal NADH pyrophosphatase NUDT12 | NUD12_MOUSE 126-460
Non-standard residues in 6o3p #7
---
AMP — adenosine monophosphate
MG — magnesium ion
ZN — zinc ion
29 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 170 N-terminal residues, 238 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 6o3p chain A to query has RMSD 1.1 using 85 of 122 paired
residues within cutoff distance 2.0
> close #6
> close #13
> show #!1 models
> select #1/N:37
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/O:37
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> open 6m6y
Summary of feedback from opening 6m6y fetched from pdb
---
note | Fetching compressed mmCIF 6m6y from http://files.rcsb.org/download/6m6y.cif
6m6y title:
Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP
[more info...]
Chain information for 6m6y #6
---
Chain | Description | UniProt
A | Hydrolase, NUDIX family protein | A0QUZ2_MYCS2 1-322
Non-standard residues in 6m6y #6
---
8DG — 8-oxo-2'-deoxyguanosine-5'-triphosphate
EDO — 1,2-ethanediol (ethylene glycol)
MG — magnesium ion
PO4 — phosphate ion
POP — pyrophosphate 2-
126 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 164 C-terminal residues, 260 non-polymer residues more than 3.0
Angstroms away.
Alignment of 6m6y chain A to query has RMSD 0.966 using 97 of 123 paired
residues within cutoff distance 2.0
> hide #!7 models
> hide #!1 models
> open 5gg5
Summary of feedback from opening 5gg5 fetched from pdb
---
note | Fetching compressed mmCIF 5gg5 from http://files.rcsb.org/download/5gg5.cif
5gg5 title:
Crystal structure of Mycobacterium smegmatis MutT1 [more info...]
Chain information for 5gg5 #8
---
Chain | Description | UniProt
A | Hydrolase, NUDIX family protein | A0QUZ2_MYCS2 1-322
Non-standard residues in 5gg5 #8
---
EDO — 1,2-ethanediol (ethylene glycol)
PEG — di(hydroxyethyl)ether
SO4 — sulfate ion
137 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 163 C-terminal residues, 2 N-terminal residues, 216 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 5gg5 chain A to query has RMSD 1.06 using 93 of 122 paired
residues within cutoff distance 2.0
> open 4hvy
Summary of feedback from opening 4hvy fetched from pdb
---
note | Fetching compressed mmCIF 4hvy from http://files.rcsb.org/download/4hvy.cif
4hvy title:
A thermostable variant of human NUDT18 NUDIX domain obtained by Hot Colony
Filtration [more info...]
Chain information for 4hvy #9
---
Chain | Description | UniProt
A | Nucleoside diphosphate-linked moiety X motif 18 | NUD18_HUMAN 26-179
Non-standard residues in 4hvy #9
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
NA — sodium ion
SO4 — sulfate ion
4hvy mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
130 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 7 C-terminal residues, 105 non-polymer residues more than 3.0
Angstroms away.
Alignment of 4hvy chain A to query has RMSD 0.987 using 79 of 119 paired
residues within cutoff distance 2.0
> close #6
> open 5ggc
Summary of feedback from opening 5ggc fetched from pdb
---
note | Fetching compressed mmCIF 5ggc from http://files.rcsb.org/download/5ggc.cif
5ggc title:
Crystal structure of Mycobacterium smegmatis MutT1 in complex with phosphate
and magnesium ions (excess magnesium, I) [more info...]
Chain information for 5ggc #6
---
Chain | Description | UniProt
A B | Hydrolase, NUDIX family protein | A0QUZ2_MYCS2 1-322
Non-standard residues in 5ggc #6
---
MG — magnesium ion
PO4 — phosphate ion
5ggc mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
40 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 163 C-terminal residues, 406 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 5ggc chain A to query has RMSD 0.984 using 96 of 123 paired
residues within cutoff distance 2.0
> open 3i7u
Summary of feedback from opening 3i7u fetched from pdb
---
notes | Fetching compressed mmCIF 3i7u from http://files.rcsb.org/download/3i7u.cif
Fetching CCD PG4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PG4/PG4.cif
Fetching CCD PGE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/PGE/PGE.cif
3i7u title:
Crystal structure of AP4A hydrolase (aq_158) from Aquifex aeolicus VF5 [more
info...]
Chain information for 3i7u #10
---
Chain | Description | UniProt
A B C D | AP4A hydrolase | O66548_AQUAE 1-134
Non-standard residues in 3i7u #10
---
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
PEG — di(hydroxyethyl)ether
PG4 — tetraethylene glycol
PGE — triethylene glycol
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
Deleted 3 extra chains, 7 C-terminal residues, 514 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 3i7u chain B to query has RMSD 0.942 using 98 of 122 paired
residues within cutoff distance 2.0
> open 6m72
Summary of feedback from opening 6m72 fetched from pdb
---
notes | Fetching compressed mmCIF 6m72 from http://files.rcsb.org/download/6m72.cif
Fetching CCD 8GD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/8GD/8GD.cif
6m72 title:
Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGDP
[more info...]
Chain information for 6m72 #11
---
Chain | Description | UniProt
A | Hydrolase, NUDIX family protein | A0QUZ2_MYCS2 1-322
Non-standard residues in 6m72 #11
---
8GD — 2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate)
(8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-diphosphate)
MG — magnesium ion
POP — pyrophosphate 2-
72 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 164 C-terminal residues, 279 non-polymer residues more than 3.0
Angstroms away.
Alignment of 6m72 chain A to query has RMSD 0.967 using 97 of 123 paired
residues within cutoff distance 2.0
> open 4hfq
Summary of feedback from opening 4hfq fetched from pdb
---
note | Fetching compressed mmCIF 4hfq from http://files.rcsb.org/download/4hfq.cif
4hfq title:
Crystal structure of UDP-X diphosphatase [more info...]
Chain information for 4hfq #12
---
Chain | Description | UniProt
A B | MutT/nudix family protein | Q97PF7_STRPN 1-203
Non-standard residues in 4hfq #12
---
EDO — 1,2-ethanediol (ethylene glycol)
GOL — glycerol (glycerin; propane-1,2,3-triol)
PEG — di(hydroxyethyl)ether
PGE — triethylene glycol
SO4 — sulfate ion
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
209 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 10 C-terminal residues, 51 N-terminal residues, 424
non-polymer residues more than 3.0 Angstroms away.
Alignment of 4hfq chain B to query has RMSD 0.944 using 72 of 132 paired
residues within cutoff distance 2.0
> close #10,12#8-9,11
> open 3id9
Summary of feedback from opening 3id9 fetched from pdb
---
note | Fetching compressed mmCIF 3id9 from http://files.rcsb.org/download/3id9.cif
3id9 title:
Crystal structure of a MutT/NUDIX family protein from Bacillus thuringiensis
[more info...]
Chain information for 3id9 #8
---
Chain | Description
A B | MutT/NUDIX family protein
Non-standard residues in 3id9 #8
---
CL — chloride ion
SO4 — sulfate ion
Deleted 1 extra chains, 9 C-terminal residues, 96 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 3id9 chain A to query has RMSD 0.995 using 77 of 115 paired
residues within cutoff distance 2.0
> open 6o3p
6o3p title:
Crystal structure of the catalytic domain of mouse Nudt12 in complex with AMP
and 3 Mg2+ ions [more info...]
Chain information for 6o3p #9
---
Chain | Description | UniProt
A B | Peroxisomal NADH pyrophosphatase NUDT12 | NUD12_MOUSE 126-460
Non-standard residues in 6o3p #9
---
AMP — adenosine monophosphate
MG — magnesium ion
ZN — zinc ion
29 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 2 C-terminal residues, 182 N-terminal residues, 243
non-polymer residues more than 3.0 Angstroms away.
Alignment of 6o3p chain B to query has RMSD 1.14 using 86 of 125 paired
residues within cutoff distance 2.0
> hide #!8 models
> hide #!9 models
> show #!9 models
> hide #!6 models
> open 3id9
3id9 title:
Crystal structure of a MutT/NUDIX family protein from Bacillus thuringiensis
[more info...]
Chain information for 3id9 #10
---
Chain | Description
A B | MutT/NUDIX family protein
Non-standard residues in 3id9 #10
---
CL — chloride ion
SO4 — sulfate ion
Deleted 1 extra chains, 12 C-terminal residues, 88 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 3id9 chain B to query has RMSD 0.993 using 73 of 115 paired
residues within cutoff distance 2.0
> open 3smd
Summary of feedback from opening 3smd fetched from pdb
---
note | Fetching compressed mmCIF 3smd from http://files.rcsb.org/download/3smd.cif
3smd title:
Crystal structure of a mut/nudix family protein from bacillus thuringiensis
[more info...]
Chain information for 3smd #11
---
Chain | Description
A | MutT/NUDIX family protein
3smd mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
Deleted 2 C-terminal residues, 3 N-terminal residues, 45 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 3smd chain A to query has RMSD 0.882 using 76 of 121 paired
residues within cutoff distance 2.0
> open 6scx
Summary of feedback from opening 6scx fetched from pdb
---
notes | Fetching compressed mmCIF 6scx from http://files.rcsb.org/download/6scx.cif
Fetching CCD CD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/CD/CD.cif
Fetching CCD MGP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/MGP/MGP.cif
6scx title:
Crystal structure of the catalytic domain of human NUDT12 in complex with
7-methyl-guanosine-5'-triphosphate [more info...]
Chain information for 6scx #12
---
Chain | Description | UniProt
A B C | Peroxisomal NADH pyrophosphatase NUDT12 | NUD12_HUMAN 111-462
Non-standard residues in 6scx #12
---
CD — cadmium ion
MGP — 7-methyl-guanosine-5'-triphosphate
6scx mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
99 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 2 extra chains, 6 C-terminal residues, 182 N-terminal residues, 14
non-polymer residues more than 3.0 Angstroms away.
Alignment of 6scx chain A to query has RMSD 1.09 using 84 of 122 paired
residues within cutoff distance 2.0
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!1 models
> open 5isy
Summary of feedback from opening 5isy fetched from pdb
---
note | Fetching compressed mmCIF 5isy from http://files.rcsb.org/download/5isy.cif
5isy title:
Crystal structure of Nudix family protein with NAD [more info...]
Chain information for 5isy #13
---
Chain | Description | UniProt
A C | NADH pyrophosphatase | NUDC_ECOLI 1-257
Non-standard residues in 5isy #13
---
NAD — nicotinamide-adenine-dinucleotide
ZN — zinc ion
6 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 70 N-terminal residues, 159 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 5isy chain C to query has RMSD 0.964 using 83 of 145 paired
residues within cutoff distance 2.0
> hide #!12 models
> open 5xd2
Summary of feedback from opening 5xd2 fetched from pdb
---
notes | Fetching compressed mmCIF 5xd2 from http://files.rcsb.org/download/5xd2.cif
Fetching CCD 5FA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/5FA/5FA.cif
5xd2 title:
Crystal structure of Mycobacterium smegmatis MutT1 in complex with Ap5A, ATP
and manganese [more info...]
Chain information for 5xd2 #14
---
Chain | Description | UniProt
A | NUDIX family protein | A0QUZ2_MYCS2 1-322
Non-standard residues in 5xd2 #14
---
5FA — adenosine-5'-pentaphosphate
ATP — adenosine-5'-triphosphate
GOL — glycerol (glycerin; propane-1,2,3-triol)
MN — manganese (II) ion
44 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 168 C-terminal residues, 205 non-polymer residues more than 3.0
Angstroms away.
Alignment of 5xd2 chain A to query has RMSD 0.953 using 89 of 120 paired
residues within cutoff distance 2.0
> hide #!13 models
> hide #!1 models
> open 5deq
Summary of feedback from opening 5deq fetched from pdb
---
notes | Fetching compressed mmCIF 5deq from http://files.rcsb.org/download/5deq.cif
Fetching CCD ARA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/ARA/ARA.cif
5deq title:
Crystal structure of transcriptional factor AraR from Bacteroides
thetaiotaomicron VPI in complex with L-arabinose [more info...]
Chain information for 5deq #15
---
Chain | Description | UniProt
A B | TRANSCRIPTIONAL REGULATOR AraR | Q8AAV8_BACTN 1-225
Non-standard residues in 5deq #15
---
ARA — alpha-L-arabinopyranose (alpha-L-arabinose; L-arabinose; arabinose)
FMT — formic acid
SO4 — sulfate ion
74 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 76 C-terminal residues, 5 N-terminal residues, 184
non-polymer residues more than 3.0 Angstroms away.
Alignment of 5deq chain A to query has RMSD 0.953 using 83 of 121 paired
residues within cutoff distance 2.0
> hide #!14 models
> open 2gb5
Summary of feedback from opening 2gb5 fetched from pdb
---
note | Fetching compressed mmCIF 2gb5 from http://files.rcsb.org/download/2gb5.cif
2gb5 title:
Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from
Escherichia coli K12 at 2.30 A resolution [more info...]
Chain information for 2gb5 #16
---
Chain | Description | UniProt
A B | NADH pyrophosphatase | NUDC_ECOLI 1-257
Non-standard residues in 2gb5 #16
---
ZN — zinc ion
45 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 8 C-terminal residues, 124 N-terminal residues, 206
non-polymer residues more than 3.0 Angstroms away.
Alignment of 2gb5 chain B to query has RMSD 0.961 using 86 of 123 paired
residues within cutoff distance 2.0
> open 5gg7
Summary of feedback from opening 5gg7 fetched from pdb
---
notes | Fetching compressed mmCIF 5gg7 from http://files.rcsb.org/download/5gg7.cif
Fetching CCD 8OG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/8OG/8OG.cif
5gg7 title:
Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP,
8-oxo-dGMP and pyrophosphate (I) [more info...]
Chain information for 5gg7 #17
---
Chain | Description | UniProt
A B | Hydrolase, NUDIX family protein | A0QUZ2_MYCS2 1-322
Non-standard residues in 5gg7 #17
---
8DG — 8-oxo-2'-deoxyguanosine-5'-triphosphate
8OG — 8-oxo-2'-deoxy-guanosine-5'-monophosphate (8-oxo-7,8-dihydro-2'-deoxy-
guanosine-5'-monophosphate)
MG — magnesium ion
POP — pyrophosphate 2-
5gg7 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
76 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 164 C-terminal residues, 546 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 5gg7 chain A to query has RMSD 0.979 using 93 of 123 paired
residues within cutoff distance 2.0
> open 3f13
Summary of feedback from opening 3f13 fetched from pdb
---
note | Fetching compressed mmCIF 3f13 from http://files.rcsb.org/download/3f13.cif
3f13 title:
Crystal structure of putative nudix hydrolase family member from
Chromobacterium violaceum [more info...]
Chain information for 3f13 #18
---
Chain | Description | UniProt
A B | putative nudix hydrolase family member | Q7NWQ3_CHRVO 4-156
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 33 C-terminal residues, 1 N-terminal residues, 142
non-polymer residues more than 3.0 Angstroms away.
Alignment of 3f13 chain B to query has RMSD 1.08 using 76 of 111 paired
residues within cutoff distance 2.0
> hide #!16 models
> hide #!15 models
> hide #!17 models
> show #!17 models
> show #!7 models
> show #!10 models
> show #!9 models
> hide #!10 models
> close #10-18
> hide #!7 models
> hide #!9 models
> open 5gp0
Summary of feedback from opening 5gp0 fetched from pdb
---
notes | Fetching compressed mmCIF 5gp0 from http://files.rcsb.org/download/5gp0.cif
Fetching CCD GPP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GPP/GPP.cif
5gp0 title:
Crystal structure of geraniol-NUDX1 complex [more info...]
Chain information for 5gp0 #10
---
Chain | Description | UniProt
A E F I | Nudix hydrolase 1 | NUDT1_ARATH 1-147 7-153
Non-standard residues in 5gp0 #10
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
GPP — geranyl diphosphate
5gp0 mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
122 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 3 extra chains, 17 C-terminal residues, 593 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 5gp0 chain I to query has RMSD 1.09 using 83 of 114 paired
residues within cutoff distance 2.0
> open 3grn
Summary of feedback from opening 3grn fetched from pdb
---
note | Fetching compressed mmCIF 3grn from http://files.rcsb.org/download/3grn.cif
3grn title:
CRYSTAL STRUCTURE OF MUTT PROTEIN FROM Methanosarcina mazei Go1 [more info...]
Chain information for 3grn #11
---
Chain | Description | UniProt
A B | MutT related protein | Q8PYE2_METMA 3-145
Non-standard residues in 3grn #11
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
3grn mmCIF Assemblies
---
1| author_defined_assembly
2| author_and_software_defined_assembly
68 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 8 C-terminal residues, 111 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 3grn chain A to query has RMSD 1.11 using 67 of 123 paired
residues within cutoff distance 2.0
> open 6dt3
Summary of feedback from opening 6dt3 fetched from pdb
---
notes | Fetching compressed mmCIF 6dt3 from http://files.rcsb.org/download/6dt3.cif
Fetching CCD EPE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/EPE/EPE.cif
6dt3 title:
1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosphatase NudI
from Klebsiella pneumoniae in Complex with HEPES [more info...]
Chain information for 6dt3 #12
---
Chain | Description | UniProt
A B | Nucleoside triphosphatase NudI | A0A1W1Q5B1_KLEPN 1-141
Non-standard residues in 6dt3 #12
---
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
275 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 5 C-terminal residues, 3 N-terminal residues, 222 non-
polymer residues more than 3.0 Angstroms away.
Alignment of 6dt3 chain A to query has RMSD 1.11 using 79 of 122 paired
residues within cutoff distance 2.0
> open 5iw5
Summary of feedback from opening 5iw5 fetched from pdb
---
notes | Fetching compressed mmCIF 5iw5 from http://files.rcsb.org/download/5iw5.cif
Fetching CCD NMN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/NMN/NMN.cif
5iw5 title:
Crystal structure of E. coli NudC in complex with NMN [more info...]
Chain information for 5iw5 #13
---
Chain | Description | UniProt
A B | NADH pyrophosphatase | D6JHV3_ECOLX 1-257
Non-standard residues in 5iw5 #13
---
NMN — β-nicotinamide ribose monophosphate (nicotinamide mononucleotide)
ZN — zinc ion
5iw5 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Deleted 1 extra chains, 10 C-terminal residues, 116 N-terminal residues, 96
non-polymer residues more than 3.0 Angstroms away.
Alignment of 5iw5 chain A to query has RMSD 1.16 using 86 of 122 paired
residues within cutoff distance 2.0
> close #10-12#13
> open 1vc9
Summary of feedback from opening 1vc9 fetched from pdb
---
note | Fetching compressed mmCIF 1vc9 from http://files.rcsb.org/download/1vc9.cif
1vc9 title:
Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase E50Q mutant-Mg2+-ATP
complex [more info...]
Chain information for 1vc9 #10
---
Chain | Description | UniProt
A B | Ndx1 | Q75UV1_THETH 1-126
Non-standard residues in 1vc9 #10
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
1vc9 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Deleted 1 extra chains, 5 C-terminal residues, 74 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 1vc9 chain B to query has RMSD 1.08 using 84 of 118 paired
residues within cutoff distance 2.0
> open 6t5j
Summary of feedback from opening 6t5j fetched from pdb
---
notes | Fetching compressed mmCIF 6t5j from http://files.rcsb.org/download/6t5j.cif
Fetching CCD MKB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/MKB/MKB.cif
6t5j title:
Structure of NUDT15 in complex with inhibitor TH1760 [more info...]
Chain information for 6t5j #11
---
Chain | Description | UniProt
A B | Probable 8-oxo-dGTP diphosphatase NUDT15 | NUD15_HUMAN 1-164
Non-standard residues in 6t5j #11
---
CL — chloride ion
MG — magnesium ion
MKB —
6-[4-(1~{H}-indol-5-ylcarbonyl)piperazin-1-yl]sulfonyl-3~{H}-1,3-benzoxazol-2-one
27 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 34 C-terminal residues, 342 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 6t5j chain B to query has RMSD 1.16 using 75 of 110 paired
residues within cutoff distance 2.0
> open 3n77
Summary of feedback from opening 3n77 fetched from pdb
---
note | Fetching compressed mmCIF 3n77 from http://files.rcsb.org/download/3n77.cif
3n77 title:
Crystal structure of Idp01880, putative NTP pyrophosphohydrolase of Salmonella
typhimurium LT2 [more info...]
Chain information for 3n77 #12
---
Chain | Description | UniProt
A B | Nucleoside triphosphatase nudI | NUDI_SALTY 1-141
3n77 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_and_software_defined_assembly
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 5 C-terminal residues, 131 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 3n77 chain A to query has RMSD 1.15 using 80 of 123 paired
residues within cutoff distance 2.0
> open 3dku
Summary of feedback from opening 3dku fetched from pdb
---
note | Fetching compressed mmCIF 3dku from http://files.rcsb.org/download/3dku.cif
3dku title:
Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1
[more info...]
Chain information for 3dku #13
---
Chain | Description | UniProt
A B C D E F G H | Putative phosphohydrolase | A1AA28_ECOK1 1-153
3dku mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
5| author_defined_assembly
6| author_defined_assembly
7| author_defined_assembly
8| author_defined_assembly
Deleted 7 extra chains, 19 C-terminal residues, 142 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 3dku chain H to query has RMSD 0.86 using 74 of 121 paired
residues within cutoff distance 2.0
> open 6scx
6scx title:
Crystal structure of the catalytic domain of human NUDT12 in complex with
7-methyl-guanosine-5'-triphosphate [more info...]
Chain information for 6scx #14
---
Chain | Description | UniProt
A B C | Peroxisomal NADH pyrophosphatase NUDT12 | NUD12_HUMAN 111-462
Non-standard residues in 6scx #14
---
CD — cadmium ion
MGP — 7-methyl-guanosine-5'-triphosphate
6scx mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
99 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 2 extra chains, 6 C-terminal residues, 179 N-terminal residues, 14
non-polymer residues more than 3.0 Angstroms away.
Alignment of 6scx chain B to query has RMSD 1.08 using 83 of 122 paired
residues within cutoff distance 2.0
> close #12-13#10-11
> open 3oga
Summary of feedback from opening 3oga fetched from pdb
---
notes | Fetching compressed mmCIF 3oga from http://files.rcsb.org/download/3oga.cif
Fetching CCD BME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/BME/BME.cif
3oga title:
1.75 Angstrom resolution crystal structure of a putative NTP
pyrophosphohydrolase (yfaO) from Salmonella typhimurium LT2 [more info...]
Chain information for 3oga #10
---
Chain | Description | UniProt
A B | Nucleoside triphosphatase nudI | NUDI_SALTY 1-141
Non-standard residues in 3oga #10
---
BME — β-mercaptoethanol
PO4 — phosphate ion
183 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 5 C-terminal residues, 175 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 3oga chain B to query has RMSD 1.11 using 82 of 116 paired
residues within cutoff distance 2.0
> open 5isy
5isy title:
Crystal structure of Nudix family protein with NAD [more info...]
Chain information for 5isy #11
---
Chain | Description | UniProt
A C | NADH pyrophosphatase | NUDC_ECOLI 1-257
Non-standard residues in 5isy #11
---
NAD — nicotinamide-adenine-dinucleotide
ZN — zinc ion
6 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 7 C-terminal residues, 118 N-terminal residues, 170
non-polymer residues more than 3.0 Angstroms away.
Alignment of 5isy chain A to query has RMSD 0.931 using 81 of 122 paired
residues within cutoff distance 2.0
> open 3ees
Summary of feedback from opening 3ees fetched from pdb
---
note | Fetching compressed mmCIF 3ees from http://files.rcsb.org/download/3ees.cif
3ees title:
Structure of the RNA pyrophosphohydrolase BdRppH [more info...]
Chain information for 3ees #12
---
Chain | Description | UniProt
A B | Probable pyrophosphohydrolase | Q6MPX4_BDEBA 1-153
Deleted 1 extra chains, 9 C-terminal residues, 69 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 3ees chain B to query has RMSD 1.04 using 78 of 118 paired
residues within cutoff distance 2.0
> open 1rya
Summary of feedback from opening 1rya fetched from pdb
---
notes | Fetching compressed mmCIF 1rya from http://files.rcsb.org/download/1rya.cif
Fetching CCD GDP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GDP/GDP.cif
1rya title:
Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex
with GDP and MG [more info...]
Chain information for 1rya #13
---
Chain | Description | UniProt
A B | GDP-mannose mannosyl hydrolase | NUDD_ECOLI 1-160
Non-standard residues in 1rya #13
---
CL — chloride ion
GDP — guanosine-5'-diphosphate
MG — magnesium ion
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
Deleted 1 extra chains, 11 C-terminal residues, 6 N-terminal residues, 563
non-polymer residues more than 3.0 Angstroms away.
Alignment of 1rya chain B to query has RMSD 0.966 using 65 of 130 paired
residues within cutoff distance 2.0
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> open 1rya
1rya title:
Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex
with GDP and MG [more info...]
Chain information for 1rya #15
---
Chain | Description | UniProt
A B | GDP-mannose mannosyl hydrolase | NUDD_ECOLI 1-160
Non-standard residues in 1rya #15
---
CL — chloride ion
GDP — guanosine-5'-diphosphate
MG — magnesium ion
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
Deleted 1 extra chains, 11 C-terminal residues, 6 N-terminal residues, 563
non-polymer residues more than 3.0 Angstroms away.
Alignment of 1rya chain B to query has RMSD 0.966 using 65 of 130 paired
residues within cutoff distance 2.0
> hide #!14 models
> open 5wy6
Summary of feedback from opening 5wy6 fetched from pdb
---
note | Fetching compressed mmCIF 5wy6 from http://files.rcsb.org/download/5wy6.cif
5wy6 title:
Crystal structure of AtNUDX1 (E56A) [more info...]
Chain information for 5wy6 #16
---
Chain | Description | UniProt
A E | Nudix hydrolase 1 | NUDT1_ARATH 1-147
Non-standard residues in 5wy6 #16
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
PEG — di(hydroxyethyl)ether
SO4 — sulfate ion
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 16 C-terminal residues, 120 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 5wy6 chain A to query has RMSD 1.09 using 83 of 114 paired
residues within cutoff distance 2.0
> open 4zbp
Summary of feedback from opening 4zbp fetched from pdb
---
notes | Fetching compressed mmCIF 4zbp from http://files.rcsb.org/download/4zbp.cif
Fetching CCD ADV from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/ADV/ADV.cif
4zbp title:
Crystal structure of the AMPCPR-bound AtNUDT7 [more info...]
Chain information for 4zbp #17
---
Chain | Description | UniProt
A B C | Nudix hydrolase 7 | NUDT7_ARATH 1-282
Non-standard residues in 4zbp #17
---
ADV — α-β methylene adp-ribose (ampcpr; {[5-(6-amino-
purin-9-yl)-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxy]-hydroxy-
phosphorylmethyl}-phosphonic acid mono-(3,4,5-trihydroxy-tetrahydro-
furan-2-ylmethyl) ester)
SO4 — sulfate ion
4zbp mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Deleted 2 extra chains, 62 C-terminal residues, 89 N-terminal residues, 86
non-polymer residues more than 3.0 Angstroms away.
Alignment of 4zbp chain B to query has RMSD 1.06 using 83 of 113 paired
residues within cutoff distance 2.0
> open 3oga
3oga title:
1.75 Angstrom resolution crystal structure of a putative NTP
pyrophosphohydrolase (yfaO) from Salmonella typhimurium LT2 [more info...]
Chain information for 3oga #18
---
Chain | Description | UniProt
A B | Nucleoside triphosphatase nudI | NUDI_SALTY 1-141
Non-standard residues in 3oga #18
---
BME — β-mercaptoethanol
PO4 — phosphate ion
183 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 5 C-terminal residues, 149 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 3oga chain A to query has RMSD 1.12 using 83 of 120 paired
residues within cutoff distance 2.0
> similarstructures sequences
> open 8dwe
Summary of feedback from opening 8dwe fetched from pdb
---
warnings | Atom HO5' is not in the residue template for DA /B:1
Atom HO5' is not in the residue template for DA /E:1
notes | Fetching compressed mmCIF 8dwe from http://files.rcsb.org/download/8dwe.cif
Fetching CCD PRN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/PRN/PRN.cif
Fetching CCD SF4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SF4/SF4.cif
8dwe title:
Adenine glycosylase MutY variant E43Q in complex with DNA containing
d(8-oxo-G) paired with substrate purine [more info...]
Chain information for 8dwe #19
---
Chain | Description | UniProt
A D | Adenine DNA glycosylase | MUTY_GEOSE 1-365
B E | DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3') |
C F | DNA (5'-D(*TP*GP*TP*CP*CP*AP*(PRN)P*GP*TP*CP*T)-3') |
Non-standard residues in 8dwe #19
---
CA — calcium ion
EDO — 1,2-ethanediol (ethylene glycol)
SF4 — iron/sulfur cluster
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
8dwe mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Deleted 5 extra chains, 6 C-terminal residues, 206 N-terminal residues, 190
non-polymer residues more than 3.0 Angstroms away.
Alignment of 8dwe chain D to query has RMSD 0.984 using 55 of 136 paired
residues within cutoff distance 2.0
> open 3x0o
Summary of feedback from opening 3x0o fetched from pdb
---
note | Fetching compressed mmCIF 3x0o from http://files.rcsb.org/download/3x0o.cif
3x0o title:
ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ESMM-state at
reaction time of 10 min [more info...]
Chain information for 3x0o #20
---
Chain | Description | UniProt
A | ADP-ribose pyrophosphatase | Q5SKW5_THET8 1-170
Non-standard residues in 3x0o #20
---
AR6 — [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
[hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl]
hydrogen phosphate (Adenosine-5-Diphosphoribose)
GOL — glycerol (glycerin; propane-1,2,3-triol)
MN — manganese (II) ion
SO4 — sulfate ion
3x0o mmCIF Assemblies
---
1| author_and_software_defined_assembly
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 9 C-terminal residues, 14 N-terminal residues, 60 non-polymer residues
more than 3.0 Angstroms away.
Alignment of 3x0o chain A to query has RMSD 0.936 using 60 of 118 paired
residues within cutoff distance 2.0
> show #!1 models
> hide #!15 models
> hide #16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> open 1viq
Summary of feedback from opening 1viq fetched from pdb
---
note | Fetching compressed mmCIF 1viq from http://files.rcsb.org/download/1viq.cif
1viq title:
Crystal structure of putative ADP ribose pyrophosphatase [more info...]
Chain information for 1viq #21
---
Chain | Description | UniProt
A B C | ADP-ribose pyrophosphatase | ADPP_ECOLI 1-208
1viq mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| software_defined_assembly
4| software_defined_assembly
5| software_defined_assembly
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 2 extra chains, 32 C-terminal residues, 45 N-terminal residues, 205
non-polymer residues more than 3.0 Angstroms away.
Alignment of 1viq chain B to query has RMSD 0.89 using 62 of 109 paired
residues within cutoff distance 2.0
> open 1khz
Summary of feedback from opening 1khz fetched from pdb
---
note | Fetching compressed mmCIF 1khz from http://files.rcsb.org/download/1khz.cif
1khz title:
Structure of the ADPR-ase in complex with AMPCPR and Mg [more info...]
Chain information for 1khz #22
---
Chain | Description | UniProt
A B | ADP-ribose pyrophosphatase | ADPP_ECOLI 1-209
Non-standard residues in 1khz #22
---
ADV — α-β methylene adp-ribose (ampcpr; {[5-(6-amino-
purin-9-yl)-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxy]-hydroxy-
phosphorylmethyl}-phosphonic acid mono-(3,4,5-trihydroxy-tetrahydro-
furan-2-ylmethyl) ester)
CL — chloride ion
MG — magnesium ion
Deleted 1 extra chains, 32 C-terminal residues, 38 N-terminal residues, 155
non-polymer residues more than 3.0 Angstroms away.
Alignment of 1khz chain B to query has RMSD 0.871 using 59 of 110 paired
residues within cutoff distance 2.0
> open 1khz
1khz title:
Structure of the ADPR-ase in complex with AMPCPR and Mg [more info...]
Chain information for 1khz #23
---
Chain | Description | UniProt
A B | ADP-ribose pyrophosphatase | ADPP_ECOLI 1-209
Non-standard residues in 1khz #23
---
ADV — α-β methylene adp-ribose (ampcpr; {[5-(6-amino-
purin-9-yl)-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxy]-hydroxy-
phosphorylmethyl}-phosphonic acid mono-(3,4,5-trihydroxy-tetrahydro-
furan-2-ylmethyl) ester)
CL — chloride ion
MG — magnesium ion
Deleted 1 extra chains, 32 C-terminal residues, 38 N-terminal residues, 155
non-polymer residues more than 3.0 Angstroms away.
Alignment of 1khz chain B to query has RMSD 0.871 using 59 of 110 paired
residues within cutoff distance 2.0
> open 1mqw
Summary of feedback from opening 1mqw fetched from pdb
---
note | Fetching compressed mmCIF 1mqw from http://files.rcsb.org/download/1mqw.cif
1mqw title:
Structure of the MT-ADPRase in complex with three Mn2+ ions and AMPCPR, a
Nudix enzyme [more info...]
Chain information for 1mqw #24
---
Chain | Description | UniProt
A | ADPR pyrophosphatase | O33199_MYCTU 1-207
Non-standard residues in 1mqw #24
---
ADV — α-β methylene adp-ribose (ampcpr; {[5-(6-amino-
purin-9-yl)-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxy]-hydroxy-
phosphorylmethyl}-phosphonic acid mono-(3,4,5-trihydroxy-tetrahydro-
furan-2-ylmethyl) ester)
MN — manganese (II) ion
1mqw mmCIF Assemblies
---
1| author_and_software_defined_assembly
Deleted 38 C-terminal residues, 40 N-terminal residues, 23 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 1mqw chain A to query has RMSD 0.86 using 64 of 112 paired
residues within cutoff distance 2.0
> hide #!20 models
> hide #!21 models
> hide #!22 models
> hide #!23 models
> close #16#10-15,17-24
> open 7ef8
Summary of feedback from opening 7ef8 fetched from pdb
---
notes | Fetching compressed mmCIF 7ef8 from http://files.rcsb.org/download/7ef8.cif
Fetching CCD 3DR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/3DR/3DR.cif
7ef8 title:
Crystal structure of mouse MUTYH in complex with DNA containing AP site
analogue:8-oxoG (Form I) [more info...]
Chain information for 7ef8 #10
---
Chain | Description | UniProt
A | Adenine DNA glycosylase | MUTYH_MOUSE 35-487
B | DNA (5'-D(*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3') |
C | DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3') |
Non-standard residues in 7ef8 #10
---
SF4 — iron/sulfur cluster
SO4 — sulfate ion
ZN — zinc ion
21 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 2 extra chains, 6 C-terminal residues, 257 N-terminal residues, 66
non-polymer residues more than 3.0 Angstroms away.
Alignment of 7ef8 chain A to query has RMSD 1.08 using 54 of 123 paired
residues within cutoff distance 2.0
> open 5j3t
5j3t title:
Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex [more
info...]
Chain information for 5j3t #11
---
Chain | Description | UniProt
A | mRNA-decapping enzyme subunit 1 | DCP1_SCHPO 1-127
B | mRNA decapping complex subunit 2 | DCP2_SCHPO 1-242
C | Edc1 | YAQ9_SCHPO 155-180
Non-standard residues in 5j3t #11
---
FMT — formic acid
MG — magnesium ion
105 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 2 extra chains, 26 C-terminal residues, 57 N-terminal residues, 152
non-polymer residues more than 3.0 Angstroms away.
Alignment of 5j3t chain B to query has RMSD 0.915 using 63 of 124 paired
residues within cutoff distance 2.0
> open 1mk1
Summary of feedback from opening 1mk1 fetched from pdb
---
note | Fetching compressed mmCIF 1mk1 from http://files.rcsb.org/download/1mk1.cif
1mk1 title:
Structure of the MT-ADPRase in complex with ADPR, a Nudix enzyme [more
info...]
Chain information for 1mk1 #12
---
Chain | Description | UniProt
A | ADPR pyrophosphatase | O33199_MYCTU 1-207
Non-standard residues in 1mk1 #12
---
APR — adenosine-5-diphosphoribose
1mk1 mmCIF Assemblies
---
1| author_and_software_defined_assembly
Deleted 41 C-terminal residues, 34 N-terminal residues, 53 non-polymer
residues more than 3.0 Angstroms away.
Alignment of 1mk1 chain A to query has RMSD 0.939 using 70 of 107 paired
residues within cutoff distance 2.0
> hide #!10 models
> hide #!11 models
> open 5c7q
Summary of feedback from opening 5c7q fetched from pdb
---
notes | Fetching compressed mmCIF 5c7q from http://files.rcsb.org/download/5c7q.cif
Fetching CCD PG0 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/PG0/PG0.cif
5c7q title:
Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate
Sugar Hydrolase [more info...]
Chain information for 5c7q #13
---
Chain | Description | UniProt
A B | NudF protein | Q6MIH8_BDEBA 1-182
Non-standard residues in 5c7q #13
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
PEG — di(hydroxyethyl)ether
PG0 — 2-(2-methoxyethoxy)ethanol (peg 6000)
PGE — triethylene glycol
SO4 — sulfate ion
31 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 1 extra chains, 29 C-terminal residues, 38 N-terminal residues, 277
non-polymer residues more than 3.0 Angstroms away.
Alignment of 5c7q chain B to query has RMSD 0.907 using 64 of 103 paired
residues within cutoff distance 2.0
> open 1viu
Summary of feedback from opening 1viu fetched from pdb
---
note | Fetching compressed mmCIF 1viu from http://files.rcsb.org/download/1viu.cif
1viu title:
Crystal structure of putative ADP ribose pyrophosphatase [more info...]
Chain information for 1viu #14
---
Chain | Description | UniProt
A B C D | ADP-ribose pyrophosphatase | YFFH_ECOLI 2-191
1viu mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Deleted 3 extra chains, 27 C-terminal residues, 42 N-terminal residues, 123
non-polymer residues more than 3.0 Angstroms away.
Alignment of 1viu chain A to query has RMSD 0.894 using 58 of 100 paired
residues within cutoff distance 2.0
> open 6u9x
Summary of feedback from opening 6u9x fetched from pdb
---
note | Fetching compressed mmCIF 6u9x from http://files.rcsb.org/download/6u9x.cif
6u9x title:
Structure of T. brucei MERS1-RNA complex [more info...]
Chain information for 6u9x #15
---
Chain | Description | UniProt
A D | Mitochondrial edited mRNA stability factor 1 | B6SBM0_9TRYP 37-395
H K | RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3') |
6u9x mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| software_defined_assembly
4| software_defined_assembly
Deleted 3 extra chains, 77 C-terminal residues, 105 N-terminal residues, 30
non-polymer residues more than 3.0 Angstroms away.
Alignment of 6u9x chain D to query has RMSD 0.939 using 57 of 98 paired
residues within cutoff distance 2.0
> open 6zse
Summary of feedback from opening 6zse fetched from pdb
---
warning | Expected gap or connection between 004 /A:7 and MHT /A:8
notes | Fetching compressed mmCIF 6zse from http://files.rcsb.org/download/6zse.cif
Fetching CCD 004 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/004/004.cif
Fetching CCD DBB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/DBB/DBB.cif
Fetching CCD DOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/DOL/DOL.cif
Fetching CCD MHT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/MHT/MHT.cif
Fetching CCD MHU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/MHU/MHU.cif
Fetching CCD MHV from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/MHV/MHV.cif
Fetching CCD MHW from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/MHW/MHW.cif
Fetching CCD P5P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/P5P/P5P.cif
Fetching CCD Y5P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/Y5P/Y5P.cif
6zse title:
Human mitochondrial ribosome in complex with mRNA, A/P-tRNA and P/E-tRNA [more
info...]
Chain information for 6zse #16
---
Chain | Description | UniProt
0 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188
1 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65
2 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92
3 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188
4 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103
5 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423
6 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380
7 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338
8 | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206
9 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137
A | Quinupristin |
A0 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 1-218
A1 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323
A2 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 | CHCH1_HUMAN 1-118
A3 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199
A4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | PTCD3_HUMAN 1-689
AA | 12S mitochondrial rRNA |
AB | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296
AC | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167
AD | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430
AE | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125
AF | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242
AG | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396
AH | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201
AI | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194
AJ | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138
AK | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128
AL | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257
AM | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137
AN | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130
AO | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258
AP | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142
AQ | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 1-87
AR | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360
AS | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190
AT | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173
AU | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205
AV | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414
AW | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187
AX | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398
AY | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395
AZ | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106
XA | 16S mitochondrial rRNA |
XB | mitochondrial tRNAVal |
XD | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305
XE | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348
XF | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311
XH | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267
XI | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261
XJ | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-190
XK | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178
XL | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145
XM | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296
XN | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251
XO | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175
XP | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 0-179
XQ | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292
XR | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149
XS | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205
XT | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 7-212
XU | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153
XV | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216
XW | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148
XX | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256
XY | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250
XZ | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161
a | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142
b | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215
c | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332
d | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 8-306
e | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279
f | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212
g | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166
h | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158
i | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128
j | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123
k | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112
l | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138
m | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-127
o | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102
p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206
q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | G45IP_HUMAN 1-222
r | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196
r1 | mRNA |
r2 | A/P-tRNA |
r3 | P/E-tRNA |
s | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439
t1 t2 t3 t4 t5 t6 | 39S ribosomal protein L12, mitochondrial | RM12_HUMAN -60-137
Non-standard residues in 6zse #16
---
004 — (2S)-amino(phenyl)ethanoic acid (L-Phenylglycine)
DBB — D-α-aminobutyric acid
DOL — 5-(2-diethylamino-
ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza-
tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone
(dalfopristin)
GTP — guanosine-5'-triphosphate
MG — magnesium ion
MHT — (3S)-3-(methylsulfanyl)-1-azabicyclo[2.2.2]octane
MHV — 4-oxo-L-pipecolic acid
MHW — 3-hydroxypicolinic acid
Y5P — 1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine (pyrimidine
riboside-5'-monophosphate)
ZN — zinc ion
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Deleted 92 extra chains, 49 N-terminal residues, 204 non-polymer residues more
than 3.0 Angstroms away.
Alignment of 6zse chain e to query has RMSD 1.29 using 6 of 134 paired
residues within cutoff distance 2.0
> close #16
> close #13#10-12,14-15
> show #!8 models
> show #!9 models
> close #8
> show #!6 models
> close #6
> show #5 models
> hide #5 models
> show #2 models
> similarstructures ligands
> hide #2 models
> show #!3 models
> hide #!3 models
> show #2 models
> show #!7 models
> hide #!7 models
> show #!7 models
> close #7
> show #5 models
> hide #5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!9 models
> hide #!3 models
> hide #2 models
> hide #!1 models
> show #!1 models
> select add #1
5458 atoms, 5210 bonds, 18 pseudobonds, 1018 residues, 2 models selected
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L MET 1
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L LYS 9
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L ARG 12
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L SER 18
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L GLU 22
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L LYS 24
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L LYS 29
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L GLU 33
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L GLU 35
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L HIS 37
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L ARG 38
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L LYS 58
ADPR-TK2284-NEB7-5_refine_061.pdb #1/L LYS 131
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ASP 2
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ARG 3
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M TYR 4
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M LEU 6
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ARG 12
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ASP 15
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M SER 18
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ARG 20
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ASP 21
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M GLU 22
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M GLU 28
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M GLU 33
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M GLU 35
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M LYS 131
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M LYS 137
ADPR-TK2284-NEB7-5_refine_061.pdb #1/M GLU 145
ADPR-TK2284-NEB7-5_refine_061.pdb #1/N LYS 24
ADPR-TK2284-NEB7-5_refine_061.pdb #1/N LYS 29
ADPR-TK2284-NEB7-5_refine_061.pdb #1/N GLU 33
ADPR-TK2284-NEB7-5_refine_061.pdb #1/N ARG 38
ADPR-TK2284-NEB7-5_refine_061.pdb #1/N GLU 91
ADPR-TK2284-NEB7-5_refine_061.pdb #1/O ARG 12
ADPR-TK2284-NEB7-5_refine_061.pdb #1/O GLU 127
ADPR-TK2284-NEB7-5_refine_061.pdb #1/O LYS 131
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for ADPR-TK2284-NEB7-5_refine_061.pdb_L SES surface #1.2:
minimum, -27.09, mean -4.38, maximum 7.80
Coulombic values for ADPR-TK2284-NEB7-5_refine_061.pdb_M SES surface #1.3:
minimum, -27.18, mean -2.21, maximum 8.76
Coulombic values for ADPR-TK2284-NEB7-5_refine_061.pdb_N SES surface #1.4:
minimum, -20.63, mean -3.56, maximum 6.22
Coulombic values for ADPR-TK2284-NEB7-5_refine_061.pdb_O SES surface #1.5:
minimum, -26.52, mean -2.91, maximum 8.80
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
Drag select of 3 atoms, 3 residues, 3 bonds
> select clear
> hide #!1 models
> show #2 models
> select :91
73 atoms, 61 bonds, 12 residues, 5 models selected
> show sel & #2 atoms
> hide #2 models
> show #!1 models
> select clear
> close #1
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb
Chain information for ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb #1
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
Drag select of 4 atoms, 38 residues, 3 bonds
> select clear
> show #2 models
> close #1-2,5#3-4,9
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure Manuscript/New
> Figure 4/Image of Assymetric Bending of the N-terminst.cxs"
> view name session-start
opened ChimeraX session
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb
Chain information for ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb #7
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/ADPR-TK2284-NEB7-5_refine_068-coot-1 copy.pdb"
Chain information for ADPR-TK2284-NEB7-5_refine_068-coot-1 copy.pdb #8
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
Cell requested for row 5 is out of bounds for table with 9 rows! Resizing
table model.
> hide #!6 models
> hide #7 models
> hide #!1 models
> select #8/L:158
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
63 atoms, 63 bonds, 8 residues, 1 model selected
> select up
1236 atoms, 1260 bonds, 166 residues, 1 model selected
> select up
5464 atoms, 5210 bonds, 1026 residues, 1 model selected
> select down
1236 atoms, 1260 bonds, 166 residues, 1 model selected
> delete sel
> select clear
> select #8/M:86
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
107 atoms, 106 bonds, 13 residues, 1 model selected
> select up
1244 atoms, 1268 bonds, 168 residues, 1 model selected
> delete sel
Drag select of 51 atoms, 28 bonds
> delete sel
> show #7 models
> hide #8 models
> select #7/N:157
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
63 atoms, 63 bonds, 8 residues, 1 model selected
> select up
1279 atoms, 1304 bonds, 167 residues, 1 model selected
> delete sel
> select clear
> select #7/O:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
107 atoms, 106 bonds, 13 residues, 1 model selected
> select up
1295 atoms, 1320 bonds, 167 residues, 1 model selected
> delete sel
> select clear
Drag select of 56 atoms, 2 residues, 34 bonds
> select clear
Drag select of 8 atoms, 3 residues, 6 bonds
> select clear
Drag select of 52 atoms, 28 bonds
> delete sel
> select clear
> show #8 models
> show #!1 models
> view #1 clip false
> mmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#1) with ADPR-
TK2284-NEB7-5_refine_068-coot-1.pdb, chain M (#7), sequence alignment score =
845
RMSD between 122 pruned atom pairs is 0.530 angstroms; (across all 166 pairs:
2.660)
> mmaker #8 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#1) with ADPR-
TK2284-NEB7-5_refine_068-coot-1 copy.pdb, chain O (#8), sequence alignment
score = 842.6
RMSD between 156 pruned atom pairs is 0.544 angstroms; (across all 166 pairs:
1.003)
> dssp
> hide #7 models
> show #7 models
> hide #8 models
Drag select of 7 residues, 1 atoms, 2 bonds
> select clear
> hide #!1 models
> show #8 models
Drag select of 12 residues, 3 atoms, 2 bonds
> select clear
Drag select of 2 residues
> select clear
Drag select of 2 atoms, 35 residues, 1 bonds
> select #7/M:81
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> show #!1 models
> hide #7 models
> hide #8 models
> show #8 models
> hide #!1 models
> show #!1 models
> select add #1
2707 atoms, 2653 bonds, 441 residues, 1 model selected
> select add #8
5640 atoms, 5306 bonds, 1108 residues, 4 models selected
> show sel atoms
> select clear
Drag select of 7 atoms, 4 residues, 6 bonds
> select clear
> hide #!1 models
> show #7 models
> show #7-8 atoms
> undo
> show #7 models
> hide #!1 models
> select #8:1-39
673 atoms, 636 bonds, 128 residues, 1 model selected
> ui tool show Axes/Planes/Centroids
> define centroid sel
Centroid 'centroid' placed at [ 11.17406686 -11.45223477 41.59986924]
> select #7:1-39
581 atoms, 543 bonds, 126 residues, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [13.33047676 59.13523064 15.96178657]
centroid #7.1 to centroid #8.1: distance: 2.913Å
> distance
> #!7/A:1#!7/A:5#!7/B:11#!7/B:12#!7/B:13#!7/B:14#!7/C:1#!7/C:2#!7/C:3#!7/C:4#!7/C:5#!7/C:17#!7/C:18#!7/C:19#!7/C:20#!7/C:22#!7/C:23#!7/C:24#!7/C:25#!7/C:26#!7/C:27#!7/C:28#!7/C:29#!7/C:30#!7/C:31#!7/C:32#!7/C:33#!7/D:2#!7/D:3#!7/D:4#!7/L:1#!7/L:2#!7/L:3#!7/L:4#!7/L:5#!7/L:6#!7/L:7#!7/L:8#!7/L:9#!7/L:10#!7/L:11#!7/L:12#!7/L:13#!7/L:14#!7/L:15#!7/L:16#!7/L:17#!7/L:18#!7/L:19#!7/L:20#!7/L:21#!7/L:22#!7/L:23#!7/L:24#!7/L:25#!7/L:26#!7/L:27#!7/L:28#!7/L:29#!7/L:30#!7/L:31#!7/L:32#!7/L:33#!7/L:34#!7/L:35#!7/L:36#!7/L:37#!7/L:38#!7/L:39#!7/M:1#!7/M:2#!7/M:3#!7/M:4#!7/M:5#!7/M:6#!7/M:7#!7/M:8#!7/M:9#!7/M:10#!7/M:11#!7/M:12#!7/M:13#!7/M:14#!7/M:15#!7/M:16#!7/M:17#!7/M:18#!7/M:19#!7/M:20#!7/M:21#!7/M:22#!7/M:23#!7/M:24#!7/M:25#!7/M:26#!7/M:27#!7/M:28#!7/M:29#!7/M:30#!7/M:31#!7/M:32#!7/M:33#!7/M:34#!7/M:35#!7/M:36#!7/M:37#!7/M:38#!7/M:39#!7/S:16#!7/S:20#!7/S:21#!7/S:23#!7/S:24#!7/S:25#!7/S:26#!7/S:27#!7/S:28#!7/S:29#!7/S:30#!7/S:31#!7/S:33#!7/S:34#!7/S:35#!7/S:36#!7/S:37#!7/S:39
> #7.1#8.1
Distance between centroid #7.1 and 581 atoms: min 1.054Å (ADPR-
TK2284-NEB7-5_refine_068-coot-1.pdb #!7/L LEU 6 N), average: 13.921Å, max
72.681Å (ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb #!7/S HOH 34 O)
Distance between centroid #8.1 and 581 atoms: min 1.534Å (ADPR-
TK2284-NEB7-5_refine_068-coot-1.pdb #!7/L LEU 6 C), average: 14.353Å, max
71.864Å (ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb #!7/S HOH 34 O)
> select clear
> hide #!7 models
> show #!7 models
> select clear
> select #7.1
1 atom, 1 residue, 1 model selected
> select add #8.1
2 atoms, 2 residues, 2 models selected
> distance #7.1 #8.1
Distance between centroid #7.1 and centroid #8.1: 2.913Å
> close #7.1#8.1
> select #7:1-37
552 atoms, 514 bonds, 121 residues, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [13.3955942 59.54851268 15.66290217]
> select #7:1-36
542 atoms, 504 bonds, 119 residues, 2 models selected
> define centroid sel
Centroid 'centroid' placed at [23.76848081 36.10778151 12.79497378]
centroid #7.1 to centroid #10: distance: 0.170Å
> close #10#7.1
> define centroid sel
Centroid 'centroid' placed at [13.36444547 59.70951017 15.61769501]
> select #8:1-36
622 atoms, 585 bonds, 119 residues, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [ 11.25092926 -11.90938424 41.93952572]
> select clear
> select #8.1
1 atom, 1 residue, 1 model selected
> select add #7.1
2 atoms, 2 residues, 2 models selected
> distance #8.1 #7.1
Distance between centroid #8.1 and centroid #7.1: 3.031Å
> hide #!7 models
> show #!1 models
> hide #!8 models
> hide #9.1 models
> hide #!9 models
> show #!8 models
> show #!7 models
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure Manuscript/New
> Figure 4/Overall View 1.cxs"
> view name session-start
opened ChimeraX session
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Last-Refinement.pdb
Chain information for Last-Refinement.pdb #6
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> mmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#1) with Last-
Refinement.pdb, chain M (#6), sequence alignment score = 845
RMSD between 123 pruned atom pairs is 0.560 angstroms; (across all 166 pairs:
2.626)
> hide #6 models
> hide #!5.1 models
> hide #!5 models
> show #6 models
> hide #!1 models
> cartoon style thickness 1.2
> cartoon style width 2.5
> show #!1 models
> show #!5 models
> hide #!5 models
> show #!5.1 models
Drag select of 47 residues
> select clear
> open /Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/Refine_82/ADPR-TK2284-NEB7-5_refine_082.pdb
Chain information for ADPR-TK2284-NEB7-5_refine_082.pdb #7
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> mmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#1) with ADPR-
TK2284-NEB7-5_refine_082.pdb, chain M (#7), sequence alignment score = 845
RMSD between 123 pruned atom pairs is 0.560 angstroms; (across all 166 pairs:
2.626)
> cartoon style thickness 1.2
> cartoon style width 2.5
> hide #!5 models
> show #!5 models
> hide #6 models
> hide #!5.1 models
> show #!5.1 models
Drag select of 10 residues
> select clear
> dssp
> close #7
> close #6
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure
> Manuscript/ADPR_TK2284_Refine_84/ADPR-TK2284-NEB7-5_refine_084.pdb"
Chain information for ADPR-TK2284-NEB7-5_refine_084.pdb #6
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure Manuscript/New
> Figure 4/Image of Assymetric Bending of the N-terminst.cxs"
> view name session-start
opened ChimeraX session
> hide #!6 models
> open "/Users/mbanco/Library/CloudStorage/OneDrive-
> NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure
> Manuscript/ADPR_TK2284_Refine_84/ADPR-TK2284-NEB7-5_refine_084.pdb"
Chain information for ADPR-TK2284-NEB7-5_refine_084.pdb #7
---
Chain | Description
L | No description available
M | No description available
N | No description available
O | No description available
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> mmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#1) with ADPR-
TK2284-NEB7-5_refine_084.pdb, chain M (#7), sequence alignment score = 845
RMSD between 123 pruned atom pairs is 0.561 angstroms; (across all 166 pairs:
2.624)
> select #7/O:161
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
63 atoms, 63 bonds, 8 residues, 1 model selected
> select up
1295 atoms, 1320 bonds, 167 residues, 1 model selected
> hide sel cartoons
> select #7/N:98
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 7 residues, 1 model selected
> select up
1274 atoms, 1299 bonds, 166 residues, 1 model selected
> select up
5463 atoms, 5210 bonds, 1025 residues, 1 model selected
> select clear
> select #7/M:168
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
48 atoms, 48 bonds, 6 residues, 1 model selected
> select up
1249 atoms, 1273 bonds, 169 residues, 1 model selected
> select clear
> select #7/N:97
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
55 atoms, 55 bonds, 7 residues, 1 model selected
> select up
1274 atoms, 1299 bonds, 166 residues, 1 model selected
> hide sel cartoons
> select clear
> hide #7#!1 atoms
> cartoon style thickness 1.2
> cartoon style width 2.5
> color #1 #009051ff
> color #1 #008f00ff
> color #1 #4f8f00ff
> color #1 #929000ff
> color #1 #fffb00ff
> color #1 #00f900ff
> color #1 #d783ffff
> color #1 #ff9300ff
> color #1 #ff2600ff
> color #1 #ff9300ff
> color #1 #945200ff
> color #1 #929000ff
> color #1 #fffb00ff
> color #1 #945200ff
> color #1 #0096ffff
> color #1 #9437ffff
> color #1 silver
> color #1 #d6d6d6ff
> color #1 silver
> color #1 darkgrey
> color #1 #00fa92ff
> color #1 #00f900ff
> color #1 #8efa00ff
> color #1 #fffb00ff
> color #1 #0433ffff
> color #1 #9437ffff
> color #1 #7a81ffff
> color #1 #d783ffff
> color #1 #73fdffff
> color #1 #73fcd6ff
> color #1 #d4fb79ff
> color #1 #fffc79ff
> color #1 #fffb00ff
> color #1 #fffc79ff
> color #1 #ffd479ff
> color #1 #7a81ffff
> color #1 #0433ffff
> color #1 #011993ff
> color #1 #005493ff
> color #1 #009193ff
> color #1 #ff40ffff
> color #1 #531b93ff
> color #1 #005493ff
> color #1 #009193ff
> color #1 #005493ff
> color #7 silver
> color #7 #929292ff
> color #7 darkgrey
> ui tool show "Side View"
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> select add #1
2707 atoms, 2653 bonds, 441 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> color sel saddle brown
> color sel brown
> color sel wheat
> color sel azure
> color sel wheat
> color sel white smoke
> color sel pale turquoise
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> color sel light blue
> color sel sky blue
> color sel light sky blue
> color sel sky blue
> select clear
> select add #7
5463 atoms, 5210 bonds, 1025 residues, 1 model selected
> color sel light coral
> color sel tan
> color sel rosy brown
> color sel dark sea green
> color sel rebecca purple
> color sel hot pink
> color sel orchid
> color sel pale violet red
> color sel midnight blue
> color sel dark slate gray
> color sel dark olive green
> color sel sea green
> color sel green
> color sel forest green
> select clear
> select add #7
5463 atoms, 5210 bonds, 1025 residues, 1 model selected
> color sel dark blue
> color sel dark green
> color sel tan
> color sel burly wood
> color sel tan
> color sel rosy brown
> color sel tan
> color sel plum
> color sel light cyan
> color sel plum
> color sel cornflower blue
> color sel medium blue
> color sel magenta
> color sel dim gray
> color sel purple
> color sel hot pink
> color sel magenta
> color sel light blue
> color sel silver
> color sel powder blue
> color sel light gray
> color sel thistle
> color sel tan
> color sel burly wood
> color sel tan
> color sel rosy brown
> color sel tan
> select add #1
8170 atoms, 7863 bonds, 1466 residues, 2 models selected
> select subtract #7
2707 atoms, 2653 bonds, 441 residues, 3 models selected
> color sel rosy brown
> color sel dark gray
> color sel rosy brown
> color sel light coral
> color sel rosy brown
> color sel dark sea green
> color sel medium sea green
> color sel sea green
> color sel cyan
> color sel deep sky blue
> color sel cadet blue
> color sel steel blue
> color sel cadet blue
> color sel steel blue
> color sel teal
> color sel steel blue
> select clear
> select add #7
5463 atoms, 5210 bonds, 1025 residues, 1 model selected
> color sel deep sky blue
> color sel steel blue
> color sel medium aquamarine
> color sel light sea green
> color sel turquoise
> color sel dodger blue
> color sel tan
> color sel rosy brown
> color sel tan
> color sel burly wood
> color sel tan
> color sel burly wood
> color sel wheat
> color sel pale goldenrod
> color sel burly wood
> select clear
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> dssp
Drag select of 16 residues
> select clear
Drag select of 22 residues
> select clear
> show #7#!1 atoms
Drag select of 4 atoms, 5 residues, 3 bonds
> select clear
> undo
Drag select of 11 atoms, 11 residues, 10 bonds
> select clear
> undo
> select clear
> undo
> select #1:40-50,70-127,150-300
1418 atoms, 1395 bonds, 219 residues, 1 model selected
> transparency #1:40-50,70-127,150-300 50 cartoons
> transparency #7:40-50,70-127,150-300 50 cartoons
> save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/test.tif width 3041 height 2001 supersample 4 transparentBackground
> true
> show #!6 models
> hide #!6 models
> transparency #7:40-50,70-127,150-300 75 cartoons
> select add #7
5463 atoms, 5210 bonds, 1025 residues, 1 model selected
> ui tool show "Color Actions"
> color sel khaki
> color sel pale goldenrod
> color sel moccasin
> color sel navajo white
> color sel peach puff
> color sel pink
> color sel light pink
> color sel antique white
> color sel linen
> color sel ivory
> color sel snow
> color sel violet
> color sel light cyan
> color sel plum
> color sel thistle
> color sel alice blue
> color sel pale violet red
> color sel dark slate gray
> color sel bisque
> color sel peach puff
> color sel pink
> color sel old lace
> color sel light goldenrod yellow
> color sel antique white
> color sel ghost white
> color sel beige
> color sel wheat
> color sel khaki
> color sel pale goldenrod
> select clear
> select ::name="OXO"
64 atoms, 68 bonds, 2 residues, 2 models selected
> show sel & #!1 atoms
> color (#!1 & sel) yellow
> color (#!1 & sel) byhetero
> select clear
> select add #7
5463 atoms, 5210 bonds, 1025 residues, 1 model selected
> color sel plum
> color sel old lace
> color sel thistle
> color sel peach puff
> select clear
> show #!6 models
> hide #!6 models
> select :rib
56 atoms, 56 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 56 atom styles
> color sel byhetero
> select clear
> transparency 0 cartoons
> transparency #7:40-50,105-117,70-127,150-300 75 cartoons
> transparency #1:40-50,105-117,70-127,150-300 75 cartoons
> transparency #1:40-50,105-117,70-127,150-300 0 cartoons
> transparency #7:40-50,105-117,70-127,150-300 75 cartoons
> transparency #1:40-50,105-117,70-127,150-300 75 cartoons
> transparency #1:40-50,70-105,117-127,150-300 75 cartoons
> transparency #1:40-50,105-117,70-127,150-300 0 cartoons
> transparency 0 cartoons
> transparency #1:40-50,70-105,117-127,150-300 75 cartoons
> transparency #7:40-50,70-105,117-127,150-300 75 cartoons
> select clear
> save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR-
> NEB7-5/test.tif width 3041 height 2001 supersample 4
> show #!6 models
> hide #!6 models
> transparency #7:40-50,70-105,117-127,150-300 85 cartoons
> transparency #1:40-50,70-105,117-127,150-300 85 cartoons
> transparency #1:40-50,70-108,117-127,150-300 85 cartoons
> transparency #7:40-50,70-108,117-127,150-300 85 cartoons
> select clear
Drag select of 14 atoms, 14 bonds
> hide sel atoms
Drag select of 13 atoms, 13 bonds
> select clear
Drag select of 14 atoms, 14 bonds
> hide sel atoms
Drag select of 4 residues
> select clear
> save "/Users/mbanco/Documents/Manuscript/TK2284 Structure Manuscript/New
> Figure 4/test.tif" width 3041 height 2001 supersample 4
> color #7 #7a81ffff
> color #7 #011993ff
> color #7 #00fa92ff
> color #7 #945200ff
> undo
> show #!6 models
> transparency 75 surfaces
> hide #!6 models
> select add #7
5463 atoms, 5210 bonds, 1025 residues, 1 model selected
> ui tool show "Color Actions"
> color sel rosy brown
> color sel honeydew
> color sel beige
> color sel wheat
> color sel linen
> color sel antique white
> color sel light goldenrod yellow
> color sel old lace
> color sel pale goldenrod
> color sel khaki
> color sel burly wood
> color sel tan
> color sel rosy brown
> select #7/L:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7
5463 atoms, 5210 bonds, 1025 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #7
5463 atoms, 5210 bonds, 1025 residues, 1 model selected
> color sel bisque
> color sel moccasin
> color sel navajo white
> color sel cornsilk
> color sel seashell
> color sel blanched almond
> color sel khaki
> color sel wheat
> color sel alice blue
> color sel khaki
> select clear
> select add #7
5463 atoms, 5210 bonds, 1025 residues, 1 model selected
> select clear
> select add #1
2707 atoms, 2653 bonds, 441 residues, 1 model selected
> color sel cadet blue
> color sel teal
> color sel medium aquamarine
> color sel dark cyan
> color sel cornflower blue
> color sel light sea green
> color sel dodger blue
> color sel deep sky blue
> color sel teal
> color sel medium aquamarine
> color sel dark cyan
> select clear
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10rc202505150242 (2025-05-15)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHE3LL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.1.2
OS Loader Version: 13822.1.2
Software:
System Software Overview:
System Version: macOS 26.0.1 (25A362)
Kernel Version: Darwin 25.0.0
Time since boot: 7 days, 21 hours, 21 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
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: Yes
Connection Type: Internal
HP V27i:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
LG HDR 4K:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.3
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.3
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.6
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.6
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10rc202505150242
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.8.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
narwhals: 2.5.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.3.3
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
plotly: 6.3.0
pluggy: 1.5.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pyKVFinder: 0.8.2
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 26.4.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tomlkit: 0.13.3
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.13.2
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 38 hours ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 37 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel said what we know about this crash:
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."
The ChimeraX daily build uses a newer version of Qt (6.9) and we have not seen this crash in the newer Qt. So you may want to try the daily build.
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Reported by Mike