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Opened 7 months ago
Closed 7 months ago
#17128 closed defect (duplicate)
Crash on Mac waking from sleep
| 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
The following bug report has been submitted:
Platform: macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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: Segmentation fault
Current thread 0x00000001f2e30840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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._imagingmath, chimerax.alignment_algs._sw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.mmcif.mmcif_write, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 60)
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"uptime" : 480000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,13",
"coalitionID" : 624,
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"build" : "24D70",
"releaseType" : "User"
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"captureTime" : "2025-03-18 22:47:58.9655 +0100",
"codeSigningMonitor" : 1,
"incident" : "9204219E-59E9-46F8-A54D-4425632D27B8",
"pid" : 34072,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-18 06:23:09.5112 +0100",
"procStartAbsTime" : 10731601110192,
"procExitAbsTime" : 11585491933618,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D3C0A8FA-DE98-58B6-8911-78CAB24779D7","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "56247536-F39C-6C4D-9024-2ED81513EB3A",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "9B7C4619-5D82-4E27-88F3-941BB03413AC",
"wakeTime" : 2137,
"sleepWakeUUID" : "DBEC9D7E-82E7-49B4-BA29-69A3B535D189",
"sip" : "enabled",
"vmRegionInfo" : "0x515e3e041fa8 is not in any region. Bytes after previous region: 88984172896169 Bytes before following region: 16087907033176\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000515e3e041fa8","rawCodes":[1,89465209233320],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000515e3e041fa8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":34072},
"vmregioninfo" : "0x515e3e041fa8 is not in any region. Bytes after previous region: 88984172896169 Bytes before following region: 16087907033176\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/closed_conformer_beforeMD.pdb
Chain information for closed_conformer_beforeMD.pdb #1
---
Chain | Description
? | No description available
Computing secondary structure
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_ETasq_Bfox_Hie290_aligned.pdb
Chain information for trueB_ETasq_Bfox_Hie290_aligned.pdb #2
---
Chain | Description
? | No description available
Computing secondary structure
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_EThq_Bfox_Hip290_aligned.pdb
Chain information for trueB_EThq_Bfox_Hip290_aligned.pdb #3
---
Chain | Description
? | No description available
Computing secondary structure
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_ETox_Bfox_Hip290_aligned.pdb
Chain information for trueB_ETox_Bfox_Hip290_aligned.pdb #4
---
Chain | Description
? | No description available
Computing secondary structure
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_withNAD_BFahq_HID290_aligned.pdb
Chain information for trueB_withNAD_BFahq_HID290_aligned.pdb #5
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/open_conformer_beforeMD_renum.pdb
Chain information for open_conformer_beforeMD_renum.pdb #6
---
Chain | Description
? | No description available
Computing secondary structure
Drag select of 55 residues
> cartoon style width 1.5
> cartoon style thickness 0.2
> hide @H*
> hide protein
> select clear
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> ui tool show "Color Actions"
> undo
> hide #6 models
> select :347
38 atoms, 36 bonds, 2 residues, 1 model selected
> show sel
> show #2 models
> hide #2 models
> hide #1 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #5 models
> open /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/4KPU.cif
4KPU.cif title:
Electron transferring flavoprotein of Acidaminococcus fermentans: Towards a
mechanism of flavin-based electron bifurcation [more info...]
Chain information for 4KPU.cif #7
---
Chain | Description | UniProt
A | Electron transfer flavoprotein alpha subunit | D2RIQ3_ACIFV 1-340
B | Electron transfer flavoprotein alpha/beta-subunit | D2RIQ2_ACIFV 1-263
Non-standard residues in 4KPU.cif #7
---
CL — chloride ion
FAD — flavin-adenine dinucleotide
115 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> cartoon style width 1.5
> cartoon style width 1.2
> cartoon style thickness 0.2
> hide #5 models
> show #4 models
> hide #4 models
> show #3 models
> hide #3 models
> show #2 models
> hide #2 models
> show #1 models
> help mm
> hide #7 models
> show #2 models
> hide #1 models
> hide #2 models
> show #1 models
> show #2 models
> show #3 models
> hide #1 models
> hide #2 models
> show #4 models
> hide #3 models
> show #5 models
> hide #4 models
> show #4 models
> close #5
> undo
> show #1 models
> show #2 models
> show #3 models
> show #4 models
> show #6 models
> show #7 models
> hide #7 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> hide #6 models
> show #4 models
> show #3 models
> hide #4 models
> show #2 models
> show #1 models
> hide #1 models
> hide #2 models
> hide #3 models
> show #2 models
> hide #2 models
> show #4 models
> show #2 models
> show #3 models
> show #6 models
> show #1 models
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> show #7 models
> hide #6 models
> select #7(/A:13-207 & /B:1-11,32-227)
Expected an objects specifier or a keyword
> select #7/A:13-207 & #7/B:1-11,32-227
Nothing selected
> select #7/A:13-207
1530 atoms, 1559 bonds, 195 residues, 1 model selected
> select #7/A:13-207 and #7/B:1-11,32-227
Expected a keyword
> select #7/A:13-207 && #7/B:1-11
Expected a keyword
> select #7/A:13-207 & #7/B:1-11
Nothing selected
> select #7/A:13-207/B:1-11
1613 atoms, 1642 bonds, 206 residues, 1 model selected
> select #7/A:13-207/B:1-11,32-227
3078 atoms, 3128 bonds, 402 residues, 1 model selected
> select #1:13-207,348-358,379-574
6173 atoms, 6223 bonds, 402 residues, 1 model selected
> show #1 models
> mmaker #7/A:13-207/B:1-11,32-227 to #1:13-207,348-358,379-574
Computing secondary structure
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 closed_conformer_beforeMD.pdb, chain (blank) (#1) with 4KPU.cif,
chain B (#7), sequence alignment score = 1029.8
RMSD between 207 pruned atom pairs is 0.102 angstroms; (across all 207 pairs:
0.102)
> hide #7 models
> show #7 models
> hide #1 models
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_withNAD_BFahq_HID290_aligned.pdb
Chain information for trueB_withNAD_BFahq_HID290_aligned.pdb #5
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> hide #7 models
> select :5:350
251 atoms, 237 bonds, 14 residues, 7 models selected
> close #5
> show #7 models
> show #1 models
> close #7
> open /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/4KPU.cif
4KPU.cif title:
Electron transferring flavoprotein of Acidaminococcus fermentans: Towards a
mechanism of flavin-based electron bifurcation [more info...]
Chain information for 4KPU.cif #5
---
Chain | Description | UniProt
A | Electron transfer flavoprotein alpha subunit | D2RIQ3_ACIFV 1-340
B | Electron transfer flavoprotein alpha/beta-subunit | D2RIQ2_ACIFV 1-263
Non-standard residues in 4KPU.cif #5
---
CL — chloride ion
FAD — flavin-adenine dinucleotide
115 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #5/A:13-207/B:1-11,32-227 to #1:13-207,348-358,379-574 reportMatrix
> true
Computing secondary structure
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 closed_conformer_beforeMD.pdb, chain (blank) (#1) with 4KPU.cif,
chain B (#5), sequence alignment score = 1029.8
Alignment matrix in structure 4KPU.cif coordinates
Matrix rotation and translation
0.99998158 0.00507753 0.00332539 -0.54964193
-0.00506508 0.99998018 -0.00373975 30.50034703
-0.00334431 0.00372283 0.99998748 26.20970306
Axis 0.52370927 0.46806599 -0.71178847
Axis point 6454.37435968 -349.74733187 0.00000000
Rotation angle (degrees) 0.40822084
Shift along axis -4.66744209
RMSD between 207 pruned atom pairs is 0.102 angstroms; (across all 207 pairs:
0.102)
Downloading file 1471-2105-7-339.pdf
> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/4KPUonClosedBeforeMD.cif
> models #5 relModel #1
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/4KPUonClosedBeforeMD.cif
Chain information for 4KPUonClosedBeforeMD.cif #7
---
Chain | Description
A | Electron transfer flavoprotein alpha subunit
B | Electron transfer flavoprotein alpha/beta-subunit
115 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #5 models
> cartoon style width 1.2
> cartoon style thickness 0.2
> select clear
> select #1:221-338,584-605
2107 atoms, 2124 bonds, 140 residues, 1 model selected
> select #7:/A:221-338/B:237-258
Expected an objects specifier or a keyword
> select #7/A:221-338/B:237-258
1045 atoms, 1062 bonds, 140 residues, 1 model selected
> help measure rotation
> select #7/A:221-338/B:237-258@CA
893 atoms, 887 bonds, 140 residues, 1 model selected
> select #1:221-338,584-605@CA
140 atoms, 140 residues, 1 model selected
> hide #1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> cartoon hide sel
> select clear
> select #7/A:221-338/B:237-258@CA
893 atoms, 887 bonds, 140 residues, 1 model selected
> hide cartoons
> hide sel
> hide #7
> select #7/A:221-338/B:237-258@CA
893 atoms, 887 bonds, 140 residues, 1 model selected
> show sel
> select #7/A:221-338/B:237-258@C*
981 atoms, 976 bonds, 21 pseudobonds, 140 residues, 2 models selected
> select #7/A:221-338/B:237-258@C*
981 atoms, 976 bonds, 21 pseudobonds, 140 residues, 2 models selected
> hide sel
> select #7/A:221-338/B:237-258@CA
893 atoms, 887 bonds, 140 residues, 1 model selected
> select #7/A:221-338/B:237-258@CA
893 atoms, 887 bonds, 140 residues, 1 model selected
> select #7/A:221-338/B:237-258@CB
893 atoms, 887 bonds, 140 residues, 1 model selected
> select #7/A:221-338/B:237-258@C
893 atoms, 887 bonds, 140 residues, 1 model selected
> select #7/A:221-338/B:237-258@CA!
Expected an objects specifier or a keyword
> select #7/A:221-338/B:237-258@N
893 atoms, 887 bonds, 140 residues, 1 model selected
> select #7/A:221-338@CA/B:237-258@CA
140 atoms, 140 residues, 1 model selected
> select #7/A:221-338@CA/B:237-258@CA
140 atoms, 140 residues, 1 model selected
> select #1:221-338,584-605@CA
140 atoms, 140 residues, 1 model selected
> show sel
> show sel ribbons
> show sel cartoons
> show #1 models
> select #7/A:221-338@CA/B:237-258@CA
140 atoms, 140 residues, 1 model selected
> show sel cartoons
> show :FAD
> hide @H
> select add #7
5265 atoms, 4751 bonds, 1201 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #7
5265 atoms, 4751 bonds, 1201 residues, 1 model selected
> select add #1
14728 atoms, 14303 bonds, 1812 residues, 2 models selected
> select subtract #1
5265 atoms, 4751 bonds, 1201 residues, 1 model selected
> select subtract #7
Nothing selected
> hide @H
> select @H*
23608 atoms, 3055 residues, 5 models selected
> hide sel
> align sel #7/A:221-338@CA/B:237-258@CA toAtoms #1:221-338,584-605@CA
> reportMatrix true
Expected a keyword
> align #7/A:221-338@CA/B:237-258@CA toAtoms #1:221-338,584-605@CA
> reportMatrix true
Alignment matrix in structure 4KPUonClosedBeforeMD.cif coordinates
Matrix rotation and translation
0.99999350 0.00110659 0.00343249 -0.11580679
-0.00108237 0.99997455 -0.00705109 0.33018451
-0.00344021 0.00704733 0.99996925 -0.16493655
Axis 0.89025523 0.43398140 -0.13822361
Axis point 0.00000000 22.35562099 42.86955782
Rotation angle (degrees) 0.45368377
Shift along axis 0.06299446
RMSD between 140 atom pairs is 0.119 angstroms
> hide #7 models
> show #2 models
> select #2:221-338,584-605@CA
140 atoms, 140 residues, 1 model selected
> show sel cartoons
> align #2:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
Alignment matrix in structure trueB_ETasq_Bfox_Hie290_aligned.pdb coordinates
Matrix rotation and translation
0.99339521 -0.09046281 0.07058633 6.24976923
0.10022218 0.98361014 -0.14988868 -3.68156891
-0.05587008 0.15597301 0.98617998 -7.67453128
Axis 0.80074167 0.33106115 0.49921067
Axis point 0.00000000 46.44098124 -29.53952257
Rotation angle (degrees) 11.01036041
Shift along axis -0.04558171
RMSD between 140 atom pairs is 0.629 angstroms
> close #2
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_ETasq_Bfox_Hie290_aligned.pdb
Chain information for trueB_ETasq_Bfox_Hie290_aligned.pdb #2
---
Chain | Description
? | No description available
Computing secondary structure
> select #2:221-338,584-605@CA
140 atoms, 140 residues, 1 model selected
> hide #2
> hide #2 ribbons
> select #2:221-338,584-605@CA
140 atoms, 140 residues, 1 model selected
> show sel ribbons
> show #2:FAD
> hide @H*
> align #2:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing
Alignment matrix in structure trueB_ETasq_Bfox_Hie290_aligned.pdb coordinates
Matrix rotation and translation
0.99339521 -0.09046281 0.07058633 6.24976923
0.10022218 0.98361014 -0.14988868 -3.68156891
-0.05587008 0.15597301 0.98617998 -7.67453128
Axis 0.80074167 0.33106115 0.49921067
Axis point 0.00000000 46.44098124 -29.53952257
Rotation angle (degrees) 11.01036041
Shift along axis -0.04558171
RMSD between 140 atom pairs is 0.629 angstroms
> align #2:13-207,348-358,379-574@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing
Alignment matrix in structure trueB_ETasq_Bfox_Hie290_aligned.pdb coordinates
Matrix rotation and translation
0.99999478 -0.00256142 -0.00196974 0.27675587
0.00255477 0.99999104 -0.00337442 -0.09504772
0.00197837 0.00336937 0.99999237 -0.45066051
Axis 0.72200816 -0.42269479 0.54775299
Axis point 0.00000000 132.57120457 -29.37762169
Rotation angle (degrees) 0.26758169
Shift along axis -0.00685447
RMSD between 402 atom pairs is 1.290 angstroms
> align #3:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing
Alignment matrix in structure trueB_EThq_Bfox_Hip290_aligned.pdb coordinates
Matrix rotation and translation
0.97255225 -0.14092020 -0.18515837 20.55175664
0.12376651 0.98713738 -0.10120097 -6.47801378
0.19703801 0.07550683 0.97748388 -18.84704686
Axis 0.35529743 -0.76846290 0.53219217
Axis point 112.02142686 0.00000000 90.07237907
Rotation angle (degrees) 14.39917143
Shift along axis 2.24984877
RMSD between 140 atom pairs is 0.926 angstroms
> hide #2 models
> show #3 models
> align #3:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing
Alignment matrix in structure trueB_EThq_Bfox_Hip290_aligned.pdb coordinates
Matrix rotation and translation
0.97255225 -0.14092020 -0.18515837 20.55175664
0.12376651 0.98713738 -0.10120097 -6.47801378
0.19703801 0.07550683 0.97748388 -18.84704686
Axis 0.35529743 -0.76846290 0.53219217
Axis point 112.02142686 0.00000000 90.07237907
Rotation angle (degrees) 14.39917143
Shift along axis 2.24984877
RMSD between 140 atom pairs is 0.926 angstroms
> show #3:221-338,584-605 ribbons
> show #3:FAD
> align #3:13-207,348-358,379-574@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing
Alignment matrix in structure trueB_EThq_Bfox_Hip290_aligned.pdb coordinates
Matrix rotation and translation
0.99999950 -0.00018786 0.00098471 -0.03403364
0.00018573 0.99999764 0.00216596 -0.10256011
-0.00098511 -0.00216578 0.99999717 0.17442726
Axis -0.90750661 0.41268129 0.07826816
Axis point 0.00000000 80.39550076 47.86029184
Rotation angle (degrees) 0.13674298
Shift along axis 0.00221322
RMSD between 402 atom pairs is 1.837 angstroms
> show #4:221-338,584-605 ribbons
> show #4 models
> hide #3 models
> align #4:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing
Alignment matrix in structure trueB_ETox_Bfox_Hip290_aligned.pdb coordinates
Matrix rotation and translation
0.99700573 -0.03057031 -0.07102834 6.46763417
0.02004192 0.98930614 -0.14447034 1.00651003
0.07468528 0.14261422 0.98695658 -14.57981578
Axis 0.88089442 -0.44710977 0.15529929
Axis point 0.00000000 106.24321778 8.33464960
Rotation angle (degrees) 9.37820164
Shift along axis 2.98304730
RMSD between 140 atom pairs is 1.014 angstroms
> align #4:13-207,348-358,379-574@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing
Alignment matrix in structure trueB_ETox_Bfox_Hip290_aligned.pdb coordinates
Matrix rotation and translation
0.99999882 -0.00056880 0.00142766 -0.10337220
0.00056511 0.99999650 0.00258477 -0.17347437
-0.00142913 -0.00258396 0.99999564 0.20941812
Axis -0.85951457 0.47505836 0.18855837
Axis point 0.00000000 77.56634079 75.66006090
Rotation angle (degrees) 0.17227567
Shift along axis 0.04592700
RMSD between 402 atom pairs is 1.854 angstroms
> show #6:221-338,584-605 ribbons
> show #6 models
> hide #4 models
> align #6:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing
Alignment matrix in structure open_conformer_beforeMD_renum.pdb coordinates
Matrix rotation and translation
0.27568379 -0.75863596 0.59031342 74.16162513
0.43350953 0.64623661 0.62805074 -26.76640737
-0.85794402 0.08276309 0.50703287 56.92569079
Axis -0.27913965 0.74138132 0.61027436
Axis point 82.74941003 0.00000000 -21.35205297
Rotation angle (degrees) 77.61517553
Shift along axis -5.80527463
RMSD between 140 atom pairs is 1.252 angstroms
> align #6:13-207,348-358,379-574@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing
Alignment matrix in structure open_conformer_beforeMD_renum.pdb coordinates
Matrix rotation and translation
0.99998133 0.00536441 0.00292695 -0.61534261
-0.00536948 0.99998410 0.00172505 0.42158678
-0.00291765 -0.00174074 0.99999423 0.38909374
Axis -0.27281435 0.46006521 -0.84493333
Axis point 75.34609027 113.28854301 0.00000000
Rotation angle (degrees) 0.36394042
Shift along axis 0.03307344
RMSD between 402 atom pairs is 1.516 angstroms
> align #7/A:221-338@CA/B:237-258@CA toAtoms #1:221-338,584-605@CA
> reportMatrix true move nothing
Alignment matrix in structure 4KPUonClosedBeforeMD.cif coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 -0.00000000
-0.00000000 -0.00000000 1.00000000 0.00000000
Axis -0.34927381 0.19934968 0.91556950
Axis point 151.54834895 118.33100974 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 140 atom pairs is 0.119 angstroms
> align #7/a:13-207@CA/B:1-11,32-227@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing
Alignment matrix in structure 4KPUonClosedBeforeMD.cif coordinates
Matrix rotation and translation
0.99999086 -0.00156786 -0.00397823 0.18454925
0.00159649 0.99997278 0.00720353 -0.39029404
0.00396682 -0.00720982 0.99996614 0.14218805
Axis -0.86000954 -0.47406186 0.18880929
Axis point 0.00000000 18.09107827 50.75113083
Rotation angle (degrees) 0.48013050
Shift along axis 0.05315582
RMSD between 402 atom pairs is 0.109 angstroms
> define axis fromPoint (0,0,0) topoint (10.9, 28.9, 23.3) id 8 color yellow
> radius 0.3
Invalid "fromPoint" argument: Expected a number
> define axis fromPoint 0,0,0 toPoint 10.9, 28.9, 23.3 id 8 color yellow
> radius 0.3
Axis 'axis' centered at [ 5.45 14.45 11.65] with direction [10.9 28.9 23.3],
radius 0.3, and length 38.6899
> define axis fromPoint 0,0,0 toPoint 8.3, -4.2, 1.5 id 9 color springgreen
> radius 0.3
Axis 'axis' centered at [ 4.15 -2.1 0.75] with direction [ 8.3 -4.2 1.5],
radius 0.3, and length 9.42231
> define axis fromPoint 0,0,0 toPoint 8.8, 3.6, 5.5 id 10 color dodgerblue
> radius 0.3
Axis 'axis' centered at [4.4 1.8 2.75] with direction [8.8 3.6 5.5], radius
0.3, and length 10.9841
> define axis fromPoint 0,0,0 toPoint 5.2, -11.1, 7.6 id 11 color orchid
> radius 0.3
Axis 'axis' centered at [ 2.6 -5.55 3.8 ] with direction [ 5.2 -11.1 7.6],
radius 0.3, and length 14.4226
> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/DomainReorientations.cxs
> define axis fromPoint 0,0,0 toPoint 5.2, -11.1, 7.6 id 11 color orchid
> radius 0.3
Axis 'axis' centered at [ 2.6 -5.55 3.8 ] with direction [ 5.2 -11.1 7.6],
radius 0.3, and length 14.4226
> hide cartoons
> hide protein
> show #2 models
> show #3 models
> show #4 models
> hide @H*
> name flavinatoms
> @N1,C2,O2,N3,C4,C4X,O4,C5X,N5,C6,C7,C7M,C8,C8M,C9,C9A,C10,N10
> hide :FAD
> hide :FDM
> show flavinatoms
> ui tool show "Side View"
> hide #11.1 models
> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/AxesRotationHead_FirstTry.png
> width 461 height 831 supersample 3
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_withNAD+_BFahq_Hid290_aligned.pdb
Chain information for trueB_withNAD+_BFahq_Hid290_aligned.pdb #12
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> close 11.1
Expected a models specifier or a keyword
> close #11.1
> color #12 #7f6919ff
> color #12 #7f5b14ff
> color #12 #7f6a25ff
> color #12 #7f6e39ff
> color #12 #e6c868ff
> color #12 #e69384ff
> color #12 #e6893aff
> color #12 #e6b02eff
> color #12 #e6a034ff
> color #12 #e68f0bff
> color #12 #ff9f0cff
> color #12 #ffad4eff
> hide protein
> select #12:347
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #12:13-207,348-358,379-574
6166 atoms, 6216 bonds, 402 residues, 1 model selected
> select #12:221-338,584-605
2114 atoms, 2131 bonds, 140 residues, 1 model selected
> close #12
> select #1:221-338,584-605
2107 atoms, 2124 bonds, 140 residues, 1 model selected
> show cartoons sel
Expected ',' or a keyword
> show sel cartoons
> measure center #1:221-338,584-605
Center of mass of 2107 atoms = (58.82, 66.36, 37.16)
> measure center #1:221-338,584-605@C*
Center of mass of 666 atoms = (58.52, 66.30, 36.92)
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/trueB_withNAD__BFahq_Hid290_aligned_renum.pdb
Chain information for trueB_withNAD__BFahq_Hid290_aligned_renum.pdb #12
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> color #12 #a97817ff
> color #12 #ffb624ff
> color #12 #ffa724ff
> color #12 #ff9727ff
> color #12 #ff8722ff
> color #12 #ffad66ff
> color #12 #ffa442ff
> select #12:13-207,348-358,379-574
6173 atoms, 6223 bonds, 402 residues, 1 model selected
> align #12:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing
Alignment matrix in structure trueB_withNAD__BFahq_Hid290_aligned_renum.pdb
coordinates
Matrix rotation and translation
0.96342787 -0.18037943 0.19816658 13.39127429
0.23666858 0.91960542 -0.31355039 -3.05142166
-0.12567702 0.34898299 0.92866364 -17.23809046
Axis 0.78202365 0.38224996 0.49226413
Axis point 0.00000000 45.95014549 -22.51339336
Rotation angle (degrees) 25.06219877
Shift along axis 0.82019388
RMSD between 140 atom pairs is 1.212 angstroms
> align #12:13-207,348-358,379-574@CA toAtoms #1:13-207,348-358,379-574@CA
> reportMatrix true move nothing
Alignment matrix in structure trueB_withNAD__BFahq_Hid290_aligned_renum.pdb
coordinates
Matrix rotation and translation
0.99999480 0.00272965 0.00171683 -0.22484504
-0.00272426 0.99999138 -0.00313200 0.27460455
-0.00172537 0.00312730 0.99999362 -0.16213848
Axis 0.69645600 0.38300456 -0.60684145
Axis point 0.00000000 42.89811732 81.81495091
Rotation angle (degrees) 0.25746986
Shift along axis 0.04697247
RMSD between 402 atom pairs is 1.594 angstroms
> define axis fromPoint 0,0,0 toPoint 19.5, 9.5, 12.3 id 13 color orange
> radius 0.3
Axis 'axis' centered at [9.75 4.75 6.15] with direction [19.5 9.5 12.3],
radius 0.3, and length 24.9357
> hide #12 cartoons
> hide #12 protein
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide protein
> name flavinatoms
> @N1,C2,O2,N3,C4,C4X,O4,C5X,N5,C6,C7,C7M,C8,C8M,C9,C9A,C10,N10
> hide
> show flavinAtoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show flavinAtom
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select @N1,C2,O2,N3,C4,C4X,O4,C5X,N5,C6,C7,C7M,C8,C8M,C9,C9A,C10,N10
300 atoms, 328 bonds, 17 residues, 8 models selected
> show sel
> name flavinAtons sel
> select clear
> select flavinAtoms
Expected an objects specifier or a keyword
> close #8
> define axis fromPoint 0,0,0 toPoint 21.8, 57.7, 46.6 id 8 color yellow
> radius 0.3
Axis 'axis' centered at [10.9 28.85 23.3 ] with direction [21.8 57.7 46.6],
radius 0.3, and length 77.3052
> hide :NDP
> help name
> name flavinatoms
> @N1,C2,O2,N3,C4,C4X,O4,C5X,N5,C6,C7,C7M,C8,C8M,C9,C9A,C10,N10
> hide flavinAtoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/DomainReorientations.cxs
> name frozen flavinatoms
> @N1,C2,O2,N3,C4,C4X,O4,C5X,N5,C6,C7,C7M,C8,C8M,C9,C9A,C10,N10
> select flavinatoms
300 atoms, 328 bonds, 17 residues, 8 models selected
> name delete flavinatons
deregistering unregistered selector "flavinatons"
> select clear
> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/DomainReorientations.cxs
> color flavinatoms byhetero
> save
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/DomainReorientations.cxs
> close #8
> close #9
> close #10
> close #11
> close #13
> define axis fromPoint 58.2,66.3,36.9 toPoint 67.3, 69.9, 42.4 id 8 color
> dodgerblue radius 0.3
Axis 'axis' centered at [62.75 68.1 39.65] with direction [9.1 3.6 5.5],
radius 0.3, and length 11.2259
> define axis fromPoint 58.2,66.3,36.9 toPoint 63.7, 55.2, 44.6 id 9 color
> orchid radius 0.3
Axis 'axis' centered at [60.95 60.75 40.75] with direction [ 5.5 -11.1 7.7],
radius 0.3, and length 14.586
> define axis fromPoint 58.2,66.3,36.9 toPoint 66.8, -62.1, 38.4 id 10 color
> springgreen radius 0.3
Axis 'axis' centered at [62.5 2.1 37.65] with direction [ 8.6 -128.4 1.5],
radius 0.3, and length 128.696
> close #10
> define axis fromPoint 58.2,66.3,36.9 toPoint 66.8, 62.1, 38.4 id 10 color
> springgreen radius 0.3
Axis 'axis' centered at [62.5 64.2 37.65] with direction [ 8.6 -4.2 1.5],
radius 0.3, and length 9.68762
> define axis fromPoint 58.2, 66.3, 36.9 toPoint 78.1, 75.8, 49.2 id 11 color
> orange radius 0.3
Axis 'axis' centered at [68.15 71.05 43.05] with direction [19.9 9.5 12.3],
radius 0.3, and length 25.2498
> define axis fromPoint 58.2, 66.3, 36.9 toPoint 36.8, 123.7, 84.3 id 12 color
> yellow radius 0.3
Axis 'axis' centered at [47.5 95. 60.6] with direction [-21.4 57.4 47.4],
radius 0.3, and length 77.4563
Drag select of 3 residues
> select clear
> show #3:221-338,584-605 ribbons
> align #3:221-338,584-605@CA toAtoms #1:221-338,584-605@CA reportMatrix true
> move nothing
Alignment matrix in structure trueB_EThq_Bfox_Hip290_aligned.pdb coordinates
Matrix rotation and translation
0.97255225 -0.14092020 -0.18515837 20.55175664
0.12376651 0.98713738 -0.10120097 -6.47801378
0.19703801 0.07550683 0.97748388 -18.84704686
Axis 0.35529743 -0.76846290 0.53219217
Axis point 112.02142686 0.00000000 90.07237907
Rotation angle (degrees) 14.39917143
Shift along axis 2.24984877
RMSD between 140 atom pairs is 0.926 angstroms
> show #3 ribbons
> show #1 ribbons
> hide #1 ribbons
> show #1:221-338,584-605 ribbons
> hide #3 ribbons
> show #3:221-338,584-605 ribbons
> define axis fromPoint 65.0, 67.3, 22.3 toPoint 73.24, 63.1, 23.8 id 10 color
> springgreen radius 0.3
Axis 'axis' centered at [69.12 65.2 23.05] with direction [ 8.24 -4.2 1.5 ],
radius 0.3, and length 9.3695
> close #10.1
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/afm/Documents/1_manuscripts/BiswajitMD/TrueB_analysis/closed_conformer_beforeMD.pdb
Chain information for closed_conformer_beforeMD.pdb #1
---
Chain | Description
? | No description available
Computing secondary structure
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,13
Model Number: Z1BV0006PLL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 2 hours, 5 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2880 x 1864 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
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: 1.2.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
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: 1.18.1
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
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: 1.41
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
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: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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