![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#18057 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-15.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000020494b200 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, psutil._psutil_osx, psutil._psutil_posix (total: 60)
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{
"uptime" : 1100000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,1",
"coalitionID" : 99029,
"osVersion" : {
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"build" : "24F74",
"releaseType" : "User"
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"captureTime" : "2025-06-23 11:34:39.0501 -0500",
"codeSigningMonitor" : 1,
"incident" : "8BB84FF5-DE6F-459C-BA03-DD42F937FC29",
"pid" : 43042,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-23 09:09:12.3710 -0500",
"procStartAbsTime" : 26205571408053,
"procExitAbsTime" : 26408926187934,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"ACF28FB2-42FE-58C2-8DE5-A9B04FE55DAD","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5CD00815-A492-345C-021D-25B424AB78F6",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["siriAssetIsNotReady","assetIsNotReady","notOptedIn"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "D0F15393-EBAE-4F26-B3FA-2E72EE20C036",
"wakeTime" : 1045,
"sleepWakeUUID" : "4470466E-2F6F-4847-8485-8B1FE4801432",
"sip" : "enabled",
"vmRegionInfo" : "0x4bd572460f28 is not in any region. Bytes after previous region: 82899080974121 Bytes before following region: 22172998955224\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, 0x00004bd572460f28","rawCodes":[1,83380117311272],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00004bd572460f28"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":43042},
"vmregioninfo" : "0x4bd572460f28 is not in any region. Bytes after previous region: 82899080974121 Bytes before following region: 22172998955224\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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"faultingThread" : 0,
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]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 9blf
Summary of feedback from opening 9blf fetched from pdb
---
warnings | Atom H1 is not in the residue template for ALA /A:2
Atom H1 is not in the residue template for PHE /B:6
Atom H1 is not in the residue template for SER /C:1
Atom H1 is not in the residue template for PHE /D:6
9blf title:
SARS-CoV-2 core polymerase complex inhibited by araCTP [more info...]
Chain information for 9blf #1
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 2-929
B D | Non-structural protein 8 | R1AB_SARS2 6-193
C | Non-structural protein 7 | R1A_SARS2 1-73
P | RNA (31-MER) |
T | RNA (33-MER) |
Non-standard residues in 9blf #1
---
CAR — cytosine arabinose-5'-phosphate
HF4 —
4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-
D-arabinofuranosyl}pyrimidin-2(1H)-one (Cytarabine-TRIPHOSPHATE)
MG — magnesium ion
ZN — zinc ion
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2 araUTP - UTP rebuild08_rnk.pdb"
Chain information for SARS2 araUTP - UTP rebuild08_rnk.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
P | No description available
T | No description available
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2 UTP-UTP_rebuild_04_rnk.pdb"
Chain information for SARS2 UTP-UTP_rebuild_04_rnk.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
P | No description available
T | No description available
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2_araUTP_15_rnk.pdb"
Chain information for SARS2_araUTP_15_rnk.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
P | No description available
T | No description available
> matchmaker #2-4 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 9blf, chain A (#1) with SARS2 araUTP - UTP rebuild08_rnk.pdb, chain
A (#2), sequence alignment score = 4671.4
RMSD between 925 pruned atom pairs is 0.443 angstroms; (across all 928 pairs:
0.464)
Matchmaker 9blf, chain A (#1) with SARS2 UTP-UTP_rebuild_04_rnk.pdb, chain A
(#3), sequence alignment score = 4682.2
RMSD between 927 pruned atom pairs is 0.364 angstroms; (across all 928 pairs:
0.379)
Matchmaker 9blf, chain A (#1) with SARS2_araUTP_15_rnk.pdb, chain A (#4),
sequence alignment score = 4681
RMSD between 925 pruned atom pairs is 0.373 angstroms; (across all 928 pairs:
0.393)
> style stick
Changed 60023 atom styles
> delete H
> view :HF4
> select HF4
Expected an objects specifier or a keyword
> select :HF4
58 atoms, 60 bonds, 2 residues, 1 model selected
> select :CAR
20 atoms, 21 bonds, 1 residue, 1 model selected
> view CAR
Expected an objects specifier or a view name or a keyword
> view :CAR
> hide #!1 models
> hide #!3 models
> hide #!4 models
> color byhetero
> open 9uo9
Fetching url http://files.rcsb.org/download/9uo9.cif failed:
HTTP Error 404: Not Found
> open 7uo9
7uo9 title:
SARS-CoV-2 replication-transcription complex bound to UTP, in a pre-catalytic
state [more info...]
Chain information for 7uo9 #5
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
P | Product RNA (35-MER) |
T | Template RNA (55-MER) |
Non-standard residues in 7uo9 #5
---
MG — magnesium ion
UTP — uridine 5'-triphosphate
ZN — zinc ion
> matchmaker #5 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 9blf, chain A (#1) with 7uo9, chain A (#5), sequence alignment
score = 4558.6
RMSD between 912 pruned atom pairs is 0.929 angstroms; (across all 926 pairs:
1.004)
> style stick
Changed 72502 atom styles
> color byhetero
> delete H
> open 7UOE
7uoe title:
SARS-CoV-2 replication-transcription complex bound to CTP, in a pre-catalytic
state [more info...]
Chain information for 7uoe #6
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
P | Product RNA (35-MER) |
T | Template RNA (55-MER) |
Non-standard residues in 7uoe #6
---
CTP — cytidine-5'-triphosphate
L2B — 3'-deoxyuridine-5'-monophosphate
([(2~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-
oxolan-2-yl]methyl dihydrogen phosphate)
MG — magnesium ion
ZN — zinc ion
> matchmaker #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 9blf, chain A (#1) with 7uoe, chain A (#6), sequence alignment
score = 4731.4
RMSD between 917 pruned atom pairs is 0.957 angstroms; (across all 928 pairs:
1.004)
> style stick
Changed 73902 atom styles
> hide #!5 models
> show #!1 models
> hide #!2 models
> color byhetero
> log metadata #1
Metadata for 9blf #1
---
Title | SARS-CoV-2 core polymerase complex inhibited by araCTP
Citation | Anderson, T.K., Kirchdoerfer, R.N. (?). Structure of the SARS-CoV-2 core-RTC bound to RNA, araCMP, and araCTP. To Be Published
Non-standard residues | CAR — cytosine arabinose-5'-phosphate
HF4 —
4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-
D-arabinofuranosyl}pyrimidin-2(1H)-one (Cytarabine-TRIPHOSPHATE)
MG — magnesium ion
ZN — zinc ion
Gene sources | synthetic construct
Severe acute respiratory syndrome coronavirus 2
CryoEM Map | EMDB 44654 — open map
Experimental method | Electron microscopy
Resolution | 3.31Å
> open 44654 fromDatabase emdb
Opened emdb 44654 as #7, grid size 256,256,256, pixel 1.06, shown at level
0.131, step 1, values float32, fit PDB 9blf
> volume #7 level 0.2424
> transparency 50
> hide #!6 models
> volume #7 level 0.1834
> select #1/A:1006@C2'
1 atom, 1 residue, 1 model selected
> select up
29 atoms, 30 bonds, 1 residue, 1 model selected
> view sel
> ui tool show "Side View"
> hide #!7 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide solvent
> ui tool show Distances
> select clear
> select #6/A:1005@O2'
1 atom, 1 residue, 1 model selected
> select add #6/A:682@OG
2 atoms, 2 residues, 1 model selected
> distance #6/A:1005@O2' #6/A:682@OG
Distance between 7uoe #6/A CTP 1005 O2' and SER 682 OG: 2.403Å
> select clear
> select #6/A:1005@O2'
1 atom, 1 residue, 1 model selected
> select add #6/A:687@OG1
2 atoms, 2 residues, 1 model selected
> distance #6/A:1005@O2' #6/A:687@OG1
Distance between 7uoe #6/A CTP 1005 O2' and THR 687 OG1: 3.493Å
> select clear
> select #6/A:1005@O2'
1 atom, 1 residue, 1 model selected
> select add #6/A:691@ND2
2 atoms, 2 residues, 1 model selected
> distance #6/A:1005@O2' #6/A:691@ND2
Distance between 7uoe #6/A CTP 1005 O2' and ASN 691 ND2: 3.769Å
> select #6/A:1005@O3'
1 atom, 1 residue, 1 model selected
> select add #6/A:622@SG
2 atoms, 2 residues, 1 model selected
> distance #6/A:1005@O3' #6/A:622@SG
Distance between 7uoe #6/A CTP 1005 O3' and CYS 622 SG: 4.129Å
> ~distance #6/A:1005@O3' #6/A:622@SG
> select clear
> select #6/A:1005@O3'
1 atom, 1 residue, 1 model selected
> select add #6/A:623@N
2 atoms, 2 residues, 1 model selected
> distance #6/A:1005@O3' #6/A:623@N
Distance between 7uoe #6/A CTP 1005 O3' and ASP 623 N: 3.782Å
> show #!4 models
> select #6/A:1005@O3'
1 atom, 1 residue, 1 model selected
> select add #6/A:680@OG1
2 atoms, 2 residues, 1 model selected
> distance #6/A:1005@O3' #6/A:680@OG1
Distance between 7uoe #6/A CTP 1005 O3' and THR 680 OG1: 4.736Å
> ~distance #6/A:1005@O3' #6/A:623@N
> ~distance #6/A:1005@O2' #6/A:691@ND2
> ~distance #6/A:1005@O2' #6/A:687@OG1
> ~distance #6/A:1005@O2' #6/A:682@OG
> ~distance #6/A:1005@O3' #6/A:680@OG1
> hide #!6 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> select clear
> select #1/A:1006@O2'
1 atom, 1 residue, 1 model selected
> select add #1/A:682@OG
2 atoms, 2 residues, 1 model selected
> distance #1/A:1006@O2' #1/A:682@OG
Distance between 9blf #1/A HF4 1006 O2' and SER 682 OG: 3.203Å
> select #1/A:555@NH1
1 atom, 1 residue, 1 model selected
> select add #1/A:1006@O2'
2 atoms, 2 residues, 1 model selected
> distance #1/A:555@NH1 #1/A:1006@O2'
Distance between 9blf #1/A ARG 555 NH1 and HF4 1006 O2': 3.739Å
> select #1/A:623@OD1
1 atom, 1 residue, 1 model selected
> select add #1/A:1006@O2'
2 atoms, 2 residues, 1 model selected
> distance #1/A:623@OD1 #1/A:1006@O2'
Distance between 9blf #1/A ASP 623 OD1 and HF4 1006 O2': 4.278Å
> ~distance #1/A:1006@O2' #1/A:682@OG
> ~distance #1/A:555@NH1 #1/A:1006@O2'
> ~distance #1/A:623@OD1 #1/A:1006@O2'
> select #1/A:1006@O3'
1 atom, 1 residue, 1 model selected
> select add #1/A:760@OD2
2 atoms, 2 residues, 1 model selected
> distance #1/A:1006@O3' #1/A:760@OD2
Distance between 9blf #1/A HF4 1006 O3' and ASP 760 OD2: 2.797Å
> select clear
> select #1/A:1006@O3'
1 atom, 1 residue, 1 model selected
> select add #1/A:691@ND2
2 atoms, 2 residues, 1 model selected
> distance #1/A:1006@O3' #1/A:691@ND2
Distance between 9blf #1/A HF4 1006 O3' and ASN 691 ND2: 4.317Å
> select #1/A:623@N
1 atom, 1 residue, 1 model selected
> select add #1/A:1006@O3'
2 atoms, 2 residues, 1 model selected
> distance #1/A:623@N #1/A:1006@O3'
Distance between 9blf #1/A ASP 623 N and HF4 1006 O3': 5.063Å
> ~distance #1/A:1006@O3' #1/A:691@ND2
> ~distance #1/A:623@N #1/A:1006@O3'
> show #!7 models
> show #!6 models
> select #1/A:760@OD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> view sel
> ui tool show "Side View"
> volume #7 level 0.2424
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!2 models
> hide #!2 models
> hide #!7 models
> hide #!8 models
> hide #8.1 models
> close #8
> show #!4 models
> show #!2 models
> hide #!1 models
> show #!1 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: Z14Z00105LL/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 25 days, 17 hours, 59 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
MZ279:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 4 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 , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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