![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 weeks ago
Closed 6 weeks ago
#18884 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 0x00007ff848cb4dc0 (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.surface._surface, chimerax.pdb_lib._load_libs, 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 (total: 54)
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{
"uptime" : 7900000,
"procRole" : "Background",
"version" : 2,
"userID" : 573055,
"deployVersion" : 210,
"modelCode" : "iMac20,2",
"coalitionID" : 2030561,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-09-23 12:10:38.9289 +0200",
"codeSigningMonitor" : 0,
"incident" : "154B0801-71E5-455A-B3EB-44E47DEE291F",
"pid" : 61966,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-17 15:21:29.7173 +0200",
"procStartAbsTime" : 7445700546530658,
"procExitAbsTime" : 7952634331341078,
"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":"779C63CD-13F5-56E9-8E6A-A12AEF46EFBB","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BF10E68F-7EB4-A7BF-BFD0-67ED6F3CDCA0",
"appleIntelligenceStatus" : {"reasons":["deviceNotCapable"],"state":"unavailable"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "68F55CCD-537A-4DC7-A4F2-8C8E14EDDEA3",
"bridgeVersion" : {"build":"22P5072","train":"9.5"},
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4429037568\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 107fdc000-107fe0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":61966},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4429037568\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 107fdc000-107fe0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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"name" : "libsystem_c.dylib"
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{
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"source" : "A",
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"uuid" : "00000000-0000-0000-0000-000000000000"
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"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
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"base" : 140703249317888,
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"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "3502.1.401"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703445082112,
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"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3020526,
"uuid" : "1ed7a7b9-e12f-348a-ac39-834f923795b6",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703310794752,
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"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 22356791,
"uuid" : "c26f6f9e-8230-3c1f-8c48-02d9de58fbc8",
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"name" : "AppKit",
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"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
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"uuid" : "e9b27e7e-c40d-3405-a371-a753e116f54f",
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"name" : "libc++.1.dylib"
},
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"path" : "\/System\/Library\/Frameworks\/IOKit.framework\/Versions\/A\/IOKit",
"name" : "IOKit"
},
{
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"arch" : "x86_64",
"base" : 140703437963264,
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"CFBundleIdentifier" : "com.apple.IOAccelerator",
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"name" : "IOAccelerator",
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"uuid" : "1fd0642a-2c8c-3e95-b3ee-d89919964340",
"path" : "\/System\/Library\/Extensions\/AMDRadeonX6000MTLDriver.bundle\/Contents\/MacOS\/AMDRadeonX6000MTLDriver",
"name" : "AMDRadeonX6000MTLDriver",
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}
],
"sharedCache" : {
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"uuid" : "57b0c2b8-36d6-3cf0-8bd0-0ac6133ec8b3"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=4.6G written=72.8M(2%) resident=0K(0%) swapped_out=72.8M(2%) unallocated=4.5G(98%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 212K 26 \nColorSync 260K 32 \nCoreAnimation 804K 116 \nCoreGraphics 8K 2 \nCoreUI image data 5160K 47 \nFoundation 36K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 3.9G 163 \nMALLOC guard page 72K 18 \nMach message 24K 5 \nOpenGL GLSL 384K 4 \nSTACK GUARD 184K 46 \nStack 166.4M 47 \nStack Guard 56.0M 1 \nVM_ALLOCATE 397.1M 405 \nVM_ALLOCATE (reserved) 160.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 42.1M 1099 \n__DATA_CONST 121.7M 999 \n__DATA_DIRTY 2590K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 192.7M 152 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2395K 2 \n__TEXT 1.4G 1123 \n__TPRO_CONST 16 2 \ndyld private memory 404K 5 \nmapped file 260.4M 56 \nshared memory 3532K 32 \n=========== ======= ======= \nTOTAL 6.7G 4737 \nTOTAL, minus reserved VM space 6.5G 4737 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "f012f69cd83fb9b412fbf7265a9e96c3a530b8f2",
"trialInfo" : {
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}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
still retrieving bundle list from toolshed
> isolde shorthand
Error running startup command 'isolde shorthand': Unknown command: isolde
shorthand
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
> /Users/jabrilg/Downloads/fold_2025_09_09_w601_rreb1_zn1_5/fold_2025_09_09_w601_rreb1_zn1_5_model_0.cif
Chain information for fold_2025_09_09_w601_rreb1_zn1_5_model_0.cif #1
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
J | .
K | .
> open
> /Users/jabrilg/Downloads/fold_2025_09_09_w601_rreb1_zn1_5/fold_2025_09_09_w601_rreb1_zn1_5_full_data_0.json
Opened AlphaFold PAE with values for 1517 residues and atoms
> hide atoms
> show cartoons
> alphafold pae #1 colorDomains true
> color bfactor #1 palette alphafold
15540 atoms, 1517 residues, atom bfactor range 8.73 to 98.3
> color /H:100-103/I:1-119 lime
> help help:user/tools/alphafold.html#pae
> color bfactor #1 palette alphafold
15540 atoms, 1517 residues, atom bfactor range 8.73 to 98.3
> color /H:29-47 lime
> color /H:68-87 magenta
> color /B:62-79 lime
> color /H:66-80 magenta
> color /B:70-77 lime
> color /H:75-80 magenta
> color /B:84 lime
> color /H:89 magenta
> color /B:72-82 lime
> color /H:82-87 magenta
> color /C:56-72 lime
> color /J:54-70 magenta
> color /J:20-82 lime
> color /D:91-93 magenta
> color /I:78-101 lime
> color /I:57-83 lime
> color /I:163-179 lime
> color /I:161-182 lime
> color /I:190-213 lime
> color /I:189-217 lime
> color /I:182-220 lime
> color /I:15-47 lime
> color /I:13-105 lime
> color /I:142-229 lime
> color /I:188-212 lime
> color /H:33-84 magenta
> color /I:185-216 lime
> color /A:19-130/B-G/H:1-94 magenta
> color /I:178-217 lime
> color /G:15-92 magenta
> color /I:180-209 lime
> color /F:41-118 magenta
> color /I:186-212 lime
> color /E:46-126 magenta
> color /I:180-213 lime
> color /D:30-119 magenta
> color /I:185-216 lime
> color /C:30-121 magenta
> color /I:188-217 lime
> color /B:27-109 magenta
> color /I:183-213 lime
> color /A:17-115 magenta
> color /J:21-76 lime
> color /J:34-82 lime
> color /J:75-86 lime
> color /F:46-125 magenta
> color /G:55-69 lime
> color /B:29-130/C/D:1-11 magenta
> color /E:31-129 lime
> color /I:63-93 magenta
> color /A:24-130/B-E/F:1-120 lime
> color /J:65-93 lime
> color /H:24-94 magenta
> color /J:65-99 lime
> color /E:39-136/F-H magenta
> color /K:89-123 lime
> color /C:18-126/D:1-102 magenta
> color /J:20-83 lime
> color /A:12-130/B-G/H:1-84 magenta
> color /I:2-230 lime
> color /F:39-136/G-H/I:1-105 lime
> color /E:25-136/F-I/J:1-7 lime
> color /A:3-130/B-K lime
> color /A:6-130/B-K lime
> color /E:66-136/F-I/J:1-18 lime
> color /I:117-233/J:1-21 lime
> open
> /Users/jabrilg/Downloads/fold_250909_w601_rreb1/fold_250909_w601_rreb1_model_0.cif
Chain information for fold_250909_w601_rreb1_model_0.cif #2
---
Chain | Description
A B | .
C D | .
E F | .
G H | .
I | .
J | .
K | .
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Refine3D/job072/run_class001.mrc
Opened run_class001.mrc as #8, grid size 256,256,256, pixel 2.1, shown at
level 0.0249, step 1, values float32
> hide #!6 models
> volume #8 level 0.00472
> volume #8 level 0.005428
> volume #8 level 0.005074
> volume #8 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #8 style surface
> volume #8 change image level -0.00116,0 level 0.02489,0.8 level 0.1599,1
> volume #8 level 0.003658
> close session
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class004.mrc
Opened run_it030_class004.mrc as #1, grid size 512,512,512, pixel 1.05, shown
at level 0.075, step 2, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class003.mrc
Opened run_it030_class003.mrc as #2, grid size 512,512,512, pixel 1.05, shown
at level 1.8, step 2, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class002.mrc
Opened run_it030_class002.mrc as #3, grid size 512,512,512, pixel 1.05, shown
at level 0.0663, step 2, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job065/run_it030_class001.mrc
Opened run_it030_class001.mrc as #4, grid size 512,512,512, pixel 1.05, shown
at level 0.00456, step 2, values float32
> hide #!2 models
> hide #!3 models
> tile
2 models tiled
> show #!3 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> volume #4 level 0.001719
> volume #4 level 0.0005333
> hide #!4 models
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job074/run_it021_class001.mrc
Opened run_it021_class001.mrc as #5, grid size 256,256,256, pixel 2.1, shown
at level 0.0242, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job074/run_it021_class002.mrc
Opened run_it021_class002.mrc as #6, grid size 256,256,256, pixel 2.1, shown
at level 0.282, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job074/run_it021_class003.mrc
Opened run_it021_class003.mrc as #7, grid size 256,256,256, pixel 2.1, shown
at level 0.0281, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job074/run_it021_class004.mrc
Opened run_it021_class004.mrc as #8, grid size 256,256,256, pixel 2.1, shown
at level 0.0667, step 1, values float32
> tile
4 models tiled
> hide #!6 models
> volume #5 level 0.009426
> volume #5 level 0.005547
> volume #7 level 0.007163
> volume #8 level 0.01913
> volume #8 level 0.01273
> close #5-8
> show #!4 models
> volume #4 level 0.0007848
> surface dust #4 size 10.5
> volume #4 step 4
> volume #4 step 1
> volume #4 level 0.0006042
> ui mousemode right "map eraser"
> volume erase #4 center 756.25,225.87,372.11 radius 246.02 outside true
Opened run_it030_class001.mrc copy as #6, grid size 512,512,512, pixel 1.05,
shown at step 1, values float32
> volume erase #6 center 641.16,309.7,-37.296 radius 245.95
> volume erase #6 center 863.62,-196.06,304.15 radius 245.95
> volume erase #6 center 806.71,334.74,747.8 radius 245.95
> ui tool show "Map Filter"
> volume gaussian #6 sDev 1.66
Opened run_it030_class001.mrc copy gaussian as #5, grid size 512,512,512,
pixel 1.05, shown at step 1, values float32
> volume #5 level 0.0004556
> surface dust #5 size 10.5
> volume #5 level 0.0006308
> ui tool show "Color Zone"
> open 7nvr
Summary of feedback from opening 7nvr fetched from pdb
---
note | Fetching compressed mmCIF 7nvr from http://files.rcsb.org/download/7nvr.cif
7nvr title:
Human Mediator with RNA Polymerase II Pre-initiation complex [more info...]
Chain information for 7nvr #7
---
Chain | Description | UniProt
0 | TFIIH basal transcription factor complex helicase XPD subunit | ERCC2_HUMAN 1-760
1 | General transcription factor IIH subunit 1 | TF2H1_HUMAN 1-548
2 | General transcription factor IIH subunit 4 | TF2H4_HUMAN 1-462
3 | CDK-activating kinase assembly factor MAT1 | MAT1_HUMAN 1-309
4 | General transcription factor IIH subunit 3 | TF2H3_HUMAN 1-308
5 | General transcription factor IIH subunit 5 | TF2H5_HUMAN 1-71
6 | General transcription factor IIH subunit 2 | TF2H2_HUMAN 1-395
7 | General transcription and DNA repair factor IIH helicase subunit XPB | ERCC3_HUMAN 1-782
8 | Cyclin-dependent kinase 7 | CDK7_HUMAN 1-346
9 | Cyclin-H | CCNH_HUMAN 1-323
A | DNA-directed RNA polymerase subunit |
B | DNA-directed RNA polymerase subunit beta | I3LGP4_PIG 1-1174
C | DNA-directed RNA polymerase II subunit RPB3 | I3LCH3_PIG 1-275
D | RPOL4c domain-containing protein | A0A287ADR4_PIG 1-142
E | DNA-directed RNA polymerase II subunit E | I3LSI7_PIG 1-210
F | DNA-directed RNA polymerase II subunit F | F1SKN8_PIG 1-127
G | DNA-directed RNA polymerase II subunit RPB7 | I3LJZ9_PIG 1-172
H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | A0A4X1ULF2_PIG 1-150
I | DNA-directed RNA polymerase II subunit RPB9 | RPB9_PIG 1-125
J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | A0A4X1VYD0_PIG 1-67
K | RNA_pol_L_2 domain-containing protein | A0A4X1UK25_PIG 1-117
L | RNA polymerase II subunit K | I3LN51_PIG 1-58
M | Transcription initiation factor IIB | TF2B_HUMAN 1-316
N | NT |
O | TATA-box-binding protein | TBP_HUMAN 1-339
Q | General transcription factor IIF subunit 1 | T2FA_HUMAN 1-517
R | General transcription factor IIF subunit 2 | T2FB_HUMAN 1-249
T | TEMPLATE |
U | Transcription initiation factor IIA subunit 1 | TF2AA_HUMAN 1-376
V | Transcription initiation factor IIA subunit 2 | T2AG_HUMAN 1-109
W | General transcription factor IIE subunit 1 | T2EA_HUMAN 1-439
X | Transcription initiation factor IIE subunit beta | T2EB_HUMAN 1-291
Y | Unassigned peptide, likely TFIIE-beta |
Z | Unassigned peptide, likely XPB |
a | Mediator of RNA polymerase II transcription subunit 6 | MED6_HUMAN 1-246
b | Mediator of RNA polymerase II transcription subunit 8 | MED8_HUMAN 1-268
c | Mediator of RNA polymerase II transcription subunit 11 | MED11_HUMAN 1-117
d | Mediator of RNA polymerase II transcription subunit 17 | MED17_HUMAN 1-651
e | Mediator of RNA polymerase II transcription subunit 18 | MED18_HUMAN 1-208
f | Mediator of RNA polymerase II transcription subunit 20 | MED20_HUMAN 1-212
g | Mediator of RNA polymerase II transcription subunit 22 | MED22_HUMAN 1-200
h | Mediator of RNA polymerase II transcription subunit 4 | MED4_HUMAN 1-271
i | Mediator of RNA polymerase II transcription subunit 7 | MED7_HUMAN 1-233
j | Mediator of RNA polymerase II transcription subunit 9 | MED9_HUMAN 1-146
k | Mediator of RNA polymerase II transcription subunit 10 | MED10_HUMAN 1-135
l | Mediator of RNA polymerase II transcription subunit 14 | MED14_HUMAN 1-1454
m | Mediator of RNA polymerase II transcription subunit 19 | MED19_HUMAN 1-244
n | Mediator of RNA polymerase II transcription subunit 21 | MED21_HUMAN 1-144
o | Mediator of RNA polymerase II transcription subunit 31 | MED31_HUMAN 1-131
p | Mediator of RNA polymerase II transcription subunit 27 | MED27_HUMAN 1-311
q | Mediator of RNA polymerase II transcription subunit 28 | MED28_HUMAN 1-178
r | unassigned peptide (MED29 or MED30) |
s | Mediator of RNA polymerase II transcription subunit 30 | MED30_HUMAN 0-177
v | unassigned peptide (MED14) |
w | unassigned peptide (MED6) |
x | unassigned peptide (MED17) |
y | unassigned peptide (MED29 or MED30) |
z | unassigned peptide (MED29 or MED30) |
Non-standard residues in 7nvr #7
---
MG — magnesium ion
SF4 — iron/sulfur cluster
ZN — zinc ion
> select add #7
96126 atoms, 98182 bonds, 305 pseudobonds, 11833 residues, 4 models selected
> ui mousemode right "rotate selected models"
> hide sel atoms
> show sel cartoons
> view matrix models
> #7,0.0040748,-0.68461,-0.7289,470.22,0.18402,0.71697,-0.67238,161.33,0.98291,-0.1314,0.12891,25.084
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.0040748,-0.68461,-0.7289,967.91,0.18402,0.71697,-0.67238,107.14,0.98291,-0.1314,0.12891,35.195
> view matrix models
> #7,0.0040748,-0.68461,-0.7289,1013.3,0.18402,0.71697,-0.67238,186.46,0.98291,-0.1314,0.12891,181.09
> fitmap #7 inMap #5
Fit molecule 7nvr (#7) to map run_it030_class001.mrc copy gaussian (#5) using
96126 atoms
average map value = 0.005769, steps = 316
shifted from previous position = 10.7
rotated from previous position = 23.6 degrees
atoms outside contour = 1034, contour level = 0.00063084
Position of 7nvr (#7) relative to run_it030_class001.mrc copy gaussian (#5)
coordinates:
Matrix rotation and translation
0.97193912 -0.09926664 0.21326152 38.11199014
0.19339999 0.85329327 -0.48423861 161.08000286
-0.13390588 0.51189523 0.84854728 -2.21898656
Axis 0.90992508 0.31712237 0.26733828
Axis point 0.00000000 119.97636930 240.52194578
Rotation angle (degrees) 33.18686313
Shift along axis 85.16790757
> color /A-L rgb (0.8, 0.8, 0.8)
> color /0-6, Z rgb (239, 187, 204)
> color /7-9 rgb (255, 158, 92)
> color /O rgb (199, 28, 0)
> color /U,V rgb (225, 173, 0)
> color /M rgb (0.2, 0.6, 0.2)
> color /X,W,Y rgb (227, 85, 123)
> color /Q,R rgb (166, 35, 248)
> color /N rgb (136, 206, 235)
> color /T rgb (48, 48, 198)
> hide #!5 models
> select clear
> color /a-z rgb (22, 86, 177)
> color /7 rgb (239, 187, 204)
> color /3 rgb (255, 158, 92)
> show #!5 models
> color zone #5 near #7 distance 33.83
> open 7enc
Summary of feedback from opening 7enc fetched from pdb
---
note | Fetching compressed mmCIF 7enc from http://files.rcsb.org/download/7enc.cif
7enc title:
TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED)
[more info...]
Chain information for 7enc #8
---
Chain | Description | UniProt
0 | CDK-activating kinase assembly factor MAT1 | MAT1_HUMAN 1-309
1 | General transcription factor IIH subunit 1 | TF2H1_HUMAN 1-548
2 | General transcription factor IIH subunit 2 | TF2H2_HUMAN 1-395
3 | General transcription factor IIH subunit 3 | TF2H3_HUMAN 1-308
4 | General transcription factor IIH subunit 4 | TF2H4_HUMAN 1-462
5 | General transcription factor IIH subunit 5 | TF2H5_HUMAN 1-71
6 | General transcription and DNA repair factor IIH helicase subunit XPB | ERCC3_HUMAN 1-782
7 | General transcription and DNA repair factor IIH helicase subunit XPD | ERCC2_HUMAN 1-760
8 | Cyclin-dependent kinase 7 | CDK7_HUMAN 1-346
9 | Cyclin-H | CCNH_HUMAN 1-323
BA | Transcription initiation factor IIB | TF2B_HUMAN 1-316
DA | Transcription initiation factor TFIID subunit 1 | TAF1_HUMAN 1-1872
DB | Transcription initiation factor TFIID subunit 2 | TAF2_HUMAN 1-1199
DD Dd | Transcription initiation factor TFIID subunit 4 | TAF4_HUMAN 1-1085
DE De | Transcription initiation factor TFIID subunit 5 | TAF5_HUMAN 1-800
DF Df | Transcription initiation factor TFIID subunit 6 | TAF6_HUMAN 1-677
DG | Transcription initiation factor TFIID subunit 7 | TAF7_HUMAN 1-349
DH | Transcription initiation factor TFIID subunit 8 | TAF8_HUMAN 1-310
DI Di | Transcription initiation factor TFIID subunit 9 | TAF9_HUMAN 1-264
DJ Dj | Transcription initiation factor TFIID subunit 10 | TAF10_HUMAN 1-218
DL Dl | Transcription initiation factor TFIID subunit 12 | TAF12_HUMAN 1-161
DO | Transcription initiation factor IIA subunit 2 | T2AG_HUMAN 1-109
DP | TATA-box-binding protein | TBP_HUMAN 1-339
DQ | TFIIA-a |
Dc | Transcription initiation factor TFIID subunit 3 | TAF3_HUMAN 1-929
Dk | Transcription initiation factor TFIID subunit 11 | TAF11_HUMAN 1-211
Dm | Transcription initiation factor TFIID subunit 13 | TAF13_HUMAN 1-124
EA | General transcription factor IIE subunit 1 | T2EA_HUMAN 1-439
EB | Transcription initiation factor IIE subunit beta | T2EB_HUMAN 1-291
FA | General transcription factor IIF subunit 1 | T2FA_HUMAN 1-517
FB | General transcription factor IIF subunit 2 | T2FB_HUMAN 1-249
PA | RPB1 |
PB | DNA-directed RNA polymerase subunit beta | A0A4X1TVZ5_PIG 1-1174
PC | DNA-directed RNA polymerase II subunit RPB3 | I3LCH3_PIG 1-275
PD | DNA-directed RNA polymerase II subunit RPB4 | A0A481BYI6_PIG 1-142
PE | DNA-directed RNA polymerase II subunit E | A0A4X1VTX4_PIG 1-210
PF | DNA-directed RNA polymerase II subunit F | A0A4X1VEK9_PIG 1-127
PG | DNA-directed RNA polymerase II subunit RPB7 | A0A4X1VKG7_PIG 1-172
PH | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | A0A4X1ULF2_PIG 1-150
PI | DNA-directed RNA polymerase II subunit RPB9 | RPB9_PIG 1-125
PJ | RPB10 |
PK | RNA_pol_L_2 domain-containing protein | A0A4X1UK25_PIG 1-117
PL | RPB12 | A0A4X1TRS6_PIG 1-58
X | DNA (69-MER) |
Y | DNA (69-MER) |
a | Mediator of RNA polymerase II transcription subunit 1 | MED1_HUMAN 1-1581
b | Mediator of RNA polymerase II transcription subunit 29 | MED29_HUMAN 1-200
c | Mediator of RNA polymerase II transcription subunit 27 | MED27_HUMAN 1-311
d | Mediator of RNA polymerase II transcription subunit 4 | MED4_HUMAN 1-270
e | Mediator of RNA polymerase II transcription subunit 28 | MED28_HUMAN 1-178
f | Mediator of RNA polymerase II transcription subunit 6 | MED6_HUMAN 1-246
g | Mediator of RNA polymerase II transcription subunit 7 | MED7_HUMAN 1-233
h | Isoform 2 of Mediator of RNA polymerase II transcription subunit 8 | MED8_HUMAN 1-268
i | Mediator of RNA polymerase II transcription subunit 9 | MED9_HUMAN 1-146
j | Mediator of RNA polymerase II transcription subunit 10 | MED10_HUMAN 1-135
k | Mediator of RNA polymerase II transcription subunit 11 | MED11_HUMAN 1-117
l | Mediator of RNA polymerase II transcription subunit 30 | MED30_HUMAN 1-178
m | Mediator of RNA polymerase II transcription subunit 31 | MED31_HUMAN 1-131
n | Mediator of RNA polymerase II transcription subunit 14 | MED14_HUMAN 1-1454
o | Mediator of RNA polymerase II transcription subunit 15 | MED15_HUMAN 1-788
p | Isoform 2 of Mediator of RNA polymerase II transcription subunit 16 | MED16_HUMAN 1-841
q | Mediator of RNA polymerase II transcription subunit 17 | MED17_HUMAN 1-651
r | Mediator of RNA polymerase II transcription subunit 18 | MED18_HUMAN 1-208
s | Mediator of RNA polymerase II transcription subunit 19 | MED19_HUMAN 1-244
t | Mediator of RNA polymerase II transcription subunit 20 | MED20_HUMAN 1-212
u | Mediator of RNA polymerase II transcription subunit 21 | MED21_HUMAN 1-144
v | Mediator of RNA polymerase II transcription subunit 22 | MED22_HUMAN 1-200
w | Mediator of RNA polymerase II transcription subunit 23 | MED23_HUMAN 1-1368
x | Mediator of RNA polymerase II transcription subunit 24 | MED24_HUMAN 1-989
z | Mediator of RNA polymerase II transcription subunit 26 | MED26_HUMAN 1-600
Non-standard residues in 7enc #8
---
MG — magnesium ion
SF4 — iron/sulfur cluster
ZN — zinc ion
> mmaker #8 to #7
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 7nvr, chain A (#7) with 7enc, chain PA (#8), sequence alignment
score = 9164.4
RMSD between 987 pruned atom pairs is 1.226 angstroms; (across all 1422 pairs:
1.826)
> select #8/DA,DB,DC,DD,DE,DF,DG,DH,DI,DJ,DL,Dc,Dd,De,Df,Di,Dj,Dk,Dl,Dm
40053 atoms, 40924 bonds, 22 pseudobonds, 5000 residues, 2 models selected
> delete sel
> color #8/a-z rgb (22, 86, 177)
> hide #!7 models
> hide #!5 models
> color #8/HA,HB,HC,HE,HF,HG,HH rgb (239, 187, 204)
> color #8/0-7 rgb (239, 187, 204)
> color #8/0,8,9 rgb (255, 158, 92)
> color #8/PA-PL rgb (0.8, 0.8, 0.8)
> color #8/DO,DQ rgb (225, 173, 0)
> color #8/DP rgb (199, 28, 0)
> color #8/BA rgb (0.2, 0.6, 0.2)
> color #8/FA,FB rgb (166, 35, 248)
> color #8/EA,EB rgb (227, 85, 123)
> color #8/X rgb (136, 206, 235)
> color #8/Y rgb (48, 48, 198)
> show #!5 models
> color single #5
> color zone #5 near #8 distance 6.66
> hide #!8 models
> show #!8 models
> color single #5
> color zone #5 near #8 distance 20.54
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> color single #5
> color zone #5 near #8 distance 334.03
> color single #5
> color zone #5 near #8 distance 72.13
> hide #!8 models
> color single #5
> color zone #5 near #8 distance 49.84
> color single #5
> color zone #5 near #8 distance 30.27
> color single #5
> color zone #5 near #8 distance 35.75
> surface dust #5 size 10.5
> volume #5 level 0.00065
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting gentle
> lighting soft
> lighting gentle
> graphics silhouettes true
> color single #5
> volume gaussian #6 sDev 3.6 modelId #5
Opened run_it030_class001.mrc copy gaussian as #5, grid size 512,512,512,
pixel 1.05, shown at step 1, values float32
> volume #5 level 0.0006114
> color zone #5 near #8 distance 30.84
> surface dust #5 size 10.5
> color single #5
> color zone #5 near #8 distance 39.93
> volume gaussian #6 sDev 2.13 modelId #5
Opened run_it030_class001.mrc copy gaussian as #5, grid size 512,512,512,
pixel 1.05, shown at step 1, values float32
> color zone #5 near #8 distance 39.93
> surface dust #5 size 10.5
> color single #5
> color zone #5 near #8 distance 34.44
> color single #5
> color zone #5 near #8 distance 28.64
> show #!6 models
> hide #!5 models
> surface dust #6 size 10.5
> volume #6 level 0.0007703
> show #!5 models
> hide #!6 models
> color single #5
> volume #5 level 0.0006573
> color zone #5 near #8 distance 28.64
> save "/Users/jabrilg/Desktop/Others/Fellowships/Walter Benjamin/preliminary-
> map.png" width 5000 height 2909 supersample 3 transparentBackground true
> hide #!5 models
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job074/run_it030_class001.mrc
Opened run_it030_class001.mrc as #9, grid size 256,256,256, pixel 2.1, shown
at level 0.0248, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job074/run_it030_class002.mrc
Opened run_it030_class002.mrc as #10, grid size 256,256,256, pixel 2.1, shown
at level 7.8, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job074/run_it030_class003.mrc
Opened run_it030_class003.mrc as #11, grid size 256,256,256, pixel 2.1, shown
at level 0.027, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job074/run_it030_class004.mrc
Opened run_it030_class004.mrc as #12, grid size 256,256,256, pixel 2.1, shown
at level 0.0697, step 1, values float32
> hide #!10 models
> tile
3 models tiled
> volume #9 level 0.006773
> volume #9 level 0.005459
> tile
3 models tiled
> volume #11 level 0.007131
> volume #12 level 0.02025
> volume #12 level 0.01606
> close #9-12
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job075/run_it019_class001.mrc
Opened run_it019_class001.mrc as #9, grid size 256,256,256, pixel 2.1, shown
at level 0.0279, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job075/run_it019_class002.mrc
Opened run_it019_class002.mrc as #10, grid size 256,256,256, pixel 2.1, shown
at level 0.0221, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job075/run_it019_class003.mrc
Opened run_it019_class003.mrc as #11, grid size 256,256,256, pixel 2.1, shown
at level 0.0337, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job075/run_it019_class004.mrc
Opened run_it019_class004.mrc as #12, grid size 256,256,256, pixel 2.1, shown
at level 0.0276, step 1, values float32
> tile
4 models tiled
> tile
4 models tiled
> volume #12 level 0.006897
> volume #11 level 0.008761
> volume #10 level 0.004438
> volume #9 level 0.007063
> close #9-12
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job076/run_it030_class004.mrc
Opened run_it030_class004.mrc as #9, grid size 256,256,256, pixel 2.1, shown
at level 0.0283, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job076/run_it030_class003.mrc
Opened run_it030_class003.mrc as #10, grid size 256,256,256, pixel 2.1, shown
at level 0.0227, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job076/run_it030_class002.mrc
Opened run_it030_class002.mrc as #11, grid size 256,256,256, pixel 2.1, shown
at level 0.0214, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job076/run_it030_class001.mrc
Opened run_it030_class001.mrc as #12, grid size 256,256,256, pixel 2.1, shown
at level 0.0286, step 1, values float32
> tile
4 models tiled
> volume #9 level 0.02216
> tile
4 models tiled
> volume #9 level 0.0131
> volume #10 level 0.01124
> volume #11 level 0.009505
> volume #12 level 0.01324
> tile
4 models tiled
> volume #9 level 0.008032
> volume #10 level 0.006078
> volume #11 level 0.006909
> volume #12 level 0.008752
> close #9-12
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job075/run_it030_class001.mrc
Opened run_it030_class001.mrc as #9, grid size 256,256,256, pixel 2.1, shown
at level 0.0265, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job075/run_it030_class002.mrc
Opened run_it030_class002.mrc as #10, grid size 256,256,256, pixel 2.1, shown
at level 0.0235, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job075/run_it030_class003.mrc
Opened run_it030_class003.mrc as #11, grid size 256,256,256, pixel 2.1, shown
at level 0.0706, step 1, values float32
> open
> /Volumes/EM11600_2/DATA/jabrilg/20250611_93_2_P4N177_S40_can_Fr18_18min/processing/Relion/Class3D/job075/run_it030_class004.mrc
Opened run_it030_class004.mrc as #12, grid size 256,256,256, pixel 2.1, shown
at level 0.0277, step 1, values float32
> tile
4 models tiled
> tile
4 models tiled
> volume #9 level 0.007432
> volume #10 level 0.005843
> volume #11 level 0.02068
> volume #12 level 0.007585
> close #9-12
> show #!5 models
> hide #!5 models
> show #!6 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
still retrieving bundle list from toolshed
> isolde shorthand
Error running startup command 'isolde shorthand': Unknown command: isolde
shorthand
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 ATI-7.0.3
OpenGL renderer: AMD Radeon Pro 5700 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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: iMac
Model Identifier: iMac20,2
Processor Name: 8-Core Intel Core i7
Processor Speed: 3,8 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0)
OS Loader Version: 583~1350
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 95 days, 4 hours, 58 minutes
Graphics/Displays:
AMD Radeon Pro 5700:
Chipset Model: AMD Radeon Pro 5700
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x731b
Revision ID: 0x0040
ROM Revision: 113-D1820Q-231
VBIOS Version: 113-D182A2XG-013
Option ROM Version: 113-D182A2XG-013
EFI Driver Version: 01.01.231
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
ROG PG278QR:
Resolution: 2048 x 1152
UI Looks like: 2048 x 1152 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: #ASOT2TO5phXd
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
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-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-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-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 , 6 weeks 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 , 6 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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