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Opened 3 months ago
Closed 3 months ago
#18377 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-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
Thread 0x0000000311b07000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000310afb000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030faef000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030eae3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030dad7000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030cacb000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030babf000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030aab3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000309aa7000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000308a9b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000307a8f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000306a83000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000305a77000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000202835f00 (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, openmm._openmm, openmm.app.internal.compiled, 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.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, psutil._psutil_osx, psutil._psutil_posix, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 61)
{"app_name":"ChimeraX","timestamp":"2025-08-04 17:16:43.00 -0500","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.5 (24F74)","roots_installed":0,"name":"ChimeraX","incident_id":"8914444F-425A-4F1C-ACF1-66A17F71B8E7"}
{
"uptime" : 2800000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,1",
"coalitionID" : 230746,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-08-04 17:16:33.1501 -0500",
"codeSigningMonitor" : 1,
"incident" : "8914444F-425A-4F1C-ACF1-66A17F71B8E7",
"pid" : 31401,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-04 12:11:43.7016 -0500",
"procStartAbsTime" : 69007303192843,
"procExitAbsTime" : 69445837293097,
"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":"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,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "D0F15393-EBAE-4F26-B3FA-2E72EE20C036",
"wakeTime" : 44,
"sleepWakeUUID" : "994483FA-C1E5-4D4C-A40D-85A84D02EB54",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4337450647\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102884000-102888000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":31401},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4337450647\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102884000-102888000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4966480536},{"value":99},{"value":112},{"value":2305948562342671808},{"value":0},{"value":5111661359506459525},{"value":5111661368138421381},{"value":14757395258967641293},{"value":4294967286},{"value":4966480466},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8649203624},{"value":0},{"value":11},{"value":259},{"value":8632098784,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4361274928,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8593248256,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSFullScreenCreateTileDropTargetController._requestedJoinSpace"},{"value":8593248256,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSFullScreenCreateTileDropTargetController._requestedJoinSpace"},{"value":5},{"value":16}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6785493132},"cpsr":{"value":1073745920},"fp":{"value":4966480608},"sp":{"value":4966480576},"esr":{"value":1442840704,"description":" 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===== Log before crash start =====
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
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/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araCTP/D_1000283555_model_P1_araCTP.cif"
Summary of feedback from opening /Users/rnkirchdoerf/Library/CloudStorage/Box-
Box/Wisconsin/2025 araNTP
structure/Chimera/araCTP/D_1000283555_model_P1_araCTP.cif
---
warnings | Atom H3 is not in the residue template for CAR /P:31
Atom H5' is not in the residue template for HF4 /A:1004
Atom H5' is not in the residue template for HF4 /A:1006
Missing or incomplete sequence information. Inferred polymer connectivity.
D_1000283555_model_P1_araCTP.cif title:
SARS-CoV-2 core polymerase complex inhibited by araCTP [more info...]
Chain information for D_1000283555_model_P1_araCTP.cif #1
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase nsp12 | R1AB_SARS2 2-929
B | Non-structural protein 8 | R1AB_SARS2 6-193
C | Non-structural protein 7 | R1A_SARS2 1-73
D | Non-structural protein 8 | R1AB_SARS2 6-193
P | Primer RNA |
T | Template RNA |
Non-standard residues in D_1000283555_model_P1_araCTP.cif #1
---
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/araCTP/cryosparc_P77_J29_005_volume_map_sharp.mrc"
Opened cryosparc_P77_J29_005_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.06, shown at level 0.111, step 1, values float32
> rename #2 araCTP_map
> rename #1 araCTP_model
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/D_1000296630_model_P1_araUTP.cif"
Summary of feedback from opening /Users/rnkirchdoerf/Library/CloudStorage/Box-
Box/Wisconsin/2025 araNTP
structure/Chimera/araUTP/D_1000296630_model_P1_araUTP.cif
---
warnings | Atom C1' is not in the residue template for UAT /P:30
Missing or incomplete sequence information. Inferred polymer connectivity.
D_1000296630_model_P1_araUTP.cif title:
SARS-CoV-2 core polymerase complex inhibited by araUTP [more info...]
Chain information for D_1000296630_model_P1_araUTP.cif #3
---
Chain | Description
A | Non-structural protein 12
B | Non-structural protein 8
C | Non-structural protein 7
D | Non-structural protein 8
P | Primer RNA
T | Template RNA
Non-standard residues in D_1000296630_model_P1_araUTP.cif #3
---
MG — magnesium ion
UAT — 4-methyl-~{N}-(phenylmethyl)piperidine-1-carboxamide
ZN — zinc ion
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2_araUTP_10.mrc"
Opened SARS2_araUTP_10.mrc as #4, grid size 256,256,256, pixel 1.06, shown at
level 0.151, step 1, values float32
> hide #1 models
> hide #!2 models
> volume #4 level 0.2972
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/D_1000296636_model_P1_araUMP_UTP.cif"
Summary of feedback from opening /Users/rnkirchdoerf/Library/CloudStorage/Box-
Box/Wisconsin/2025 araNTP
structure/Chimera/araUTP/D_1000296636_model_P1_araUMP_UTP.cif
---
warnings | Atom C1' is not in the residue template for UAT /P:30
Atom H5' is not in the residue template for UTP /P:31
Missing or incomplete sequence information. Inferred polymer connectivity.
D_1000296636_model_P1_araUMP_UTP.cif title:
SARS-CoV-2 core polymerase complex bound to RNA, araUMP, and UTP [more
info...]
Chain information for D_1000296636_model_P1_araUMP_UTP.cif #5
---
Chain | Description
A | Non-structural protein 12
B | Non-structural protein 8
C | Non-structural protein 7
D | Non-structural protein 8
P | Primer RNA
T | Template RNA
Non-standard residues in D_1000296636_model_P1_araUMP_UTP.cif #5
---
MG — magnesium ion
UAT — 4-methyl-~{N}-(phenylmethyl)piperidine-1-carboxamide
UTP — uridine 5'-triphosphate
ZN — zinc ion
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2 araUTP - UTP chase map.mrc"
Opened SARS2 araUTP - UTP chase map.mrc as #6, grid size 256,256,256, pixel
1.06, shown at level 0.122, step 1, values float32
> hide #3 models
> hide #!4 models
> volume #6 level 0.2433
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/D_1000296137_model_P1_2XUTP.cif"
Summary of feedback from opening /Users/rnkirchdoerf/Library/CloudStorage/Box-
Box/Wisconsin/2025 araNTP
structure/Chimera/araUTP/D_1000296137_model_P1_2XUTP.cif
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
D_1000296137_model_P1_2XUTP.cif title:
SARS-CoV-2 core polymerase complex with two UTP incorporation [more info...]
Chain information for D_1000296137_model_P1_2XUTP.cif #7
---
Chain | Description
A | Non-structural protein 12
B | Non-structural protein 8
C | Non-structural protein 7
D | Non-structural protein 8
P | Primer RNA
T | Template RNA
Non-standard residues in D_1000296137_model_P1_2XUTP.cif #7
---
ZN — zinc ion
> hide #5 models
> hide #!6 models
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 araNTP
> structure/Chimera/araUTP/SARS2_2xUTP_map.mrc"
Opened SARS2_2xUTP_map.mrc as #8, grid size 256,256,256, pixel 1.06, shown at
level 0.157, step 1, values float32
> volume #8 level 0.2794
> rename #3 araUTP_model
> rename #4 araUTP_map
> rename #5 araUMP_UTP_model
> rename #6 araUMP_UTP_map
> rename #7 2XUMP_model
> rename #8 2XUMP_map
> view name overall
> matchmaker #3,5,7 to #1
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 araCTP_model, chain A (#1) with araUTP_model, chain A (#3),
sequence alignment score = 4756.6
RMSD between 925 pruned atom pairs is 0.366 angstroms; (across all 928 pairs:
0.386)
Matchmaker araCTP_model, chain A (#1) with araUMP_UTP_model, chain A (#5),
sequence alignment score = 4768.6
RMSD between 926 pruned atom pairs is 0.444 angstroms; (across all 928 pairs:
0.460)
Matchmaker araCTP_model, chain A (#1) with 2XUMP_model, chain A (#7), sequence
alignment score = 4768.6
RMSD between 927 pruned atom pairs is 0.363 angstroms; (across all 928 pairs:
0.378)
> hide #7 models
> hide #!8 models
> show #!2 models
> show #3 models
> hide #!2 models
> show #!4 models
> view position #4 sameAsModels #3
> hide #3 models
> hide #!4 models
> show #5 models
> show #!6 models
> view position #6 sameAsModels #5
> view position #8 sameAsModels #7
> hide #5 models
> hide #!6 models
> show #7 models
> show #!8 models
> cartoon
> ~show
> style stick
Changed 93979 atom styles
> view ligand
No displayed objects specified.
> color #2,4,6,8 grey
> transparency 50
> view /P:31
> ~ribbon nucleic
> show nucleic
> hide H
> hide #!8 models
> select #7/P:31@C2'
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> show sel : hide H
> color /A goldenrod
> color /B forest green
> color /D forest green
> color /C dodger blue
> color /P light pink
> color /T purple
> color /T medium blue
> ui tool show "Color Actions"
> color /T medium purple
> set bgColor white
> view sel
> show #!8 models
> volume zone #2 nearAtoms sel range 5
> unzone #2
Unknown command: unzone #2
> unzone
Unknown command: unzone
> volume unzone #2
> volume zone #8 nearAtoms sel range 5
> volume zone #8 nearAtoms #7 range 5
> volume zone #8 nearAtoms #7 range 4
> volume #8 level 0.4624
> volume zone #8 nearAtoms #7 range 3
> transparency 70
> lighting soft
> lighting full
> volume #!8 style mesh
> show #!6 models
> hide #!8 models
> hide #!6 models
> show #!8 models
> volume #8 level 0.5234
> color byhetero
> hide #!8 models
> hide #7 models
> show #!6 models
> show #5 models
> volume #!6 style mesh
> volume #6 level 0.5596
> volume zone #6 nearAtoms #5 range 3
> select #5/P:29@O3'
1 atom, 1 residue, 1 model selected
> select add #5/P:30@P
2 atoms, 2 residues, 1 model selected
> ui tool show "Build Structure"
> bond sel
Created 1 bond
> ~ribbon nucleic
> ui tool show "Side View"
> hide #5 models
> hide #!6 models
> show #3 models
> show #!4 models
> volume #!4 style mesh
> volume #4 level 0.645
> select #4
2 models selected
> hide #!4 models
> select #3/P:29@O3'
1 atom, 1 residue, 1 model selected
> select add #3/P:30@P
2 atoms, 2 residues, 1 model selected
> ui tool show "Build Structure"
> bond sel
Created 1 bond
> ~ribbon nucleic
> hide #3 models
> show #1 models
> show #!2 models
> volume #!2 style mesh
> volume #2 level 0.2799
> select #1/A:1006@C2'
1 atom, 1 residue, 1 model selected
> select up
41 atoms, 42 bonds, 1 residue, 1 model selected
> select up
14777 atoms, 14964 bonds, 934 residues, 1 model selected
> select down
41 atoms, 42 bonds, 1 residue, 1 model selected
> color sel light pink
> color byhetero
> show #3 models
> show #5 models
> show #7 models
> ui tool show "Side View"
> camera walleye
> hide #7 models
> hide #5 models
> hide #3 models
> camera stereo
Could not switch graphics mode. Graphics driver did not create OpenGL context.
> camera mono
> volume zone #2 nearAtoms #1 range 3
> select #1/P:31@O2'
1 atom, 1 residue, 1 model selected
> select up
34 atoms, 35 bonds, 1 residue, 1 model selected
> select add #1/A:1006@C2'
35 atoms, 35 bonds, 2 residues, 1 model selected
> select up
75 atoms, 77 bonds, 2 residues, 1 model selected
> show sel : hide H
> hide #1 models
> hide #!2 models
> show #3 models
> show #!4 models
> hide #3 models
> hide #!4 models
> show #5 models
> show #!6 models
> hide #5 models
> hide #!6 models
> show #7 models
> show #!8 models
> show #5 models
> hide #5 models
> save /Users/rnkirchdoerf/Desktop/2XUMP_density1.png width 800 height 917
> supersample 3 transparentBackground true
> turn y 6
> save /Users/rnkirchdoerf/Desktop/2XUMP_density1_6.png width 546 height 626
> supersample 3
> turn y -12
> save /Users/rnkirchdoerf/Desktop/2XUMP_density1_-6.png width 800 height 917
> supersample 3 transparentBackground true
> turn y 12
> save /Users/rnkirchdoerf/Desktop/2XUMP_density1_6.png width 800 height 917
> supersample 3 transparentBackground true
> save /Users/rnkirchdoerf/Desktop/araNTP.cxs
> volume #2,4,6,8 subdivisionLevels 2
> volume #2,4,6,8 subdivisionLevels 3
> show #!2 models
> hide #!8 models
> hide #7 models
> show #1 models
> volume #2,4,6,8 subdivisionLevels 2
> volume #2,4,6,8 subdivideSurface true
> volume #2,4,6,8 subdivisionLevels 1
> hide #1 models
> hide #!2 models
> show #5 models
> show #!6 models
> graphics silhouettes true
> graphics silhouettes false
> volume #!6 style surface
> lighting soft
> lighting full
> lighting simple
> lighting full
> hide #5 models
> hide #!6 models
> show #!2 models
> volume #!2 style surface
> hide #!2 models
> show #!4 models
> volume #!4 style surface
> hide #!4 models
> show #!6 models
> show #!8 models
> hide #!6 models
> volume #!8 style surface
> hide #!8 models
> show #1 models
> show #!2 models
> select clear
> save /Users/rnkirchdoerf/Desktop/araCTP_density1.png width 800 height 917
> supersample 3 transparentBackground true
> turn y -6
> save /Users/rnkirchdoerf/Desktop/araCTP_density2.png width 800 height 917
> supersample 3 transparentBackground true
> turn y 6
> view name active
> transparency 50
> save /Users/rnkirchdoerf/Desktop/araCTP_density1.png width 800 height 917
> supersample 3 transparentBackground true
> turn y -6
> save /Users/rnkirchdoerf/Desktop/araCTP_density2.png width 800 height 917
> supersample 3 transparentBackground true
> turn y 6
> hide #1 models
> hide #!2 models
> show #3 models
> show #!4 models
> save /Users/rnkirchdoerf/Desktop/araUTP_density1.png width 800 height 917
> supersample 3 transparentBackground true
> turn y -6
> save /Users/rnkirchdoerf/Desktop/araUTP_density2.png width 800 height 917
> supersample 3 transparentBackground true
> hide #3 models
> hide #!4 models
> show #5 models
> show #!6 models
> turn y 6
> save /Users/rnkirchdoerf/Desktop/araUTPUTP_density1.png width 800 height 917
> supersample 3 transparentBackground true
> turn y -6
> save /Users/rnkirchdoerf/Desktop/araUTPUTP_density2.png width 546 height 626
> supersample 3
> save /Users/rnkirchdoerf/Desktop/araUTPUTP_density2.png width 800 height 917
> supersample 3 transparentBackground true
> turn y 6
> hide #5 models
> hide #!6 models
> show #7 models
> show #!8 models
> save /Users/rnkirchdoerf/Desktop/2XUTP_density1.png width 800 height 917
> supersample 3 transparentBackground true
> turn y -6
> save /Users/rnkirchdoerf/Desktop/2XUTP_density2.png width 800 height 917
> supersample 3 transparentBackground true
> turn y 6
> view active
> hide #!8 models
> show #1 models
> show #3 models
> show #5 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #7 models
> show #7 models
> open 6yyt
6yyt title:
Structure of replicating SARS-CoV-2 polymerase [more info...]
Chain information for 6yyt #9
---
Chain | Description | UniProt
A | nsp12 | R1AB_SARS2 1-932
B D | nsp8 | R1AB_SARS2 1-198
C | nsp7 | R1AB_SARS2 1-83
P Q T U | RNA product |
Non-standard residues in 6yyt #9
---
ZN — zinc ion
> matchmaker #9 to #1
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 araCTP_model, chain A (#1) with 6yyt, chain A (#9), sequence
alignment score = 4625.8
RMSD between 841 pruned atom pairs is 0.709 angstroms; (across all 853 pairs:
0.857)
> style stick
Changed 105354 atom styles
> cartoon #9
> ~ribbon nucleic
> color /A goldenrod
> color /B forest green
> color /D forest green
> color /C dodger blue
> color /P light pink
> color /T medium purple
> hide H
> hide pseudobonds
> color byhetero
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #7 models
> hide #5 models
> hide #3 models
> hide #1 models
> close #9
> open 7cyq
7cyq title:
Cryo-EM structure of an extended SARS-CoV-2 replication and transcription
complex reveals an intermediate state in cap synthesis [more info...]
Chain information for 7cyq #9
---
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
E F | Helicase | R1AB_SARS2 1-601
G | Non-structural protein 9 | R1AB_SARS2 1-113
I | Primer |
J | Template |
Non-standard residues in 7cyq #9
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
ZN — zinc ion
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #9 to #1
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 araCTP_model, chain A (#1) with 7cyq, chain A (#9), sequence
alignment score = 4690.6
RMSD between 912 pruned atom pairs is 0.658 angstroms; (across all 926 pairs:
0.743)
> style stick
Changed 115820 atom styles
> close #9
> open 7bzf
Summary of feedback from opening 7bzf fetched from pdb
---
note | Fetching compressed mmCIF 7bzf from http://files.rcsb.org/download/7bzf.cif
7bzf title:
COVID-19 RNA-dependent RNA polymerase post-translocated catalytic complex
[more info...]
Chain information for 7bzf #9
---
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
F | RNA (31-MER) |
G | RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*A)-3') |
Non-standard residues in 7bzf #9
---
ZN — zinc ion
> matchmaker #9 to #1
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 araCTP_model, chain A (#1) with 7bzf, chain A (#9), sequence
alignment score = 4405.6
RMSD between 766 pruned atom pairs is 0.996 angstroms; (across all 913 pairs:
1.537)
> style stick
Changed 103911 atom styles
> color /A goldenrod
> color /B forest green
> color /D forest green
> color /C dodger blue
> color #9/G light pink
> color #9/F medium purple
> hide pseudobonds
> ribbon #9
> ~ribbon nucleic
> show #5 models
> hide #!9 models
> select #5/P:30@C3'
1 atom, 1 residue, 1 model selected
> select add #5/P:31@O3B
2 atoms, 2 residues, 1 model selected
> hide protein
> select up
71 atoms, 73 bonds, 2 residues, 1 model selected
> show sel nearAtom 5
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel : hide H
> color byhetero
> show #!9 models
> hide #5 models
> show #3 models
> hide #3 models
> show #1 models
> hide #!9 models
> color ligand light pink
> color byhetero
> show #!9 models
> hide #1 models
> show #1 models
> hide #!9 models
> show #!9 models
> hide #1 models
> show #3 models
> hide #3 models
> show #5 models
> show #1 models
> hide #1 models
> hide #!9 models
> hide #5 models
> show #1 models
> show #!9 models
> show sel : hide H
> show #5 models
> ui tool show "Side View"
> ~ribbon /A:830-940
> view sel
> hide #5 models
> hide #!9 models
> show #5 models
> ~ribbon /A:800-940
> ~show /A:800-940
> hide #1 models
> hide #5 models
> show #1 models
> show #!9 models
> hide #1 models
> show #3 models
> hide #3 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> select clear
> hide #!9 models
> show #1 models
> show #!9 models
> hide #!9 models
> save /Users/rnkirchdoerf/Desktop/araCTPmodel.png width 800 height 758
> supersample 3 transparentBackground true
> hide #1 models
> show #3 models
> save /Users/rnkirchdoerf/Desktop/araUTPmodel.png width 800 height 758
> supersample 3
> hide #3 models
> show #5 models
> save /Users/rnkirchdoerf/Desktop/araUMP_UTPmodel.png width 800 height 758
> supersample 3 transparentBackground true
> hide #5 models
> show #!9 models
> save /Users/rnkirchdoerf/Desktop/7bzfmodel.png width 800 height 758
> supersample 3 transparentBackground true
> show #1 models
> select ~sel & ##selected
Nothing selected
> ~show /A:1-700
> show /A:615-620
> hide H
> ~show /A:1-700
> show /A:618-619
> ~show /A:1-700
> show /A:617-618
> ~show /A:1-700
> show /A:618
> show /A:620
> hide H
> hide /A:798
> show #5 models
> hide #5 models
> hide #!9 models
> save /Users/rnkirchdoerf/Desktop/araCTPmodel.png width 800 height 758
> supersample 3 transparentBackground true
> hide #1 models
> show #3 models
> save /Users/rnkirchdoerf/Desktop/araUTPmodel.png width 800 height 758
> supersample 3 transparentBackground true
> hide #3 models
> show #5 models
> save /Users/rnkirchdoerf/Desktop/araUMP_UTPmodel.png width 800 height 758
> supersample 3 transparentBackground true
> hide #5 models
> show #!9 models
> save /Users/rnkirchdoerf/Desktop/7bzfmodel.png width 800 height 758
> supersample 3 transparentBackground true
> save /Users/rnkirchdoerf/Desktop/araNTP_models.cxs
> open 7c2k
7c2k title:
COVID-19 RNA-dependent RNA polymerase pre-translocated catalytic complex [more
info...]
Chain information for 7c2k #10
---
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
F | RNA (29-MER) |
G | RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*CP*AP*CP*AP*GP*G*(F86)P*G)-3') |
Non-standard residues in 7c2k #10
---
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate (Remdesivir, bound form)
ZN — zinc ion
> matchmaker #10 to #1/A
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 araCTP_model, chain A (#1) with 7c2k, chain A (#10), sequence
alignment score = 4718.8
RMSD between 914 pruned atom pairs is 0.676 angstroms; (across all 926 pairs:
0.783)
> style stick
Changed 114603 atom styles
> close #10
> open 7dte
Summary of feedback from opening 7dte fetched from pdb
---
note | Fetching compressed mmCIF 7dte from http://files.rcsb.org/download/7dte.cif
7dte title:
SARS-CoV-2 RdRP catalytic complex with T33-1 RNA [more info...]
Chain information for 7dte #10
---
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
F | RNA (57-MER) |
G | RNA (33-MER) |
Non-standard residues in 7dte #10
---
ZN — zinc ion
> matchmaker #10 to #1/A
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 araCTP_model, chain A (#1) with 7dte, chain A (#10), sequence
alignment score = 4711
RMSD between 914 pruned atom pairs is 0.644 angstroms; (across all 928 pairs:
0.767)
> style stick
Changed 116041 atom styles
> hide #!9 models
> view active
> color /A goldenrod
> color /B forest green
> color /C dodger blue
> color /D forest green
> ribbon protein
> ~show
> show nucleic
> show ligand
> ~ribbon /A:800-94-
> hide pseudobonds
> open 7uoe
7uoe title:
SARS-CoV-2 replication-transcription complex bound to CTP, in a pre-catalytic
state [more info...]
Chain information for 7uoe #11
---
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 #11
---
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
> open 7uo9
7uo9 title:
SARS-CoV-2 replication-transcription complex bound to UTP, in a pre-catalytic
state [more info...]
Chain information for 7uo9 #12
---
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 #12
---
MG — magnesium ion
UTP — uridine 5'-triphosphate
ZN — zinc ion
> matchmaker #11,12 to #1
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 araCTP_model, chain A (#1) with 7uoe, chain A (#11), sequence
alignment score = 4746.4
RMSD between 918 pruned atom pairs is 0.966 angstroms; (across all 928 pairs:
1.011)
Matchmaker araCTP_model, chain A (#1) with 7uo9, chain A (#12), sequence
alignment score = 4593.4
RMSD between 910 pruned atom pairs is 0.929 angstroms; (across all 926 pairs:
1.009)
> style stick
Changed 152609 atom styles
> hide solvent
> hide H
> ribbon protein
> ~show
> show nucleic
> show ligand
> color /A goldenrod
> color /B forest green
> color /C dodger blue
> color /D forest green
> color nucleic light pink
> hide #!12 models
> hide #!11 models
> color #10/F medium purple
> hide #!10 models
> show #!11 models
> show #!12 models
> hide #!11 models
> color /T medium purple
> color byhetero
> select #12/P:35@C3'
1 atom, 1 residue, 1 model selected
> select add #12/A:1004@PA
2 atoms, 2 residues, 1 model selected
> select up
50 atoms, 53 bonds, 2 residues, 1 model selected
> show /A:758-761
> hide H
> show /A:755-761
> show /A:618
> show /A:620
> show /A:623
> show /A:620-23
> show /A:620-623
> hide H
> show #5 models
> hide #!12 models
> show #!9 models
> hide #!9 models
> show #!10 models
> save /Users/rnkirchdoerf/Desktop/araNTP_models2.cxs
> hide #!10 models
> show #!10 models
> hide #5 models
> show #5 models
> hide #5 models
> show #1 models
> show #3 models
> hide #3 models
> show #5 models
> color ligand light pink
> color byhetero
> save /Users/rnkirchdoerf/Desktop/araNTP_models2.cxs
> hide #1 models
> lighting shadows false
> hide #!10 models
> show #!11 models
> hide #5 models
> show #5 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!10 models
> hide #!10 models
> select #5/P:30@O3'
1 atom, 1 residue, 1 model selected
> select add #5/A:760@OD1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #5/P:30@O3' #5/A:760@OD1
Distance between araUMP_UTP_model #5/P UAT 30 O3' and /A ASP 760 OD1: 2.560Å
> distance style color black
> hide #13.1 models
> show #13.1 models
> hide #5 models
> show #!10 models
> select #10/G:4@O3'
1 atom, 1 residue, 1 model selected
> select add #10/A:760@OD2
2 atoms, 2 residues, 1 model selected
> distance #10/G:4@O3' #10/A:760@OD2
Distance between 7dte #10/G A 4 O3' and /A ASP 760 OD2: 2.757Å
> hide #!10 models
> show #!10 models
> distance style symbol false
> distance style symbol true
> hide #13.1 models
> hide #!13 models
> show #!13 models
> show #5 models
> distance #10/G:4@O3' #10/A:760@OD2
Distance already exists; modify distance properties with 'distance style'
> show #13.1 models
> hide #13.1 models
> hide #!13 models
> show #!13 models
> select clear
Exactly two atoms must be selected!
> distance style decimalPlaces 2
> show #13.1 models
> distance style decimalPlaces 1
> distance style decimalPlaces 2
> distance style decimalPlaces 1
> distance style radius 0.2
> distance style radius 0.1
> distance style symbol false
> distance style symbol true
> distance style color #73fcd6
> distance style color black
> hide #!10 models
> show #!10 models
> hide #13.1 models
> hide #!13 models
> hide #!10 models
> show #!13 models
> select #5/P:30@C3'
1 atom, 1 residue, 1 model selected
> select add #5/P:30@O3'
2 atoms, 1 residue, 1 model selected
> select add #5/A:760@OD1
3 atoms, 2 residues, 1 model selected
> ui tool show Distances
> show #13.1 models
> hide #5 models
> show #!10 models
> select #10/G:4@C3'
1 atom, 1 residue, 1 model selected
> select add #10/G:4@O3'
2 atoms, 1 residue, 1 model selected
Either three or four atoms must be selected!
> select clear
> select #10/G:4@C3'
1 atom, 1 residue, 1 model selected
> select add #10/G:4@O3'
2 atoms, 1 residue, 1 model selected
> select add #10/A:760@OD2
3 atoms, 2 residues, 1 model selected
> show #5 models
> hide #!10 models
> show #!10 models
> hide #5 models
> select clear
> ~ribbon /A:800-940
> show #5 models
> hide #5 models
> hide #13.1 models
> hide #!13 models
> show #5 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!10 models
> save /Users/rnkirchdoerf/Desktop/araUMP_UTPmodel2.png width 800 height 758
> supersample 3 transparentBackground true
> hide #5 models
> show #!10 models
> save /Users/rnkirchdoerf/Desktop/7dte_model2.png width 800 height 758
> supersample 3 transparentBackground true
> hide #!10 models
> show #!12 models
> hide pseudobonds
> save /Users/rnkirchdoerf/Desktop/7uo9_model2.png width 800 height 758
> supersample 3 transparentBackground true
> hide #!12 models
> show #!11 models
> show #1 models
> hide #!11 models
> save /Users/rnkirchdoerf/Desktop/araCTP_model2.png width 800 height 758
> supersample 3 transparentBackground true
> hide #1 models
> show #!11 models
> save /Users/rnkirchdoerf/Desktop/7uoe_model2.png width 800 height 758
> supersample 3 transparentBackground true
> hide #!11 models
> show #!12 models
===== 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
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 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: Z14Z00105LL/A
Chip: Apple M1 Pro
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: 68 days, 20 hours, 50 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
Rotation: Supported
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
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-Clipper: 0.24.0
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-ISOLDE: 1.9
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
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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
more-itertools: 10.3.0
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
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
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
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 3 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 , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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