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Opened 5 months ago
Closed 5 months ago
#17972 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.1-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 0x000000031b163000 (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 0x000000031a157000 (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 0x000000031914b000 (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 0x000000031813f000 (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 0x0000000317133000 (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 0x0000000316127000 (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 0x000000031511b000 (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 0x000000031410f000 (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 0x0000000313103000 (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 0x00000003120f7000 (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 0x00000003110eb000 (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 0x00000003100df000 (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 0x000000030f0d3000 (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 0x00000001fc094840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 57)
{"app_name":"ChimeraX","timestamp":"2025-06-12 14:10:55.00 -0700","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 15.3.1 (24D70)","roots_installed":0,"name":"ChimeraX","incident_id":"1AF3C5BF-0C3E-4DA6-87E0-BD8A32E41030"}
{
"uptime" : 160000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,1",
"coalitionID" : 2556,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-06-12 14:10:50.8659 -0700",
"codeSigningMonitor" : 2,
"incident" : "1AF3C5BF-0C3E-4DA6-87E0-BD8A32E41030",
"pid" : 2282,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-27 09:40:59.8130 -0700",
"procStartAbsTime" : 56197126743,
"procExitAbsTime" : 3963005517196,
"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":"944615D9-5819-5599-8EFD-159607085CDB","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "24CC7EE5-AF2E-8312-594D-1EBA91DB79F0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "F1FE2483-5299-4B02-8988-6287CE3BC28D",
"wakeTime" : 456,
"sleepWakeUUID" : "3BF50FE5-A877-4194-A1C9-AFFCD046E5F3",
"sip" : "enabled",
"vmRegionInfo" : "0x641fd6bf2948 is not in any region. Bytes after previous region: 4534092802377 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [156.1M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000e41fd6bf2948","rawCodes":[1,250825397971272],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000e41fd6bf2948 -> 0x0000641fd6bf2948 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":2282},
"vmregioninfo" : "0x641fd6bf2948 is not in any region. Bytes after previous region: 4534092802377 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [156.1M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"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":4563696280},{"value":99},{"value":119},{"value":1153027057758535360},{"value":4552384826},{"value":9190397861199395108},{"value":9190397857239527780},{"value":14757395258967641293},{"value":4294967286},{"value":4563696210},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8664212160},{"value":0},{"value":11},{"value":259},{"value":8523434272,"symbolLocation":224,"symbol":"_main_thread"},{"value":316},{"value":1},{"value":4361750064,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8486424576,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":8486424576,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6751928176},"cpsr":{"value":1073741824},"fp":{"value":4563696352},"sp":{"value":4563696320},"esr":{"value":1442840704,"description":" Address size 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"name" : "_psutil_osx.abi3.so"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
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"uuid" : "3133c77c-8bf7-32a3-b5db-cbfe2e50ce9d",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/matplotlib\/backends\/_backend_agg.cpython-311-darwin.so",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> lighting soft
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/aorta/Downloads/cryosparc_P405_J285_class_01_00400_volume.mrc
Opened cryosparc_P405_J285_class_01_00400_volume.mrc as #1, grid size
64,64,64, pixel 2.89, shown at level 0.0544, step 1, values float32
> open "/Users/aorta/Downloads/cryosparc_P405_J251_002_volume_map (1).mrc"
Opened cryosparc_P405_J251_002_volume_map (1).mrc as #2, grid size
100,100,100, pixel 2.96, shown at level 0.00914, step 1, values float32
> hide #!2 models
> volume #1 level 0.3495
> show #!2 models
> volume #2 level 0.3601
> open /Users/aorta/Downloads/cryosparc_P402_J837_003_volume_map_sharp.mrc
Opened cryosparc_P402_J837_003_volume_map_sharp.mrc as #3, grid size
350,350,350, pixel 0.74, shown at level 0.0294, step 2, values float32
> open /Users/aorta/Downloads/cryosparc_P402_J837_003_volume_map.mrc
Opened cryosparc_P402_J837_003_volume_map.mrc as #4, grid size 350,350,350,
pixel 0.74, shown at level 0.0288, step 2, values float32
> hide #!2 models
> hide #!1 models
> volume #3 step 1
> volume #4 step 1
> ui tool show "Side View"
> open /Users/aorta/Documents/p450/phenix/p450_trimer_Start5.pdb
Chain information for p450_trimer_Start5.pdb #5
---
Chain | Description
A B C | No description available
> select clear
Drag select of 8 residues
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.014042,-0.44774,0.89405,80.854,-0.076946,0.89101,0.44742,-8.0799,-0.99694,-0.075077,-0.02194,250.14
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> hide #!3 models
> fitmap #5 inMap #4
Fit molecule p450_trimer_Start5.pdb (#5) to map
cryosparc_P402_J837_003_volume_map.mrc (#4) using 11571 atoms
average map value = 0.04953, steps = 120
shifted from previous position = 7.72
rotated from previous position = 7.16 degrees
atoms outside contour = 2574, contour level = 0.028826
Position of p450_trimer_Start5.pdb (#5) relative to
cryosparc_P402_J837_003_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.02929752 -0.39469402 0.91834540 69.02294252
0.03111921 0.91865459 0.39383413 -20.42510557
-0.99908620 0.01703982 0.03919687 240.58756768
Axis -0.18840104 0.95873560 0.21291101
Axis point 155.11604041 0.00000000 84.97593883
Rotation angle (degrees) 90.36815682
Shift along axis 18.63747281
> hide #!4 models
> select /B:508@FE
1 atom, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> view sel
> show #!4 models
> color #4 #b2b2ff9a models
> color #4 #b2b2ff89 models
> hide #!4 models
> show #!3 models
> color #3 #b2ffff82 models
> volume #3 level 0.0393
> select /B:215
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
73 atoms, 74 bonds, 8 residues, 1 model selected
> show sel atoms
> hide #!3 models
> select /B:305
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
127 atoms, 129 bonds, 16 residues, 1 model selected
> show sel atoms
> show #!3 models
> select clear
> select /B:211@CG
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
73 atoms, 74 bonds, 8 residues, 1 model selected
> select up
2097 atoms, 2151 bonds, 260 residues, 1 model selected
> color sel white
> select up
2141 atoms, 2195 bonds, 266 residues, 1 model selected
> select up
3814 atoms, 3908 bonds, 474 residues, 1 model selected
> color sel #ff9bdcff
> color sel #706effff
> color sel #6c6effff
> color sel #6970ffff
> color sel #6375ffff
> color sel #6478ffff
> color sel #6799ffff
> color sel #689cffff
> color sel #699effff
> color sel #6da7ffff
> color sel #6faaffff
> color sel #75b6ffff
> color sel #75b7ffff
> color sel #76b7ffff
> color sel #75b7ffff
> color sel #74b7ffff
> color sel #6db5ffff
> color sel #6cb5ffff
> color sel #62b0ffff
> color sel #60b0ffff
> color sel #5fafffff
> color sel #5eafffff
> color sel #59acffff
> color sel #57abffff
> color sel #55a9ffff
> color sel #52a5ffff
> color sel #51a3ffff
> color sel #4e9effff
> color sel #4a97ffff
> color sel #4894ffff
> color sel #4995ffff
> color sel #4a96ffff
> select clear
> color byhetero
> volume #3 level 0.04001
> select add #5
11571 atoms, 11862 bonds, 18 pseudobonds, 1425 residues, 3 models selected
> show sel atoms
> select clear
> volume #3 level 0.03506
> volume #3 level 0.04142
> view name inh
> view
> color #3 #b2ffffff models
> open /Users/aorta/Downloads/cryosparc_P402_J820_004_volume_map_sharp.mrc
Opened cryosparc_P402_J820_004_volume_map_sharp.mrc as #6, grid size
400,400,400, pixel 0.74, shown at level 0.0301, step 2, values float32
> volume #6 step 1
> volume #6 level 0.07703
> hide #!5 models
> select #6
2 models selected
> view matrix models #6,1,0,0,-13.959,0,1,0,-17.085,0,0,1,5.1992
> view matrix models
> #6,0.95721,0.28868,-0.020171,-47.538,-0.2865,0.95519,0.07433,18.151,0.040724,-0.06537,0.99703,9.6243
> fitmap #6 inMap #3
Fit map cryosparc_P402_J820_004_volume_map_sharp.mrc in map
cryosparc_P402_J837_003_volume_map_sharp.mrc using 205942 points
correlation = 0.8619, correlation about mean = 0.3974, overlap = 2327
steps = 204, shift = 25, angle = 4.54 degrees
Position of cryosparc_P402_J820_004_volume_map_sharp.mrc (#6) relative to
cryosparc_P402_J837_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.95226164 0.30528295 0.00028219 -56.66301923
-0.30528294 0.95226169 -0.00006788 33.79384754
-0.00028944 -0.00002151 0.99999996 -18.99733894
Axis 0.00007595 0.00093623 -0.99999956
Axis point 79.66538249 198.07053863 0.00000000
Rotation angle (degrees) 17.77519561
Shift along axis 19.02466585
> show #!5 models
> hide #!3 models
> surface dust #6 size 7.4
> select clear
> view inh
> color #6 #ffb2ff7f models
> color #6 #ffb2ff60 models
> color #6 #ffb2ff61 models
> color #6 #ffb2ffa4 models
> ui tool show "Color Zone"
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
25 atoms, 24 bonds, 3 residues, 1 model selected
> select up
2097 atoms, 2151 bonds, 260 residues, 1 model selected
> select up
2141 atoms, 2195 bonds, 266 residues, 1 model selected
> select up
3814 atoms, 3908 bonds, 474 residues, 1 model selected
> color #6 #cac0ffa3 models
> color #6 #a39dffa3 models
> undo
> redo
> color sel #9aedffa3
> color sel #a0bdffa3
> color sel #9fbbffa3
> color sel #a5d1ffa3
> color sel #b6e7ffa3
> color sel #b8e9ffa3
> color sel #b7e8ffa3
> color sel #b5e6ffa3
> color sel #b4e2ffa3
> color sel #b1ddffa3
> color sel #7f82ffa3
> color sel #7d7cffa3
> color sel #7d78ffa3
> color sel #7e75ffa3
> color sel #7e72ffa3
> color sel #7e6fffa3
> color sel #7d6bffa3
> color sel #7a6affa3
> color sel #7366ffa3
> color sel #6c62ffa3
> color sel #675fffa3
> color sel #5e5bffa3
> color sel #5e5bffa4
> color sel #5e5bffff
> select #6
4 models selected
> select clear
> hide #!6 models
> select /B:508@FE
1 atom, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> color sel #ffb999ff
> color sel #ffa676ff
> color sel #ffab74ff
> color sel #ff875eff
> color sel #ff755eff
> color sel #ff9977ff
> color sel #ffa174ff
> select clear
> show #!6 models
> color zone #6 near #5 distance 4.44
> color zone #6 near #5 distance 3
> color zone #6 near #5 distance 2
> color zone #6 near #5 distance 2.5
> transparency #6.1 0
> color zone #6 near #5 distance 2.5 transparency #6 50
Expected a keyword
> hide #!6 models
Drag select of 26 atoms, 12 residues, 19 bonds
> select up
113 atoms, 112 bonds, 13 residues, 1 model selected
> select down
103 atoms, 19 bonds, 13 residues, 1 model selected
> select up
113 atoms, 112 bonds, 13 residues, 1 model selected
> select up
424 atoms, 429 bonds, 50 residues, 1 model selected
> select up
3814 atoms, 3908 bonds, 474 residues, 1 model selected
> color sel #bcbaffff
> color sel #9fabffff
> color sel #99a0ffff
> color sel #9190ffff
> color sel #918fffff
> color sel #685fffff
> color sel #685effff
> color sel #675dffff
> color sel #675cffff
> color sel #5e50ffff
> color sel #6253ffff
> color sel #6656ffff
> color sel #6a5affff
> color sel #6d5cffff
> color sel #6f5effff
> color sel #6f5eff88
> color sel #6f5eff7a
> select /B:508@FE
1 atom, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> select up
3857 atoms, 3954 bonds, 475 residues, 1 model selected
> select down
43 atoms, 46 bonds, 1 residue, 1 model selected
> color sel #ff97687a
> color sel #ff4d4f7a
> color sel #ff6f617a
> color sel #ff6e617a
> color sel #ff6e637a
> color sel #ff6e667a
> color sel #ff6f6a7a
> color sel #ff965c7a
> select clear
> color zone #6 near #5 distance 2.5
> hide #!6 models
Drag select of 26 atoms, 8 residues, 25 bonds
Drag select of 3 atoms, 3 residues, 2 bonds
> select clear
Drag select of 77 atoms, 30 residues, 80 bonds
> select up
593 atoms, 616 bonds, 73 residues, 1 model selected
> select up
4194 atoms, 4302 bonds, 520 residues, 1 model selected
> select up
4282 atoms, 4390 bonds, 532 residues, 1 model selected
> select up
7628 atoms, 7816 bonds, 948 residues, 1 model selected
> select up
7714 atoms, 7908 bonds, 950 residues, 1 model selected
> select up
11571 atoms, 11862 bonds, 1425 residues, 1 model selected
> color sel #8dabff7a
> color sel #909eff7a
> color sel #909dff7a
> color sel #8899ff7a
> color sel #8798ff7a
> color sel #8596ff7a
> color sel #7f91ff7a
> color sel #7b8eff7a
> color sel #778cff7a
> color sel #768cff7a
> color sel #788eff7a
> color sel #7c99ff7a
> color sel #7e9fff7a
> color sel #7fa6ff7a
> color sel #7fa9ff7a
> color sel #7ba7ff7a
> color sel #79a6ff7a
> color sel #78a6ff7a
> color sel #78a8ff7a
> color sel #79abff7a
> color sel #79b0ff7a
> color sel #79b5ff7a
> color sel #79beff7a
> color sel #7abcff7a
> color sel #7abbff7a
> select /B:508@FE
1 atom, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> select up
3857 atoms, 3954 bonds, 475 residues, 1 model selected
> select down
43 atoms, 46 bonds, 1 residue, 1 model selected
> color sel #ff996c7a
> color sel #ff8e637a
> color sel #ff91677a
> color sel #ff966c7a
> color sel #ffa87e7a
> color sel #ffb5897a
> color sel #ffbd8f7a
> color sel #ffc0917a
> color sel #ffbe8f7a
> color sel #ffba8d7a
> color sel #ffb3897a
> color sel #ffa27d7a
> color sel #ff9a787a
> color sel #ff94747a
> color sel #ff93747a
> color sel #ff92727a
> color sel #ff8e6f7a
> color sel #ff87697a
> color sel #ff85677a
> color sel #ff83657a
> color sel #ff7f627a
> color sel #ff7d607a
> color sel #ff7a5d7a
> color sel #ff795d7a
> color sel #ff785b7a
> color sel #ff74587a
> color sel #ff72567a
> color sel #ff71537a
> color sel #ff70517a
> color sel #ff6f507a
> color sel #ff704f7a
> color sel #ff6f4f7a
> color sel #ff6f4e7a
> color sel #ff69447a
> color sel #ff68417a
> color sel #ff683e7a
> color sel #ff683c7a
> color sel #ff683b7a
> color sel #ff683a7a
> color sel #ff69367a
> color sel #ff6a347a
> color sel #ff6b327a
> color sel #ff6c307a
> color sel #ff6e2e7a
> color sel #ff6f2c7a
> color sel #ff722b7a
> color sel #ff732a7a
> select clear
> color zone #6 near #5 distance 2.5
> select add #5
11571 atoms, 11862 bonds, 18 pseudobonds, 1425 residues, 3 models selected
> hide #!6 target m
> show #!6 target m
> hide #!5 target m
> show #!5 target m
> hide #!6 target m
> show #!4 target m
> hide #!5 target m
> show #!5 target m
> hide #!4 target m
> show #!6 target m
> hide #!5 target m
> select clear
> hide #!6 models
> show #!5 models
Drag select of 117 atoms, 28 residues, 104 bonds
> select up
260 atoms, 255 bonds, 36 residues, 1 model selected
> select up
312 atoms, 311 bonds, 36 residues, 1 model selected
> select up
685 atoms, 694 bonds, 84 residues, 1 model selected
> select up
3814 atoms, 3908 bonds, 474 residues, 1 model selected
> select up
3857 atoms, 3954 bonds, 475 residues, 1 model selected
> select up
11571 atoms, 11862 bonds, 1425 residues, 1 model selected
> select down
3857 atoms, 3954 bonds, 475 residues, 1 model selected
> select down
3814 atoms, 3908 bonds, 474 residues, 1 model selected
> color sel #b2b9ff7a
> color sel #a3c2ff7a
> color sel #8596ff7a
> color sel #8596ff7c
> color sel #8596ffbb
> color sel #8596ffff
> color sel #8c9effff
> color sel #7b92ffff
> color sel #7790ffff
> color sel #6a80ffff
> show #!6 models
> hide #!6 models
> select /B:508@FE
1 atom, 1 residue, 1 model selected
> select up
43 atoms, 46 bonds, 1 residue, 1 model selected
> color sel #ffb9a8ff
> color sel #ff9a74ff
> color sel #ff9975ff
> color sel #ffaf55ff
> color sel #ffaf54ff
> color sel #ffaf50ff
> color sel #ffae4fff
> color sel #ffa242ff
> color sel #ffa241ff
> color sel #ffa43eff
> color sel #ffa43dff
> color sel #ffa53cff
> color sel #ffa135ff
> color sel #ffa035ff
> color sel #ff9f34ff
> color sel #ff9030ff
> color sel #ffa43eff
> color sel #ffa236ff
> color sel #ff9d31ff
> color sel #ff921fff
> color sel #ff9019ff
> color sel #ff911aff
> color sel #ff931cff
> select clear
> view inh
> hide #!6 models
Drag select of 72 atoms, 16 residues, 62 bonds
> select up
154 atoms, 152 bonds, 19 residues, 1 model selected
> select up
174 atoms, 175 bonds, 19 residues, 1 model selected
> select up
603 atoms, 612 bonds, 73 residues, 1 model selected
> select up
3814 atoms, 3908 bonds, 474 residues, 1 model selected
> hide sel atoms
> select clear
> show #!6 models
> volume splitbyzone #6
Opened cryosparc_P402_J820_004_volume_map_sharp.mrc 0 as #7.1, grid size
400,400,400, pixel 0.74, shown at level 0.077, step 1, values float32
Opened cryosparc_P402_J820_004_volume_map_sharp.mrc 1 as #7.2, grid size
400,400,400, pixel 0.74, shown at level 0.077, step 1, values float32
Opened cryosparc_P402_J820_004_volume_map_sharp.mrc 2 as #7.3, grid size
400,400,400, pixel 0.74, shown at level 0.077, step 1, values float32
> surface dust #7.1 size 7.4
> surface dust #7.2 size 7.4
> surface dust #7.3 size 7.4
> volume #7.1 level 0.07359
> volume #7.1 level 0.0737
> volume #7.1 level 0.077
> select clear
> view name inh
> view
> select add #5
11571 atoms, 11862 bonds, 18 pseudobonds, 1425 residues, 3 models selected
> select clear
> hide #!5 models
> show #!6 models
> hide #!7 models
> color #6 #b0aeffa3 models
> color #6 #b0aeffff models
> color #6 #6c91ffff models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> open /Users/aorta/Downloads/fold_gfp_dimer/fold_gfp_dimer_model_0.cif
Chain information for fold_gfp_dimer_model_0.cif #8
---
Chain | Description
A B | .
Computing secondary structure
> view
> select clear
Drag select of 13 residues
> view matrix models
> #8,0.96683,-0.12759,-0.22126,98.402,0.22227,0.84707,0.48278,39.823,0.12582,-0.51595,0.84733,66.961
> view matrix models
> #8,0.96683,-0.12759,-0.22126,63.954,0.22227,0.84707,0.48278,65.008,0.12582,-0.51595,0.84733,76.849
> view matrix models
> #8,0.97545,-0.16714,-0.1434,65.876,0.21921,0.79927,0.55957,83.326,0.021087,-0.57726,0.81629,79.746
> view matrix models
> #8,0.86187,-0.37484,-0.34158,67.015,0.50353,0.71268,0.48842,83.938,0.060358,-0.59294,0.80298,79.852
> view matrix models
> #8,0.86187,-0.37484,-0.34158,68.521,0.50353,0.71268,0.48842,84.166,0.060358,-0.59294,0.80298,83.317
> select up
397 atoms, 401 bonds, 51 residues, 1 model selected
> select up
1903 atoms, 1946 bonds, 239 residues, 1 model selected
> fitmap #8 inMap #1
Fit molecule fold_gfp_dimer_model_0.cif (#8) to map
cryosparc_P405_J285_class_01_00400_volume.mrc (#1) using 3806 atoms
average map value = 0.154, steps = 352
shifted from previous position = 11.7
rotated from previous position = 60.2 degrees
atoms outside contour = 3119, contour level = 0.34953
Position of fold_gfp_dimer_model_0.cif (#8) relative to
cryosparc_P405_J285_class_01_00400_volume.mrc (#1) coordinates:
Matrix rotation and translation
0.98149312 0.11064508 0.15629752 69.88765237
-0.08190877 0.98031958 -0.17962313 95.14970690
-0.17309593 0.16349673 0.97123973 89.45719463
Axis 0.66867272 0.64192267 -0.37524936
Axis point 0.00000000 -658.34794788 336.53054224
Rotation angle (degrees) 14.86650817
Shift along axis 74.24196461
> undo
> view matrix models
> #8,0.98149,0.11065,0.1563,65.9,-0.081909,0.98032,-0.17962,96.459,-0.1731,0.1635,0.97124,89.333
> view matrix models
> #8,0.96562,0.059612,0.25304,65.656,-0.13604,0.94532,0.29642,94.773,-0.22153,-0.32065,0.92093,90.602
> close #8
> open
> /Users/aorta/Downloads/fold_gfp_dimer_with_nanobody/fold_gfp_dimer_with_nanobody_model_0.cif
Chain information for fold_gfp_dimer_with_nanobody_model_0.cif #8
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> select #8/D:189
6 atoms, 5 bonds, 1 residue, 1 model selected
> view matrix models
> #8,0.025962,-0.21925,0.97532,53.155,-0.6384,-0.75443,-0.1526,12.594,0.76927,-0.61868,-0.15955,12.412
> view matrix models
> #8,0.75514,-0.54435,-0.3653,66.249,-0.001304,0.55598,-0.83119,5.6769,0.65556,0.62815,0.41913,17.788
> view matrix models
> #8,0.75514,-0.54435,-0.3653,54.358,-0.001304,0.55598,-0.83119,89.595,0.65556,0.62815,0.41913,71.017
> view matrix models
> #8,0.80863,-0.58094,0.092867,92.37,0.54344,0.67713,-0.49616,72.17,0.22536,0.45168,0.86325,71.285
> view matrix models
> #8,0.93485,-0.32194,0.14969,95.806,0.32539,0.6082,-0.72403,85.959,0.14205,0.72556,0.67333,72.893
> view matrix models
> #8,0.93485,-0.32194,0.14969,160.58,0.32539,0.6082,-0.72403,99.417,0.14205,0.72556,0.67333,113.33
> select clear
> color #8 bychain
> hide #!1 models
Drag select of 145 residues
> select clear
Drag select of 37 residues
> select up
536 atoms, 536 bonds, 84 residues, 1 model selected
> select up
4068 atoms, 4134 bonds, 558 residues, 1 model selected
> select up
7874 atoms, 8026 bonds, 1036 residues, 1 model selected
> select down
4068 atoms, 4134 bonds, 558 residues, 1 model selected
> select ::name="CYS"
186 atoms, 155 bonds, 31 residues, 2 models selected
> show sel & #8 atoms
> close #8
> open
> /Users/aorta/Downloads/fold_gfp_dimer_with_nanobody/fold_gfp_dimer_with_nanobody_model_1.cif
Chain information for fold_gfp_dimer_with_nanobody_model_1.cif #8
---
Chain | Description
A B | .
C D | .
Computing secondary structure
> view
> color #8 bychain
> select ::name="CYS"
186 atoms, 155 bonds, 31 residues, 2 models selected
> select #8/D:273
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/C:274
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> interfaces #8 & ~solvent
4 buried areas: D B 1531, C A 1484, C D 1259, A B 638
> show sel atoms
> color sel byhetero
> select clear
> save /Users/aorta/Documents/TEST/test1.png width 739 height 705 supersample
> 4 transparentBackground true
> select #8/C:246
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
51 atoms, 51 bonds, 6 residues, 1 model selected
> select up
2034 atoms, 2067 bonds, 279 residues, 1 model selected
> color sel cornflower blue
> select clear
> save /Users/aorta/Documents/TEST/test1.png width 739 height 705 supersample
> 4 transparentBackground true
> hide #8 models
> open
> /Users/aorta/Downloads/fold_atad329_dimer/fold_atad329_dimer_model_0.cif
Chain information for fold_atad329_dimer_model_0.cif #9
---
Chain | Description
A B | .
Computing secondary structure
> color #9 bychain
> select #9/B:258
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
129 atoms, 131 bonds, 17 residues, 1 model selected
> select up
2429 atoms, 2473 bonds, 306 residues, 1 model selected
> hide sel cartoons
> open /Users/aorta/Downloads/cryosparc_P405_J337_class_03_final_volume.mrc
Opened cryosparc_P405_J337_class_03_final_volume.mrc as #10, grid size
192,192,192, pixel 1.54, shown at level 0.0175, step 1, values float32
> view
> volume #10 level 0.05597
> select clear
Drag select of 26 residues
> view matrix models #9,1,0,0,116.39,0,1,0,104.06,0,0,1,211.72
> view matrix models
> #9,0.38328,-0.26563,-0.88461,126.36,-0.46773,0.77005,-0.43389,103.73,0.79645,0.58006,0.1709,213.83
> view matrix models
> #9,0.38328,-0.26563,-0.88461,143.65,-0.46773,0.77005,-0.43389,131.22,0.79645,0.58006,0.1709,216.47
> view matrix models
> #9,0.38328,-0.26563,-0.88461,136.38,-0.46773,0.77005,-0.43389,134.26,0.79645,0.58006,0.1709,179.77
> surface dust #10 size 15.4
> fitmap #9 inMap #10
Fit molecule fold_atad329_dimer_model_0.cif (#9) to map
cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 4858 atoms
average map value = 0.06642, steps = 340
shifted from previous position = 17.9
rotated from previous position = 31.3 degrees
atoms outside contour = 3154, contour level = 0.055966
Position of fold_atad329_dimer_model_0.cif (#9) relative to
cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates:
Matrix rotation and translation
0.78847871 -0.08610931 -0.60900452 151.35768216
-0.42736971 0.63537969 -0.64315456 137.34779106
0.44233070 0.76738376 0.46418284 168.28176002
Axis 0.78711621 -0.58667175 -0.19043197
Axis point 0.00000000 -48.46518572 246.96935300
Rotation angle (degrees) 63.63930450
Shift along axis 6.51178854
> view matrix models
> #9,0.79137,-0.062038,-0.60818,151.41,-0.38616,0.72051,-0.57598,139.28,0.47393,0.69067,0.54623,170.44
> volume #10 level 0.1328
> view matrix models
> #9,0.78957,-0.059353,-0.61078,151.32,-0.39075,0.71882,-0.57499,139.21,0.47317,0.69266,0.54437,170.39
> view matrix models
> #9,0.76035,-0.1246,-0.63746,151.13,-0.37484,0.71733,-0.58731,139.4,0.53044,0.68551,0.49871,171.08
> view matrix models
> #9,0.36113,-0.23281,-0.90299,138.8,-0.46091,0.79722,-0.38987,141.3,0.81065,0.55699,0.18059,170.71
> view matrix models
> #9,0.36113,-0.23281,-0.90299,142.62,-0.46091,0.79722,-0.38987,142.06,0.81065,0.55699,0.18059,173.82
> fitmap #9 inMap #10
Fit molecule fold_atad329_dimer_model_0.cif (#9) to map
cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 4858 atoms
average map value = 0.06642, steps = 292
shifted from previous position = 10.2
rotated from previous position = 32.9 degrees
atoms outside contour = 3937, contour level = 0.13282
Position of fold_atad329_dimer_model_0.cif (#9) relative to
cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates:
Matrix rotation and translation
0.78809691 -0.08609755 -0.60950019 151.32659082
-0.42771762 0.63548755 -0.64281663 137.35216893
0.44267472 0.76729576 0.46400033 168.27638923
Axis 0.78677925 -0.58706624 -0.19060862
Axis point 0.00000000 -48.40174972 246.91892487
Rotation angle (degrees) 63.65389777
Shift along axis 6.35086933
> hide #9 models
> show #8 models
Drag select of 21 atoms, 238 residues, 16 bonds
> select up
1839 atoms, 1862 bonds, 239 residues, 1 model selected
> select up
2888 atoms, 2930 bonds, 396 residues, 1 model selected
> select up
5971 atoms, 6080 bonds, 797 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
Drag select of 239 residues
> view matrix models
> #8,0.88051,0.46779,-0.076663,157.75,-0.35874,0.55186,-0.75284,114.74,-0.30987,0.69038,0.65373,141.6
> view matrix models
> #8,0.36593,0.11179,0.9239,159.54,-0.67867,0.71135,0.18273,146.21,-0.63679,-0.6939,0.33617,147.57
> view matrix models
> #8,0.36593,0.11179,0.9239,163.37,-0.67867,0.71135,0.18273,143.29,-0.63679,-0.6939,0.33617,150.94
> fitmap #8 inMap #10
Fit molecule fold_gfp_dimer_with_nanobody_model_1.cif (#8) to map
cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 7874 atoms
average map value = 0.05868, steps = 292
shifted from previous position = 18.2
rotated from previous position = 64 degrees
atoms outside contour = 6524, contour level = 0.13282
Position of fold_gfp_dimer_with_nanobody_model_1.cif (#8) relative to
cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates:
Matrix rotation and translation
-0.24060228 -0.69113193 0.68150363 152.62194254
-0.45173709 0.70118603 0.55160833 151.37558460
-0.85909496 -0.17514225 -0.48091688 139.23598980
Axis -0.42249226 0.89561810 0.13917081
Axis point 152.28219193 -0.00000000 -2.82241039
Rotation angle (degrees) 120.67492509
Shift along axis 90.47070984
> select clear
> color #10 #99bfe5a1 models
> select clear
> select #8/A:117
4 atoms, 3 bonds, 1 residue, 1 model selected
> view matrix models
> #8,-0.27676,-0.66343,0.69518,150.22,-0.45131,0.72842,0.51548,150.03,-0.84836,-0.17108,-0.50101,135.57
> view matrix models
> #8,-0.28778,-0.75054,0.59487,150.16,-0.66791,0.60244,0.43698,145.18,-0.68635,-0.27157,-0.67467,139.65
> fitmap #8 inMap #10
Fit molecule fold_gfp_dimer_with_nanobody_model_1.cif (#8) to map
cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 7874 atoms
average map value = 0.06221, steps = 252
shifted from previous position = 10.4
rotated from previous position = 41.3 degrees
atoms outside contour = 6450, contour level = 0.13282
Position of fold_gfp_dimer_with_nanobody_model_1.cif (#8) relative to
cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates:
Matrix rotation and translation
-0.39299873 -0.91592827 0.08140881 145.66133610
-0.45028465 0.26888116 0.85143799 154.75052529
-0.80174542 0.29795691 -0.51809840 139.61892558
Axis -0.48485230 0.77364770 0.40790623
Axis point 140.84131681 0.00000000 -10.90722527
Rotation angle (degrees) 145.19586190
Shift along axis 106.04958316
> undo
> select #8/A:204
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #8,-0.92834,-0.3169,-0.19429,131.72,-0.32256,0.42701,0.84476,155.05,-0.18474,0.8469,-0.49864,146.37
> view matrix models
> #8,-0.93302,-0.24776,-0.26092,130.9,-0.32085,0.9011,0.29166,150.11,0.16286,0.35585,-0.92024,158.78
> view matrix models
> #8,-0.79835,-0.60219,-0.0030833,130.91,-0.59774,0.79305,-0.11736,139.35,0.073118,-0.09185,-0.99308,155.34
> fitmap #8 inMap #10
Fit molecule fold_gfp_dimer_with_nanobody_model_1.cif (#8) to map
cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 7874 atoms
average map value = 0.05102, steps = 144
shifted from previous position = 11.4
rotated from previous position = 10.2 degrees
atoms outside contour = 6756, contour level = 0.13282
Position of fold_gfp_dimer_with_nanobody_model_1.cif (#8) relative to
cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates:
Matrix rotation and translation
-0.77795001 -0.61049006 0.14864611 139.00440758
-0.62010903 0.78411673 -0.02501490 146.72596161
-0.10128456 -0.11163714 -0.98857402 152.17601903
Axis -0.32725809 0.94423595 -0.03634042
Axis point 100.39651883 0.00000000 73.01113281
Rotation angle (degrees) 172.39485181
Shift along axis 87.52347074
> volume #10 level 0.1328
> view matrix models
> #8,-0.77795,-0.61049,0.14865,163.29,-0.62011,0.78412,-0.025015,154.98,-0.10128,-0.11164,-0.98857,163.24
> view matrix models
> #8,-0.62824,-0.76608,0.13577,134.17,-0.77543,0.63077,-0.028983,142.14,-0.063439,-0.12349,-0.99032,153.8
> view matrix models
> #8,-0.62824,-0.76608,0.13577,133.27,-0.77543,0.63077,-0.028983,141.79,-0.063439,-0.12349,-0.99032,152.94
> select up
81 atoms, 82 bonds, 10 residues, 1 model selected
> select up
1903 atoms, 1946 bonds, 239 residues, 1 model selected
> fitmap #8 inMap #10
Fit molecule fold_gfp_dimer_with_nanobody_model_1.cif (#8) to map
cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 7874 atoms
average map value = 0.06221, steps = 384
shifted from previous position = 21.3
rotated from previous position = 60.6 degrees
atoms outside contour = 6452, contour level = 0.13282
Position of fold_gfp_dimer_with_nanobody_model_1.cif (#8) relative to
cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates:
Matrix rotation and translation
-0.39296935 -0.91593970 0.08142207 145.64878333
-0.45019525 0.26884261 0.85149744 154.77153450
-0.80181003 0.29795657 -0.51799861 139.61449382
Axis -0.48484931 0.77362756 0.40794797
Axis point 140.84205807 0.00000000 -10.92652726
Rotation angle (degrees) 145.19131351
Shift along axis 106.07326236
> undo
> select up
81 atoms, 82 bonds, 10 residues, 1 model selected
> select up
1903 atoms, 1946 bonds, 239 residues, 1 model selected
> ui tool show "Fit in Map"
> fitmap sel inMap #10
Fit molecule fold_gfp_dimer_with_nanobody_model_1.cif (#8) to map
cryosparc_P405_J337_class_03_final_volume.mrc (#10) using 1903 atoms
average map value = 0.1408, steps = 88
shifted from previous position = 2.78
rotated from previous position = 16.9 degrees
atoms outside contour = 1015, contour level = 0.13282
Position of fold_gfp_dimer_with_nanobody_model_1.cif (#8) relative to
cryosparc_P405_J337_class_03_final_volume.mrc (#10) coordinates:
Matrix rotation and translation
-0.50315903 -0.81044765 0.30000933 139.05500724
-0.79921935 0.56845295 0.19521698 143.32764189
-0.32875433 -0.14154808 -0.93374768 146.07696079
Axis -0.47208381 0.88141314 0.01574004
Axis point 123.08753529 0.00000000 54.10220943
Rotation angle (degrees) 159.10359942
Shift along axis 62.98450599
> select clear
> show #9 models
> hide #9 models
> show #9 models
> color #9 #d95bf2ff
> select add #9
4858 atoms, 4946 bonds, 612 residues, 1 model selected
> view matrix models
> #9,0.98679,-0.11025,-0.11872,165.48,-0.028938,0.60103,-0.7987,131.4,0.15941,0.79158,0.5899,124.18
> view matrix models
> #9,0.98679,-0.11025,-0.11872,169.35,-0.028938,0.60103,-0.7987,177.95,0.15941,0.79158,0.5899,117.51
> view matrix models
> #9,0.98679,-0.11025,-0.11872,165.77,-0.028938,0.60103,-0.7987,165.6,0.15941,0.79158,0.5899,128.63
> view matrix models
> #9,0.75203,0.22798,0.61844,174.46,0.4061,0.57877,-0.70718,175.55,-0.51916,0.78297,0.34267,111.24
> view matrix models
> #9,0.75203,0.22798,0.61844,177.22,0.4061,0.57877,-0.70718,207.96,-0.51916,0.78297,0.34267,94.077
> close #9
> open
> /Users/aorta/Downloads/fold_gfpatad329_dimer/fold_gfpatad329_dimer_model_0.cif
Chain information for fold_gfpatad329_dimer_model_0.cif #9
---
Chain | Description
A B | .
Computing secondary structure
> select clear
> color #8-9 bychain
> select clear
Drag select of 91 residues
> select up
1114 atoms, 1131 bonds, 139 residues, 1 model selected
> select up
4404 atoms, 4494 bonds, 554 residues, 1 model selected
> select down
1114 atoms, 1131 bonds, 139 residues, 1 model selected
> select up
4404 atoms, 4494 bonds, 554 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 553 residues
> view matrix models #9,1,0,0,12.531,0,1,0,35.385,0,0,1,51.688
> view matrix models
> #9,-0.31285,-0.19585,0.92939,163.27,0.56121,0.75131,0.34724,93.163,-0.76627,0.63022,-0.12513,128.46
> select clear
> mmaker #9 to #8
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 fold_gfp_dimer_with_nanobody_model_1.cif, chain A (#8) with
fold_gfpatad329_dimer_model_0.cif, chain A (#9), sequence alignment score =
1226.7
RMSD between 231 pruned atom pairs is 0.255 angstroms; (across all 239 pairs:
2.159)
> select clear
Drag select of 2 residues
> view matrix models
> #9,-0.90216,0.11625,0.41545,149.95,0.39246,0.62101,0.67847,157.12,-0.17913,0.77513,-0.60587,125.15
> view matrix models
> #9,-0.90216,0.11625,0.41545,150.01,0.39246,0.62101,0.67847,160.8,-0.17913,0.77513,-0.60587,124.03
> open /Users/aorta/Downloads/cryosparc_P405_J346_003_volume_map_sharp.mrc
Opened cryosparc_P405_J346_003_volume_map_sharp.mrc as #11, grid size
200,200,200, pixel 1.48, shown at level 0.0176, step 1, values float32
> volume #11 level 0.07876
> volume #11 level 0.1558
> view matrix models
> #9,-0.90216,0.11625,0.41545,150.82,0.39246,0.62101,0.67847,160.67,-0.17913,0.77513,-0.60587,125.21
> view matrix models
> #9,-0.63121,0.52898,0.56723,145.33,0.72635,0.65964,0.19312,155.14,-0.27201,0.53391,-0.8006,127.36
> view matrix models
> #9,-0.78761,0.01165,0.61607,151.31,0.55865,0.43532,0.70598,160.64,-0.25996,0.9002,-0.34937,125.99
> undo
> hide #8 models
> view matrix models
> #9,-0.32589,0.74048,0.58778,138.91,0.93922,0.18256,0.29076,156.2,0.108,0.64681,-0.75496,124.69
> view matrix models
> #9,-0.32589,0.74048,0.58778,141.9,0.93922,0.18256,0.29076,161.3,0.108,0.64681,-0.75496,128.2
> view matrix models
> #9,-0.2218,0.70839,0.67007,150.61,0.9496,0.00081365,0.31346,158.78,0.22151,0.70583,-0.67286,122.77
> view matrix models
> #9,-0.3239,0.1945,0.92588,156.83,0.84327,0.50304,0.18933,155.25,-0.42893,0.84209,-0.32696,129.49
> view matrix models
> #9,-0.40876,0.49605,0.76606,150.93,0.91102,0.17172,0.37492,161.88,0.054435,0.85114,-0.5221,126.39
> hide #9 models
> show #!10 models
> hide #!10 models
> hide #!11 models
> show #!6 models
> hide #!6 models
> show #!4 models
> open /Users/aorta/Downloads/Refine5_coot1.pdb
Summary of feedback from opening /Users/aorta/Downloads/Refine5_coot1.pdb
---
warning | End residue of secondary structure not found: HELIX 28 28 THR A 375 TRP A 396 1 22
Chain information for Refine5_coot1.pdb #12
---
Chain | Description
A | No description available
> hide #!4 models
> rainbow #!12
> dssp
Computing secondary structure
===== 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
> lighting soft
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 - 89.3
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,1
Model Number: MW2V3LL/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 16 days, 5 hours, 9 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
SE2717H/HX:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
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 , 5 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 , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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