![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#17020 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-14.6.1-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
Current thread 0x00000001e8744f40 (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, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.pdb._pdbio, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 60)
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{
"uptime" : 100000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 3131,
"osVersion" : {
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"build" : "23G93",
"releaseType" : "User"
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"captureTime" : "2025-03-04 22:54:28.8361 -0800",
"codeSigningMonitor" : 1,
"incident" : "3D21AB16-13C6-4946-8085-300BE531395F",
"pid" : 62621,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-04 10:08:16.9476 -0800",
"procStartAbsTime" : 1739775384726,
"procExitAbsTime" : 2605234813981,
"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":"F506FC31-E65F-55B7-A7FD-67F69D994358","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "855BD8A2-3578-60DB-C765-483583A8AFCC",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 24835,
"sleepWakeUUID" : "43FB8199-5FBC-4B8A-BF5B-834002DB6AA1",
"sip" : "enabled",
"vmRegionInfo" : "0x168 is not in any region. Bytes before following region: 4307123864\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100b98000-100b9c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000168","rawCodes":[1,360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000168"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":62621},
"vmregioninfo" : "0x168 is not in any region. Bytes before following region: 4307123864\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100b98000-100b9c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/hhokamoto/Downloads/cryosparc_P67_J415_class_03_00186_volume_sharp.mrc
Opened cryosparc_P67_J415_class_03_00186_volume_sharp.mrc as #1, grid size
480,480,480, pixel 0.819, shown at level 0.0702, step 2, values float32
> volume #1 level 0.0522
> open
> /Users/hhokamoto/Downloads/cryosparc_P67_J415_class_03_00187_volume_sharp.mrc
Opened cryosparc_P67_J415_class_03_00187_volume_sharp.mrc as #2, grid size
480,480,480, pixel 0.819, shown at level 0.0703, step 2, values float32
> lighting simple
> set bgColor white
> lighting soft
> volume #2 level 0.1726
> close #1
> close #2
> open /Users/hhokamoto/Downloads/cryosparc_P67_J407_004_volume_map.mrc
> /Users/hhokamoto/Downloads/cryosparc_P67_J413_002_volume_map_sharp.mrc
Opened cryosparc_P67_J407_004_volume_map.mrc as #1.1, grid size 480,480,480,
pixel 0.819, shown at level 0.0802, step 2, values float32
Opened cryosparc_P67_J413_002_volume_map_sharp.mrc as #1.2, grid size
480,480,480, pixel 0.819, shown at level 0.0755, step 2, values float32
> windowsize 1000 1000
> volume #1.1 level 0.219
> volume #1.1 level 0.1762
> volume #1.2 level 0.2222
> volume #1.2 level 0.2521
> volume #1.2 level 0.1533
> hide #!1.2 models
> close #1.2
> open "/Users/hhokamoto/Downloads/cryosparc_P67_J407_004_volume_map_sharp
> (1).mrc"
Opened cryosparc_P67_J407_004_volume_map_sharp (1).mrc as #2, grid size
480,480,480, pixel 0.819, shown at level 0.0778, step 2, values float32
Drag select of 2 cryosparc_P67_J407_004_volume_map_sharp (1).mrc
> volume #2 level 0.1995
> hide #!2 models
> show #!2 models
> volume #2 level 0.1547
> open /Users/hhokamoto/Downloads/cryosparc_P67_J414_map_sharp.mrc
Opened cryosparc_P67_J414_map_sharp.mrc as #3, grid size 480,480,480, pixel
0.819, shown at level 0.0824, step 2, values float32
> ui tool show "Side View"
> open pdb:7k65
Summary of feedback from opening 7k65 fetched from pdb
---
notes | Fetching compressed mmCIF 7k65 from http://files.rcsb.org/download/7k65.cif
Fetching CCD Q7G from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/Q7G/Q7G.cif
7k65 title:
Hedgehog receptor Patched (PTCH1) in complex with conformation selective
nanobody TI23 [more info...]
Chain information for 7k65 #4
---
Chain | Description | UniProt
A | Protein patched homolog 1 | PTC1_MOUSE 1-1291
B | nanobody TI23 |
Non-standard residues in 7k65 #4
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Q7G — 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-
glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl
4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
> hide #4/B
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select add #4
8796 atoms, 9038 bonds, 1 pseudobond, 1131 residues, 5 models selected
> select subtract #2
8796 atoms, 9038 bonds, 1 pseudobond, 1131 residues, 3 models selected
> view matrix models #4,1,0,0,20.612,0,1,0,34.563,0,0,1,-11.01
> view matrix models #4,1,0,0,23.646,0,1,0,84.822,0,0,1,34.527
> view matrix models #4,1,0,0,30.247,0,1,0,48.293,0,0,1,78.721
> view matrix models #4,1,0,0,33.295,0,1,0,32.055,0,0,1,93.207
> view matrix models #4,1,0,0,21.343,0,1,0,15.796,0,0,1,124.06
> open
> /Users/hhokamoto/Downloads/cryosparc_P67_J415_class_03_00190_volume_sharp.mrc
Opened cryosparc_P67_J415_class_03_00190_volume_sharp.mrc as #5, grid size
480,480,480, pixel 0.819, shown at level 0.0708, step 2, values float32
> hide #4 target ar
> show #4/A target r
> view matrix models #4,1,0,0,29.995,0,1,0,13.159,0,0,1,126.64
> view matrix models #4,1,0,0,48.927,0,1,0,3.5068,0,0,1,128.72
> graphics silhouettes true width 1
> view matrix models #4,1,0,0,70.665,0,1,0,-14.628,0,0,1,124.65
> view matrix models #4,1,0,0,45.128,0,1,0,17.587,0,0,1,110.91
> view matrix models #4,1,0,0,56.844,0,1,0,17.969,0,0,1,116.41
> volume #2 level 0.2448
> view matrix models #4,1,0,0,57.888,0,1,0,39.719,0,0,1,106.15
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.15314,-0.081951,-0.9848,310.01,-0.97583,0.14469,-0.16378,315.7,0.15591,0.98608,-0.057813,78.29
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.15314,-0.081951,-0.9848,310.93,-0.97583,0.14469,-0.16378,313.71,0.15591,0.98608,-0.057813,66.569
> transparency #2 50
> view matrix models
> #4,0.15314,-0.081951,-0.9848,313.57,-0.97583,0.14469,-0.16378,315.67,0.15591,0.98608,-0.057813,57.642
> view matrix models
> #4,0.15314,-0.081951,-0.9848,315.68,-0.97583,0.14469,-0.16378,315.68,0.15591,0.98608,-0.057813,58.002
> fitmap #4 inMap #2
Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc
(#2) using 8796 atoms
average map value = 0.1558, steps = 448
shifted from previous position = 4.49
rotated from previous position = 42.8 degrees
atoms outside contour = 6829, contour level = 0.24477
Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp
(1).mrc (#2) coordinates:
Matrix rotation and translation
-0.36862113 -0.52443212 -0.76752161 421.46017226
-0.92869643 0.17177853 0.32865647 241.43183594
-0.04051428 0.83394430 -0.55035943 174.37950066
Axis 0.51915673 -0.74696189 -0.41536037
Axis point 266.76554319 0.00000000 96.40552375
Rotation angle (degrees) 150.87983581
Shift along axis -33.96683035
> color #4/a red
> view matrix models
> #4,-0.36862,-0.52443,-0.76752,420.48,-0.9287,0.17178,0.32866,239.27,-0.040514,0.83394,-0.55036,175.95
> volume #2 level 0.1854
> fitmap #4 inMap #2
Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc
(#2) using 8796 atoms
average map value = 0.1558, steps = 88
shifted from previous position = 2.84
rotated from previous position = 0.0203 degrees
atoms outside contour = 5507, contour level = 0.18544
Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp
(1).mrc (#2) coordinates:
Matrix rotation and translation
-0.36847569 -0.52420703 -0.76774517 421.43751213
-0.92876140 0.17173829 0.32849387 241.46820786
-0.04034755 0.83409409 -0.55014464 174.30904219
Axis 0.51917141 -0.74692224 -0.41541331
Axis point 266.76617874 0.00000000 96.40010383
Rotation angle (degrees) 150.86100478
Shift along axis -33.96996388
> fitmap #4 inMap #2
Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc
(#2) using 8796 atoms
average map value = 0.1558, steps = 48
shifted from previous position = 0.0195
rotated from previous position = 0.0126 degrees
atoms outside contour = 5508, contour level = 0.18544
Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp
(1).mrc (#2) coordinates:
Matrix rotation and translation
-0.36857929 -0.52407406 -0.76778622 421.43788404
-0.92871705 0.17168109 0.32864913 241.43403127
-0.04042211 0.83418942 -0.54999461 174.27364805
Axis 0.51912017 -0.74690265 -0.41551255
Axis point 266.75460032 0.00000000 96.37357466
Rotation angle (degrees) 150.86163841
Shift along axis -33.96369953
> fitmap #4 inMap #2
Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc
(#2) using 8796 atoms
average map value = 0.1558, steps = 44
shifted from previous position = 0.00979
rotated from previous position = 0.0556 degrees
atoms outside contour = 5512, contour level = 0.18544
Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp
(1).mrc (#2) coordinates:
Matrix rotation and translation
-0.36894540 -0.52471305 -0.76717371 421.49784766
-0.92855134 0.17177357 0.32906877 241.35283479
-0.04088651 0.83376859 -0.55059808 174.47756509
Axis 0.51909666 -0.74700495 -0.41535800
Axis point 266.76019170 0.00000000 96.39076318
Rotation angle (degrees) 150.91328360
Shift along axis -33.96428918
> fitmap #4 inMap #2
Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc
(#2) using 8796 atoms
average map value = 0.1558, steps = 76
shifted from previous position = 0.00905
rotated from previous position = 0.0399 degrees
atoms outside contour = 5509, contour level = 0.18544
Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp
(1).mrc (#2) coordinates:
Matrix rotation and translation
-0.36860182 -0.52434639 -0.76758945 421.45356097
-0.92870606 0.17176990 0.32863377 241.43676107
-0.04046917 0.83399998 -0.55027837 174.35454845
Axis 0.51914943 -0.74695156 -0.41538806
Axis point 266.76280618 0.00000000 96.40111713
Rotation angle (degrees) 150.87443600
Shift along axis -33.96898890
> view matrix models
> #4,-0.3686,-0.52435,-0.76759,418.65,-0.92871,0.17177,0.32863,234.47,-0.040469,0.834,-0.55028,178.25
> view matrix models
> #4,-0.3686,-0.52435,-0.76759,412.98,-0.92871,0.17177,0.32863,234.28,-0.040469,0.834,-0.55028,173.85
> view matrix models
> #4,-0.3686,-0.52435,-0.76759,413.5,-0.92871,0.17177,0.32863,239.41,-0.040469,0.834,-0.55028,174.95
> fitmap #4 inMap #2
Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc
(#2) using 8796 atoms
average map value = 0.1558, steps = 132
shifted from previous position = 8.23
rotated from previous position = 0.0118 degrees
atoms outside contour = 5505, contour level = 0.18544
Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp
(1).mrc (#2) coordinates:
Matrix rotation and translation
-0.36851605 -0.52421767 -0.76771854 421.44101994
-0.92874464 0.17175326 0.32853344 241.45561337
-0.04036487 0.83408432 -0.55015818 174.31320956
Axis 0.51915797 -0.74693066 -0.41541496
Axis point 266.76221477 0.00000000 96.39944300
Rotation angle (degrees) 150.86329476
Shift along axis -33.96845107
> volume #2 level 0.214
> transparency #2 70
> transparency #2 20
> view matrix models
> #4,-0.36852,-0.52422,-0.76772,419.02,-0.92874,0.17175,0.32853,238.38,-0.040365,0.83408,-0.55016,176.4
> fitmap #4 inMap #2
Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc
(#2) using 8796 atoms
average map value = 0.1558, steps = 88
shifted from previous position = 4.44
rotated from previous position = 0.0132 degrees
atoms outside contour = 6206, contour level = 0.21401
Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp
(1).mrc (#2) coordinates:
Matrix rotation and translation
-0.36860757 -0.52430361 -0.76761591 421.45296020
-0.92869966 0.17167058 0.32870375 241.44144191
-0.04056349 0.83404732 -0.55019966 174.34967800
Axis 0.51915142 -0.74691815 -0.41544564
Axis point 266.76990936 0.00000000 96.38440910
Rotation angle (degrees) 150.87598775
Shift along axis -33.97190649
> save /Users/hhokamoto/Desktop/image45.png supersample 3
> open "/Users/hhokamoto/Downloads/cryosparc_P67_J418_006_volume_map_sharp
> (1).mrc"
Opened cryosparc_P67_J418_006_volume_map_sharp (1).mrc as #6, grid size
480,480,480, pixel 0.819, shown at level 0.087, step 2, values float32
> volume #6 level 0.2602
> transparency #6 20
> fitmap #4 inMap #6
Fit molecule 7k65 (#4) to map cryosparc_P67_J418_006_volume_map_sharp (1).mrc
(#6) using 8796 atoms
average map value = 0.1686, steps = 76
shifted from previous position = 1.61
rotated from previous position = 3.65 degrees
atoms outside contour = 6028, contour level = 0.26016
Position of 7k65 (#4) relative to cryosparc_P67_J418_006_volume_map_sharp
(1).mrc (#6) coordinates:
Matrix rotation and translation
-0.32768508 -0.56593133 -0.75653435 422.94801383
-0.94164438 0.13037470 0.31033578 252.55869210
-0.07699580 0.81407872 -0.57562790 185.28835356
Axis 0.54424839 -0.73417954 -0.40592375
Axis point 276.19374296 0.00000000 96.25571768
Rotation angle (degrees) 152.43285936
Shift along axis -30.44759286
> view matrix models
> #4,-0.32769,-0.56593,-0.75653,420.07,-0.94164,0.13037,0.31034,250.7,-0.076996,0.81408,-0.57563,187.31
> view matrix models
> #4,-0.32769,-0.56593,-0.75653,418.44,-0.94164,0.13037,0.31034,249.87,-0.076996,0.81408,-0.57563,188.01
> fitmap #4 inMap #6
Fit molecule 7k65 (#4) to map cryosparc_P67_J418_006_volume_map_sharp (1).mrc
(#6) using 8796 atoms
average map value = 0.1686, steps = 88
shifted from previous position = 5.91
rotated from previous position = 0.0125 degrees
atoms outside contour = 6027, contour level = 0.26016
Position of 7k65 (#4) relative to cryosparc_P67_J418_006_volume_map_sharp
(1).mrc (#6) coordinates:
Matrix rotation and translation
-0.32778688 -0.56606069 -0.75639345 422.96656831
-0.94160552 0.13045850 0.31041848 252.52375828
-0.07703774 0.81397535 -0.57576845 185.33248924
Axis 0.54422598 -0.73422298 -0.40587521
Axis point 276.18503632 0.00000000 96.27079609
Rotation angle (degrees) 152.44267635
Shift along axis -30.44121398
> save /Users/hhokamoto/Desktop/image46.png supersample 3
> color #4/a yellow
> color #4/a cyan
> transparency #6 70
> view matrix models
> #4,-0.32779,-0.56606,-0.75639,421.59,-0.94161,0.13046,0.31042,250.81,-0.077038,0.81398,-0.57577,186.81
> transparency #6 50
> fitmap #4 inMap #6
Fit molecule 7k65 (#4) to map cryosparc_P67_J418_006_volume_map_sharp (1).mrc
(#6) using 8796 atoms
average map value = 0.1686, steps = 76
shifted from previous position = 2.65
rotated from previous position = 0.0318 degrees
atoms outside contour = 6027, contour level = 0.26016
Position of 7k65 (#4) relative to cryosparc_P67_J418_006_volume_map_sharp
(1).mrc (#6) coordinates:
Matrix rotation and translation
-0.32755428 -0.56572566 -0.75674479 422.93517217
-0.94168803 0.13018469 0.31028311 252.59530661
-0.07701853 0.81425207 -0.57537963 185.24355534
Axis 0.54427969 -0.73409521 -0.40603430
Axis point 276.20912601 0.00000000 96.23515800
Rotation angle (degrees) 152.42115910
Shift along axis -30.44921733
> open /Users/hhokamoto/Downloads/cryosparc_P67_J423_003_volume_map_sharp.mrc
Opened cryosparc_P67_J423_003_volume_map_sharp.mrc as #7, grid size
480,480,480, pixel 0.819, shown at level 0.0752, step 2, values float32
> hide #!4 models
> select subtract #4
Nothing selected
> hide #!6 models
> volume #7 level 0.2145
> volume #7 level 0.168
> open /Users/hhokamoto/Downloads/cryosparc_P67_J424_map.mrc
Opened cryosparc_P67_J424_map.mrc as #8, grid size 480,480,480, pixel 0.819,
shown at level 0.0802, step 2, values float32
> show #!4 models
> select add #4
8796 atoms, 9038 bonds, 1 pseudobond, 1131 residues, 3 models selected
> volume #8 style mesh
> volume #8
> volume #8 style surface
> view matrix models
> #4,-0.32755,-0.56573,-0.75674,418.79,-0.94169,0.13018,0.31028,239.51,-0.077019,0.81425,-0.57538,146.67
> view matrix models
> #4,-0.32755,-0.56573,-0.75674,391.28,-0.94169,0.13018,0.31028,298.6,-0.077019,0.81425,-0.57538,99.312
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.11759,-0.67914,-0.72453,377.91,0.94475,-0.30129,0.12909,151.99,-0.30597,-0.66932,0.67705,186.33
> view matrix models
> #4,-0.62469,-0.18511,0.75861,165.55,0.18168,-0.97929,-0.089355,381.41,0.75944,0.082002,0.64539,-58.565
> view matrix models
> #4,-0.672,-0.3325,0.66171,207.19,0.16584,-0.93841,-0.30312,406.02,0.72175,-0.093961,0.68575,-32.301
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.672,-0.3325,0.66171,233.74,0.16584,-0.93841,-0.30312,366.37,0.72175,-0.093961,0.68575,7.7846
> view matrix models
> #4,-0.672,-0.3325,0.66171,242.95,0.16584,-0.93841,-0.30312,355.78,0.72175,-0.093961,0.68575,5.7838
> ui tool show "Selection Inspector"
> fitmap #4 inMap #8
Fit molecule 7k65 (#4) to map cryosparc_P67_J424_map.mrc (#8) using 8796 atoms
average map value = 0.1749, steps = 124
shifted from previous position = 2.3
rotated from previous position = 8.25 degrees
atoms outside contour = 1772, contour level = 0.08023
Position of 7k65 (#4) relative to cryosparc_P67_J424_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.56741469 -0.31893831 0.75915673 212.91070558
0.14417348 -0.94618067 -0.28975190 358.54016586
0.81071240 -0.05495922 0.58285925 2.67107640
Axis 0.44998096 -0.09880661 0.88755529
Axis point 78.50261282 193.22888080 0.00000000
Rotation angle (degrees) 164.87701510
Shift along axis 62.75035483
> transparency #8 50
> volume #8 level 0.1314
> view matrix models
> #4,-0.56741,-0.31894,0.75916,216.69,0.14417,-0.94618,-0.28975,361.8,0.81071,-0.054959,0.58286,3.7942
> fitmap #4 inMap #8
Fit molecule 7k65 (#4) to map cryosparc_P67_J424_map.mrc (#8) using 8796 atoms
average map value = 0.1749, steps = 104
shifted from previous position = 5.11
rotated from previous position = 0.0116 degrees
atoms outside contour = 3178, contour level = 0.13138
Position of 7k65 (#4) relative to cryosparc_P67_J424_map.mrc (#8) coordinates:
Matrix rotation and translation
-0.56744258 -0.31890643 0.75914928 212.91233669
0.14431604 -0.94620176 -0.28961202 358.50789722
0.81066751 -0.05478078 0.58293848 2.64993439
Axis 0.44995837 -0.09871370 0.88757708
Axis point 78.50619786 193.21392212 -0.00000000
Rotation angle (degrees) 164.87369499
Shift along axis 62.76406836
> volume #8 level 0.2002
> volume #8 level 0.1561
> volume #8 level 0.1684
> save /Users/hhokamoto/Desktop/image47.png supersample 3
> volume #8 level 0.2072
> volume #8 level 0.1614
> save /Users/hhokamoto/Desktop/image48.png supersample 3
> rotate 180
Unknown command: rotate 180
> turn x 180
> turn y 180
> save /Users/hhokamoto/Desktop/image49.png supersample 3
> open /Users/hhokamoto/Downloads/cryosparc_P67_J425_003_volume_map_sharp.mrc
Opened cryosparc_P67_J425_003_volume_map_sharp.mrc as #9, grid size
480,480,480, pixel 0.819, shown at level 0.0777, step 2, values float32
> volume #9 level 0.2198
> save /Users/hhokamoto/Downloads/2025-03-04_Hiro_2in1-Krios.cxs includeMaps
> true
> save /Users/hhokamoto/Downloads/250304.cxs includeMaps true
> close #1.1
> close #2
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> hide #1 models
> show #1 models
> close #1
> close #3
> close #5
> close #6
> close #7
> close #9
> save /Users/hhokamoto/Downloads/250304.cxs includeMaps true
> hide #!4 models
> hide #!8 models
> close #8
> close #4
> open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
> Mapping/smo_mtr_1.defattr format defattr
Summary of feedback from opening
/Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
Mapping/smo_mtr_1.defattr
---
note | Assigned attribute 'mtr' to 0 residues using match mode: any
> open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
> Mapping/smo_mtr_1.defattr format defattr
Summary of feedback from opening
/Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
Mapping/smo_mtr_1.defattr
---
note | Assigned attribute 'mtr' to 0 residues using match mode: any
> open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
> Mapping/smo_mtr_1.defattr format defattr
Summary of feedback from opening
/Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
Mapping/smo_mtr_1.defattr
---
note | Assigned attribute 'mtr' to 0 residues using match mode: any
> open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
> Mapping/smo_mtr_1.defattr format defattr
Summary of feedback from opening
/Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
Mapping/smo_mtr_1.defattr
---
note | Assigned attribute 'mtr' to 0 residues using match mode: any
> open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-
> PTCH1/AF3/fold_smo_ptch1b/fold_smo_ptch1b_model_4.cif
Chain information for fold_smo_ptch1b_model_4.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> lighting soft
> open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
> Mapping/smo_mtr_1.defattr /Users/hhokamoto/Library/CloudStorage/OneDrive-
> UCSF/SMO-PTCH1/Variants-Mapping/ptch1_mtr_1.defattr
Summary of feedback from opening
/Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
Mapping/smo_mtr_1.defattr
---
note | Assigned attribute 'mtr' to 632 residues using match mode: any
Summary of feedback from opening
/Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
Mapping/ptch1_mtr_1.defattr
---
note | Assigned attribute 'mtr' to 1266 residues using match mode: any
> color #1 by attribute
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1 byattribute
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color byattribute
Missing or invalid "attrName" argument: Expected a text string
> color byattribute mtr palette red:yellow:green
14895 atoms, 1900 residues, atom mtr range 0.596 to 1.17
> save /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants-
> Mapping/Generon_color_byattribute_mtr_palette_red:yellow:green.cxs
> save /Users/hhokamoto/Desktop/image50.png supersample 3
> open /Users/hhokamoto/Downloads/cryosparc_P67_J425_006_volume_map_sharp.mrc
Opened cryosparc_P67_J425_006_volume_map_sharp.mrc as #2, grid size
480,480,480, pixel 0.819, shown at level 0.0779, step 2, values float32
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> volume #2 level 0.2306
> volume #2 level 0.1853
> ui mousemode right "translate selected models"
> select add #1
14895 atoms, 15281 bonds, 1900 residues, 1 model selected
> view matrix models #1,1,0,0,1.5457,0,1,0,5.1242,0,0,1,4.8305
> view matrix models #1,1,0,0,61.819,0,1,0,206.37,0,0,1,220.08
> view matrix models #1,1,0,0,90.361,0,1,0,187.27,0,0,1,229.95
> view matrix models #1,1,0,0,85.947,0,1,0,167.79,0,0,1,181.59
> view matrix models #1,1,0,0,178.44,0,1,0,159.78,0,0,1,221.03
> view matrix models #1,1,0,0,169.22,0,1,0,161.68,0,0,1,218.16
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.17871,0.34169,-0.92266,193.82,0.18072,0.93321,0.31059,155.68,0.96716,-0.11124,-0.22852,224.22
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.17871,0.34169,-0.92266,194.86,0.18072,0.93321,0.31059,196.23,0.96716,-0.11124,-0.22852,191.83
> fitmap #1 inMap #2
Fit molecule fold_smo_ptch1b_model_4.cif (#1) to map
cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) using 14895 atoms
average map value = 0.1377, steps = 272
shifted from previous position = 3.88
rotated from previous position = 18.8 degrees
atoms outside contour = 9925, contour level = 0.18526
Position of fold_smo_ptch1b_model_4.cif (#1) relative to
cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.00639741 0.11184534 -0.99370503 193.84570252
0.02342669 0.99346940 0.11166800 193.80140545
0.99970509 -0.02256483 -0.00897580 193.99111741
Axis -0.06712044 -0.99676484 -0.04421198
Axis point -1.14163012 0.00000000 181.72364887
Rotation angle (degrees) 90.62751041
Shift along axis -214.76216753
> volume #2 level 0.2163
> select subtract #1
Nothing selected
> transparency #2 20
> fitmap #1 inMap #2
Fit molecule fold_smo_ptch1b_model_4.cif (#1) to map
cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) using 14895 atoms
average map value = 0.1377, steps = 24
shifted from previous position = 0.00534
rotated from previous position = 0.00559 degrees
atoms outside contour = 10984, contour level = 0.21628
Position of fold_smo_ptch1b_model_4.cif (#1) relative to
cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.00644873 0.11188558 -0.99370017 193.84555061
0.02335451 0.99346663 0.11170772 193.79745453
0.99970645 -0.02248701 -0.00901963 193.98752207
Axis -0.06710142 -0.99676363 -0.04426821
Axis point -1.12752304 0.00000000 181.71407165
Rotation angle (degrees) 90.63031569
Shift along axis -214.76504671
> surface dust #2 size 8.19
> volume #2 level 0.1876
> fitmap #1 inMap #2
Fit molecule fold_smo_ptch1b_model_4.cif (#1) to map
cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) using 14895 atoms
average map value = 0.1377, steps = 24
shifted from previous position = 0.00398
rotated from previous position = 0.00362 degrees
atoms outside contour = 9999, contour level = 0.18764
Position of fold_smo_ptch1b_model_4.cif (#1) relative to
cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.00647074 0.11186222 -0.99370266 193.84906215
0.02330000 0.99347054 0.11168436 193.79570991
0.99970758 -0.02243059 -0.00903488 193.98660209
Axis -0.06706155 -0.99676562 -0.04428380
Axis point -1.11812123 0.00000000 181.71666739
Rotation angle (degrees) 90.63127131
Shift along axis -214.75918181
> hide #!2 models
> show #1/A:367 atoms
===== 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 - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,3
Model Number: Z1C80001DLL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 2 days, 18 hours, 18 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LG HDR WQHD:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 100.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 8 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 , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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