![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 23 months ago
Closed 23 months ago
#10430 closed defect (nonchimerax)
Graphics crash, macOS 14.2.1, Radeon Pro 580X
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff846636b80 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio (total: 52)
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{
"uptime" : 460000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMac19,1",
"coalitionID" : 2200,
"osVersion" : {
"train" : "macOS 14.2.1",
"build" : "23C71",
"releaseType" : "User"
},
"captureTime" : "2024-01-04 19:57:37.4379 -0800",
"codeSigningMonitor" : 0,
"incident" : "6E1D0995-A3FA-4208-B746-F2927979090D",
"pid" : 2221,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-12-30 11:32:31.8186 -0800",
"procStartAbsTime" : 1142258543911,
"procExitAbsTime" : 463431995629268,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"704DEA82-91EA-5FB4-B10E-780E94F1EBE8","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "35E0750B-3B07-7A66-FE22-DC6C1F8D560E",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":2221},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics kernel error: 0x1bcf85f9\n"],
"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,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/donghuachen/Downloads/PIC34_2Gamma/job145_run_it054_class005.mrc
> /Users/donghuachen/Downloads/PIC34_2Gamma/job145_run_it054_class006.mrc
Opened job145_run_it054_class005.mrc as #1.1, grid size 288,288,288, pixel
1.4, shown at level 0.0128, step 2, values float32
Opened job145_run_it054_class006.mrc as #1.2, grid size 288,288,288, pixel
1.4, shown at level 0.0119, step 2, values float32
> hide #!1.1 models
> hide #!1.2 models
> show #!1.1 models
> volume #1.1 step 1
> volume #1.1 level 0.02391
> volume #1.2 step 1
> volume #1.2 level 0.0331
> volume #1.1 level 0.03838
> open /Users/donghuachen/Downloads/PIC34_2Gamma/job142_run_it060_class002.mrc
> /Users/donghuachen/Downloads/PIC34_2Gamma/job142_run_it060_class003.mrc
Opened job142_run_it060_class002.mrc as #2.1, grid size 288,288,288, pixel
1.4, shown at level 0.0129, step 2, values float32
Opened job142_run_it060_class003.mrc as #2.2, grid size 288,288,288, pixel
1.4, shown at level 0.0121, step 2, values float32
> volume #2.1 step 1
> volume #2.1 level 0.03006
> volume #2.1 level 0.02607
> volume #2.1 level 0.03205
> volume #2.1 level 0.0313
> fitmap #1.1 inMap #2.1
Fit map job145_run_it054_class005.mrc in map job142_run_it060_class002.mrc
using 11369 points
correlation = 0.9981, correlation about mean = 0.893, overlap = 19.54
steps = 88, shift = 8.47, angle = 3.18 degrees
Position of job145_run_it054_class005.mrc (#1.1) relative to
job142_run_it060_class002.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99851668 0.05398373 -0.00708443 -16.22327236
-0.05390650 0.99848895 0.01067305 5.02532244
0.00764990 -0.01027533 0.99991794 1.50344818
Axis -0.18891409 -0.13287531 -0.97296229
Axis point 87.12643935 299.64608148 0.00000000
Rotation angle (degrees) 3.17834849
Shift along axis 0.93426507
> volume #2.1 level 0.03399
> show #!2.2 models
> hide #!2.1 models
> volume #2.2 step 1
> volume #2.2 level 0.02404
> open /Users/donghuachen/Downloads/PIC34_2Gamma/job143_run_it060_class001.mrc
> /Users/donghuachen/Downloads/PIC34_2Gamma/job143_run_it060_class002.mrc
> /Users/donghuachen/Downloads/PIC34_2Gamma/job143_run_it060_class003.mrc
> /Users/donghuachen/Downloads/PIC34_2Gamma/job143_run_it060_class004.mrc
> /Users/donghuachen/Downloads/PIC34_2Gamma/job143_run_it060_class005.mrc
> /Users/donghuachen/Downloads/PIC34_2Gamma/job143_run_it060_class006.mrc
Opened job143_run_it060_class001.mrc as #3.1, grid size 288,288,288, pixel
1.4, shown at level 0.0181, step 2, values float32
Opened job143_run_it060_class002.mrc as #3.2, grid size 288,288,288, pixel
1.4, shown at level 0.0188, step 2, values float32
Opened job143_run_it060_class003.mrc as #3.3, grid size 288,288,288, pixel
1.4, shown at level 0.0197, step 2, values float32
Opened job143_run_it060_class004.mrc as #3.4, grid size 288,288,288, pixel
1.4, shown at level 0.0155, step 2, values float32
Opened job143_run_it060_class005.mrc as #3.5, grid size 288,288,288, pixel
1.4, shown at level 0.00306, step 2, values float32
Opened job143_run_it060_class006.mrc as #3.6, grid size 288,288,288, pixel
1.4, shown at level 0.0161, step 2, values float32
> volume #3.1 level 0.02555
> volume #3.2 level 0.02303
> volume #3.3 level 0.03111
> volume #3.3 level 0.0234
> volume #3.4 level 0.01891
> volume #3.5 level 0.003604
> volume #3.6 level 0.02164
> open /Users/donghuachen/Downloads/PIC34_2Gamma/J143_006_volume_map_sharp.mrc
Opened J143_006_volume_map_sharp.mrc as #4, grid size 288,288,288, pixel 1.4,
shown at level 0.223, step 2, values float32
> volume #4 step 1
> volume #4 level 0.7356
> volume #4 level 0.8638
> close #4
> open
> /Users/donghuachen/Downloads/PIC34_2Gamma/J143_006_volume_map_sharp_3A.mrc
> /Users/donghuachen/Downloads/PIC34_2Gamma/J143_006_volume_map.mrc
Opened J143_006_volume_map_sharp_3A.mrc as #4.1, grid size 288,288,288, pixel
1.4, shown at level 0.223, step 2, values float32
Opened J143_006_volume_map.mrc as #4.2, grid size 288,288,288, pixel 1.4,
shown at level 0.209, step 2, values float32
> volume #4.2 step 1
> volume #4.2 level 0.6212
> volume #4.2 level 0.5169
> volume #4.1 step 1
> volume #4.1 level 0.6203
> volume #4.1 level 1.415
> volume #4.1 level 0.7228
> volume #4.1 level 0.8894
> volume #4.1 level 0.364
> volume #4.2 level 0.6212
> close #1
> open /Users/donghuachen/Downloads/PIC34_2Gamma/job145_run_it060_class005.mrc
Opened job145_run_it060_class005.mrc as #1, grid size 288,288,288, pixel 1.4,
shown at level 0.0129, step 2, values float32
> volume #4.2 level 0.2449
> volume #4.2 level 0.2132
> volume #4.2 level 0.1
> volume #4.2 level 0.2
> volume #4.2 level 0.1
> volume #4.2 level 0.15
> open /Users/donghuachen/Downloads/PIC34_2Gamma/cryosparc_P21_J162_mask.mrc
Opened cryosparc_P21_J162_mask.mrc as #5, grid size 288,288,288, pixel 1.4,
shown at level 1, step 2, values float32
> volume #5 level 1
> volume #5 step 1
> open
> /Users/donghuachen/Downloads/PICSAGA/J132_class_00_00262_volume_sharp.mrc
> /Users/donghuachen/Downloads/PICSAGA/J132_class_01_00262_volume_sharp.mrc
> /Users/donghuachen/Downloads/PICSAGA/J132_class_02_00262_volume_sharp.mrc
> /Users/donghuachen/Downloads/PICSAGA/J132_class_03_00262_volume_sharp.mrc
> /Users/donghuachen/Downloads/PICSAGA/J132_class_04_00262_volume_sharp.mrc
> /Users/donghuachen/Downloads/PICSAGA/J132_class_05_00262_volume_sharp.mrc
Opened J132_class_00_00262_volume_sharp.mrc as #6.1, grid size 160,160,160,
pixel 5.6, shown at level 1.43, step 1, values float32
Opened J132_class_01_00262_volume_sharp.mrc as #6.2, grid size 160,160,160,
pixel 5.6, shown at level 1.18, step 1, values float32
Opened J132_class_02_00262_volume_sharp.mrc as #6.3, grid size 160,160,160,
pixel 5.6, shown at level 1.05, step 1, values float32
Opened J132_class_03_00262_volume_sharp.mrc as #6.4, grid size 160,160,160,
pixel 5.6, shown at level 1.39, step 1, values float32
Opened J132_class_04_00262_volume_sharp.mrc as #6.5, grid size 160,160,160,
pixel 5.6, shown at level 1.24, step 1, values float32
Opened J132_class_05_00262_volume_sharp.mrc as #6.6, grid size 160,160,160,
pixel 5.6, shown at level 1.22, step 1, values float32
> volume #6.1 level 1.107
> volume #6.2 level 1.065
> volume #6.2 level 1.315
> volume #6.1 level 1.448
> volume #6.2 level 1.775
> volume #6.2 level 1.454
> volume #6.3 level 1.265
> volume #6.3 level 1.206
> volume #6.1 level 1.429
> volume #6.6 level 1.104
> volume #6.6 level 1.315
> volume #6.6 level 1.048
> volume #6.6 level 1.469
> volume #6.6 level 1.343
> volume #6.6 level 1.903
> volume #6.6 level 1.553
> volume #6.5 level 1.243
> volume #6.6 level 1.09
> volume #6.6 level 1.147
> volume #6.6 level 1.427
> volume #4.1 level 0.7741
> close #6
> open
> /Users/donghuachen/Downloads/PIC34_2Gamma/J154_005_volume_map_sharp_3A.mrc
Opened J154_005_volume_map_sharp_3A.mrc as #6, grid size 288,288,288, pixel
1.4, shown at level 0.22, step 2, values float32
> volume #6 color #0dff88
> volume #6 step 1
> volume #6 level 0.8003
> volume #6 level 2.281
> volume #4.1 level 2.517
> volume #4.1 level 1.812
> volume #4.1 level 0.9022
> volume #6 level 1.037
> fitmap #4.1 inMap #6
Fit map J143_006_volume_map_sharp_3A.mrc in map
J154_005_volume_map_sharp_3A.mrc using 27451 points
correlation = 0.9848, correlation about mean = 0.8485, overlap = 4.852e+04
steps = 80, shift = 8.65, angle = 2.71 degrees
Position of J143_006_volume_map_sharp_3A.mrc (#4.1) relative to
J154_005_volume_map_sharp_3A.mrc (#6) coordinates:
Matrix rotation and translation
0.99892416 -0.04630708 0.00248580 16.01124358
0.04632799 0.99888445 -0.00914170 -2.90051969
-0.00205971 0.00924703 0.99995512 -2.36541190
Axis 0.19448286 0.04807424 0.97972715
Axis point 71.50943572 341.34159638 0.00000000
Rotation angle (degrees) 2.70972261
Shift along axis 0.65701387
> volume #6 level 0.8713
> open 7c4j
7c4j title:
Cryo-EM structure of the yeast Swi/Snf complex in a nucleosome free state
[more info...]
Chain information for 7c4j #7
---
Chain | Description | UniProt
A | Transcription regulatory protein SNF12 | SNF12_YEAST 1-566
B D | SWI/SNF complex subunit SWI3 | SWI3_YEAST 1-825
C | Transcription regulatory protein SNF6 | SNF6_YEAST 1-332
E | SWI/SNF global transcription activator complex subunit SWP82 | SWP82_YEAST
1-623
F | SWI/SNF chromatin-remodeling complex subunit SNF5 | SNF5_YEAST 1-905
G | Unkown |
H | Transcription regulatory protein SNF2 | SNF2_YEAST 1-1703
I | SWI/SNF chromatin-remodeling complex subunit SWI1 | SWI1_YEAST 1-1314
J | Regulator of Ty1 transposition protein 102 | RT102_YEAST 1-157
K | Actin-related protein 7 | ARP7_YEAST 1-477
L | Actin-like protein ARP9 | ARP9_YEAST 1-467
> show cartoons
> show atoms
> show cartoons
> style stick
Changed 29730 atom styles
> style stick
Changed 29730 atom styles
> style ball
Changed 29730 atom styles
> style ball
Changed 29730 atom styles
> style stick
Changed 29730 atom styles
> hide atoms
> rainbow
> ui mousemode right "translate selected models"
> ui mousemode right "move picked models"
> view matrix models #7,1,0,0,7.4573,0,1,0,-2.4801,0,0,1,19.146
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select /E:25
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /E:27
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 34 residues
> select clear
> select /D:462
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right "rotate selected models"
> hide #!4.1 models
Drag select of 3660 residues, 56 pseudobonds
> show #!4.1 models
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.40593,0.4624,-0.7883,169.14,0.66087,0.44727,0.60267,-127.99,0.63125,-0.7656,-0.12402,236.08
> view matrix models
> #7,0.041595,0.84696,-0.53002,121.76,-0.26434,0.5209,0.81165,-21.535,0.96353,0.10635,0.24556,-27.788
> ui mousemode right "move picked models"
> view matrix models
> #7,0.041595,0.84696,-0.53002,152.02,-0.26434,0.5209,0.81165,25.068,0.96353,0.10635,0.24556,-13.61
> view matrix models
> #4.1,0.99892,-0.046307,0.0024858,17.228,0.046328,0.99888,-0.0091417,-0.014273,-0.0020597,0.009247,0.99996,-2.4413
> view matrix models
> #7,0.041595,0.84696,-0.53002,151.38,-0.26434,0.5209,0.81165,12.694,0.96353,0.10635,0.24556,-6.6404
> view matrix models
> #7,0.041595,0.84696,-0.53002,156.7,-0.26434,0.5209,0.81165,23.948,0.96353,0.10635,0.24556,-6.11
> view matrix models
> #7,0.041595,0.84696,-0.53002,167.18,-0.26434,0.5209,0.81165,52.045,0.96353,0.10635,0.24556,-8.8308
> fitmap #7 inMap #4.1
Fit molecule 7c4j (#7) to map J143_006_volume_map_sharp_3A.mrc (#4.1) using
29730 atoms
average map value = 0.2182, steps = 120
shifted from previous position = 9.1
rotated from previous position = 5.3 degrees
atoms outside contour = 28006, contour level = 0.90225
Position of 7c4j (#7) relative to J143_006_volume_map_sharp_3A.mrc (#4.1)
coordinates:
Matrix rotation and translation
0.04913786 0.88095659 -0.47063889 139.94673941
-0.17329072 0.47158129 0.86462790 21.78106153
0.98364414 0.03907139 0.17583410 6.51066448
Axis -0.41761296 -0.73565823 -0.53329764
Axis point 84.23799896 0.00000000 58.00547408
Rotation angle (degrees) 98.72681201
Shift along axis -77.93911167
> fitmap #7 inMap #4.1
Fit molecule 7c4j (#7) to map J143_006_volume_map_sharp_3A.mrc (#4.1) using
29730 atoms
average map value = 0.2182, steps = 44
shifted from previous position = 0.00522
rotated from previous position = 0.00176 degrees
atoms outside contour = 28009, contour level = 0.90225
Position of 7c4j (#7) relative to J143_006_volume_map_sharp_3A.mrc (#4.1)
coordinates:
Matrix rotation and translation
0.04912292 0.88094570 -0.47066083 139.95542440
-0.17330063 0.47159982 0.86461581 21.77856600
0.98364314 0.03909337 0.17583481 6.51120220
Axis -0.41759559 -0.73566858 -0.53329697
Axis point 84.24276573 0.00000000 58.01191299
Rotation angle (degrees) 98.72668727
Shift along axis -77.93897926
> view matrix models
> #4.1,0.99892,-0.046307,0.0024858,23.166,0.046328,0.99888,-0.0091417,9.4979,-0.0020597,0.009247,0.99996,-6.3028
> view matrix models
> #7,0.05954,0.85826,-0.50976,144.58,-0.17982,0.51153,0.84024,12.822,0.9819,0.041638,0.18479,-3.1883
> view matrix models
> #7,0.05954,0.85826,-0.50976,144.4,-0.17982,0.51153,0.84024,13.426,0.9819,0.041638,0.18479,-4.7337
> fitmap #7 inMap #4.1
Fit molecule 7c4j (#7) to map J143_006_volume_map_sharp_3A.mrc (#4.1) using
29730 atoms
average map value = 0.5404, steps = 172
shifted from previous position = 15.5
rotated from previous position = 18.2 degrees
atoms outside contour = 23092, contour level = 0.90225
Position of 7c4j (#7) relative to J143_006_volume_map_sharp_3A.mrc (#4.1)
coordinates:
Matrix rotation and translation
0.21448301 0.85081764 -0.47969405 105.68554164
0.09549040 0.47050493 0.87721531 -37.55522446
0.97204867 -0.23395396 0.01967040 86.14908944
Axis -0.56174327 -0.73391762 -0.38185001
Axis point 31.14173024 0.00000000 93.55425966
Rotation angle (degrees) 98.49197190
Shift along axis -64.70173145
> fitmap #7 inMap #4.1
Fit molecule 7c4j (#7) to map J143_006_volume_map_sharp_3A.mrc (#4.1) using
29730 atoms
average map value = 0.5403, steps = 28
shifted from previous position = 0.032
rotated from previous position = 0.0159 degrees
atoms outside contour = 23083, contour level = 0.90225
Position of 7c4j (#7) relative to J143_006_volume_map_sharp_3A.mrc (#4.1)
coordinates:
Matrix rotation and translation
0.21434033 0.85072877 -0.47991539 105.73385564
0.09553427 0.47071960 0.87709535 -37.56661990
0.97207583 -0.23384527 0.01962044 86.14668787
Axis -0.56162675 -0.73404203 -0.38178227
Axis point 31.16826072 0.00000000 93.58061761
Rotation angle (degrees) 98.49133364
Shift along axis -64.69676143
> volume #4.1 color #ffffb2c2
> volume #4.1 color #ffffb2cc
> select clear
> save /Users/donghuachen/Desktop/image1.png supersample 3
> hide #!7 models
> save /Users/donghuachen/Desktop/image1.png supersample 3
> volume #1 step 1
> volume #1 level 0.0224
> volume #2.1 level 0.0243
> fitmap #2.1 inMap #1
Fit map job142_run_it060_class002.mrc in map job145_run_it060_class005.mrc
using 43377 points
correlation = 0.9974, correlation about mean = 0.9377, overlap = 47.22
steps = 84, shift = 8.74, angle = 2.84 degrees
Position of job142_run_it060_class002.mrc (#2.1) relative to
job145_run_it060_class005.mrc (#1) coordinates:
Matrix rotation and translation
0.99881072 -0.04860978 0.00377315 16.24813062
0.04864234 0.99877498 -0.00908063 -3.30283228
-0.00332712 0.00925337 0.99995165 -2.16913366
Axis 0.18478206 0.07156124 0.98017069
Axis point 77.15092317 329.93644976 0.00000000
Rotation angle (degrees) 2.84359857
Shift along axis 0.63988705
> volume #2.1 level 0.02245
> volume #1 level 0.02427
> open /Users/donghuachen/Downloads/PIC34_2Gamma/job153_run_it016_class001.mrc
> /Users/donghuachen/Downloads/PIC34_2Gamma/job153_run_it016_class002.mrc
> /Users/donghuachen/Downloads/PIC34_2Gamma/job153_run_it016_class003.mrc
> /Users/donghuachen/Downloads/PIC34_2Gamma/job153_run_it016_class004.mrc
Opened job153_run_it016_class001.mrc as #8.1, grid size 288,288,288, pixel
1.4, shown at level 0.00703, step 2, values float32
Opened job153_run_it016_class002.mrc as #8.2, grid size 288,288,288, pixel
1.4, shown at level 0.0052, step 2, values float32
Opened job153_run_it016_class003.mrc as #8.3, grid size 288,288,288, pixel
1.4, shown at level 0.00879, step 2, values float32
Opened job153_run_it016_class004.mrc as #8.4, grid size 288,288,288, pixel
1.4, shown at level 0.00917, step 2, values float32
> hide #!2.1 models
> volume #8.1 step 1
> volume #8.1 level 0.01726
> volume #8.1 level 0.01465
> volume #8.2 step 1
> volume #8.2 level 0.009575
> volume #8.3 step 1
> volume #8.3 level 0.0191
> volume #8.4 step 1
> volume #8.4 level 0.01745
> open
> /Users/donghuachen/Downloads/PIC34_2Gamma/run_it016_class001_angdist.bild
> /Users/donghuachen/Downloads/PIC34_2Gamma/run_it016_class002_angdist.bild
> /Users/donghuachen/Downloads/PIC34_2Gamma/run_it016_class003_angdist.bild
> /Users/donghuachen/Downloads/PIC34_2Gamma/run_it016_class004_angdist.bild
Opened BILD data containing 191 objects
Opened BILD data containing 192 objects
Opened BILD data containing 192 objects
Opened BILD data containing 192 objects
> hide #12 models
> hide #11 models
> hide #10 models
> hide #9 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #11 models
> show #12 models
> hide #11 models
> hide #12 models
> show #12 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #12 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> volume #8.4 level 0.01604
> volume #8.4 level 0.01846
> volume #8.4 level 0.04046
> volume #8.4 level 0.01543
> volume #8.3 level 0.0178
> volume #8.2 level 0.02886
> volume #8.2 level 0.01043
> fitmap #8.3 inMap #8.4
Fit map job153_run_it016_class003.mrc in map job153_run_it016_class004.mrc
using 52993 points
correlation = 0.9934, correlation about mean = 0.8802, overlap = 30.28
steps = 84, shift = 1.02, angle = 4.78 degrees
Position of job153_run_it016_class003.mrc (#8.3) relative to
job153_run_it016_class004.mrc (#8.4) coordinates:
Matrix rotation and translation
0.99690881 -0.04961799 0.06091692 -2.02761202
0.05128304 0.99834357 -0.02608002 -4.78347134
-0.05952197 0.02912341 0.99780207 6.53497635
Axis 0.33148214 0.72320391 0.60588423
Axis point 110.14196521 0.00000000 37.93744495
Rotation angle (degrees) 4.77641164
Shift along axis -0.17210326
> open
> /Users/donghuachen/Downloads/PIC34_2Gamma/J184_007_volume_map_sharp_3p3A.mrc
Opened J184_007_volume_map_sharp_3p3A.mrc as #13, grid size 288,288,288, pixel
1.4, shown at level 0.206, step 2, values float32
> volume #13 step 1
> volume #13 level 0.7622
> fitmap #4.1 inMap #13
Fit map J143_006_volume_map_sharp_3A.mrc in map
J184_007_volume_map_sharp_3p3A.mrc using 27451 points
correlation = 0.5455, correlation about mean = 0.03109, overlap = 9980
steps = 176, shift = 1.96, angle = 7.43 degrees
Position of J143_006_volume_map_sharp_3A.mrc (#4.1) relative to
J184_007_volume_map_sharp_3p3A.mrc (#13) coordinates:
Matrix rotation and translation
0.99526381 0.04878524 -0.08408302 24.46704329
-0.04804237 0.99878651 0.01083691 22.07891149
0.08450967 -0.00674603 0.99639982 -17.78521045
Axis -0.09007039 -0.86363311 -0.49600924
Axis point 294.64636227 0.00000000 261.05326035
Rotation angle (degrees) 5.60136785
Shift along axis -12.45020653
> fitmap #4.1 inMap #13
Fit map J143_006_volume_map_sharp_3A.mrc in map
J184_007_volume_map_sharp_3p3A.mrc using 27451 points
correlation = 0.5455, correlation about mean = 0.03111, overlap = 9980
steps = 104, shift = 0.00335, angle = 0.0108 degrees
Position of J143_006_volume_map_sharp_3A.mrc (#4.1) relative to
J184_007_volume_map_sharp_3p3A.mrc (#13) coordinates:
Matrix rotation and translation
0.99525914 0.04883356 -0.08411020 24.46365883
-0.04810560 0.99878536 0.01066118 22.13146115
0.08452866 -0.00656447 0.99639942 -17.82266065
Axis -0.08821151 -0.86358927 -0.49641948
Axis point 294.93105234 0.00000000 261.20000476
Rotation angle (degrees) 5.60319225
Shift along axis -12.42295270
> view matrix models #13,1,0,0,12.399,0,1,0,17.697,0,0,1,-1.9109
> fitmap #4.1 inMap #13
Fit map J143_006_volume_map_sharp_3A.mrc in map
J184_007_volume_map_sharp_3p3A.mrc using 27451 points
correlation = 0.9836, correlation about mean = 0.837, overlap = 4.865e+04
steps = 76, shift = 4.19, angle = 5.59 degrees
Position of J143_006_volume_map_sharp_3A.mrc (#4.1) relative to
J184_007_volume_map_sharp_3p3A.mrc (#13) coordinates:
Matrix rotation and translation
0.99999998 0.00017171 -0.00005090 -0.06288907
-0.00017169 0.99999989 0.00043386 -0.05915087
0.00005097 -0.00043385 0.99999990 0.10383231
Axis -0.92433775 -0.10852371 -0.36581735
Axis point 0.00000000 261.70016798 129.75745374
Rotation angle (degrees) 0.02689273
Shift along axis 0.02656636
> fitmap #4.1 inMap #13
Fit map J143_006_volume_map_sharp_3A.mrc in map
J184_007_volume_map_sharp_3p3A.mrc using 27451 points
correlation = 0.9835, correlation about mean = 0.8358, overlap = 4.83e+04
steps = 36, shift = 0.0241, angle = 0.0125 degrees
Position of J143_006_volume_map_sharp_3A.mrc (#4.1) relative to
J184_007_volume_map_sharp_3p3A.mrc (#13) coordinates:
Matrix rotation and translation
0.99999999 0.00009743 0.00008545 -0.08233659
-0.00009748 0.99999982 0.00058665 -0.09928754
-0.00008540 -0.00058665 0.99999982 0.18140517
Axis -0.97645725 0.14218447 -0.16221844
Axis point 0.00000000 319.35726695 178.27464327
Rotation angle (degrees) 0.03442297
Shift along axis 0.03685375
> fitmap #4.1 inMap #13
Fit map J143_006_volume_map_sharp_3A.mrc in map
J184_007_volume_map_sharp_3p3A.mrc using 27451 points
correlation = 0.9835, correlation about mean = 0.8362, overlap = 4.843e+04
steps = 40, shift = 0.0101, angle = 0.0118 degrees
Position of J143_006_volume_map_sharp_3A.mrc (#4.1) relative to
J184_007_volume_map_sharp_3p3A.mrc (#13) coordinates:
Matrix rotation and translation
0.99999999 0.00014584 -0.00005653 -0.06318836
-0.00014581 0.99999989 0.00044549 -0.05921233
0.00005659 -0.00044548 0.99999990 0.11784076
Axis -0.94353214 -0.11979934 -0.30886115
Axis point 0.00000000 285.51841880 124.83382692
Rotation angle (degrees) 0.02705178
Shift along axis 0.03031742
> hide #!4.1 models
> show #!7 models
> fitmap #7 inMap #13
Fit molecule 7c4j (#7) to map J184_007_volume_map_sharp_3p3A.mrc (#13) using
29730 atoms
average map value = 0.4776, steps = 64
shifted from previous position = 3.58
rotated from previous position = 2.69 degrees
atoms outside contour = 22853, contour level = 0.76216
Position of 7c4j (#7) relative to J184_007_volume_map_sharp_3p3A.mrc (#13)
coordinates:
Matrix rotation and translation
0.21441520 0.85060293 -0.48010497 105.79671417
0.09533735 0.47096400 0.87698558 -37.56765329
0.97207866 -0.23381097 0.01988761 86.14814484
Axis -0.56152908 -0.73410684 -0.38180132
Axis point 31.19393204 0.00000000 93.62256713
Rotation angle (degrees) 98.47434771
Shift along axis -64.72073576
> fitmap #7 inMap #13
Fit molecule 7c4j (#7) to map J184_007_volume_map_sharp_3p3A.mrc (#13) using
29730 atoms
average map value = 0.4776, steps = 44
shifted from previous position = 0.0195
rotated from previous position = 0.0113 degrees
atoms outside contour = 22857, contour level = 0.76216
Position of 7c4j (#7) relative to J184_007_volume_map_sharp_3p3A.mrc (#13)
coordinates:
Matrix rotation and translation
0.21449117 0.85067697 -0.47993982 105.72643440
0.09530437 0.47080327 0.87707546 -37.54871347
0.97206513 -0.23386530 0.01990991 86.16219660
Axis -0.56160463 -0.73401996 -0.38185722
Axis point 31.14501013 0.00000000 93.58800079
Rotation angle (degrees) 98.47615669
Shift along axis -64.71660602
> volume #13 color #b2ffb2cc
> volume #13 color #f8faf6cc
> volume #13 color #fafaf8cc
> volume #13 color #d4fac6cc
> volume #13 color #eefaeccc
> open /Users/donghuachen/Downloads/MedIIDPIC/job041_postprocess_4p55A.mrc
Opened job041_postprocess_4p55A.mrc as #14, grid size 512,512,512, pixel 1.11,
shown at level 0.00586, step 2, values float32
> close #14
> open /Users/donghuachen/Downloads/PIC34_2Gamma/job032_run_it060_class001.mrc
Opened job032_run_it060_class001.mrc as #14, grid size 160,160,160, pixel 2.8,
shown at level 0.0269, step 1, values float32
> volume #13 level 0.7526
> volume #14 level 0.04928
> hide #!7 models
> fitmap #13 inMap #14
Fit map J184_007_volume_map_sharp_3p3A.mrc in map
job032_run_it060_class001.mrc using 28519 points
correlation = 0.9208, correlation about mean = 0.1399, overlap = 1740
steps = 100, shift = 28.2, angle = 1.77 degrees
Position of J184_007_volume_map_sharp_3p3A.mrc (#13) relative to
job032_run_it060_class001.mrc (#14) coordinates:
Matrix rotation and translation
0.99994255 -0.00881667 -0.00609569 24.40334512
0.00898965 0.99954018 0.02895879 17.19820102
0.00583756 -0.02901193 0.99956202 28.18000976
Axis -0.93793540 -0.19307362 0.28809681
Axis point 0.00000000 1157.83811874 -454.88658662
Rotation angle (degrees) 1.77091443
Shift along axis -18.09070913
> volume #14 level 0.06277
> show #!7 models
> fitmap #7 inMap #13
Fit molecule 7c4j (#7) to map J184_007_volume_map_sharp_3p3A.mrc (#13) using
29730 atoms
average map value = 0.2522, steps = 124
shifted from previous position = 18.4
rotated from previous position = 3.29 degrees
atoms outside contour = 27410, contour level = 0.75257
Position of 7c4j (#7) relative to J184_007_volume_map_sharp_3p3A.mrc (#13)
coordinates:
Matrix rotation and translation
0.20648833 0.82963689 -0.51871495 110.84337257
0.09437526 0.51078067 0.85451531 -42.28365683
0.97388700 -0.22540130 0.02717305 75.13490563
Axis -0.54442111 -0.75246921 -0.37066932
Axis point 39.02391771 0.00000000 94.81851054
Rotation angle (degrees) 97.34126664
Shift along axis -56.37852541
> fitmap #7 inMap #13
Fit molecule 7c4j (#7) to map J184_007_volume_map_sharp_3p3A.mrc (#13) using
29730 atoms
average map value = 0.2522, steps = 40
shifted from previous position = 0.0212
rotated from previous position = 0.00953 degrees
atoms outside contour = 27415, contour level = 0.75257
Position of 7c4j (#7) relative to J184_007_volume_map_sharp_3p3A.mrc (#13)
coordinates:
Matrix rotation and translation
0.20641438 0.82971818 -0.51861435 110.84054820
0.09427840 0.51069733 0.85457581 -42.26448804
0.97391205 -0.22529086 0.02719077 75.12376225
Axis -0.54440087 -0.75243795 -0.37076249
Axis point 39.02936445 0.00000000 94.80418759
Rotation angle (degrees) 97.34529801
Shift along axis -56.39335878
> view matrix models
> #13,0.99994,-0.0088167,-0.0060957,23.17,0.0089897,0.99954,0.028959,18.51,0.0058376,-0.029012,0.99956,21.789
> fitmap #7 inMap #13
Fit molecule 7c4j (#7) to map J184_007_volume_map_sharp_3p3A.mrc (#13) using
29730 atoms
average map value = 0.4776, steps = 60
shifted from previous position = 5.94
rotated from previous position = 2.62 degrees
atoms outside contour = 22718, contour level = 0.75257
Position of 7c4j (#7) relative to J184_007_volume_map_sharp_3p3A.mrc (#13)
coordinates:
Matrix rotation and translation
0.21434898 0.85056981 -0.48019321 105.80533598
0.09535053 0.47105041 0.87693773 -37.57090620
0.97209197 -0.23375738 0.01986689 86.14784865
Axis -0.56147783 -0.73415820 -0.38177793
Axis point 31.19741375 0.00000000 93.62844468
Rotation angle (degrees) 98.47436292
Shift along axis -64.71370843
> open
> /Users/donghuachen/Downloads/PIC34_2Gamma/J15_007_volume_map_sharp_3p2A.mrc
Opened J15_007_volume_map_sharp_3p2A.mrc as #15, grid size 320,320,320, pixel
1.4, shown at level 0.226, step 2, values float32
> volume #15 step 1
> volume #15 level 0.8384
> volume #15 color #00d539
> hide #!7 models
> fitmap #13 inMap #15
Fit map J184_007_volume_map_sharp_3p3A.mrc in map
J15_007_volume_map_sharp_3p2A.mrc using 28519 points
correlation = 0.93, correlation about mean = 0.5031, overlap = 3.128e+04
steps = 124, shift = 7.01, angle = 1.89 degrees
Position of J184_007_volume_map_sharp_3p3A.mrc (#13) relative to
J15_007_volume_map_sharp_3p2A.mrc (#15) coordinates:
Matrix rotation and translation
0.99949581 0.01630622 -0.02724394 21.94633165
-0.01559339 0.99953574 0.02617534 20.92884165
0.02765812 -0.02573731 0.99928605 23.33782298
Axis -0.63295194 -0.66940071 -0.38894026
Axis point -325.02622008 0.00000000 -47.53155760
Rotation angle (degrees) 2.35026541
Shift along axis -36.97777366
> show #!7 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> fitmap #7 inMap #13
Fit molecule 7c4j (#7) to map J184_007_volume_map_sharp_3p3A.mrc (#13) using
29730 atoms
average map value = 0.4776, steps = 76
shifted from previous position = 7.57
rotated from previous position = 1.9 degrees
atoms outside contour = 22731, contour level = 0.75257
Position of 7c4j (#7) relative to J184_007_volume_map_sharp_3p3A.mrc (#13)
coordinates:
Matrix rotation and translation
0.21455263 0.85070358 -0.47986517 105.71913491
0.09529147 0.47073070 0.87711581 -37.54771430
0.97205283 -0.23391456 0.01993172 86.16156687
Axis -0.56164947 -0.73397542 -0.38187689
Axis point 31.14273659 0.00000000 93.58374179
Rotation angle (degrees) 98.47584687
Shift along axis -64.72110773
> fitmap #7 inMap #13
Fit molecule 7c4j (#7) to map J184_007_volume_map_sharp_3p3A.mrc (#13) using
29730 atoms
average map value = 0.4776, steps = 40
shifted from previous position = 0.00449
rotated from previous position = 0.00092 degrees
atoms outside contour = 22732, contour level = 0.75257
Position of 7c4j (#7) relative to J184_007_volume_map_sharp_3p3A.mrc (#13)
coordinates:
Matrix rotation and translation
0.21454917 0.85071182 -0.47985211 105.71268930
0.09528566 0.47071856 0.87712296 -37.54858693
0.97205416 -0.23390902 0.01993164 86.16008080
Axis -0.56165095 -0.73397036 -0.38188444
Axis point 31.14032551 0.00000000 93.58086309
Rotation angle (degrees) 98.47630098
Shift along axis -64.71727681
> volume #15 level 0.7922
> volume #15 color #d5ba80
> volume #15 color #d58879
> volume #15 color #7aa5d5
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.2.4
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 3.6 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2020.40.3.0.0
OS Loader Version: 580~1053
SMC Version (system): 2.46f12
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 5 days, 8 hours, 44 minutes
Graphics/Displays:
Radeon Pro 580X:
Chipset Model: Radeon Pro 580X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A1X-009
EFI Driver Version: 01.B1.042
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 23 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in Qt drawing after volume coloring |
comment:2 by , 23 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash in Qt drawing after volume coloring → Graphics crash, macOS 14.2.1, Radeon Pro 580X |
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Crash in Apple AMD graphics driver. Unfortunately Apple's AMD and Intel graphics drivers are unstable and frequently crash. Nothing the ChimeraX team can do to fix that and it is unpredictable when the crashes will occur. All currently sold Macs use M1/M2 GPUs that have completely stable OpenGL drivers. More details here
https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#maccrash