![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17737 closed defect (can't reproduce)
Crash restoring many alignments from session
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x0000000200d34840 (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, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 62)
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"procRole" : "Foreground",
"version" : 2,
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"modelCode" : "Mac15,3",
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"build" : "24D81",
"releaseType" : "User"
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"captureTime" : "2025-05-19 22:12:13.9966 -0700",
"codeSigningMonitor" : 1,
"incident" : "DA92814A-D534-4B3F-8980-A93710A21C83",
"pid" : 89049,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-19 21:50:34.8053 -0700",
"procStartAbsTime" : 4658959615558,
"procExitAbsTime" : 4690130736992,
"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":"8CF9F00A-F9C4-51E7-9E13-65C1A512E697","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B98ECC04-B986-FF1F-F1A7-A00069269010",
"lowPowerMode" : 1,
"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" : "2A97F82F-2E47-4669-AA18-C077ED53CBD5",
"wakeTime" : 3963,
"sleepWakeUUID" : "B640E3CD-2935-4D87-A91B-CCC11722E72C",
"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":89049},
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System Profile:
Network Service: Wi-Fi, AirPort, en0
Thunderbolt Bus: MacBook Pro, Apple Inc.
Thunderbolt Bus: MacBook Pro, Apple Inc.
Boot Volume File System Type: apfs
Memory Module: LPDDR5, Hynix
USB Device: USB31Bus
USB Device: USB31Bus
Display: Color LCD, 3024 x 1964 Retina, Main, MirrorOff, Online
Model: Mac15,3, BootROM 11881.81.4, proc 8:4:4 processors, 8 GB, SMC
Graphics: Apple M3, Apple M3, Built-In
AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4388), wl0: Oct 31 2024 06:18:43 version 23.10.900.20.41.51.176 FWID 01-24228154
IO80211_driverkit-1345.10 "IO80211_driverkit-1345.10" Dec 14 2024 17:47:07
AirPort:
Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports
===== 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/evitatsiolaki/Downloads/run_it026_half1_class001.mrc
Opened run_it026_half1_class001.mrc as #1, grid size 384,384,384, pixel 0.819,
shown at level 0.0016, step 2, values float32
> close
> open
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/new_fig_comparison/hHsp70_mutations_comparison.cxs
> format session
opened ChimeraX session
> open /Users/evitatsiolaki/Downloads/run_it026_half1_class001.mrc
Opened run_it026_half1_class001.mrc as #2, grid size 384,384,384, pixel 0.819,
shown at level 0.0016, step 2, values float32
> ui mousemode right "rotate selected models"
> select add #2
2 models selected
> view matrix models
> #2,0.19881,-0.97267,0.11991,267.78,0.59306,0.21681,0.77542,-86.524,-0.78023,-0.083043,0.61996,196.56
> view matrix models
> #2,-0.86151,0.22485,-0.45525,327.45,-0.44064,0.11441,0.89037,74.622,0.25229,0.96765,0.00051086,-41.308
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.86151,0.22485,-0.45525,331.53,-0.44064,0.11441,0.89037,59.488,0.25229,0.96765,0.00051086,-43.591
> fitmap #1 inMap #2
Fit molecule HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb
(#1) to map run_it026_half1_class001.mrc (#2) using 18912 atoms
average map value = 0.009092, steps = 148
shifted from previous position = 12.9
rotated from previous position = 13.7 degrees
atoms outside contour = 525, contour level = 0.0015965
Position of HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#1)
relative to run_it026_half1_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.02895178 0.21461974 -0.97626849 273.24994857
0.91288240 0.39218779 0.11328934 -55.59145916
0.40719471 -0.89449825 -0.18456805 259.76286793
Axis -0.54517417 -0.74840017 0.37773313
Axis point 39.22144795 0.00000000 235.71888993
Rotation angle (degrees) 112.43990677
Shift along axis -9.24311442
> volume #2 level 0.002463
> color #2 #fffc79ff models
> color zone #2 near #1 distance 4.91
> select clear
> volume #2 level 0.002959
> volume #2 level 0.003
> open
> /Users/evitatsiolaki/Downloads/Masks/RELION_it010_half1_class001_region_116.mrc
Failed opening file
/Users/evitatsiolaki/Downloads/Masks/RELION_it010_half1_class001_region_116.mrc:
MRC file is truncated. Failed reading 1 values, type int32
> open /Users/evitatsiolaki/Downloads/run_it025_class001.mrc
Opened run_it025_class001.mrc as #3, grid size 384,384,384, pixel 0.819, shown
at level 1.09e-06, step 2, values float32
> open /Users/evitatsiolaki/Downloads/run_it025_class002.mrc
Opened run_it025_class002.mrc as #4, grid size 384,384,384, pixel 0.819, shown
at level 2.01e-06, step 2, values float32
> open /Users/evitatsiolaki/Downloads/run_it025_class003.mrc
Opened run_it025_class003.mrc as #5, grid size 384,384,384, pixel 0.819, shown
at level 1.1e-06, step 2, values float32
> hide #!2 models
> select add #3
2 models selected
> select add #4
4 models selected
> select add #5
6 models selected
> view matrix models
> #3,1,0,0,3.7366,0,1,0,-30.527,0,0,1,-20.302,#4,1,0,0,3.7366,0,1,0,-30.527,0,0,1,-20.302,#5,1,0,0,3.7366,0,1,0,-30.527,0,0,1,-20.302
> volume all level 0.1
> volume all level 0.04
> volume #3 level 0.02173
> volume #3 level 0.009598
> volume all level 0.01
> view matrix models
> #3,1,0,0,-4.6811,0,1,0,-28.575,0,0,1,-7.8067,#4,1,0,0,-4.6811,0,1,0,-28.575,0,0,1,-7.8067,#5,1,0,0,-4.6811,0,1,0,-28.575,0,0,1,-7.8067
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.77694,0.4611,-0.42866,258.91,-0.25819,0.38762,0.88492,-26.315,0.57419,0.79821,-0.18211,-42.528,#4,-0.77694,0.4611,-0.42866,258.91,-0.25819,0.38762,0.88492,-26.315,0.57419,0.79821,-0.18211,-42.528,#5,-0.77694,0.4611,-0.42866,258.91,-0.25819,0.38762,0.88492,-26.315,0.57419,0.79821,-0.18211,-42.528
> view matrix models
> #3,-0.63859,0.75081,-0.1688,140.07,-0.074204,0.15825,0.98461,-29.916,0.76596,0.64128,-0.045342,-67.015,#4,-0.63859,0.75081,-0.1688,140.07,-0.074204,0.15825,0.98461,-29.916,0.76596,0.64128,-0.045342,-67.015,#5,-0.63859,0.75081,-0.1688,140.07,-0.074204,0.15825,0.98461,-29.916,0.76596,0.64128,-0.045342,-67.015
> hide #!4 models
> hide #!5 models
> fitmap #1 inMap #3
Fit molecule HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb
(#1) to map run_it025_class001.mrc (#3) using 18912 atoms
average map value = 0.003121, steps = 516
shifted from previous position = 20.7
rotated from previous position = 50.3 degrees
atoms outside contour = 17244, contour level = 0.01
Position of HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#1)
relative to run_it025_class001.mrc (#3) coordinates:
Matrix rotation and translation
-0.08664378 0.27655191 -0.95708511 279.77064374
0.57727599 0.79690985 0.17800879 -51.41203834
0.81193922 -0.53707890 -0.22869405 153.62772861
Axis -0.37019722 -0.91581479 0.15568331
Axis point 83.82088737 0.00000000 184.55014492
Rotation angle (degrees) 105.02342814
Shift along axis -32.56913521
> hide #!3 models
> hide #1 models
> show #!2 models
> show #!3 models
> fitmap #3 inMap #2
Fit map run_it025_class001.mrc in map run_it026_half1_class001.mrc using 4436
points
correlation = 0.8474, correlation about mean = 0.1091, overlap = 0.4952
steps = 140, shift = 13.1, angle = 20.2 degrees
Position of run_it025_class001.mrc (#3) relative to
run_it026_half1_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.92007490 -0.39062787 -0.02953057 88.03713042
0.39137813 0.91985419 0.02629516 -60.58876085
0.01689220 -0.03575114 0.99921795 3.06678271
Axis -0.07895578 -0.05907438 0.99512622
Axis point 192.91256946 185.83750897 0.00000000
Rotation angle (degrees) 23.13618782
Shift along axis -0.31996128
> hide #!3 models
> show #!4 models
> fitmap #4 inMap #2
Fit map run_it025_class002.mrc in map run_it026_half1_class001.mrc using 4324
points
correlation = 0.8226, correlation about mean = 0.09163, overlap = 0.4463
steps = 152, shift = 5.82, angle = 15.3 degrees
Position of run_it025_class002.mrc (#4) relative to
run_it026_half1_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.87131427 -0.34580499 -0.34818150 149.07915961
0.36335536 0.93151543 -0.01587096 -56.01505290
0.32982470 -0.11268502 0.93729278 -22.73888766
Axis -0.09819992 -0.68771167 0.71931178
Axis point 207.05061259 356.19434669 -0.00000000
Rotation angle (degrees) 29.53424321
Shift along axis 7.52629405
> hide #!4 models
> show #!5 models
> fitmap #5 inMap #2
Fit map run_it025_class003.mrc in map run_it026_half1_class001.mrc using 4348
points
correlation = 0.8328, correlation about mean = 0.01819, overlap = 0.4622
steps = 228, shift = 11.6, angle = 32 degrees
Position of run_it025_class003.mrc (#5) relative to
run_it026_half1_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.98538033 -0.16998159 0.01148316 34.59060775
0.17024111 0.98501269 -0.02771212 -26.37287744
-0.00660051 0.02926188 0.99954999 -4.81178440
Axis 0.16493461 0.05235061 0.98491420
Axis point 171.43962160 189.15346325 0.00000000
Rotation angle (degrees) 9.94582444
Shift along axis -0.41464233
> hide #!5 models
> show #1 models
> fitmap #1 inMap #2
Fit molecule HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb
(#1) to map run_it026_half1_class001.mrc (#2) using 18912 atoms
average map value = 0.009092, steps = 392
shifted from previous position = 20.7
rotated from previous position = 50.3 degrees
atoms outside contour = 11399, contour level = 0.01
Position of HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#1)
relative to run_it026_half1_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.02900610 0.21451632 -0.97628961 273.25960931
0.91288029 0.39219057 0.11329668 -55.60276150
0.40719556 -0.89452184 -0.18445180 259.76079826
Axis -0.54516979 -0.74838307 0.37777331
Axis point 39.21904168 -0.00000000 235.73561476
Rotation angle (degrees) 112.43453451
Shift along axis -9.23002082
> hide #!2 models
> show #!3 models
> color zone #3 near #1 distance 4.91
> hide #!3 models
> show #!4 models
> color zone #4 near #1 distance 4.91
> show #!5 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> volume all color #fffc79
> hide #!4 models
> color zone #5 near #1 distance 4.91
> hide #!5 models
> show #!4 models
> color zone #4 near #1 distance 4.91
> hide #!4 models
> show #!3 models
> color zone #3 near #1 distance 4.91
> hide #1 models
> show #!4 models
> show #!5 models
> tile
3 models tiled
> volume all level 0.01
> volume all level 0.005
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #!3 models
> select subtract #4
4 models selected
> select subtract #3
2 models selected
> view matrix models
> #5,0.56306,0.8253,-0.042966,-49.8,-0.015777,0.062715,0.99791,-135.34,0.82627,-0.5612,0.048333,129.54
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.56306,0.8253,-0.042966,-47.204,-0.015777,0.062715,0.99791,-17.523,0.82627,-0.5612,0.048333,-99.471
> view matrix models
> #5,0.56306,0.8253,-0.042966,-47.668,-0.015777,0.062715,0.99791,-14.832,0.82627,-0.5612,0.048333,-100.43
> select clear
> open
> /Users/evitatsiolaki/Documents/ChimeraSessions/ChimeraSessions/Model_Angelo_noseq_prediction.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Redust" returned None
opened ChimeraX session
Alignment identifier is 2/A
Alignment identifier is 2/B
Alignment identifier is 2/C
Alignment identifier is 2/E
Alignment identifier is 2/F
Alignment identifier is 2/G
Alignment identifier is 2/H
Alignment identifier is 2/I
Alignment identifier is 1
Alignment identifier is 2/K
Alignment identifier is 2/L
Alignment identifier is 2/M
Alignment identifier is 2
Alignment identifier is 2/R
Alignment identifier is 2/S
Alignment identifier is 2/T
Alignment identifier is 3
Alignment identifier is 2/V
Alignment identifier is 2/W
Alignment identifier is 2/X
Alignment identifier is 2/Z
Alignment identifier is 2/c
Alignment identifier is 2/e
Alignment identifier is 2/f
Alignment identifier is 2/g
Alignment identifier is 4
Alignment identifier is 2/k
Alignment identifier is 5
Alignment identifier is 2/p
Alignment identifier is 6
Alignment identifier is 2/u
Alignment identifier is 7
Alignment identifier is 2/y
Alignment identifier is 2/1
Alignment identifier is 2/2
Alignment identifier is 2/8
Alignment identifier is 2/9
Alignment identifier is 2/AA
Alignment identifier is 2/AC
Alignment identifier is 2/AF
Alignment identifier is 2/AG
Alignment identifier is 2/AL
Alignment identifier is 2/AN
Alignment identifier is 2/AO
Alignment identifier is 8
Alignment identifier is 2/AS
Alignment identifier is 2/AT
Alignment identifier is 2/AU
Alignment identifier is 2/AW
Alignment identifier is 2/AX
Alignment identifier is 2/AZ
Alignment identifier is 2/Ac
Alignment identifier is 2/Am
Alignment identifier is 2/An
Alignment identifier is 2/Ao
Alignment identifier is 2/As
Alignment identifier is 2/Ay
Alignment identifier is 2/A0
Alignment identifier is 2/A1
Alignment identifier is 2/A5
Alignment identifier is 2/BA
Alignment identifier is 2/BM
Alignment identifier is 2/BO
Alignment identifier is 2/Bj
Alignment identifier is 2/Bo
Alignment identifier is 2/Bq
Alignment identifier is 2/Br
Alignment identifier is 2/Bs
Alignment identifier is 2/Bt
Alignment identifier is 2/Bu
Alignment identifier is 2/Bv
Alignment identifier is 2/Bw
Alignment identifier is 2/Bx
Alignment identifier is 2/By
Alignment identifier is 2/Bz
Alignment identifier is 2/B0
Alignment identifier is 2/B1
Alignment identifier is 2/B2
Alignment identifier is 2/B3
Alignment identifier is 2/B4
Alignment identifier is 2/B5
Alignment identifier is 2/B6
Alignment identifier is 2/B7
Alignment identifier is 2/B8
Alignment identifier is 2/B9
Alignment identifier is 2/CA
Alignment identifier is 2/CB
Alignment identifier is 2/CC
Alignment identifier is 2/CD
Alignment identifier is 2/CE
Alignment identifier is 2/CF
Alignment identifier is 2/CG
Alignment identifier is 2/CH
Alignment identifier is 2/CI
Alignment identifier is 2/CJ
Alignment identifier is 2/CK
Alignment identifier is 2/CL
Alignment identifier is 2/CM
Alignment identifier is 2/CN
Alignment identifier is 2/CO
Alignment identifier is 2/CP
Alignment identifier is 2/CQ
Alignment identifier is 2/CR
Alignment identifier is 2/CS
Alignment identifier is 2/CT
Alignment identifier is 2/CV
Alignment identifier is 2/CW
Alignment identifier is 2/CX
Alignment identifier is 2/CY
Alignment identifier is 2/CZ
Alignment identifier is 2/Ca
Alignment identifier is 2/Cb
Alignment identifier is 2/Cc
Alignment identifier is 2/Cd
Alignment identifier is 2/Ce
Alignment identifier is 2/Cf
Alignment identifier is 2/Cg
Alignment identifier is 2/Ch
Alignment identifier is 2/Ci
Alignment identifier is 2/Cj
Alignment identifier is 2/Ck
Alignment identifier is 2/Cl
Alignment identifier is 2/Cm
Alignment identifier is 2/Cn
Alignment identifier is 2/Co
Alignment identifier is 2/Cp
Alignment identifier is 2/Cq
Alignment identifier is 2/Cr
Alignment identifier is 2/Cs
Alignment identifier is 2/Ct
Alignment identifier is 2/Cu
Alignment identifier is 2/Cv
Alignment identifier is 2/Cw
Alignment identifier is 2/Cx
Alignment identifier is 2/Cy
Alignment identifier is 2/Cz
Alignment identifier is 2/C0
Alignment identifier is 2/C1
Alignment identifier is 2/C2
===== 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
> open /Users/evitatsiolaki/Downloads/volumes/volume_half1_000.mrc
Opened volume_half1_000.mrc as #1, grid size 192,192,192, pixel 0.819, shown
at level 35, step 1, values float32
OpenGL version: 4.1 Metal - 89.3
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: MR7K3LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 21 days, 6 hours, 9 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:
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
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-NIHPresets: 1.2.7
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-StarMap: 1.2.15
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
pyqtgraph: 0.13.7
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 , 5 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash restoring many alignments from session |
comment:2 by , 5 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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