![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Closed 12 months ago
#16260 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.0-x86_64-i386-64bit
ChimeraX Version: 1.9rc202410310525 (2024-10-31 05:25:41 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff85b9c6680 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 116)
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{
"uptime" : 1900000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 6435,
"osVersion" : {
"train" : "macOS 15.0",
"build" : "24A335",
"releaseType" : "User"
},
"captureTime" : "2024-11-07 14:02:26.7441 +0800",
"codeSigningMonitor" : 0,
"incident" : "6539BCDA-5A48-42E0-9C3B-FAC5F24E9640",
"pid" : 28363,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-07 10:31:13.1162 +0800",
"procStartAbsTime" : 1960833670368431,
"procExitAbsTime" : 1973507095371347,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"AF0E444E-37B4-593A-957D-B5CF6828D46F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F7A40BD4-636A-5D03-BCEB-C22CD08BD04B",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "E6E85802-84A6-4D7F-A09D-CDB88C487001",
"wakeTime" : 13992,
"bridgeVersion" : {"build":"22P353","train":"9.0"},
"sleepWakeUUID" : "C431757C-0A07-4D43-B6DC-B242C8CEFD16",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4524281856\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10dab1000-10dab5000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":28363},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4524281856\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10dab1000-10dab5000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_ufuncs_cxx.cpython-311-darwin.so",
"name" : "_ufuncs_cxx.cpython-311-darwin.so"
},
{
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_cdflib.cpython-311-darwin.so",
"name" : "_cdflib.cpython-311-darwin.so"
},
{
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_specfun.cpython-311-darwin.so",
"name" : "_specfun.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 5958422528,
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"uuid" : "2d2e18f9-d234-3cac-81ed-447d252c8fa6",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_comb.cpython-311-darwin.so",
"name" : "_comb.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6131228672,
"size" : 65536,
"uuid" : "ee0c90a6-01f4-3e5e-bf07-3e758786822f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/special\/_ellip_harm_2.cpython-311-darwin.so",
"name" : "_ellip_harm_2.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6515621888,
"size" : 425984,
"uuid" : "c7fc9a60-2940-3dda-bf1c-e24d687981fd",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_distance_pybind.cpython-311-darwin.so",
"name" : "_distance_pybind.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6514421760,
"size" : 704512,
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/transform\/_rotation.cpython-311-darwin.so",
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},
{
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"base" : 6164594688,
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"uuid" : "a9d30c5d-d3aa-3add-81c1-8d192b60c73b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_direct.cpython-311-darwin.so",
"name" : "_direct.cpython-311-darwin.so"
},
{
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{
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
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"arch" : "x86_64",
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"uuid" : "a0aee5ca-4298-3070-82f9-ea72229f36e5",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
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"uuid" : "c0db9cf9-86ec-31d4-a557-2c07945fd8f2",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
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"name" : "libsystem_c.dylib"
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"uuid" : "2568a05f-3db8-3b09-9ea2-aaf2fc264a52",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
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"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
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{
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"uuid" : "6c0ff4e0-6f75-36fa-b45f-0075a398132d",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
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{
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"name" : "HIToolbox"
},
{
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb
Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
95 messages similar to the above omitted
Chain information for c34_job27_ILS-coot-41.pdb #1
---
Chain | Description
0 | No description available
2 | No description available
5 | No description available
6 | No description available
7 | No description available
A | No description available
B | No description available
C | No description available
CY | No description available
Cb | No description available
Cc | No description available
Ci | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
P | No description available
R | No description available
S | No description available
T | No description available
U | No description available
W | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
> open /Users/lijuanyin/project/prp43/deposit/ils/run_class001.mrc
Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at
level 0.00799, step 2, values float32
> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_body_high.mrc
Opened multi_ctf_c34_job27_body_high.mrc as #3, grid size 480,480,480, pixel
0.932, shown at level 0.0045, step 2, values float32
> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_bottom_high.mrc
Opened multi_ctf_c34_job27_bottom_high.mrc as #4, grid size 480,480,480, pixel
0.932, shown at level 0.000984, step 2, values float32
> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_ntr_high.mrc
Opened multi_ctf_c34_job27_ntr_high.mrc as #5, grid size 480,480,480, pixel
0.932, shown at level 0.000544, step 2, values float32
> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_prp43_high.mrc
Opened multi_ctf_c34_job27_prp43_high.mrc as #6, grid size 480,480,480, pixel
0.932, shown at level 0.00086, step 2, values float32
> volume #3 step 1 level 0.01
> volume #4 step 1 level 0.01
> volume #5 step 1 level 0.01
> volume #6 step 1 level 0.01
> surface dust #1-15 size 20
> set bgColor white
> windowsize 800 800
> color #1 #3-10 silver
> color #1 cyan
> color #2-10 silver
> color #1/a-g /j-p /u sienna
> color #1/K /L /P /R /T /q-t /CW wheat
> color #1/F /V /W /Z /CN sky blue
> color #1/B /Ca plum
> color #1/D /G /H /Q /X green
> color #1/I /Y /CV light green
> color #1/J /M /N /S /CY /Cb /Cc pink
> color #1/CD /CK /CL orange
> color #1/CR /CT /CX /CZ lime
> color #1/O /CA /CC /CU purple
> color #1/2 /h /i /CS cornflower blue
> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green
> color #1/5 /A /C /E /CM deep pink
> color #1/6 /CB blue
> color #1/A hot pink
> color #1/7 red
> color #1/8 magenta
> color #1/M dark red
> color #1/Cc orange
> color #1/U cyan
> color #1/Cb dodger blue
> color #1/CY dark red
> color #1/0 dark khaki
> color #1/Ch aquamarine
> color #1/Cf cyan
> color #1/Cd teal
> color #1/z tomato
> color #1/1 forest green
> color #1/Cg chocolate
> color #1/R dark violet
> color #1/F deep sky blue
> color #1/2 lime
> color #1/5 hot pink
> color #1/Y olive
> color #1/E tomato
> color #1/Ci dark blue
> color zone #2-10 near #1 distance 6
> view matrix camera
> 0.50258,-0.032433,0.86392,748.17,-0.84845,0.17337,0.50008,539.22,-0.166,-0.98432,0.059613,259.91
> color #1/0 green yellow
> color zone #2-10 near #1 distance 6
> hide #!1 models
> save /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_view1.jpg
> view matrix camera
> 0.50258,-0.032433,0.86392,748.17,-0.84845,0.17337,0.50008,539.22,-0.166,-0.98432,0.059613,259.91
> save /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_view1.jpg
> view matrix camera
> 0.83999,0.11234,-0.53085,-119.57,0.50587,0.19174,0.84103,757.51,0.19627,-0.97499,0.10422,288.88
> save /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_view2.jpg
> hide #1 target a
> show #1 target r
> hide #1/CM target r
> show #1/2-8 target a
> nucleotides #1/2-8 ladder
> ribbon style protein modeh tube rad 2 sides 24
> ribbon style nucleic xsect rect width 3.2 thick 1.6
> cartoon style protein xsection oval width 3.2 thickness 1
> cartoon style strand xsection rectangle width 3.2 thickness 1.6
> show #!1 models
> hide #!1 models
> graphics silhouettes true
> view matrix camera
> 0.50258,-0.032433,0.86392,748.17,-0.84845,0.17337,0.50008,539.22,-0.166,-0.98432,0.059613,259.91
> save /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_view1.jpg
> view matrix camera
> 0.83999,0.11234,-0.53085,-119.57,0.50587,0.19174,0.84103,757.51,0.19627,-0.97499,0.10422,288.88
> save /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_view2.jpg
> show #!1 models
> hide #1.2 models
> view matrix camera
> 0.50258,-0.032433,0.86392,748.17,-0.84845,0.17337,0.50008,539.22,-0.166,-0.98432,0.059613,259.91
> save
> /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_model_view1.jpg
> view matrix camera
> 0.83999,0.11234,-0.53085,-119.57,0.50587,0.19174,0.84103,757.51,0.19627,-0.97499,0.10422,288.88
> save
> /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_model_view2.jpg
> close
> open /Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-41.pdb
Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-41.pdb
---
warnings | Duplicate atom serial number found: 4205
Duplicate atom serial number found: 4206
Duplicate atom serial number found: 4207
Duplicate atom serial number found: 4208
Duplicate atom serial number found: 4209
1144 messages similar to the above omitted
Chain information for c34_job28_Q1-coot-41.pdb #1
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
5 | No description available
6 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
CV | No description available
CY | No description available
Cb | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
P | No description available
R | No description available
S | No description available
T | No description available
V | No description available
W | No description available
Y | No description available
Z | No description available
j | No description available
k | No description available
l | No description available
m | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
z | No description available
> open /Users/lijuanyin/project/prp43/deposit/q1/run_class001.mrc
Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at
level 0.00702, step 2, values float32
> open
> /Users/lijuanyin/project/prp43/deposit/q1/local_ctf_c34_job28_2/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #3, grid size 480,480,480, pixel 0.932,
shown at level 0.00705, step 2, values float32
> open
> /Users/lijuanyin/project/prp43/deposit/q1/multi/local_multi_ctf_c34_job28_body_2/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #4, grid size 480,480,480, pixel 0.932,
shown at level 0.00635, step 2, values float32
> open
> /Users/lijuanyin/project/prp43/deposit/q1/multi/local_multi_ctf_c34_job28_dhx_2/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #5, grid size 480,480,480, pixel 0.932,
shown at level 0.00258, step 2, values float32
> open
> /Users/lijuanyin/project/prp43/deposit/q1/multi/local_multi_ctf_c34_job28_head_2/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #6, grid size 480,480,480, pixel 0.932,
shown at level 0.00276, step 2, values float32
> volume #2-10 step 1 level 0.005
> volume #4 step 1 level 0.0075
> volume #5 step 1 level 0.0065
> volume #6 step 1 level 0.005
> surface dust #1-15 size 20
> set bgColor white
> windowsize 800 800
> color #1 #3-10 silver
> color #1 cyan
> color #2-10 silver
> color #1/a-g /j-p /u sienna
> color #1/K /L /P /T /q-t /CW wheat
> color #1/F /V /W /Z /CN sky blue
> color #1/B /Ca plum
> color #1/D /G /H /Q /X green
> color #1/I /Y /CV light green
> color #1/J /M /N /S /CY /Cb /Cc /R pink
> color #1/CD /CK /CL orange
> color #1/CR /CT /CX /CZ lime
> color #1/O /CA /CC /CU purple
> color #1/2 /h /i /CS cornflower blue
> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green
> color #1/5 /A /C /E /CM hot pink
> color #1/6 /CB blue
> color #1/7 red
> color #1/8 magenta
> color #1/M dark red
> color #1/Cc orange
> color #1/U cyan
> color #1/Cb dodger blue
> color #1/CY dark red
> color #1/0 green yellow
> color #1/Ch aquamarine
> color #1/Cf cyan
> color #1/Cd teal
> color #1/z tomato
> color #1/1 forest green
> color #1/Cg chocolate
> color #1/R dark violet
> color #1/F deep sky blue
> color #1/2 lime
> color #1/5 hot pink
> color #1/Y olive
> color #1/E tomato
> color #1/C deep pink
> color #1/V steel blue
> color #1/CV yellow green
> color #1/8 red
> color zone #2-10 near #1 distance 6
> view matrix camera
> 0.52209,0.083337,-0.84881,-258.37,0.81484,0.24518,0.52528,513.08,0.25189,-0.96589,0.060097,268.61
> hide #!1 models
> show #!1 models
> color #1/CV magenta
> color zone #2-10 near #1 distance 6
> hide #!1 models
> view matrix camera
> 0.52209,0.083337,-0.84881,-258.37,0.81484,0.24518,0.52528,513.08,0.25189,-0.96589,0.060097,268.61
> save /Users/lijuanyin/project/prp43/figure_new/figure2/q1_full_view1.jpg
> view matrix camera
> 0.10901,-0.19598,0.97453,779.23,-0.90425,0.38763,0.1791,312.85,-0.41285,-0.90074,-0.13496,161.59
> save /Users/lijuanyin/project/prp43/figure_new/figure2/q1_full_view2.jpg
> hide #1 target a
> show #1 target r
> hide #1/CM target r
> show #1/2-8 target a
> nucleotides #1/2-8 ladder
> ribbon style protein modeh tube rad 2 sides 24
> ribbon style nucleic xsect rect width 3.2 thick 1.6
> cartoon style protein xsection oval width 3.2 thickness 1
> cartoon style strand xsection rectangle width 3.2 thickness 1.6
> show #!1 models
> view matrix camera
> 0.52209,0.083337,-0.84881,-258.37,0.81484,0.24518,0.52528,513.08,0.25189,-0.96589,0.060097,268.61
> save
> /Users/lijuanyin/project/prp43/figure_new/figure2/q1_full_model_view1.jpg
> view matrix camera
> 0.10901,-0.19598,0.97453,779.23,-0.90425,0.38763,0.1791,312.85,-0.41285,-0.90074,-0.13496,161.59
> save
> /Users/lijuanyin/project/prp43/figure_new/figure2/q1_full_model_view2.jpg
> close
> open /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-45.pdb
Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-45.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
95 messages similar to the above omitted
Chain information for c6_job26_Q2-coot-45.pdb #1
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
5 | No description available
6 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
CY | No description available
Cb | No description available
Cc | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
P | No description available
R | No description available
S | No description available
T | No description available
V | No description available
W | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
z | No description available
> open /Users/lijuanyin/project/prp43/deposit/q2/run_class001.mrc
Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at
level 0.00639, step 2, values float32
> open
> /Users/lijuanyin/project/prp43/deposit/q2/local_c6_job26_2/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #3, grid size 480,480,480, pixel 0.932,
shown at level 0.00615, step 2, values float32
> open
> /Users/lijuanyin/project/prp43/deposit/q2/multi/local_multi_c6_job26_body/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #4, grid size 480,480,480, pixel 0.932,
shown at level 0.0055, step 2, values float32
> open
> /Users/lijuanyin/project/prp43/deposit/q2/multi/local_multi_c6_job26_head/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #5, grid size 480,480,480, pixel 0.932,
shown at level 0.00246, step 2, values float32
> volume #2-10 step 1 level 0.0045
> volume #4 step 1 level 0.0075
> volume #5 step 1 level 0.003
> volume #4 step 1 level 0.0055
> surface dust #1-15 size 20
> set bgColor white
> windowsize 800 800
> color #1 #3-10 silver
> color #1 cyan
> color #2-10 silver
> color #1/a-g /j-p /u sienna
> color #1/K /L /P /R /T /q-t /CW wheat
> color #1/F /V /W /Z /CN sky blue
> color #1/B /Ca plum
> color #1/D /G /H /Q /X green
> color #1/I /Y /CV light green
> color #1/J /M /N /S /CY /Cb /Cc pink
> color #1/CD /CK /CL orange
> color #1/CR /CT /CX /CZ lime
> color #1/O /CA /CC /CU purple
> color #1/2 /h /i /CS cornflower blue
> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green
> color #1/5 /A /C /E /CM hot pink
> color #1/6 /CB blue
> color #1/7 red
> color #1/8 magenta
> color #1/M dark red
> color #1/Cc orange
> color #1/U cyan
> color #1/Cb dodger blue
> color #1/CY dark red
> color #1/0 green yellow
> color #1/Ch aquamarine
> color #1/Cf cyan
> color #1/Cd teal
> color #1/z tomato
> color #1/1 forest green
> color #1/Cg chocolate
> color #1/R dark violet
> color #1/F deep sky blue
> color #1/2 lime
> color #1/5 hot pink
> color #1/Y olive
> color #1/E tomato
> color #1/C deep pink
> color #1/V steel blue
> color #1/CV magenta
> color #1/8 red
> color zone #2-10 near #1 distance 6
> view matrix camera
> 0.52209,0.083337,-0.84881,-259.14,0.81484,0.24518,0.52528,513.87,0.25189,-0.96589,0.060097,250.86
> hide #!1 models
> view matrix camera
> 0.52209,0.083337,-0.84881,-259.14,0.81484,0.24518,0.52528,513.87,0.25189,-0.96589,0.060097,250.86
> save /Users/lijuanyin/project/prp43/figure_new/figure2/q2_full_view1.jpg
> view matrix camera
> 0.10901,-0.19598,0.97453,776.31,-0.90425,0.38763,0.1791,317.57,-0.41285,-0.90074,-0.13496,146.75
> save /Users/lijuanyin/project/prp43/figure_new/figure2/q2_full_view2.jpg
> hide #1 target a
> show #1 target r
> hide #1/CM target r
> show #1/2-8 target a
> nucleotides #1/2-8 ladder
> ribbon style protein modeh tube rad 2 sides 24
> ribbon style nucleic xsect rect width 3.2 thick 1.6
> cartoon style protein xsection oval width 3.2 thickness 1
> cartoon style strand xsection rectangle width 3.2 thickness 1.6
> show #!1 models
> view matrix camera
> 0.52209,0.083337,-0.84881,-259.14,0.81484,0.24518,0.52528,513.87,0.25189,-0.96589,0.060097,250.86
> save
> /Users/lijuanyin/project/prp43/figure_new/figure2/q2_full_model_view1.jpg
> view matrix camera
> 0.10901,-0.19598,0.97453,776.31,-0.90425,0.38763,0.1791,317.57,-0.41285,-0.90074,-0.13496,146.75
> save
> /Users/lijuanyin/project/prp43/figure_new/figure2/q2_full_model_view2.jpg
> close
> open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb
Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
95 messages similar to the above omitted
Chain information for c34_job27_ILS-coot-41.pdb #1
---
Chain | Description
0 | No description available
2 | No description available
5 | No description available
6 | No description available
7 | No description available
A | No description available
B | No description available
C | No description available
CY | No description available
Cb | No description available
Cc | No description available
Ci | No description available
D | No description available
E | No description available
F | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
P | No description available
R | No description available
S | No description available
T | No description available
U | No description available
W | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
> open /Users/lijuanyin/project/prp43/deposit/published/8ro1-ils_2.cif-
> coot-0.cif
Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/published/8ro1-ils_2.cif-coot-0.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 141
Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' on line 120723
Skipping chem_comp category: Missing column 'type' on line 120750
Skipping chem_comp category: Missing column 'type' on line 120777
Skipping chem_comp category: Missing column 'type' on line 121056
Skipping chem_comp category: Missing column 'type' on line 121308
3 messages similar to the above omitted
Chain information for 8ro1-ils_2.cif-coot-0.cif #2
---
Chain | Description
2 | No description available
5 | No description available
6 | No description available
A | No description available
C | No description available
D | No description available
DX | No description available
E | No description available
I | No description available
IN | No description available
J | No description available
K | No description available
L | No description available
L1 | No description available
L2 | No description available
M | No description available
N | No description available
O | No description available
P | No description available
PX | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
TF | No description available
W | No description available
X | No description available
Z | No description available
a h | No description available
b | No description available
c j | No description available
d | No description available
e l | No description available
f m | No description available
g n | No description available
i | No description available
k | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
y | No description available
> open /Users/lijuanyin/project/prp43/deposit/published/5y88-ILS.cif-
> coot-0.pdb
Chain information for 5y88-ILS.cif-coot-0.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
a | No description available
b i | No description available
c j | No description available
d k | No description available
e l | No description available
f m | No description available
g | No description available
h | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
x | No description available
> surface dust #1-15 size 20
No surfaces specified
> set bgColor white
> windowsize 800 800
> color #1 #3-10 silver
> color #1 cyan
> color #2-10 silver
> color #1/a-g /j-p /u sienna
> color #1/K /L /P /R /T /q-t /CW wheat
> color #1/F /V /W /Z /CN sky blue
> color #1/B /Ca plum
> color #1/D /G /H /Q /X green
> color #1/I /Y /CV light green
> color #1/J /M /N /S /CY /Cb /Cc pink
> color #1/CD /CK /CL orange
> color #1/CR /CT /CX /CZ lime
> color #1/O /CA /CC /CU purple
> color #1/2 /h /i /CS cornflower blue
> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green
> color #1/5 /A /C /E /CM hot pink
> color #1/6 /CB blue
> color #1/7 red
> color #1/8 magenta
> color #1/M dark red
> color #1/Cc orange
> color #1/U lime
> color #1/Cb dodger blue
> color #1/CY dark red
> color #1/0 green yellow
> color #1/Ch aquamarine
> color #1/Cf cyan
> color #1/Cd teal
> color #1/z tomato
> color #1/1 forest green
> color #1/Cg chocolate
> hide #1-2 target a
> show #1-2 target r
> hide #1/CM target r
> show #1-2/2-8 target a
> nucleotides #1-2/2-8 #2/N ladder
> color #1-2 silver
> color #2/L1 purple
> color #1/Cb #2/TF dodger blue
> color #1/CY #2/PX dark red
> color #1/M dark red
> color #1/0 #2/O green yellow
> color #1/Cc #2/DX orange
> color #1/B #2/M plum
> color #1/D #2/X green
> color #1-2/6 blue
> color #1-2/I light green
> ribbon style protein modeh tube rad 2 sides 24
> ribbon style nucleic xsect rect width 3.2 thick 1.6
> cartoon style protein xsection oval width 3.2 thickness 1
> cartoon style strand xsection rectangle width 3.2 thickness 1.6
> hide #!1 models
> hide #!2 models
> show #!3 cartoons
> hide #!3 atoms
> show #!1 models
> color #1-2 silver
> color #1/M #3/M dark red
> color #1/0 #2/O #3/N green yellow
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> hide #1.2 models
> hide #2.1 models
> hide #3.1 models
> show #!2 models
> show #!3 models
> ui tool show "Side View"
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> view matrix
view matrix camera
-0.7213,0.50409,0.47499,348.06,-0.51049,0.076562,-0.85647,37.098,-0.4681,-0.86025,0.20211,231.59
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0
> show #!1 models
> hide #!3 models
> save
> /Users/lijuanyin/project/prp43/figure_new/figure_s2/ils_ecm2_model_view3.jpg
> show #!2 models
> hide #!1 models
> save
> /Users/lijuanyin/project/prp43/figure_new/figure_s2/8ro1_ecm2_model_view3.jpg
> show #!3 models
> hide #!2 models
> save
> /Users/lijuanyin/project/prp43/figure_new/figure_s2/5y88_ecm2_model_view3.jpg
===== Log before crash end =====
Log:
Startup Messages
---
warning | QCoreApplication::postEvent: Unexpected null receiver
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202410310525 (2024-10-31)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2,3 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: 64 GB
System Firmware Version: 2069.0.0.0.0 (iBridge: 22.16.10353.0.0,0)
OS Loader Version: 582~1023
Software:
System Software Overview:
System Version: macOS 15.0 (24A335)
Kernel Version: Darwin 24.0.0
Time since boot: 32天2小时30分钟
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
C34H89x:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 50.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: H1AK500000
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Apple USB-C Digital AV Adapter
Adapter Firmware Version: 2,35
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.17
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: 1.58.7
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: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
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: 1.9rc202410310525
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: 1.2.5
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
ChimeraX-Label: 1.1.11
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: 2.7.1
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: 1.5.17
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: 1.6.1
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: 3.2.3
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: 1.3.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.7
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.54.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
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: 2.10.1
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: 2.4.1
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
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: 6.4.1
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 , 12 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 , 12 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Crashed in 1.8, reported with 1.9rc. Phew!
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I guess the release candidate is getting more widely used...