![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Closed 12 months ago
#16296 closed defect (fixed)
Color key runs command during session close
| 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-14.4-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00000001f1f9fac0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 91 in get_prop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1255 in _changes_cb
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1069 in proxy_handler
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 54 in check_for_changes
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 77 in
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3318 in command_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 144 in __exit__
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3203 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py", line 225 in delete
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py", line 308 in _key_closed
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/model.py", line 105 in delete
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 1010 in close
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 676 in reset_state
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 552 in reset
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 723 in restore
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1027 in open
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 464 in cxcmd
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 446 in defer
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 423 in thread_safe
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 455 in chimerax_intercept
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 353 in intercept
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 93 in _intercept
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 320 in interceptRequest
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, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 62)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,10",
"coalitionID" : 6839,
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"releaseType" : "User"
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"captureTime" : "2024-11-12 14:41:39.1512 +0100",
"codeSigningMonitor" : 1,
"incident" : "83E2D9EF-9BDA-4628-B044-46DDB177E9BA",
"pid" : 72859,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-12 13:50:39.9197 +0100",
"procStartAbsTime" : 13232151063358,
"procExitAbsTime" : 13266641751998,
"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":"27DF656B-9E89-50F5-A945-632FCB7F7DE3","thirdParty":true},
"parentProc" : "launchd",
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"crashReporterKey" : "87816E32-FB80-B4A1-1C8A-5670F63155F7",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"exception" : {"codes":"0x0000000000000001, 0xfffffffffffffff8","rawCodes":[1,-8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0xfffffffffffffff8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":72859},
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=7.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=7.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 912K 40 \nColorSync 656K 31 \nCoreAnimation 2336K 114 \nCoreGraphics 32K 2 \nCoreServices 624K 2 \nCoreUI image data 5520K 39 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 7.1G 178 \nMALLOC guard page 384K 24 \nMach message 96K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 896K 56 \nStack 179.9M 57 \nStack Guard 56.0M 1 \nVM_ALLOCATE 279.4M 199 \nVM_ALLOCATE (reserved) 320.0M 4 reserved VM address space (unallocated)\n__AUTH 2205K 407 \n__AUTH_CONST 31.9M 625 \n__CTF 824 1 \n__DATA 22.2M 779 \n__DATA_CONST 42.6M 788 \n__DATA_DIRTY 2030K 234 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 555.5M 158 \n__OBJC_RO 71.7M 1 \n__OBJC_RW 2195K 1 \n__TEXT 941.7M 805 \ndyld private memory 320K 4 \nmapped file 259.7M 69 \nshared memory 3136K 22 \n=========== ======= ======= \nTOTAL 9.8G 4658 \nTOTAL, minus reserved VM space 9.5G 4658 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "64a9de3e1781b5d853a9a3380cddfda9794a4eae",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "648a2601f74c42732876cb5b",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "66b55f4e9142fa69576cb851"
},
"deploymentId" : 240000266
},
{
"rolloutId" : "63f9578e238e7b23a1f3030a",
"factorPackIds" : {
},
"deploymentId" : 240000005
}
],
"experiments" : [
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
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/lucastafur/Documents/TORC2_paper/Figures/Fig1/last_oct2024/model_PH.cxs
> format session
Opened cryosparc_P11_J211_006_volume_map_sharp (1).mrc as #6, grid size
512,512,512, pixel 0.908, shown at level 0.0851, step 1, values float32
Opened composite_Lst8_PH.mrc as #3, grid size 512,512,512, pixel 0.908, shown
at level 0.205, step 1, values float32
Opened cryosparc_P11_J448_007_volume_map.mrc as #4, grid size 512,512,512,
pixel 0.908, shown at level 0.0402, step 1, values float32
Opened composite_lst8_NRD.mrc as #7, grid size 512,512,512, pixel 0.908, shown
at level 0.179, step 1, values float32
opened ChimeraX session
> open
> /Users/lucastafur/Downloads/fold_avo3_bit61_slm1dimer/fold_avo3_bit61_slm1dimer_model_0.cif
> format mmcif
Chain information for fold_avo3_bit61_slm1dimer_model_0.cif #8
---
Chain | Description
A B | .
C | .
D | .
> mmaker #8/C to #1/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Monomer_PH_rspr21.pdb, chain E (#1) with
fold_avo3_bit61_slm1dimer_model_0.cif, chain C (#8), sequence alignment score
= 1015.8
RMSD between 213 pruned atom pairs is 0.550 angstroms; (across all 215 pairs:
0.621)
> select #8/B:1-686
5490 atoms, 5585 bonds, 686 residues, 1 model selected
> select #8/A:1-686
5490 atoms, 5585 bonds, 686 residues, 1 model selected
> select #8/A:1-686
5490 atoms, 5585 bonds, 686 residues, 1 model selected
> select #8/B:1-686
5490 atoms, 5585 bonds, 686 residues, 1 model selected
> select #8/B:1-686
5490 atoms, 5585 bonds, 686 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide #8 models
> hide #5 models
> volume #3 level 0.1607
> volume #4 level 0.04637
> ui tool show "Color Zone"
> color single #4
> ui tool show "Surface Zone"
> surface unzone #4
> volume #4 level 0.03877
> volume #4 color #b6b6b6
> volume #4 color #b6b6b680
> select #1/E
1776 atoms, 1806 bonds, 215 residues, 1 model selected
> select #1/D
1518 atoms, 1550 bonds, 189 residues, 1 model selected
> select #1/F
Nothing selected
> select #1/B
2386 atoms, 2442 bonds, 302 residues, 1 model selected
> ui tool show "Fit in Map"
> fitmap #1 inMap #4
Fit molecule Monomer_PH_rspr21.pdb (#1) to map
cryosparc_P11_J448_007_volume_map.mrc (#4) using 34465 atoms
average map value = 0.03408, steps = 100
shifted from previous position = 0.537
rotated from previous position = 1.18 degrees
atoms outside contour = 26556, contour level = 0.038775
Position of Monomer_PH_rspr21.pdb (#1) relative to
cryosparc_P11_J448_007_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99980557 0.00876122 0.01766559 -6.50612569
-0.00884252 0.99995065 0.00452923 1.71174420
-0.01762504 -0.00468456 0.99983369 6.16455489
Axis -0.22750360 0.87138306 -0.43466502
Axis point 353.49189356 0.00000000 368.42083304
Rotation angle (degrees) 1.16030626
Shift along axis 0.29223555
> fitmap #1 inMap #4
Fit molecule Monomer_PH_rspr21.pdb (#1) to map
cryosparc_P11_J448_007_volume_map.mrc (#4) using 34465 atoms
average map value = 0.03408, steps = 80
shifted from previous position = 0.0103
rotated from previous position = 0.00293 degrees
atoms outside contour = 26558, contour level = 0.038775
Position of Monomer_PH_rspr21.pdb (#1) relative to
cryosparc_P11_J448_007_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99980643 0.00872323 0.01763555 -6.48161394
-0.00880411 0.99995106 0.00451370 1.71067439
-0.01759531 -0.00466809 0.99983429 6.15544365
Axis -0.22723251 0.87189973 -0.43376982
Axis point 353.62800026 0.00000000 367.62030912
Rotation angle (degrees) 1.15765443
Shift along axis 0.29432429
> select clear
> ui tool show "Side View"
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> save /Users/lucastafur/Documents/TORC2_paper/Figures/ExtFig6/map-CRIM.png
> pixelSize 0.05 transparentBackground true
> save /Users/lucastafur/Documents/TORC2_paper/Figures/ExtFig6/mapCRIM.cxs
> includeMaps true
> hide #!4 models
> open /Users/lucastafur/Downloads/AF-Q08236-F1-model_v4_avo1.pdb
AF-Q08236-F1-model_v4_avo1.pdb title:
Alphafold monomer V2.0 prediction for target of rapamycin complex 2 subunit
AVO1 (Q08236) [more info...]
Chain information for AF-Q08236-F1-model_v4_avo1.pdb #9
---
Chain | Description | UniProt
A | target of rapamycin complex 2 subunit AVO1 | AVO1_YEAST 1-1176
> select #1/G:620-644
195 atoms, 197 bonds, 25 residues, 1 model selected
> mmaker #9/A to sel
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Monomer_PH_rspr21.pdb, chain G (#1) with
AF-Q08236-F1-model_v4_avo1.pdb, chain A (#9), sequence alignment score = 116.8
RMSD between 12 pruned atom pairs is 0.998 angstroms; (across all 25 pairs:
8.619)
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #9/A:620-791
1376 atoms, 1398 bonds, 172 residues, 1 model selected
> color bfactor palette alphafold key true
> key alphafold :0 :50 :70 :90 :100 showTool true
> ui mousemode right "color key"
106067 atoms, 13195 residues, atom bfactor range 15.6 to 516
> ui mousemode right translate
> undo
> select #9/A:620-791
1376 atoms, 1398 bonds, 172 residues, 1 model selected
> select ~sel & ##selected
7847 atoms, 7978 bonds, 1004 residues, 1 model selected
> hide sel cartoons
> color bfactor palette alphafold key true
> key alphafold :0 :50 :70 :90 :100 showTool true
> ui mousemode right "color key"
106067 atoms, 13195 residues, atom bfactor range 15.6 to 516
> key pos 0.24394,0.0436712 size 0.040483,0.459698
> key pos 0.903582,0.126491 size 0.038899,0.585498
> key pos 0.845577,0.666627 size 0.0358525,0.105018
> key pos 0.880929,0.314265 size 0.0405764,0.501559
> save /Users/lucastafur/Documents/TORC2_paper/Figures/ExtFig6/AFCRIM.png
> pixelSize 0.05 transparentBackground true
> save /Users/lucastafur/Documents/TORC2_paper/Figures/ExtFig6/AFCRIM.cxs
> includeMaps true
> show #!1 models
> open /Users/lucastafur/Documents/TORC2_paper/Figures/ExtFig6/mapCRIM.cxs
> format session
> ui mousemode right translate
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,10
Model Number: MRX53Y/A
Chip: Apple M3 Max
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 36 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4 (23E214)
Kernel Version: Darwin 23.4.0
Time since boot: 27 days, 18 hours, 40 minutes
Graphics/Displays:
Apple M3 Max:
Chipset Model: Apple M3 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
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: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
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: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
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: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 12 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Color key runs command during session close |
comment:2 by , 12 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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