![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#18241 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-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x000000020b8c5f00 (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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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.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, PIL._imagingmath (total: 58)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 16983,
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"build" : "24F74",
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"captureTime" : "2025-07-22 15:18:44.5791 +0200",
"codeSigningMonitor" : 1,
"incident" : "FB4A6046-23B4-4F2D-A628-164CB251BA1D",
"pid" : 40769,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-22 10:22:10.3757 +0200",
"procStartAbsTime" : 1871842538939,
"procExitAbsTime" : 2228123717793,
"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":"6B169C76-CA35-514E-8B10-F8F8A1295F79","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "9575A0BD-1234-9581-1E01-974F4B4A7465",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguage"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "0E34CD9E-8DA6-40EA-A799-A74415A33E98",
"sleepWakeUUID" : "98CBCDB4-91C4-495C-B39B-9D8F8D63BDB3",
"sip" : "enabled",
"vmRegionInfo" : "0x6502743f08f8 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x00006502743f08f8","rawCodes":[1,111061214628088],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00006502743f08f8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":40769},
"vmregioninfo" : "0x6502743f08f8 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
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"name" : "_version.cpython-311-darwin.so"
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"uuid" : "87eed069-25fc-30f6-aa30-1e54859d92e2",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
"name" : "_frame.cpython-311-darwin.so"
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{
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"uuid" : "c1a3c2d3-b21b-3231-839d-fcbc83ca2028",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
"name" : "_serialize.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
"name" : "_cmsgpack.cpython-311-darwin.so"
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{
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"uuid" : "cc06500d-d418-3365-b197-36b1304a819e",
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"name" : "QtOpenGL.abi3.so"
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{
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"uuid" : "b32a8c32-a5e0-3a8b-9a0d-00a26b160215",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
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{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
},
{
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"uuid" : "0c6e9a11-e483-3d7d-a88f-8ad0507af167",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
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"uuid" : "1e310bc7-5f96-396b-816d-5b40a3dde12c",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
{
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
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===== Log before crash start =====
Startup Messages
---
warning | Registration file '/Users/u0159610/Library/Application Support/ChimeraX/registration' has expired
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
> ui tool show Registration
> open "/Users/u0159610/SwitchLab Dropbox/brajabandhu
> pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_2_Models/morph2_foldxmodel.cxs"
> format session
Opened cryosparc_P7_J438_map_sharp.mrc z flip as #5, grid size 256,256,256,
pixel 1.39, shown at level 0.129, step 1, values float32
Opened cryosparc_P7_J418_009_volume_map_sharp (1).mrc z flip as #2, grid size
256,256,256, pixel 1.39, shown at level 0.359, step 1, values float32
Opened cryosparc_P7_J438_map_sharp.mrc z flip zone as #1, grid size
256,256,256, pixel 1.39, shown at level 0.041, step 1, values float32
Opened cryosparc_P7_J438_map_sharp.mrc z flip zone as #6, grid size
256,256,256, pixel 1.39, shown at level 0.0509, step 1, values float32
Opened cryosparc_P7_J418_009_volume_map_sharp (1).mrc z flip zone as #7, grid
size 256,256,256, pixel 1.39, shown at level 0.384, step 1, values float32
Opened cryosparc_P7_J418_009_volume_map_sharp (1).mrc z flip zone as #8, grid
size 256,256,256, pixel 1.39, shown at level 0.368, step 1, values float32
opened ChimeraX session
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> hide #!9 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> volume #5 style surface
> view name p1
> view name p2
> show #!1 models
> hide #!1 models
> volume #5 style mesh
> show #!8 models
> hide #!8 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!9 models
> hide #!9 models
> hide #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> ui tool show "Side View"
> show #!8 models
> show #!2 models
> lighting soft
> volume #2 color #d783ff
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> view name p3
> hide #!8 models
> show #!8 models
> show #!1 models
> hide #!1 models
> hide #!8 models
> show #!1 models
> hide #!7 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!8 models
> hide #!8 models
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> show #!8 models
> show #!7 models
> view name p4
> show #!9 models
> view name p5
> view p1
> show #!1 models
> show #!2 models
> hide #!9 models
> view p2
> view p3
> view p5
> view p4
> fly p1 p2 p3 p4
> hide #!8 models
> hide #!7 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> movie record
> volume #2 level 0.469
> volume #2 level 0.4941
> volume #2 level 0.7098
> movie record
Already recording a movie
> movie stop
> roll y 10 36 #2
Expected a keyword
> roll y 10 36 center #2
> roll y 20 18 center #2
> roll y 4 90 center #2
> roll y 2 180 center #2
> turn y 90
> turn z 90
> turn x 90
> turn y 90
> turn x 90
> volume #2 level 0.3537
> show #!9 models
> volume #2 style mesh
> hide #!2 models
> show #!2 models
> hide #!9 models
> show #!9 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!9 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!9 models
> hide #!4 models
> hide #!3 models
> show #!8 models
> show #!7 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!7 models
> hide #!8 models
> hide #!6 models
> show #!6 models
> show #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> hide #!9 models
> hide #!1 models
> show #!1 models
> show #!7 models
> hide #!8 models
> show #!8 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!2 models
> hide #!2 models
> show #!9 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #2 style surface
> volume #2 level 0.6195
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!2 models
> show #!2 models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> graphics silhouettes true
> volume #2 level 0.6345
> roll y 4 90 center #2
> turn x 90
> zoom 0.75
moved plane near -336.7457502740981 [ 0.00715726 0.03333838 -0.9994185 ]
moved plane far -336.7457502740981 [ 0.00715726 0.03333838 -0.9994185 ]
> zoom 1.5
moved plane near 448.9943346236103 [ 0.00715726 0.03333838 -0.9994185 ]
moved plane far 448.9943346236103 [ 0.00715726 0.03333838 -0.9994185 ]
> zoom 5
moved plane near 718.3909324383754 [ 0.00715726 0.03333838 -0.9994185 ]
moved plane far 718.3909324383754 [ 0.00715726 0.03333838 -0.9994185 ]
> zoom 3
moved plane near 119.73181812719434 [ 0.00715726 0.03333838 -0.9994185 ]
moved plane far 119.73181812719434 [ 0.00715726 0.03333838 -0.9994185 ]
> zoom 0.2
moved plane near -239.46363230852052 [ 0.00715726 0.03333838 -0.9994185 ]
moved plane far -239.46363230852052 [ 0.00715726 0.03333838 -0.9994185 ]
> zoom 0.2
moved plane near -1197.3181697663215 [0.99051076 0.10057255 0.09366753]
moved plane far -1197.3181697663215 [0.99051076 0.10057255 0.09366753]
> zoom 0.4
moved plane near -2244.971583606832 [0.99051076 0.10057255 0.09366753]
moved plane far -2244.971583606832 [0.99051076 0.10057255 0.09366753]
> zoom 1
moved plane near -0.0 [0.99051076 0.10057255 0.09366753]
moved plane far -0.0 [0.99051076 0.10057255 0.09366753]
> zoom 1.5
moved plane near 1247.2064417100366 [0.99051076 0.10057255 0.09366753]
moved plane far 1247.2064417100366 [0.99051076 0.10057255 0.09366753]
> zoom 1.5
moved plane near 831.4709575995204 [0.99051076 0.10057255 0.09366753]
moved plane far 831.4709575995204 [0.99051076 0.10057255 0.09366753]
> zoom 1.5
moved plane near 554.3139693726773 [0.99051076 0.10057255 0.09366753]
moved plane far 554.3139693726773 [0.99051076 0.10057255 0.09366753]
> zoom 1.5
moved plane near 369.5426446748941 [0.99051076 0.10057255 0.09366753]
moved plane far 369.5426446748941 [0.99051076 0.10057255 0.09366753]
> zoom 1.5
moved plane near 246.36176206755792 [0.99051076 0.10057255 0.09366753]
moved plane far 246.36176206755792 [0.99051076 0.10057255 0.09366753]
> zoom 1.5
moved plane near 164.24117401234642 [0.99051076 0.10057255 0.09366753]
moved plane far 164.24117401234642 [0.99051076 0.10057255 0.09366753]
> zoom 1.5
moved plane near 109.49411554199169 [0.99051076 0.10057255 0.09366753]
moved plane far 109.49411554199169 [0.99051076 0.10057255 0.09366753]
> turn x 90
> rotate z 90
Unknown command: rotate z 90
> turn z 90
> turn x 90
> turn y
> roll y 4 90 center #2
> turn x 90
> zoom 3
moved plane near 757.8687109848526 [ 0.04187114 -0.01361814 -0.99903029]
moved plane far 757.8687109848526 [ 0.04187114 -0.01361814 -0.99903029]
> turn z50
Expected an axis vector or a keyword
> turn z 50
> volume #2 level 0.3587
> show #!8 models
> hide #!8 models
> hide #!2 models
> show #!8 models
> hide #!8 models
> graphics silhouettes false
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!7 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> orient #2
Unknown command: orient #2
> select add #2
4 models selected
> hide #!2 models
> show #!2 models
> select add #2
4 models selected
> select subtract #2
Nothing selected
> volume #2 level 0.6997
> volume #2 level 0.6897
> graphics silhouettes false
> graphics silhouettes true
> view name p1
> roll y 4 90 #2
Expected a keyword
> roll y 4 90 center #2
> turn x 90
> show #!9 models
> roll y 4 90 center #2
> turn x 90
> zoom 4
moved plane near 956.2278958008205 [ 0.06741475 0.06378036 -0.99568445]
moved plane far 956.2278958008205 [ 0.06741475 0.06378036 -0.99568445]
> volume #2 level 0.3587
> hide #!2 models
> show #!8 models
> hide #!8 models
> graphics silhouettes false
> show #!8 models
> show #!7 models
> show #7,8
> hide #7,8
> show #7,8
> view p1
> show #!2 models
> hide #!8 models
> hide #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #9
> show #!9 models
> hide #!9 models
> roll y 4 90 center #2
> turn x 90
> view name p2
> zoom 4
moved plane near 774.4056942753766 [ 0.03176016 0.02803891 -0.99910224]
moved plane far 774.4056942753766 [ 0.03176016 0.02803891 -0.99910224]
> zoom 0.75
moved plane near -86.04503129289363 [ 0.03176016 0.02803891 -0.99910224]
moved plane far -86.04503129289363 [ 0.03176016 0.02803891 -0.99910224]
> turn z 50
> turn z 32
> turn z 20
> turn z 5
> view name p3
> volume #2 level 0.3587
> volume #2 level 0.2835
> volume #2 level 0.2835
> volume #2 level 0.283
> volume #2 level 0.27
> hide #2
> graphics silhouettes false
> show #7,8
> show #!9 models
> hide #!9 models
> show #!3 models
> show #!4 models
> show #!3,4 models
> hide #!3,4 models
> show #!3,4 models
> zoom 1.5
moved plane near 113.76157937209423 [ 0.03382792 0.02426317 -0.99913313]
moved plane far 113.76157937209423 [ 0.03382792 0.02426317 -0.99913313]
> turn z 5
> turn z -5
> turn z 5
> view p1
> view p2
> view p4
> view p5
> view p1
> view p2
> view p3
> view pp4
Expected an objects specifier or a view name or a keyword
> view p4
> view p1
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> hide #!8 models
> hide #!4 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color #2 #ff85ffff models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select #9/p
66 atoms, 65 bonds, 9 residues, 1 model selected
> select #9/p,F
372 atoms, 377 bonds, 49 residues, 1 model selected
> select #9/p,F,H
678 atoms, 689 bonds, 89 residues, 1 model selected
> select ~sel & ##selected
4374 atoms, 4446 bonds, 574 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> color #2 #d783ffff models
> hide #!9 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.6812
> graphics silhouettes true
> view name p1
> roll y 4 90 center #2
> turn x 90
> view name p2
> zoom 3
moved plane near 702.6577642138668 [ 0.00539731 -0.00371411 0.99997855]
moved plane far 702.6577642138668 [ 0.00539731 -0.00371411 0.99997855]
> volume #2 level 0.28
> view name p4
> hide #2
> graphics silhouettes false
> show #7,8
> view name p5
> show #!9 models
> turn z 5
> fly p1
> fly p1 p2
> fly p1 p2 p3 p4
> show #!1 models
> show #!2 models
> fly p1 p2 p3 p4
> volume #2 level 0.2599
> fly p1 p2 p3 p4
> fly p2 p3 p4
> fly p1 p2
> fly p2 p3
> fly p3 p4
> fly p3 p5
> hide #!1 models
> show #!1 models
> close #1
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> close #3
> close #4
> show #!5 models
> hide #!5 models
> hide #!7 models
> show #!7 models
> hide #!2 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> show #!6 models
> hide #!6 models
> close #6
> close #5
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> show #!2 models
> select add #2
3 models selected
> view sel
> select subtract #2
Nothing selected
> select add #7
2 models selected
> select subtract #7
Nothing selected
> select add #8
2 models selected
> select subtract #8
Nothing selected
> select add #9
678 atoms, 689 bonds, 89 residues, 2 models selected
> select subtract #9
Nothing selected
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.621
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> scene side_view
Unknown command: scene side_view
> show #!9 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> hide #!9 models
> show #!9 models
> show #!7 models
> show #!8 models
> show #!2 models
> movie record
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.3352
> show #!7 models
> show #!8 models
> show #!9 models
> movie stop
> save /Users/u0159610/Desktop/image34.png supersample 3
> movie encode /Users/u0159610/Desktop/itieam.mp4
Movie saved to /Users/u0159610/Desktop/itieam.mp4
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!2 models
> volume #2 level 0.6511
> movie record
> roll y 4 90 center #2
> turn x 90
> volume #2 level 0.3903
> show #!7 models
> show #!8 models
> hide #!2 models
> show #!9 models
> movie stop
> movie encode /Users/u0159610/Desktop/itieam.mp4
Movie saved to /Users/u0159610/Desktop/itieam.mp4
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!2 models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> volume #2 level 0.7163
> movie record
> roll y 4 90 center #2
> turn x 90
> volume #2 level 0.3753
> graphics silhouettes false
> show #!7 models
> show #!8 models
> hide #!2 models
> show #!9 models
> movie stop
> movie encode /Users/u0159610/Desktop/itieam.mp4
Movie saved to /Users/u0159610/Desktop/itieam.mp4
> view name p5
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!2 models
> volume #2 level 0.6762
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> view name p1
> turn x 90
> view name p2
> view name p3
> show #!7 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> show #!8 models
> show #!7 models
> show #!9 models
> hide #!9 models
> hide #!2 models
> hide #!7 models
> hide #!8 models
> view p1
> show #!2 models
> graphics silhouettes true
> movie record
> roll y 4 90 center #2
> flyby p1 p2
Unknown command: flyby p1 p2
> fly p1 p2
> fly p2 p3
> show #!8 models
> hide #!8 models
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> hide #!2 models
> show #!7 models
> show #!8 models
> fly p3 p5
> show #!9 models
> movie stop
> movie encode /Users/u0159610/Desktop/itieam.mp4
Movie saved to /Users/u0159610/Desktop/itieam.mp4
> view p1
> show #!2 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> view p2
> view p3
> fly p2 p3
> fly p1 p2 p3
> view p1
> view p2
> view name p2
> view p3
> fly p1 p2 p3
> hide #!2 models
> show #!2 models
> select add #2
2 models selected
> view sel
> select add #2
3 models selected
> select subtract #2
Nothing selected
> view #2 clip false
> view clip false
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> fly p1
> fly p1 p2
> fly p1 p2 p3
> fly p1 p2
> volume #2 level 0.6685
> view name p2
> fly p1 p2
> ui tool show "Side View"
> view name p3
> fly p1 p2 p3
> fly p2 p3
> view p2
> view p3
> fly p2 p3
> fly p1 p3
> view p3
> view name p3
> fly p1 p2 p3
> view p1
> view name p1
> turn x 90
> view p2
> view p1
> turn x 90
> zoom 3
moved plane near 588.9770379832257 [-0.01605782 0.05060235 -0.99858977]
moved plane far 588.9770379832257 [-0.01605782 0.05060235 -0.99858977]
> zoom 0.3
moved plane near -369.46825134938763 [-0.01605782 0.05060235 -0.99858977]
moved plane far -369.46825134938763 [-0.01605782 0.05060235 -0.99858977]
> view p§
Expected an objects specifier or a view name or a keyword
> view name p1
> turn x 90
> view p2
> fly p1 p2
> view name p3
> fly p1 p2 p3
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> graphics silhouettes false
> volume #2 level 0.5066
> graphics silhouettes true
> graphics silhouettes false
> show #!7 models
> show #!8 models
> show #!8,9 models
> hide #!2 models
> view name o4
> view name p4
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!2 models
> view p1
> video record
Unknown command: video record
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/u0159610/Desktop/movie8.mp4
Movie saved to /Users/u0159610/Desktop/movie8.mp4
> volume #2 level 0.4835
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> movie encode
No frames have been recorded
> movie record
> roll y 4 90 center #2
> fly p1 p2
> fly p2 p3
> volume #2 level 0.3679
> fly p3 p4
> hide #!2 models
> show #!7 models
> show #!8 models
> show #!9 models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> movie stop
> view p1
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!2 models
> view p2
> view p3
> fly p2 p3
> fly p1 p3
> volume #2 level 0.2985
> view name p4
> fly p1 p4
> graphics silhouettes false
> show #!8,9 models
> hide #!9 models
> show #!7 models
> show #!7,8 models
> hide #!2 models
> view name p4
> show #!9 models
> view name p5
> fly p1 p5
> show #!2 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> View p1
Unknown command: View p1
> view p1
> roll y 4 90 center #2
> roll y 5 72 center #2
> roll y 3 120 center #2
> fly p1 p3
> view name p3
> fly p1 p3
> fly p1 p2 p3
> view p2
> fly p1 p2
> fly p1 p2 p3
> view p2
> view name p3
> fly p1 p2 p3
> view p1
> turn y 90
> view p1
> turn x 90
> view name p2
> fly p1 p2
> view name p3
> fly p1 p2 p3
> view p1
> view p2
> view p3
> fly p1 p3
> view p1
> turn y 90
> view p1
> turn x 90
> view name p2
> fly p1 p2
> view name p2
> fly p1 p2
> view p1
> view name p1
> fly p1 p2
> fly p1 p2 p3
> view name p4
> fly p1 p4
> fly p1 p2 p3 p4
> fly p1 p2 p4
> show #!8 models
> show #!7 models
> graphics silhouettes false
> show #!7,8 models
> hide #!2 models
> view name p4
> fly p1 p4
> hide #!8 models
> hide #!7 models
> show #!2 models
> show #!9 models
> hide #!9 models
> view p1
> view p2
> view p3
> view p1
> view p2
> view p3
> view p2
> view name p3
> fly p1 p2 p3
> view p1
> fly p1 p3
> fly p1 p2
> view name p3
> fly p1 p2 p3
> fly p1 p2
> view name p3
> fly p1 p2 p3
> fly p1 p2
> fly p2 p3
> show #!7,8 models
> hide #!2 models
> show #!9 models
> view name p4
> fly p3 p4
> view p1
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!2 models
> movie record
> roll y 3 120 center #2
> fly p1 p2
> fly p2 p3
> graphics silhouettes false
> show #!7,8 models
> hide #!2 models
> show #!9 models
> fly p3 p4
> movie stop
> movie encode /Users/u0159610/Desktop/itieam.mp4
Movie saved to /Users/u0159610/Desktop/itieam.mp4
> view p1
> hide #!7 models
> hide #!8 models
> hide #!9 models
> view p1
> show #!2 models
> graphics silhouettes true
> fly p1 p2
> fly p2 p3
> view p2
> view name p3
> fly p2
> fly p2 p3
> fly p1 p2 p3
> fly p1 p2
> view p1
> view p2
> view p3
> view p1
> view p2
> fly p1 p2
> view name p2
> fly p1 p2
> view p1
> view name p1
> view name p2
> view name p1
> view p2
> turn x 90
> view p2
> turn x 90
> view name p2
> view name p3
> view p2
> view p3
> fly p1 p3
> fly p1 p2
> fly p1 p23
fly: Unknown position name "p23"
> fly p1 p2 p3
> view name p3
> view p1 p3
Expected an integer >= 1 or a keyword
> fly p1 p3
> fly p1 p2
> fly p1 p2 p3
> show #!7 models
> show #!8 models
> graphics silhouettes false
> hide #!2 models
> view name p4
> fly p3 p4
> show #!9 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!2 models
> view p1
> fly p1 p2 p3
> fly p1 p3
> fly p2 p3
> View p1
Unknown command: View p1
> view p1
> movie record
> roll y 3 120 center #2
> fly p1 p2 p3
> graphics silhouettes false
> show #!7,8 models
> hide #!2 models
> fly p3 p4
> show #!9 models
> movie stop
> view p1
> show #!2 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> graphics silhouettes true
> fly p1 p3
> view name p5
> fly p1 p2 p3
> view p1
> fly p1 p2 p3
> view p5
> fly p3 p5
> view p1
> view p2
> view p3
> view p1 p2
Expected an integer >= 1 or a keyword
> fly p1 p2
> fly p2 p3
> view p1
> fly p1 p2
> fly p2 p3
> fly p3 p5
> view name p4
> fly p3 p4
> view p5
> view p4
> show #!7 models
> show #!8 models
> show #!9 models
> hide #!9 models
> hide #!2 models
> graphics silhouettes false
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!7 models
> hide #!8 models
> show #!2 models
> View p1
Unknown command: View p1
> View p1
Unknown command: View p1
> view p1
> movie record
> roll y 3 120 center #2
> fly p1 p2 p3
> fly p3 p4
> show #!7,8 models
> hide #!2 models
> fly p3 p4
> show #!9 models
> movie stop
> movie encode /Users/u0159610/Desktop/itieam.mp4
Movie saved to /Users/u0159610/Desktop/itieam.mp4
> movie reset
No movie being recorded.
> hide #!7 models
> hide #!9 models
> hide #!8 models
> show #!2 models
> view p1
> fly p1 p3
> view p4
> fly p3 p4
> view p1
> fly p1 p4
> view p4
> fly p3 p4
> view p1
> fly p3 p4
> view p4
> show #!8 models
> show #!7 models
> hide #!2 models
> view name p5
> show #!9 models
> hide #!9 models
> fly p4 p5
> hide #!7 models
> hide #!8 models
> show #!2 models
> hide #!2 models
> show #!2 models
> view p1
> fly p1 p2 p3
> view p4
> view p3 p4
Expected an integer >= 1 or a keyword
> fly p3 p4
> view p3
> view p2
> view p4
> view name p3
> fly p1 p3
> view p1
> fly p1 p3
> view p3
> graphics silhouettes false
> show #!7,8 models
> hide #!2 models
> show #!2 models
> view name p3
> fly p2 p3
> view p1
> fly p1 p2
> fly p2 p3
> view p3
> fly p2 p3
> view pe
Expected an objects specifier or a view name or a keyword
> view p1
> view p3
> fly p1 p3
> view p1
> view p3
> view p1
> view p2
> view p3
> fly p1 p3
> view p1
> view p3
> view p1
> fly p1 p3
> view p3
> view p1
> view name p1
> view p3
> fly p1 p3
> view p1
> view p2
> fly p1 p3
> view p3
> view name p2
> fly p1 p2
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> view p4
> hide #!2 models
> view name p3
> fly p2 p3
> show #!9 models
> view p1
> show #!2 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> movie record
> roll y 3 120 center #2
> fly p1 p2
> show #!7,8 models
> hide #!2 models
> fly p3 p4
> fly p2 p3
> movie stop
> movie reset
> view p1
> hide #!7 models
> hide #!8 models
> show #!2 models
> view p2
> view p1
> view p2
> view p3
> view p2
> hide #!2 models
> show #!7 models
> show #!8 models
> view name p3
> view name p4
> show #!9 models
> hide #!9 models
> view p1
> hide #!7 models
> hide #!8 models
> show #!2 models
> view p2
> fly p1 p2
> view p1
> fly p1 p2
> view p1
> view p2
> show #!7 models
> show #!8 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> view p2
> view p1
> view p2
> view p3
> fly p1 p2
> view p1
> fly p1 p2
> view p2
> graphics silhouettes true
> view p1
> movie record
> movie stop
> movie reset
> view p1
> fly p1 p2
> view p1
> view name p1
> fly p1 p2
> view p2
> view p1
> view p3
> fly p2 p3
> view p1 p3
Expected an integer >= 1 or a keyword
> fly p1 p3
> hide #!2 models
> show #!2 models
> graphics silhouettes false
> hide #!2 models
> fly p4 p5
> fly p2 p3
> view p3
> view p4
> view p1
> show #!2 models
> graphics silhouettes true
> movie record
> roll y 3 120 center #2
> fly p1 p2
> graphics silhouettes false
> hide #!2 models
> fly p3 p4
> show #!9 models
> movie stop
> movie reset
> view p1
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!2 models
> fly p1 p2
> hide #!2 models
> show #!7 models
> show #!8 models
> fly p3 p4
> view p3
> view name p4
> view p1
> fly p1 p2
> fly p3 p4
> view p2
> view name p3
> fly p1 p2
> view p1
> fly p1 p2
> fly p2 p3
> view p2
> fly p2 p3
> view p2
> show #!2 models
> view name p2
> fly p2 p3
> hide #!2 models
> hide #!7 models
> show #!7 models
> view p3
> fly p2 p3
> fly p1 p2
> fly p2 p3
> view p1
> fly p1 p2
> fly p2 p3
> view p1
> view name p1
> fly p1 p2
> fly p2 p3
> hide #!7 models
> hide #!8 models
> show #!2 models
> view p1
> fly p1 p2
> fly p2 p3
> fly p1 p2
> fly p2 p3
> view p1
> graphics silhouettes false
> show #!7 models
> show #!8 models
> view p3
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!7 models
> hide #!8 models
> fly p1 p3
fly: Nothing displayed to calculate center of rotation
> show #!2 models
> fly p1 p3
> fly p3 p4
> hide #!2 models
> show #!7 models
> show #!8 models
> fly p3 p4
> view p3
> show #!2 models
> hide #!2 models
> show #!9 models
> hide #!9 models
> view p1
> show #!2 models
> fly p1 p3
> view p2
> fly p1 p3
> view p3
> fly p1 p3
> view p1
> view p2
> fly p1 p2
> view p1
> view name p1
> view name p1
> view p1
> fly p1 p2
> view p2
> view p3
> fly p2 p3
> fly p1 p3
> view p1
> view p3
> movie record
> fly p1 p3
> movie stop
> movie encode /Users/u0159610/Desktop/itieam.mp4
Movie saved to /Users/u0159610/Desktop/itieam.mp4
> movie reset
No movie being recorded.
> movie encode
No frames have been recorded
> movie record
> fly p1 p3
> movie stop
> movie encode /Users/u0159610/Desktop/itieam.mp4
Movie saved to /Users/u0159610/Desktop/itieam.mp4
> movie reset
No movie being recorded.
> view p1
> movie record
> roll y 3 120 center #2
> movie stop
> view p3
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> crossfade
> show #!2 models
> crossfade
> hide #2
> crossfade
> hide #2
> crossfade
> hide #2
> crossfade
> hide #2: wait 20
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> movie crossfade
> hide #2: wait 20
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> movie crossfade
> crossfade
> hide #2: wait 20
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> crossfade
> hide #2: wait 20
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> crossfade
> hide #2: wait 20
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #!2 models
> movie crossfade
> hide #2: wait 20
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #!2 models
> show #!2 models
> view p1
> hide #!2 models
> show #!2 models
> select add #2
2 models selected
> view sel
No displayed objects specified.
> color #2 #ff85ffff models
> color #2 #d783ffff models
> hide #!7 models
> hide #!8 models
> view p1
> view p2
> view p3
> select add #2
3 models selected
> select subtract #2
Nothing selected
> show #!7 models
> show #!8 models
> view p1
> crossfade fade; hide #2
Expected an integer >= 1 or a keyword
> hide #!2 models
> show #!2 models
> crossfade fade;hide #!2 models
Expected an integer >= 1 or a keyword
> crossfade
> hide #!2 models
> crossfade
> hide #!2 models
> crossfade
> hide #!2 models
> show #!2 models
> crossfade
> hide #!2 models
> crossfade
> hide #!2 models
> crossfade
> hide #!2 models
> crossfade
> show #!2 models
> crossfade
> show #!2 models
> crossfade
> show #!2 models
> crossfade
> show #!2 models
> crossfade
> show #!2 models
> crossfade
> show #!2 models
> view p2
> volume morph #2 #3
volume morph requires 2 or more volumes, got 1
> hide #!7 models
> hide #!8 models
> hide #!2 models
===== Log before crash end =====
Log:
Startup Messages
---
warning | Registration file '/Users/u0159610/Library/Application Support/ChimeraX/registration' has expired
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: Mac14,7
Model Number: Z16S000UNFN/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 2 days, 22 hours, 51 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
S24R65x:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 4 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 , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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