id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18434	Mac wake from sleep crash	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.6-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

Thread 0x000000032ba43000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000032aa37000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000329a2b000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000328a1f000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000327a13000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000326a07000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x00000003259fb000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x00000003249ef000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x00000003239e3000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x00000003229d7000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x00000003219cb000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x00000003209bf000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031f9b3000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031e9a7000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031d99b000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031c98f000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000031b983000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00000001fd9760c0 (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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, 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, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 56)


{""app_name"":""ChimeraX"",""timestamp"":""2025-08-14 19:32:42.00 +0800"",""app_version"":""1.9.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.6 (24G84)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""CCDEA146-D5B3-4866-950F-5C8795729062""}
{
  ""uptime"" : 440000,
  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""Mac16,8"",
  ""coalitionID"" : 84552,
  ""osVersion"" : {
    ""train"" : ""macOS 15.6"",
    ""build"" : ""24G84"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2025-08-14 19:32:16.8500 +0800"",
  ""codeSigningMonitor"" : 2,
  ""incident"" : ""CCDEA146-D5B3-4866-950F-5C8795729062"",
  ""pid"" : 70559,
  ""translated"" : false,
  ""cpuType"" : ""ARM-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2025-08-14 14:27:50.3571 +0800"",
  ""procStartAbsTime"" : 10301456736556,
  ""procExitAbsTime"" : 10675179057606,
  ""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"":""DD5D85C7-085B-5484-B9CC-7F123C5DE0A3"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""C646FE3B-2D8A-E277-3F5C-DC4F9C216704"",
  ""appleIntelligenceStatus"" : {""state"":""unavailable"",""reasons"":[""countryBillingIneligible"",""countryLocationIneligible""]},
  ""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"" : ""155F7035-1114-4294-B194-2EAB2E6A39BC"",
  ""wakeTime"" : 2,
  ""sleepWakeUUID"" : ""27A792CD-480F-4150-AD37-ED48638D8F59"",
  ""sip"" : ""enabled"",
  ""vmRegionInfo"" : ""0x169 is not in any region.  Bytes before following region: 4329832087\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      102140000-102144000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX"",
  ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000169"",""rawCodes"":[1,361],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000169""},
  ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":70559},
  ""vmregioninfo"" : ""0x169 is not in any region.  Bytes before following region: 4329832087\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      102140000-102144000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX"",
  ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""warnings"":0},
  ""faultingThread"" : 0,
  ""threads"" : [{""threadState"":{""x"":[{""value"":0},{""value"":0},{""value"":1},{""value"":4563696280},{""value"":99},{""value"":116},{""value"":1152921511031020864},{""value"":0},{""value"":14823324183470528851},{""value"":14823324185842989459},{""value"":14757395258967641293},{""value"":4294967286},{""value"":4563696210},{""value"":0},{""value"":53},{""value"":4294967280},{""value"":328},{""value"":8566658392},{""value"":0},{""value"":11},{""value"":259},{""value"":8549523872,""symbolLocation"":224,""symbol"":""_main_thread""},{""value"":0},{""value"":1},{""value"":4350346800,""symbolLocation"":0,""symbol"":""faulthandler_handlers""},{""value"":8510689280,""symbolLocation"":0,""symbol"":""OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list""},{""value"":8510689280,""symbolLocation"":0,""symbol"":""OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list""},{""value"":5},{""value"":1}],""flavor"":""ARM_THREAD_STATE64"",""lr"":{""value"":6704478348},""cpsr"":{""value"":1073741824},""fp"":{""value"":4563696352},""sp"":{""value"":4563696320},""esr"":{""value"":1442840704,""description"":"" 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===== Log before crash start =====
Startup Messages  
---  
warning | Registration file '/Users/hongwenchen/Library/Application Support/ChimeraX/registration' has expired  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/hongwenchen/Desktop/MS_OSTalpha-beta/Map-and-
> Model/apo_cryosparc_P95_J1807_003_volume_map_sharp_2.86.mrc

Opened apo_cryosparc_P95_J1807_003_volume_map_sharp_2.86.mrc as #1, grid size
224,224,224, pixel 1.1, shown at level 0.101, step 1, values float32  

> ui tool show Registration

Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  
hongwen.chen@sjtu.edu.cn has been invited to the ChimeraX announcements list  

> set bgColor white

> volume #1 level 0.1961

> ui tool show ""Side View""

> open ""/Users/hongwenchen/Desktop/MS_OSTalpha-beta/Map-and-
> Model/apo_cryosparc_P95_J1807_003_volume_map_sharp_2.86 copy.mrc""

Opened apo_cryosparc_P95_J1807_003_volume_map_sharp_2.86 copy.mrc as #2, grid
size 224,224,224, pixel 1.1, shown at level 0.101, step 1, values float32  

> volume #2 color #7a81ff

> volume #2 color #0433ff

> volume #2 color #0096ff

> volume #2 level 0.2594

> volume #1 color #b2b2b249

> volume #1 level 0.101

> ui tool show ""Hide Dust""

> surface dust #1 size 6.6

> volume #1 color darkgrey

> volume #1 color #a9a9a917

> volume #1 color #a9a9a914

> volume #1 level 0.1141

> volume #1 level 0.1075

> volume #1 step 2

> volume #1 step 16

> volume #1 step 1

> volume #1 style image

> volume #1 style mesh

> volume #1 style image

> volume #1 level -0.02944,0 level 0.1008,0.8 level 2.166,1

> volume #1 level -0.02944,0 level 0.1008,0.8 level 2.133,0.03077

> volume #1 level -0.02944,0 level 0.09431,0.6154 level 2.133,0.03077

> volume #1 level -0.02944,0 level 0.09431,0.6154 level 2.133,1

> volume #1 level 0.003188,0.01538 level 0.09431,0.6154 level 2.133,1

> volume #1 color #929292 color white color white

> volume #1 color #929292a2 color white color white

> volume #1 color #929292b0 color white color white

> volume #1 style surface

> volume #1 color #929292a4

> volume #1 color #92929200

> volume #1 color #9292920a

> volume #1 color #9292920d

> volume #1 style image region 0,0,111,223,223,111 step 1 showOutlineBox true

> volume #1 region 0,0,0,223,223,223 step 1

> volume #1 region 0,0,0,223,223,223 step 1 colorMode opaque8 orthoplanes xyz
> positionPlanes 111,111,111 imageMode orthoplanes

> volume #1 imageMode ""box faces""

> volume #1 colorMode auto8 imageMode ""tilted slab"" tiltedSlabAxis
> -0.7615,0.6301,0.1521 tiltedSlabOffset -21.67 tiltedSlabSpacing 1.1
> tiltedSlabPlaneCount 44

> volume #1 maximumIntensityProjection true imageMode ""full region""

> volume #1 maximumIntensityProjection false

> volume #1 style surface

> volume #1 color #424242

> volume #1 color #4242420f

> volume #1 color darkgrey

> volume #1 color #a9a9a90d

> surface dust #1 size 5.86

> surface dust #1 size 1.79

> surface dust #1 size 5

> open /Users/hongwenchen/Desktop/MS_OSTalpha-beta/Map-and-
> Model/R_apo_2.86.pdb

Chain information for R_apo_2.86.pdb #3  
---  
Chain | Description  
A C | No description available  
B D | No description available  
  

> volume #1 tiltedSlabAxis -0.7959,0.6004,-0.07808 tiltedSlabOffset -60.3

> volume #1 tiltedSlabAxis -0.7654,0.4927,-0.4141 tiltedSlabOffset -116.5

> turn x 90

> turn x -90

> turn x 90

> turn x -90

> turn x 90

> turn x -90

> turn x 90

> select #2:A

Nothing selected  

> select #3:A

Nothing selected  

> select #3/A

3205 atoms, 3267 bonds, 340 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel forest green

> color sel #00ffffff

> color sel #00ff00ff

> color sel #00fa92ff

> color sel #00f900ff

> color sel #00fa00ff

> color sel #00fb00ff

> color sel #00fd00ff

> color sel #00ff00ff

> select #3/C

3205 atoms, 3274 bonds, 340 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel cyan

> select clear

> select #3/b

426 atoms, 434 bonds, 53 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel orange

> select #3/d

426 atoms, 434 bonds, 53 residues, 1 model selected  

> color sel magenta

> select #3

7262 atoms, 7409 bonds, 786 residues, 1 model selected  

> select #3/a/b/c/d

7262 atoms, 7409 bonds, 786 residues, 1 model selected  

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> ui tool show ""Color Zone""

> color zone #2 near #3 distance 6.6

> color zone #2 near #3 distance 5

> volume #2 color #d6d6d6

> color zone #2 near #3 distance 5

> color zone #2 near #3 distance 4.9

> color zone #2 near #3 distance 4.8

> color zone #2 near #3 distance 4.7

> color zone #2 near #3 distance 4.6

> color zone #2 near #3 distance 4.5

> color zone #2 near #3 distance 4.4

> color zone #2 near #3 distance 3

> volume #2 tiltedSlabAxis -0.7647,0.1135,-0.6343 tiltedSlabOffset -195.8

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> select clear

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> color zone #2 near #3 distance 3

> volume #2 tiltedSlabAxis 0.7825,-0.6224,0.014 tiltedSlabOffset 18.6

> select clear

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> select clear

> select backbone

3008 atoms, 3004 bonds, 752 residues, 1 model selected  

> color zone #2 near #3 distance 3

> color single #2

> color zone #2 near #3 distance 3

> color single #2

> color zone #2 near #3 distance 3

> volume #2 tiltedSlabAxis -0.5036,0.6449,0.5748 tiltedSlabOffset 45.17

> ui tool show ""Side View""

> open ""/Users/hongwenchen/Desktop/MS_OSTalpha-beta/Map-and-Model/R_apo_2.86
> copy.pdb""

Summary of feedback from opening /Users/hongwenchen/Desktop/MS_OSTalpha-
beta/Map-and-Model/R_apo_2.86 copy.pdb  
---  
warnings | CONECT record to nonexistent atom: (1196, 3093)  
CONECT record to nonexistent atom: (1202, 3144)  
CONECT record to nonexistent atom: (1208, 3110)  
CONECT record to nonexistent atom: (1214, 3127)  
CONECT record to nonexistent atom: (1220, 3161)  
2 messages similar to the above omitted  
CONECT record for nonexistent atom: 2512  
Cannot find LINK/SSBOND residue PLM (501 )  
Cannot find LINK/SSBOND residue PLM (504 )  
Cannot find LINK/SSBOND residue PLM (502 )  
Cannot find LINK/SSBOND residue PLM (503 )  
Cannot find LINK/SSBOND residue PLM (505 )  
2 messages similar to the above omitted  
  
Chain information for R_apo_2.86 copy.pdb #4  
---  
Chain | Description  
A C | No description available  
B D | No description available  
  

> close #3

> select #3/a/b/c/d

Nothing selected  

> color single #2

> color zone #2 near #4 distance 3

> color single #2

> select #3/a/b/c/d

Nothing selected  

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> color zone #2 near #4 distance 3

> color zone #2 near #4 distance 3.06

> color zone #2 near #4 distance 11.74

> color single #2

> select #3/a

Nothing selected  

> ui tool show ""Color Actions""

> color light sea green

> select /A

2510 atoms, 2565 bonds, 323 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel forest green

> color sel sea green

> select /C

2510 atoms, 2565 bonds, 323 residues, 1 model selected  

> color sel turquoise

> color sel dark turquoise

> select /B

426 atoms, 434 bonds, 53 residues, 1 model selected  

> color sel deep sky blue

> color sel bychain

> color sel dark orange

> color sel sandy brown

> color sel dark salmon

> color sel sandy brown

> color sel dark salmon

> select /D

426 atoms, 434 bonds, 53 residues, 1 model selected  

> color sel orange

> color sel dark orange

> color sel orange

> color sel sandy brown

> select clear

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> color zone #2 near #4 distance 11.74

> color zone #2 near #4 distance 5

> volume #2 color #d6d6d6

> color zone #2 near #4 distance 5

> color zone #2 near #4 distance 3

> surface dust #2 size 5

> surface dust #2 size 5.1

> surface dust #2 size 5.2

> surface dust #2 size 5.3

> surface dust #2 size 5.4

> surface dust #2 size 5.5

> surface dust #2 size 5.6

> surface dust #2 size 5.7

> surface dust #2 size 5.8

> surface dust #2 size 5.9

> surface dust #2 size 6

> surface dust #2 size 6.1

> surface dust #2 size 6.2

> surface dust #2 size 6.3

> surface dust #2 size 6.4

> surface dust #2 size 6.5

> surface dust #2 size 6.6

> surface dust #2 size 6.7

> surface dust #2 size 6.8

> surface dust #2 size 6.9

> color zone #2 near #4 distance 2

> color zone #2 near #4 distance 1.82

> color zone #2 near #4 distance 1.54

> color zone #2 near #4 distance 1.57

> color zone #2 near #4 distance 2.22

> volume #1 color #d6d6d6

> volume #1 color #d6d6d60e

> volume #1 color #d6d6d60d

> volume #1 tiltedSlabAxis 0.5781,-0.8108,0.09155 tiltedSlabOffset -18.43

> volume #1 tiltedSlabAxis -0.6739,-0.5874,-0.4481 tiltedSlabOffset -191.6

> volume #1 tiltedSlabAxis -0.8986,0.4256,0.107 tiltedSlabOffset -12.68

> volume #1 tiltedSlabAxis -0.2212,0.6595,0.7185 tiltedSlabOffset 122.3

> volume #1 tiltedSlabAxis 0.02117,0.8896,0.4562 tiltedSlabOffset 136.9

> volume #1 tiltedSlabAxis 0.8534,0.4668,0.2319 tiltedSlabOffset 118.8

> volume #1 tiltedSlabAxis 0.07207,0.9432,0.3244 tiltedSlabOffset 154.7

> volume #1 tiltedSlabAxis 0.01583,0.7326,-0.6805 tiltedSlabOffset -18.59

> volume #1 tiltedSlabAxis 0.9353,0.2476,-0.2529 tiltedSlabOffset 22.19

> volume #1 tiltedSlabAxis 0.4005,-0.9033,0.1539 tiltedSlabOffset -87.4

> volume #1 tiltedSlabAxis 0.3787,-0.5673,0.7313 tiltedSlabOffset 34.41

> volume #1 tiltedSlabAxis -0.9146,-0.2582,-0.3113 tiltedSlabOffset -182.9

> surface dust #1 size 6.9

> surface dust #1 size 7.08

> surface dust #1 size 7.89

> surface dust #1 size 8.06

> surface dust #1 size 8

> surface dust #2 size 6.9

> surface dust #2 size 7

> surface dust #2 size 7.1

> surface dust #2 size 7.2

> surface dust #2 size 7.1

> surface dust #2 size 7

> volume #1 tiltedSlabAxis -0.2134,-0.1246,0.969 tiltedSlabOffset 59.07

> volume #1 tiltedSlabAxis 0.4435,-0.8226,0.3558 tiltedSlabOffset -33.53

> turn x 90

> turn x -90

> volume #2 tiltedSlabAxis -0.2602,0.3572,0.8971 tiltedSlabOffset 85.73

> color zone #2 near #4 distance 2.32

> color zone #2 near #4 distance 2.42

> color zone #2 near #4 distance 2.52

> color zone #2 near #4 distance 2.62

> color zone #2 near #4 distance 2.72

> color zone #2 near #4 distance 2.82

> color zone #2 near #4 distance 2.92

> color zone #2 near #4 distance 3.02

> color zone #2 near #4 distance 3.12

> color zone #2 near #4 distance 3.22

> color zone #2 near #4 distance 3.12

> color zone #2 near #4 distance 3.02

> color zone #2 near #4 distance 2.92

> color zone #2 near #4 distance 3.02

> color zone #2 near #4 distance 3

> color zone #2 near #4 distance 2

> color zone #2 near #4 distance 2.8

> surface dust #2 size 10

> surface dust #2 size 5

> surface undust #2

> surface dust #2 size 5

> surface undust #2

> surface dust #2 size 5

> surface dust #2 size 15

> surface dust #2 size 5

> surface dust #2 size 10

> surface dust #2 size 5

> surface dust #2 size 8

> volume #2 tiltedSlabAxis 0.4785,-0.5277,0.7018 tiltedSlabOffset 59.68

> select clear

> turn x -90

> turn x 90

> volume #2 tiltedSlabAxis -0.6778,0.6923,-0.2476 tiltedSlabOffset -53.3

> turn x -90

> turn x 90

> volume #2 tiltedSlabAxis -0.4628,0.769,0.441 tiltedSlabOffset 61.28

> save /Users/hongwenchen/Desktop/Overall_map.png width 2715 height 1920
> supersample 3 transparentBackground true

> hide #4 models

> save /Users/hongwenchen/Desktop/Overall_map.png width 2941 height 2080
> supersample 3 transparentBackground true

> save /Users/hongwenchen/Desktop/Overall_micell.png width 2941 height 2080
> supersample 3

> save /Users/hongwenchen/Desktop/Overall_micell.png width 2941 height 2080
> supersample 3 transparentBackground true

> volume #1 step 2

> volume #1 step 1

> save /Users/hongwenchen/Desktop/Overall_map.png width 2941 height 2080
> supersample 3 transparentBackground true

> volume #1 color #d6d6d613

> volume #1 color darkgrey

> volume #1 color #a9a9a90c

> volume #1 color #a9a9a90d

> save ""/Users/hongwenchen/Desktop/Overall structure.cxs"" includeMaps true

> ui tool show ""Color Actions""

> turn x 90

> turn x -90

> volume #1 color #a9a9a91a

> volume #1 color #929292

> volume #1 color #9292921a

> volume #1 color #797979

> volume #1 color #7979791a

> save /Users/hongwenchen/Desktop/Overall_micell.png width 2715 height 1920
> supersample 3 transparentBackground true

> turn x -90

> volume #2 tiltedSlabAxis -0.3547,0.6697,0.6524 tiltedSlabOffset 87.27

> turn x 90

> turn x -90

> turn x 90

> turn x -90

> turn x 90

> turn x -90

> save /Users/hongwenchen/Desktop/Overall_map-2.png width 2715 height 1920
> supersample 3 transparentBackground true

> save /Users/hongwenchen/Desktop/Overall_micell.png width 2715 height 1920
> supersample 3 transparentBackground true

> turn x -90

> turn x 90

> turn x -90

> turn x 90

> turn x -90

> turn x 90

> turn x -90

> save /Users/hongwenchen/Desktop/Overall_map-2.png width 2715 height 1920
> supersample 3 transparentBackground true

> save /Users/hongwenchen/Desktop/Overall_micell.png width 2715 height 1920
> supersample 3 transparentBackground true

> volume #1 level 0.1167


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/hongwenchen/Desktop/Overall structure.cxs""

Opened apo_cryosparc_P95_J1807_003_volume_map_sharp_2.86.mrc as #1, grid size
224,224,224, pixel 1.1, shown at level 0.108, step 1, values float32  
Opened apo_cryosparc_P95_J1807_003_volume_map_sharp_2.86 copy.mrc as #2, grid
size 224,224,224, pixel 1.1, shown at level 0.259, step 1, values float32  
Log from Thu Aug 14 16:18:15 2025 Startup Messages  
---  
warning | Registration file '/Users/hongwenchen/Library/Application Support/ChimeraX/registration' has expired  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/hongwenchen/Desktop/MS_OSTalpha-beta/Map-and-
> Model/apo_cryosparc_P95_J1807_003_volume_map_sharp_2.86.mrc

Opened apo_cryosparc_P95_J1807_003_volume_map_sharp_2.86.mrc as #1, grid size
224,224,224, pixel 1.1, shown at level 0.101, step 1, values float32  

> ui tool show Registration

Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  
hongwen.chen@sjtu.edu.cn has been invited to the ChimeraX announcements list  

> set bgColor white

> volume #1 level 0.1961

> ui tool show ""Side View""

> open ""/Users/hongwenchen/Desktop/MS_OSTalpha-beta/Map-and-
> Model/apo_cryosparc_P95_J1807_003_volume_map_sharp_2.86 copy.mrc""

Opened apo_cryosparc_P95_J1807_003_volume_map_sharp_2.86 copy.mrc as #2, grid
size 224,224,224, pixel 1.1, shown at level 0.101, step 1, values float32  

> volume #2 color #7a81ff

> volume #2 color #0433ff

> volume #2 color #0096ff

> volume #2 level 0.2594

> volume #1 color #b2b2b249

> volume #1 level 0.101

> ui tool show ""Hide Dust""

> surface dust #1 size 6.6

> volume #1 color darkgrey

> volume #1 color #a9a9a917

> volume #1 color #a9a9a914

> volume #1 level 0.1141

> volume #1 level 0.1075

[Repeated 1 time(s)]

> volume #1 step 2

> volume #1 step 16

> volume #1 step 1

> volume #1 style image

> volume #1 style mesh

> volume #1 style image

> volume #1 level -0.02944,0 level 0.1008,0.8 level 2.166,1

> volume #1 level -0.02944,0 level 0.1008,0.8 level 2.133,0.03077

> volume #1 level -0.02944,0 level 0.09431,0.6154 level 2.133,0.03077

> volume #1 level -0.02944,0 level 0.09431,0.6154 level 2.133,1

> volume #1 level 0.003188,0.01538 level 0.09431,0.6154 level 2.133,1

> volume #1 color #929292 color white color white

> volume #1 color #929292a2 color white color white

> volume #1 color #929292b0 color white color white

> volume #1 style surface

> volume #1 color #929292a4

> volume #1 color #92929200

> volume #1 color #9292920a

> volume #1 color #9292920d

> volume #1 style image region 0,0,111,223,223,111 step 1 showOutlineBox true

> volume #1 region 0,0,0,223,223,223 step 1

> volume #1 region 0,0,0,223,223,223 step 1 colorMode opaque8 orthoplanes xyz
> positionPlanes 111,111,111 imageMode orthoplanes

> volume #1 imageMode ""box faces""

> volume #1 colorMode auto8 imageMode ""tilted slab"" tiltedSlabAxis
> -0.7615,0.6301,0.1521 tiltedSlabOffset -21.67 tiltedSlabSpacing 1.1
> tiltedSlabPlaneCount 44

> volume #1 maximumIntensityProjection true imageMode ""full region""

> volume #1 maximumIntensityProjection false

> volume #1 style surface

> volume #1 color #424242

> volume #1 color #4242420f

> volume #1 color darkgrey

> volume #1 color #a9a9a90d

> surface dust #1 size 5.86

> surface dust #1 size 1.79

> surface dust #1 size 5

[Repeated 2 time(s)]

> open /Users/hongwenchen/Desktop/MS_OSTalpha-beta/Map-and-
> Model/R_apo_2.86.pdb

Chain information for R_apo_2.86.pdb #3  
---  
Chain | Description  
A C | No description available  
B D | No description available  
  

> volume #1 tiltedSlabAxis -0.7959,0.6004,-0.07808 tiltedSlabOffset -60.3

> volume #1 tiltedSlabAxis -0.7654,0.4927,-0.4141 tiltedSlabOffset -116.5

> turn x 90

> turn x -90

> turn x 90

> turn x -90

> turn x 90

> turn x -90

> turn x 90

> select #2:A

Nothing selected  

> select #3:A

Nothing selected  

> select #3/A

3205 atoms, 3267 bonds, 340 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel forest green

> color sel #00ffffff

> color sel #00ff00ff

> color sel #00fa92ff

> color sel #00f900ff

> color sel #00fa00ff

[Repeated 1 time(s)]

> color sel #00fb00ff

> color sel #00fd00ff

> color sel #00ff00ff

> select #3/C

3205 atoms, 3274 bonds, 340 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel cyan

> select clear

> select #3/b

426 atoms, 434 bonds, 53 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel orange

> select #3/d

426 atoms, 434 bonds, 53 residues, 1 model selected  

> color sel magenta

> select #3

7262 atoms, 7409 bonds, 786 residues, 1 model selected  

> select #3/a/b/c/d

7262 atoms, 7409 bonds, 786 residues, 1 model selected  

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> ui tool show ""Color Zone""

> color zone #2 near #3 distance 6.6

> color zone #2 near #3 distance 5

> volume #2 color #d6d6d6

> color zone #2 near #3 distance 5

> color zone #2 near #3 distance 4.9

> color zone #2 near #3 distance 4.8

> color zone #2 near #3 distance 4.7

> color zone #2 near #3 distance 4.6

> color zone #2 near #3 distance 4.5

> color zone #2 near #3 distance 4.4

[Repeated 1 time(s)]

> color zone #2 near #3 distance 3

[Repeated 1 time(s)]

> volume #2 tiltedSlabAxis -0.7647,0.1135,-0.6343 tiltedSlabOffset -195.8

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> select clear

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> color zone #2 near #3 distance 3

> volume #2 tiltedSlabAxis 0.7825,-0.6224,0.014 tiltedSlabOffset 18.6

> select clear

[Repeated 2 time(s)]

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> select clear

> select backbone

3008 atoms, 3004 bonds, 752 residues, 1 model selected  

> color zone #2 near #3 distance 3

[Repeated 1 time(s)]

> color single #2

> color zone #2 near #3 distance 3

> color single #2

> color zone #2 near #3 distance 3

> volume #2 tiltedSlabAxis -0.5036,0.6449,0.5748 tiltedSlabOffset 45.17

> ui tool show ""Side View""

> open ""/Users/hongwenchen/Desktop/MS_OSTalpha-beta/Map-and-Model/R_apo_2.86
> copy.pdb""

Summary of feedback from opening /Users/hongwenchen/Desktop/MS_OSTalpha-
beta/Map-and-Model/R_apo_2.86 copy.pdb  
---  
warnings | CONECT record to nonexistent atom: (1196, 3093)  
CONECT record to nonexistent atom: (1202, 3144)  
CONECT record to nonexistent atom: (1208, 3110)  
CONECT record to nonexistent atom: (1214, 3127)  
CONECT record to nonexistent atom: (1220, 3161)  
2 messages similar to the above omitted  
CONECT record for nonexistent atom: 2512  
Cannot find LINK/SSBOND residue PLM (501 )  
Cannot find LINK/SSBOND residue PLM (504 )  
Cannot find LINK/SSBOND residue PLM (502 )  
Cannot find LINK/SSBOND residue PLM (503 )  
Cannot find LINK/SSBOND residue PLM (505 )  
2 messages similar to the above omitted  
  
Chain information for R_apo_2.86 copy.pdb #4  
---  
Chain | Description  
A C | No description available  
B D | No description available  
  

> close #3

> select #3/a/b/c/d

Nothing selected  

> color single #2

> color zone #2 near #4 distance 3

> color single #2

> select #3/a/b/c/d

Nothing selected  

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> color zone #2 near #4 distance 3

> color zone #2 near #4 distance 3.06

> color zone #2 near #4 distance 11.74

[Repeated 1 time(s)]

> color single #2

> select #3/a

Nothing selected  

> ui tool show ""Color Actions""

> color light sea green

> select /A

2510 atoms, 2565 bonds, 323 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel forest green

> color sel sea green

> select /C

2510 atoms, 2565 bonds, 323 residues, 1 model selected  

> color sel turquoise

> color sel dark turquoise

> select /B

426 atoms, 434 bonds, 53 residues, 1 model selected  

> color sel deep sky blue

> color sel bychain

> color sel dark orange

> color sel sandy brown

> color sel dark salmon

> color sel sandy brown

> color sel dark salmon

> select /D

426 atoms, 434 bonds, 53 residues, 1 model selected  

> color sel orange

> color sel dark orange

> color sel orange

> color sel sandy brown

> select clear

> select protein

5872 atoms, 5998 bonds, 752 residues, 1 model selected  

> color zone #2 near #4 distance 11.74

> color zone #2 near #4 distance 5

[Repeated 1 time(s)]

> volume #2 color #d6d6d6

> color zone #2 near #4 distance 5

> color zone #2 near #4 distance 3

[Repeated 1 time(s)]

> surface dust #2 size 5

> surface dust #2 size 5.1

> surface dust #2 size 5.2

> surface dust #2 size 5.3

> surface dust #2 size 5.4

> surface dust #2 size 5.5

> surface dust #2 size 5.6

> surface dust #2 size 5.7

> surface dust #2 size 5.8

> surface dust #2 size 5.9

> surface dust #2 size 6

> surface dust #2 size 6.1

> surface dust #2 size 6.2

> surface dust #2 size 6.3

> surface dust #2 size 6.4

> surface dust #2 size 6.5

> surface dust #2 size 6.6

> surface dust #2 size 6.7

> surface dust #2 size 6.8

> surface dust #2 size 6.9

[Repeated 1 time(s)]

> color zone #2 near #4 distance 2

[Repeated 3 time(s)]

> color zone #2 near #4 distance 1.82

> color zone #2 near #4 distance 1.54

> color zone #2 near #4 distance 1.57

> color zone #2 near #4 distance 2.22

> volume #1 color #d6d6d6

> volume #1 color #d6d6d60e

> volume #1 color #d6d6d60d

> volume #1 tiltedSlabAxis 0.5781,-0.8108,0.09155 tiltedSlabOffset -18.43

> volume #1 tiltedSlabAxis -0.6739,-0.5874,-0.4481 tiltedSlabOffset -191.6

> volume #1 tiltedSlabAxis -0.8986,0.4256,0.107 tiltedSlabOffset -12.68

> volume #1 tiltedSlabAxis -0.2212,0.6595,0.7185 tiltedSlabOffset 122.3

> volume #1 tiltedSlabAxis 0.02117,0.8896,0.4562 tiltedSlabOffset 136.9

> volume #1 tiltedSlabAxis 0.8534,0.4668,0.2319 tiltedSlabOffset 118.8

> volume #1 tiltedSlabAxis 0.07207,0.9432,0.3244 tiltedSlabOffset 154.7

> volume #1 tiltedSlabAxis 0.01583,0.7326,-0.6805 tiltedSlabOffset -18.59

> volume #1 tiltedSlabAxis 0.9353,0.2476,-0.2529 tiltedSlabOffset 22.19

> volume #1 tiltedSlabAxis 0.4005,-0.9033,0.1539 tiltedSlabOffset -87.4

> volume #1 tiltedSlabAxis 0.3787,-0.5673,0.7313 tiltedSlabOffset 34.41

> volume #1 tiltedSlabAxis -0.9146,-0.2582,-0.3113 tiltedSlabOffset -182.9

> surface dust #1 size 6.9

> surface dust #1 size 7.08

> surface dust #1 size 7.89

> surface dust #1 size 8.06

> surface dust #1 size 8

[Repeated 1 time(s)]

> surface dust #2 size 6.9

> surface dust #2 size 7

> surface dust #2 size 7.1

> surface dust #2 size 7.2

> surface dust #2 size 7.1

> surface dust #2 size 7

[Repeated 1 time(s)]

> volume #1 tiltedSlabAxis -0.2134,-0.1246,0.969 tiltedSlabOffset 59.07

> volume #1 tiltedSlabAxis 0.4435,-0.8226,0.3558 tiltedSlabOffset -33.53

> turn x 90

> turn x -90

> volume #2 tiltedSlabAxis -0.2602,0.3572,0.8971 tiltedSlabOffset 85.73

> color zone #2 near #4 distance 2.32

> color zone #2 near #4 distance 2.42

> color zone #2 near #4 distance 2.52

> color zone #2 near #4 distance 2.62

> color zone #2 near #4 distance 2.72

> color zone #2 near #4 distance 2.82

> color zone #2 near #4 distance 2.92

> color zone #2 near #4 distance 3.02

> color zone #2 near #4 distance 3.12

> color zone #2 near #4 distance 3.22

> color zone #2 near #4 distance 3.12

> color zone #2 near #4 distance 3.02

> color zone #2 near #4 distance 2.92

> color zone #2 near #4 distance 3.02

> color zone #2 near #4 distance 3

[Repeated 1 time(s)]

> color zone #2 near #4 distance 2

> color zone #2 near #4 distance 2.8

[Repeated 1 time(s)]

> surface dust #2 size 10

[Repeated 2 time(s)]

> surface dust #2 size 5

[Repeated 1 time(s)]

> surface undust #2

> surface dust #2 size 5

> surface undust #2

> surface dust #2 size 5

> surface dust #2 size 15

[Repeated 1 time(s)]

> surface dust #2 size 5

[Repeated 1 time(s)]

> surface dust #2 size 10

> surface dust #2 size 5

> surface dust #2 size 8

[Repeated 1 time(s)]

> volume #2 tiltedSlabAxis 0.4785,-0.5277,0.7018 tiltedSlabOffset 59.68

> select clear

> turn x -90

> turn x 90

> volume #2 tiltedSlabAxis -0.6778,0.6923,-0.2476 tiltedSlabOffset -53.3

> turn x -90

> turn x 90

> volume #2 tiltedSlabAxis -0.4628,0.769,0.441 tiltedSlabOffset 61.28

> save /Users/hongwenchen/Desktop/Overall_map.png width 2715 height 1920
> supersample 3 transparentBackground true

> hide #4 models

> save /Users/hongwenchen/Desktop/Overall_map.png width 2941 height 2080
> supersample 3 transparentBackground true

> save /Users/hongwenchen/Desktop/Overall_micell.png width 2941 height 2080
> supersample 3

> save /Users/hongwenchen/Desktop/Overall_micell.png width 2941 height 2080
> supersample 3 transparentBackground true

> volume #1 step 2

> volume #1 step 1

> save /Users/hongwenchen/Desktop/Overall_map.png width 2941 height 2080
> supersample 3 transparentBackground true

> volume #1 color #d6d6d613

> volume #1 color darkgrey

> volume #1 color #a9a9a90c

> volume #1 color #a9a9a90d

> save ""/Users/hongwenchen/Desktop/Overall structure.cxs"" includeMaps true

——— End of log from Thu Aug 14 16:18:15 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
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: Mac16,8
      Model Number: MX2J3LL/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6 (24G84)
      Kernel Version: Darwin 24.6.0
      Time since boot: 7 days, 19 hours, 37 minutes

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        HP M27fq QHD:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          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
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX