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Opened 13 months ago
Closed 13 months ago
#16003 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 (last modified by )
The following bug report has been submitted:
Platform: macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070002d6e0000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070002c6dd000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070002b6da000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070002a6d7000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000296d4000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000286d1000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000276ce000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000266cb000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000256c8000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000246c5000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000236c2000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000226bf000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000216bc000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000206b9000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001f6b6000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001e6b3000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001d6b0000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001c6ad000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001b6aa000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff85683bfc0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 62)
{"app_name":"ChimeraX","timestamp":"2024-09-24 10:47:31.00 +1000","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.5 (23F79)","roots_installed":0,"name":"ChimeraX","incident_id":"7EDB3D2F-8F0E-4D4F-93BD-42F25546889B"}
{
"uptime" : 73000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 9052,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-09-24 10:47:16.2949 +1000",
"codeSigningMonitor" : 0,
"incident" : "7EDB3D2F-8F0E-4D4F-93BD-42F25546889B",
"pid" : 40507,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-23 17:24:08.5000 +1000",
"procStartAbsTime" : 72180791856272,
"procExitAbsTime" : 73720859885521,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"C3BA8B9E-1138-5FA2-8C81-49936FF253EE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "324B8216-C495-C2F1-1769-3322C698A086",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 8,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "A7C2F5A5-A2ED-4422-9809-82B4FC869088",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4524302336\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10dab6000-10daba000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":40507},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4524302336\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10dab6000-10daba000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.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" : 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level 0.396, step 2, values float32
Opened emd_38015_8X2K.map copy as #6, grid size 320,320,320, pixel 0.85, shown
at level 0.396, step 1, values float32
Opened emd_37881_8WW2.map as #5, grid size 256,256,256, pixel 1.1, shown at
level 0.526, step 1, values float32
Opened emd_37881_8WW2.map copy as #8, grid size 256,256,256, pixel 1.1, shown
at level 0.526, step 1, values float32
Log from Mon Jun 17 15:55:50 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_174_v3.cxs" format session
Opened emd_33479_7XV3.map as #3, grid size 256,256,256, pixel 1.1, shown at
level 1.52, step 1, values float32
Opened emd_33479_7XV3.map copy as #6, grid size 256,256,256, pixel 1.1, shown
at level 1.52, step 1, values float32
Opened emd_35838_8IZB.map as #5, grid size 192,192,192, pixel 1.07, shown at
level 0.31, step 1, values float32
Opened emd_35838_8IZB.map copy as #9, grid size 192,192,192, pixel 1.07, shown
at level 0.31, step 1, values float32
Opened emd_35838_8IZB.map copy as #10, grid size 192,192,192, pixel 1.07,
shown at level 0.31, step 1, values float32
Not registering illegal selector name "1_hydrophobic_cleft"
Not registering illegal selector name "1_head_interact"
Log from Sun Jun 16 23:57:53 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_174_v3.cxs"
Opened emd_33479_7XV3.map as #3, grid size 256,256,256, pixel 1.1, shown at
level 1.52, step 1, values float32
Opened emd_33479_7XV3.map copy as #6, grid size 256,256,256, pixel 1.1, shown
at level 1.52, step 1, values float32
Opened emd_35838_8IZB.map as #5, grid size 192,192,192, pixel 1.07, shown at
level 0.31, step 1, values float32
Opened emd_35838_8IZB.map copy as #9, grid size 192,192,192, pixel 1.07, shown
at level 0.31, step 1, values float32
Opened emd_35838_8IZB.map copy as #10, grid size 192,192,192, pixel 1.07,
shown at level 0.31, step 1, values float32
Not registering illegal selector name "1_hydrophobic_cleft"
Not registering illegal selector name "1_head_interact"
Log from Fri Jun 14 01:29:38 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4A_119_LPC.cxs" format session
Opened emd_33525_7xz5.map as #2, grid size 200,200,200, pixel 1.07, shown at
level 0.0208, step 1, values float32
Opened emd_33525_7xz5.map copy as #4, grid size 200,200,200, pixel 1.07, shown
at level 0.0208, step 1, values float32
Log from Mon Jun 10 00:01:24 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 7/Figure7C.cxs"
Log from Thu May 30 20:40:46 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/All Figures-
> draft/Figure7/Figure 7D-GPR61-BRIL fused structure v2.cxs"
Log from Thu Apr 4 16:40:01 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
> draft/Figure 7D-GPR61-BRIL fused structure.cxs"
Log from Mon Apr 1 18:14:01 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
> draft/Fig3B_inactive GPR20 with the map.cxs"
Opened emd_34993_8HSC.map as #4, grid size 288,288,288, pixel 0.832, shown at
level 0.13, step 2, values float32
Opened emd_34984_8HS3.map as #5, grid size 256,256,256, pixel 0.832, shown at
level 0.148, step 1, values float32
Opened emd_34983_8HS2.map as #6, grid size 288,288,288, pixel 0.832, shown at
level 0.0931, step 1, values float32
Opened emd_34983_8HS2.map copy as #8, grid size 288,288,288, pixel 0.832,
shown at level 0.0678, step 1, values float32
Log from Wed Feb 28 18:29:12 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-
> Monash/NRE/Figure2_DL/Fig2B_GPR21 and 52.cxs"
Not registering illegal selector name "GPR21_binding sites"
Log from Tue Feb 27 18:06:41 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NRE/Figure2_DL/Aligned
> overall_17_21_52_161.cxs" format session
Log from Wed Feb 14 23:29:37 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NRE/Figure 2 -
> Autoactivated/20240206_Figure_2.cxs"
Log from Tue Feb 6 18:08:29 2024UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231026_Figure_2.cxs
Log from Thu Oct 26 20:27:55 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> C:\Users\Midget\OneDrive\MIPS\papers\GPR_mini_review\Figures\20231025_Figure_2.cxs
> format session
Log from Thu Oct 26 16:19:56 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> C:\Users\Midget\OneDrive\MIPS\papers\GPR_mini_review\Figures\20231025_Figure_2.cxs
> format session
Log from Thu Oct 26 00:31:26 2023You can double click a model's Name or ID in
the model panel to edit those fields
Updating list of available bundles failed: [Errno 11001] getaddrinfo failed
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/structures/GPR12_Gs.pdb
GPR12_Gs.pdb title:
Cryo-em structure of A class A orphan GPCR [more info...]
Chain information for GPR12_Gs.pdb #1
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN
B | transducin β chain 1 | GBB1_HUMAN
G | G γ-I | GBG2_HUMAN
N | nanobody 35 |
R | G-protein coupled receptor 12 | GPR12_HUMAN
> open
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/structures/GPR17_7y89.pdb
GPR17_7y89.pdb title:
Structure of the GPR17-gi complex [more info...]
Chain information for GPR17_7y89.pdb #2
---
Chain | Description | UniProt
A | uracil nucleotide/cysteinyl leukotriene receptor | GPR17_HUMAN
B | transducin β chain 1 | GBB1_HUMAN
C | adenylate cyclase-inhibiting G α protein | GNAI1_HUMAN
G | guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit β-1 |
S | guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit γ-2 |
> open
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/structures/GPR21_8hmv.pdb
GPR21_8hmv.pdb title:
Structure of GPR21-GS complex [more info...]
Chain information for GPR21_8hmv.pdb #3
---
Chain | Description | UniProt
A | probable G-protein coupled receptor 21 | GPR21_HUMAN
B | transducin β chain 1 | GBB1_HUMAN
C | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN
G | G γ-I | GBG2_HUMAN
N | nanobody NB35 |
[deleted to fit within ticket limits]
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.92025,0.34341,-0.18765,-13.265,-0.39131,0.81279,-0.43157,144.43,0.0043142,0.47058,0.88235,-44.314
> fitmap #2 inMap #5
Fit molecule 8ww2 (#2) to map emd_37881_8WW2.map (#5) using 2048 atoms
average map value = 1.485, steps = 140
shifted from previous position = 4.53
rotated from previous position = 25.6 degrees
atoms outside contour = 546, contour level = 0.7885
Position of 8ww2 (#2) relative to emd_37881_8WW2.map (#5) coordinates:
Matrix rotation and translation
0.99999996 0.00012222 0.00026537 -0.07513565
-0.00012223 0.99999999 0.00004628 0.01029297
-0.00026536 -0.00004631 0.99999996 0.04239788
Axis -0.15650920 0.89709431 -0.41319083
Axis point 165.14679237 0.00000000 281.11680356
Rotation angle (degrees) 0.01694827
Shift along axis 0.00347477
> view matrix models
> #5,0.91866,0.34702,-0.18877,-13.418,-0.39502,0.81217,-0.42934,144.76,0.0043231,0.46899,0.88319,-44.193
> view matrix models
> #5,0.91891,0.34712,-0.18738,-13.651,-0.39446,0.81283,-0.42862,144.49,0.0035265,0.46777,0.88384,-43.985
> fitmap #2 inMap #5
Fit molecule 8ww2 (#2) to map emd_37881_8WW2.map (#5) using 2048 atoms
average map value = 1.485, steps = 44
shifted from previous position = 0.108
rotated from previous position = 0.247 degrees
atoms outside contour = 548, contour level = 0.7885
Position of 8ww2 (#2) relative to emd_37881_8WW2.map (#5) coordinates:
Matrix rotation and translation
0.99999993 -0.00012631 0.00036012 -0.04066985
0.00012642 0.99999995 -0.00030626 0.02288320
-0.00036008 0.00030630 0.99999989 -0.00138601
Axis 0.62591382 0.73589748 0.25823787
Axis point 2.55653855 0.00000000 97.33758639
Rotation angle (degrees) 0.02803672
Shift along axis -0.00897406
> ui mousemode right select
> select clear
> volume #5 level 0.8177
> volume #!5 style image
[Repeated 1 time(s)]
> volume #!5 style surface
> transparency #5.1 50
> volume #5 change image level -0.1034,0 level 0.3212,0.8 level 9.069,1
> volume #5 level 0.526
> ui mousemode right "map eraser"
> volume erase #5 center 129.08,126.26,175.65 radius 14.086 outside true
Opened emd_37881_8WW2.map copy as #8, grid size 256,256,256, pixel 1.1, shown
at step 1, values float32
> hide #!2 cartoons
> volume erase #8 center 132.73,134.06,181.07 radius 8.8704
> volume erase #8 center 123.22,143.01,175.92 radius 8.8704
> volume erase #8 center 126.34,138.23,176.54 radius 8.8704
> volume erase #8 center 123.1,136.44,172.4 radius 8.8704
> volume erase #8 center 133.5,118.49,184.72 radius 8.8704
> volume erase #8 center 130.68,114.11,180.62 radius 8.8704
> volume erase #8 center 133.71,110.82,173.85 radius 8.8704
> volume erase #8 center 139.97,119.37,181.39 radius 8.8704
> volume erase #8 center 128.97,125.27,186.28 radius 8.8704
> volume erase #8 center 138.92,115.29,172.66 radius 8.8704
> volume erase #8 center 126.08,128.57,164.84 radius 8.8704
> volume erase #8 center 131.88,123.79,163.63 radius 8.8704
> volume erase #8 center 131.8,119.64,171.9 radius 2.6752
> volume erase #8 center 127.99,116.9,169.62 radius 2.6752
> volume erase #8 center 127.72,114.89,165.99 radius 2.6752
> volume erase #8 center 125.74,117.48,172.43 radius 2.6752
> volume erase #8 center 124.41,115.77,170.2 radius 2.6752
> volume erase #8 center 124.9,114.59,173.59 radius 2.6752
> volume erase #8 center 126.71,114.11,171.83 radius 2.6752
> volume erase #8 center 122.83,114.96,172.56 radius 2.6752
> volume erase #8 center 124.04,114.17,173.93 radius 2.6752
> volume erase #8 center 123.28,117.16,179.85 radius 2.6752
> volume erase #8 center 119.13,117.47,182.77 radius 2.6752
> volume erase #8 center 119.63,118.49,183.56 radius 2.6752
> volume erase #8 center 120.36,122.2,181.63 radius 2.6752
> volume erase #8 center 120.12,126.6,185.16 radius 2.6752
> volume erase #8 center 120.53,131.8,185 radius 2.6752
> volume erase #8 center 119.62,130.25,185.06 radius 2.6752
> volume erase #8 center 118.43,127.92,184.85 radius 2.6752
> volume erase #8 center 122.49,133.78,183.77 radius 2.6752
> volume erase #8 center 115.19,130.14,180.01 radius 2.6752
> volume erase #8 center 113.75,128.84,180.2 radius 2.6752
> volume erase #8 center 115.67,132.32,180.14 radius 2.6752
> volume erase #8 center 115.13,127.99,176.33 radius 2.6752
> volume erase #8 center 117.62,127.49,170.29 radius 2.6752
> volume erase #8 center 121.06,128.17,173.73 radius 2.6752
> volume erase #8 center 118.41,127.89,171.18 radius 2.6752
> volume erase #8 center 118.46,129.16,172.58 radius 2.6752
> volume erase #8 center 118.1,126.3,171.9 radius 2.6752
> volume erase #8 center 116.68,121.64,172.99 radius 2.6752
> volume erase #8 center 119.78,122.6,168.51 radius 2.6752
> volume erase #8 center 119.32,117.8,168.12 radius 2.6752
> volume erase #8 center 125.46,123.88,170.24 radius 2.6752
> volume erase #8 center 123.18,120.41,167.11 radius 2.6752
> volume erase #8 center 121.58,116.58,167.74 radius 2.6752
> volume erase #8 center 125.47,119.8,170.75 radius 2.6752
> volume erase #8 center 120.87,116.15,178.38 radius 2.6752
> volume erase #8 center 138.19,128.06,185.02 radius 2.6752
> volume erase #8 center 126.82,126.58,178.55 radius 2.6752
> volume erase #8 center 125.47,127.68,175.58 radius 2.6752
> volume erase #8 center 125,127.48,174.51 radius 2.6752
> volume erase #8 center 123.46,129.67,180.61 radius 2.6752
> volume erase #8 center 124.49,129.56,182.67 radius 2.6752
> volume erase #8 center 126.72,124.17,178.91 radius 2.6752
> volume erase #8 center 115.36,123.16,169.06 radius 2.6752
> volume erase #8 center 137.76,130.39,167.52 radius 2.6752
> volume erase #8 center 137.44,133.42,169.51 radius 2.6752
> volume erase #8 center 134.92,135.56,168.98 radius 2.6752
> volume erase #8 center 131.73,135.74,167.68 radius 2.6752
> volume erase #8 center 134.23,134.44,164.63 radius 2.6752
> volume erase #8 center 136.07,137.48,172.31 radius 2.6752
> volume erase #8 center 133.32,132.73,171.21 radius 2.6752
> volume erase #8 center 132.66,129.88,171.79 radius 2.6752
> volume erase #8 center 136.37,131.27,172.58 radius 2.6752
> volume erase #8 center 139.33,134.06,173.1 radius 2.6752
> volume erase #8 center 137.19,130.43,169.86 radius 2.6752
> volume erase #8 center 141.58,131.99,171.85 radius 2.6752
> volume erase #8 center 140.33,131.13,174.85 radius 2.6752
> volume erase #8 center 143.02,125.79,175.07 radius 2.6752
> volume erase #8 center 142.74,124.1,167.11 radius 2.6752
> volume erase #8 center 140.07,127.39,178.97 radius 2.6752
> volume erase #8 center 141.7,129.37,175.9 radius 2.6752
> volume erase #8 center 139.07,133.03,177.52 radius 2.6752
> ui mousemode right select
> select clear
[Repeated 3 time(s)]
> show #!2 cartoons
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> select #8
2 models selected
Drag select of 24 atoms, 76 residues, 21 bonds, 7 pseudobonds, 8
emd_37881_8WW2.map copy
Drag select of 39 atoms, 144 residues, 35 bonds, 7 pseudobonds, 8
emd_37881_8WW2.map copy
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> select clear
[Repeated 4 time(s)]
> hide #!8 models
> hide #!2 cartoons
> select clear
[Repeated 9 time(s)]
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> select clear
[Repeated 4 time(s)]
> show #!2 cartoons
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_GPR3_with maps.cxs"
> show #!8 models
> color #8 #ffd09280 models
> color #8 #ffd6ac80 models
> color #8 #ffeabc80 models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_GPR3_8WW2.png" width 3000
> height 1903 supersample 3 transparentBackground true
> hide #!2 cartoons
> color #8 #ffeabc41 models
> color #8 #ffeabc40 models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8WW2_surface.png" width 2000
> height 1269 supersample 3 transparentBackground true
> volume #!8 style mesh
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8WW2_mesh.png" width 2000
> height 1269 supersample 3 transparentBackground true
[Repeated 1 time(s)]
> volume #!8 style surface
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8WW2_surface.png" width 2000
> height 1269 supersample 3 transparentBackground true
> hide #!2 models
> show #!1 models
> hide #!8 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 cartoons
> volume #!6 style mesh
> color #6 #bf888342 models
> color #6 #bf888370 models
> hide #!6 models
> show #!6 models
> show #!1 cartoons
> select add #6
2 models selected
> volume sel style surface
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8X2K_overall.png" width 3000
> height 1903 supersample 3 transparentBackground true
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_GPR3_with maps.cxs"
——— End of log from Mon Jun 17 15:55:50 2024 ———
opened ChimeraX session
> show #!3 models
> hide #!1 models
> hide #!6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/R
Alignment identifier is 3/R
> select #3/R:96
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 17 atom styles
> show #!1 models
> show #!2 models
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show (sel-residues & sidechain) target ab
> ribbon suppressBackboneDisplay true
> ribbon sel suppressBackboneDisplay true
> ribbon sel suppressBackboneDisplay false
> ribbon sel suppressBackboneDisplay true
> ui mousemode right select
> select #3/R:280
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select H
2121 atoms, 266 residues, 1 model selected
> hide sel atoms
> select clear
> color #1-3 byhetero
> select clear
> hide #!2 models
> hide #!3 models
> select #1/A:96
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Side View"
> show #!6 models
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8X2K_overall_v2.png" width
> 3000 height 1949 supersample 3 transparentBackground true
> show #!4 models
> hide #!6 models
> volume #!4 style mesh
> volume #!4 style surface
> volume #!4 style image
> volume #!4 style surface
> transparency #4.1 50
> ui mousemode right "map eraser"
> volume erase #4 center 130.88,123.09,167.02 radius 18.278 outside true
Opened emd_38015_8X2K.map copy as #9, grid size 320,320,320, pixel 0.85, shown
at step 1, values float32
> volume erase #9 center 122.31,133.94,154.24 radius 18.224
> volume erase #9 center 130.45,95.963,162.54 radius 18.224
> volume erase #9 center 113.96,122.5,174.48 radius 5.032
> volume erase #9 center 117.33,126.37,181.13 radius 5.032
> volume erase #9 center 114.61,113.69,166.43 radius 5.032
> volume erase #9 center 114.43,117.27,169.78 radius 5.032
> volume erase #9 center 112.55,123.4,174.17 radius 5.032
> volume erase #9 center 113.05,123.04,170.37 radius 5.032
> volume erase #9 center 112.2,123.8,174.29 radius 5.032
> volume erase #9 center 115.88,113.27,169.86 radius 5.032
> volume erase #9 center 119.55,110.6,171.85 radius 5.032
> volume erase #9 center 114.48,125.87,179.79 radius 5.032
> volume erase #9 center 115.96,128.51,173.78 radius 5.032
> volume erase #9 center 112.94,123.39,172.63 radius 5.032
> volume erase #9 center 114.54,125.68,171.75 radius 5.032
> volume erase #9 center 116.25,119.68,169.12 radius 5.032
> volume erase #9 center 115.68,117.02,173.09 radius 5.032
> volume erase #9 center 116.7,111.14,166.69 radius 5.032
> volume erase #9 center 119.76,111.36,170.61 radius 5.032
> volume erase #9 center 128.92,112.06,178.21 radius 5.032
> volume erase #9 center 129.87,116.48,179.29 radius 5.032
> volume erase #9 center 129.72,114.86,178.03 radius 5.032
> volume erase #9 center 129.67,116,178.13 radius 5.032
> volume erase #9 center 134.38,135.13,171.54 radius 8.976
> volume erase #9 center 130.19,134.29,176.08 radius 8.976
> volume erase #9 center 140.54,122.46,178.15 radius 8.976
> show #!6 models
> select add #6
2 models selected
> volume sel style mesh
> select subtract #6
Nothing selected
> select add #6
2 models selected
> select subtract #6
Nothing selected
> select add #6
2 models selected
Can only have one displayed volume when erasing
[Repeated 5 time(s)]
> select add #9
5 models selected
Can only have one displayed volume when erasing
> hide #7 models
> show #7 models
> hide #!6 models
> select subtract #6
3 models selected
> volume erase #9 center 128.67,127.89,182.98 radius 8.976
> volume erase #9 center 135.16,122.88,184.6 radius 8.976
> volume erase #9 center 133.56,128.01,180.51 radius 8.976
> volume erase #9 center 144.06,134.86,172.66 radius 8.976
> volume erase #9 center 147.26,131.12,171.99 radius 8.976
> volume erase #9 center 142.66,112.71,164.07 radius 8.976
> volume erase #9 center 136.26,113.68,176.37 radius 8.976
> volume erase #9 center 122.49,118.9,180.94 radius 5.032
> volume erase #9 center 115.89,125.37,170.33 radius 5.032
> volume erase #9 center 113.13,124.28,164.48 radius 5.032
> volume erase #9 center 114.01,122.51,161.81 radius 5.032
> volume erase #9 center 112.22,124,172.46 radius 5.032
> volume erase #9 center 117.31,128.31,180.82 radius 5.032
> volume erase #9 center 116.07,129.07,178.69 radius 5.032
> volume erase #9 center 114.96,129.74,176.68 radius 5.032
> volume erase #9 center 116.6,130.62,177.6 radius 5.032
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!9 models
> show #!9 models
> hide #!4 models
> volume erase #9 center 118.75,129.42,176.96 radius 5.032
> volume erase #9 center 125.45,124.61,174.09 radius 2.04
> volume erase #9 center 128.33,124.58,172.93 radius 2.04
> volume erase #9 center 128.51,125.45,171.18 radius 2.72
> volume erase #9 center 118.93,117.37,166.13 radius 2.72
> volume erase #9 center 118.58,116.66,164.63 radius 2.72
> volume erase #9 center 117.38,111.67,162.72 radius 2.72
> volume erase #9 center 121.01,112.56,164.66 radius 2.72
> volume erase #9 center 123.99,112.79,165.74 radius 2.72
> volume erase #9 center 127.29,113.97,167.19 radius 2.72
> hide #!1 models
> volume erase #9 center 133.61,117.17,163.38 radius 5.032
> volume erase #9 center 136.77,116.29,160.24 radius 5.032
> volume erase #9 center 129.96,114.16,163.19 radius 5.032
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> volume erase #9 center 129.2,119.46,162.27 radius 5.032
> volume erase #9 center 127.03,121.47,166.53 radius 1.224
> volume erase #9 center 126.53,120.62,166.5 radius 1.224
[Repeated 1 time(s)]
> volume erase #9 center 126.44,120.3,166.88 radius 1.224
> show #!6 models
> hide #!9 models
> show #!9 models
> show #!1 models
> select add #1
1921 atoms, 1956 bonds, 2 pseudobonds, 263 residues, 5 models selected
> hide sel ribbons
Can only have one displayed volume when erasing
> select subtract #1
2 models selected
> select add #9
3 models selected
> select subtract #9
Nothing selected
> select add #9
3 models selected
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> hide #!6 models
> volume erase #9 center 127.8,120.24,167.11 radius 1.224
> volume erase #9 center 125.19,124.29,171.41 radius 1.224
> volume erase #9 center 125.08,124.08,170.24 radius 1.224
> volume erase #9 center 126.56,127.49,170.12 radius 1.224
> volume erase #9 center 124.92,124.39,170.78 radius 1.224
> volume erase #9 center 124.74,124.72,169.85 radius 1.224
> volume erase #9 center 127.29,123.4,175.53 radius 1.224
> volume erase #9 center 131.79,124.97,171.95 radius 2.312
> volume erase #9 center 130.89,116.38,173.27 radius 2.312
> volume erase #9 center 129.09,114.05,169.51 radius 2.312
> volume erase #9 center 129.32,114.2,169.61 radius 2.312
> volume erase #9 center 128.8,115.77,168.17 radius 2.312
> volume erase #9 center 134.3,114.04,168.46 radius 2.312
> volume erase #9 center 127.46,110.48,164.59 radius 2.312
> volume erase #9 center 125.58,111.26,168.38 radius 2.312
> volume erase #9 center 121,110.06,162.03 radius 2.312
> volume erase #9 center 119.25,109.36,159.33 radius 2.312
> volume erase #9 center 115.95,111.86,160.9 radius 2.312
> volume erase #9 center 117.47,113.27,160.44 radius 2.312
> volume erase #9 center 119.74,114.34,163.23 radius 2.312
> volume erase #9 center 125.52,115.68,165.69 radius 2.312
> volume erase #9 center 124.21,114.54,162.44 radius 2.312
> volume erase #9 center 120.24,114.83,161.49 radius 2.312
> volume erase #9 center 119.8,116.84,161.74 radius 2.312
> volume erase #9 center 122.34,116.24,160.05 radius 2.312
> volume erase #9 center 124.53,114.83,159.05 radius 2.312
> volume erase #9 center 121.96,115.22,155.5 radius 2.312
> volume erase #9 center 127.2,114.33,155.42 radius 2.312
> volume erase #9 center 128.19,114.83,154.14 radius 2.312
> volume erase #9 center 130.64,115.42,156.52 radius 2.312
> volume erase #9 center 135.89,121.73,159.88 radius 5.576
> volume erase #9 center 135.52,121.76,160.87 radius 5.576
> volume erase #9 center 135.22,117.93,152.41 radius 5.576
> volume erase #9 center 138.94,122.29,153.73 radius 5.576
> volume erase #9 center 145.1,119.1,156.14 radius 5.576
> volume erase #9 center 139.18,114.57,166.48 radius 5.576
[Repeated 1 time(s)]
> volume erase #9 center 140.34,118.64,167.69 radius 5.576
> volume erase #9 center 147.86,119.27,167.6 radius 5.576
> volume erase #9 center 150.46,124.56,165.65 radius 5.576
> volume erase #9 center 139.04,133.44,166.28 radius 5.576
> volume erase #9 center 128.35,128.21,165.71 radius 5.576
> volume erase #9 center 129.27,127.58,165.78 radius 5.576
> volume erase #9 center 137.2,131.35,160.79 radius 5.576
> volume erase #9 center 141.71,134.24,163.24 radius 5.576
> volume erase #9 center 142.69,133.06,162.59 radius 5.576
> volume erase #9 center 143.9,132.93,161 radius 5.576
> volume erase #9 center 141.89,131.71,158.06 radius 5.576
> volume erase #9 center 148.29,129.69,156.01 radius 5.576
> volume erase #9 center 145.13,130.71,154.65 radius 5.576
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> hide #7 models
> show #7 models
> hide #!6 models
> volume erase #9 center 147.87,123.94,162.78 radius 3.536
> volume erase #9 center 117.89,120.64,165.62 radius 3.536
> volume erase #9 center 125.65,117.5,168.53 radius 1.768
> volume erase #9 center 124.39,123.38,175.14 radius 1.768
> volume sel style mesh
> ui mousemode right select
> select clear
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #1/A
Alignment identifier is 1/A
Could not find virtual screen for QCocoaScreen(0x6000002f27e0, "DELL P2422H",
QRect(-1920,0 1920x1080), dpr=1, displayId=4128833, ) with displayId 4128833
> select #1/A:96
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:96
10 atoms, 10 bonds, 1 residue, 1 model selected
> ribbon sel suppressBackboneDisplay true
> hide sel ribbons
> ribbon sel suppressBackboneDisplay true
> select clear
> hide #!9 models
> select #1/A:96
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel ribbons
> select clear
> select #1/A:96@C
1 atom, 1 residue, 1 model selected
Drag select of 2 atoms, 1 bonds
Drag select of 2 atoms, 2 bonds
> hide sel atoms
Drag select of 2 atoms, 1 bonds
> hide sel atoms
> show #!9 models
> ui mousemode right "map eraser"
> volume erase #9 center 120.66,116.98,161.77 radius 3.5995
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8X2K_ligand_mesh_v2.png" width
> 2000 height 1299 supersample 3 transparentBackground true
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> ui mousemode right distance
> distance #1/A:96@NE2 #1/A:502@O
Distance between 8x2k #1/A HIS 96 NE2 and HOH 502 O: 4.321Å
> hide #7.1 models
> color #7 black models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8X2K_ligand_mesh_v3.png" width
> 2000 height 1299 supersample 3 transparentBackground true
> hide #!1 models
> hide #!9 models
> show #!2 models
> show #!5 models
> ui mousemode right "map eraser"
> volume erase #5 center 127.27,124.6,175.16 radius 14.985 outside true
Opened emd_37881_8WW2.map copy as #11, grid size 256,256,256, pixel 1.1, shown
at step 1, values float32
> select add #2
2050 atoms, 2091 bonds, 8 pseudobonds, 274 residues, 4 models selected
> hide sel ribbons
> select subtract #2
2 atoms, 1 bond, 1 residue, 1 model selected
> hide #!2 models
> show #!2 models
> show #!8 models
> hide #!11 models
> hide #10 models
> ui mousemode right select
Drag select of 44 atoms, 46 bonds
> hide sel atoms
Drag select of 9 atoms, 7 bonds
> hide sel atoms
> select add #8
9 atoms, 7 bonds, 1 residue, 3 models selected
> volume sel style mesh
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8WW2_mesh_v2.png" width 2000
> height 1299 supersample 3 transparentBackground true
> hide #!2 models
> show #!3 models
> hide #!8 models
> hide #!7 models
> open /Users/dongju/Downloads/emd_42023.map.gz
File reader requires uncompressed file;
'/Users/dongju/Downloads/emd_42023.map.gz' is compressed
> open /Users/dongju/Downloads/emd_42023.map
Opened emd_42023.map as #10, grid size 256,256,256, pixel 0.86, shown at level
0.167, step 1, values float32
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #3 inMap #10
Fit molecule 8u8f (#3) to map emd_42023.map (#10) using 4141 atoms
average map value = 0.1101, steps = 192
shifted from previous position = 16.7
rotated from previous position = 9.16 degrees
atoms outside contour = 2995, contour level = 0.16691
Position of 8u8f (#3) relative to emd_42023.map (#10) coordinates:
Matrix rotation and translation
0.88449228 -0.43560265 -0.16710398 92.49693760
-0.33231245 -0.83960005 0.42969779 210.58389705
-0.32747801 -0.32453365 -0.88737594 304.93232510
Axis -0.96947337 0.20614143 0.13276707
Axis point 0.00000000 147.04753663 136.68586676
Rotation angle (degrees) 157.10831354
Shift along axis -5.77828007
> rename #10 emd_42023_8U8F.map
> undo
[Repeated 4 time(s)]
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!7 models
> show #!7 models
> show #7.1 models
> hide #7.1 models
> show #7.1 models
> hide #!8 models
> hide #!2 models
> show #!2 models
> show #!1 models
> show #!3 models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4_GPR3_updated_no8U9F.cxs"
——— End of log from Mon Sep 23 15:26:47 2024 ———
opened ChimeraX session
Could not find virtual screen for QCocoaScreen(0x6000002f27e0, "DELL P2422H",
QRect(-1920,0 1920x1080), dpr=1, displayId=4128833, ) with displayId 4128833
[Repeated 1 time(s)]
> show #!10 models
> ui mousemode right translate
> select add #10
9 atoms, 7 bonds, 1 residue, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.91902,0.34695,-0.18716,-23.279,-0.3942,0.81275,-0.42901,138.04,0.0032674,0.46804,0.8837,-28.74,#10,1,0,0,-9.5979,0,1,0,-6.4832,0,0,1,15.236
> view matrix models
> #2,0.91902,0.34695,-0.18716,-28.621,-0.3942,0.81275,-0.42901,135.08,0.0032674,0.46804,0.8837,-20.164,#10,1,0,0,-14.94,0,1,0,-9.443,0,0,1,23.812
> view matrix models
> #2,0.91902,0.34695,-0.18716,-19.32,-0.3942,0.81275,-0.42901,147.7,0.0032674,0.46804,0.8837,-34.002,#10,1,0,0,-5.6394,0,1,0,3.1727,0,0,1,9.9738
> view matrix models
> #2,0.91902,0.34695,-0.18716,-22.6,-0.3942,0.81275,-0.42901,146.72,0.0032674,0.46804,0.8837,-28.615,#10,1,0,0,-8.9194,0,1,0,2.1914,0,0,1,15.361
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.55026,-0.35997,0.75342,101.56,-0.41995,0.89919,0.1229,66.698,-0.7217,-0.24877,-0.64595,338.13,#10,-0.7716,-0.39887,0.49552,170.44,-0.096972,0.84363,0.52809,-33.331,-0.62868,0.35942,-0.68962,247.26
> view matrix models
> #2,-0.4284,-0.60842,0.66806,117.88,-0.16046,0.77881,0.60639,-24.337,-0.88923,0.15258,-0.43127,297.28,#10,-0.72983,-0.61222,0.30419,209.76,0.0092519,0.43609,0.89986,-47.663,-0.68356,0.65956,-0.31261,178.86
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.4284,-0.60842,0.66806,127.97,-0.16046,0.77881,0.60639,12.444,-0.88923,0.15258,-0.43127,285.66,#10,-0.72983,-0.61222,0.30419,219.84,0.0092519,0.43609,0.89986,-10.883,-0.68356,0.65956,-0.31261,167.24
> ui mousemode right select
> select clear
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 1 maps.
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #3 inMap #10
Fit molecule 8u8f (#3) to map emd_42023_8U8F.map (#10) using 4141 atoms
average map value = 0.1039, steps = 140
shifted from previous position = 6.04
rotated from previous position = 13.2 degrees
atoms outside contour = 3150, contour level = 0.16691
Position of 8u8f (#3) relative to emd_42023_8U8F.map (#10) coordinates:
Matrix rotation and translation
-0.58378611 0.39230421 0.71083837 40.11433254
-0.81057672 -0.33172350 -0.48262294 278.52181831
0.04646678 -0.85793760 0.51164823 136.24670506
Axis -0.26347291 0.46639243 -0.84442888
Axis point 67.32370020 166.66693468 0.00000000
Rotation angle (degrees) 134.58210932
Shift along axis 4.28077393
> hide #!1 models
> hide #!2 models
> volume #10 level 0.3641
> ui mousemode right "translate selected models"
> select add #10
2 models selected
> view matrix models
> #10,-0.72983,-0.61222,0.30419,232.85,0.0092519,0.43609,0.89986,-3.0164,-0.68356,0.65956,-0.31261,178.23
> view matrix models
> #10,-0.72983,-0.61222,0.30419,239.92,0.0092519,0.43609,0.89986,-11.331,-0.68356,0.65956,-0.31261,177.48
> hide #!10 models
> show #!10 models
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.34978,-0.91732,-0.19019,203.67,-0.74194,-0.3952,0.54161,197.32,-0.572,-0.048329,-0.81883,292.62
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.34978,-0.91732,-0.19019,199.94,-0.74194,-0.3952,0.54161,195.51,-0.572,-0.048329,-0.81883,291.08
> view matrix models
> #10,0.34978,-0.91732,-0.19019,197.99,-0.74194,-0.3952,0.54161,193.99,-0.572,-0.048329,-0.81883,291.98
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.71492,-0.67613,-0.17814,131.3,-0.60499,-0.72591,0.32717,235.51,-0.35053,-0.12613,-0.92802,286.93
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.71492,-0.67613,-0.17814,132.86,-0.60499,-0.72591,0.32717,236.4,-0.35053,-0.12613,-0.92802,287.2
> view matrix models
> #10,0.71492,-0.67613,-0.17814,134.6,-0.60499,-0.72591,0.32717,236.6,-0.35053,-0.12613,-0.92802,287.56
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.71493,-0.67692,-0.17506,134.32,-0.6059,-0.72476,0.32805,236.49,-0.34894,-0.12846,-0.9283,287.64
> view matrix models
> #10,0.56403,-0.79822,-0.21144,167.64,-0.68901,-0.59607,0.41227,223.65,-0.45512,-0.086851,-0.88618,290.83
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.56403,-0.79822,-0.21144,167.91,-0.68901,-0.59607,0.41227,222.99,-0.45512,-0.086851,-0.88618,292.1
> view matrix models
> #10,0.56403,-0.79822,-0.21144,168.12,-0.68901,-0.59607,0.41227,222.47,-0.45512,-0.086851,-0.88618,292.89
> view matrix models
> #10,0.56403,-0.79822,-0.21144,167.68,-0.68901,-0.59607,0.41227,222.06,-0.45512,-0.086851,-0.88618,292.78
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.9451,-0.30826,-0.10842,64.336,-0.24932,-0.89473,0.37054,205.73,-0.21123,-0.32317,-0.92247,292.14
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.9451,-0.30826,-0.10842,64.792,-0.24932,-0.89473,0.37054,207.28,-0.21123,-0.32317,-0.92247,291.09
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.95406,-0.28402,-0.095414,59.891,-0.23096,-0.90001,0.36966,205.79,-0.19086,-0.33064,-0.92426,289.69
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.95406,-0.28402,-0.095414,54.61,-0.23096,-0.90001,0.36966,206.3,-0.19086,-0.33064,-0.92426,289.49
> ui mousemode right select
> select clear
> ui tool show "Fit in Map"
> fitmap #3 inMap #10
Fit molecule 8u8f (#3) to map emd_42023_8U8F.map (#10) using 4141 atoms
average map value = 0.1356, steps = 60
shifted from previous position = 2.97
rotated from previous position = 3.78 degrees
atoms outside contour = 3428, contour level = 0.36411
Position of 8u8f (#3) relative to emd_42023_8U8F.map (#10) coordinates:
Matrix rotation and translation
0.98885725 -0.13046063 0.07170335 9.70268642
0.11910430 0.98228692 0.14466024 -33.06462280
-0.08930573 -0.13450815 0.98687996 22.31914980
Axis -0.68489987 0.39501286 0.61227200
Axis point 0.00000000 170.70498206 232.97410918
Rotation angle (degrees) 11.75939778
Shift along axis -6.04092928
> select clear
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select add #10
2 models selected
> view matrix models
> #10,0.95406,-0.28402,-0.095414,60.021,-0.23096,-0.90001,0.36966,210.43,-0.19086,-0.33064,-0.92426,294.16
> view matrix models
> #10,0.95406,-0.28402,-0.095414,59.925,-0.23096,-0.90001,0.36966,210.25,-0.19086,-0.33064,-0.92426,294.21
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.95276,-0.26606,-0.1465,64.268,-0.21159,-0.92746,0.30831,217.85,-0.2179,-0.26274,-0.93994,292.51
> view matrix models
> #10,0.94455,-0.26808,-0.18966,70.424,-0.18725,-0.91414,0.35956,207.8,-0.26976,-0.30411,-0.91364,299.42
> view matrix models
> #10,0.96895,-0.23928,-0.062312,50.009,-0.21977,-0.94892,0.22637,230.41,-0.11329,-0.20564,-0.97205,278.71
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.96895,-0.23928,-0.062312,48.309,-0.21977,-0.94892,0.22637,229.48,-0.11329,-0.20564,-0.97205,277.8
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.96809,-0.24111,-0.068264,49.278,-0.22119,-0.95024,0.21935,230.58,-0.11775,-0.19725,-0.97326,277.64
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.96809,-0.24111,-0.068264,49.089,-0.22119,-0.95024,0.21935,230.35,-0.11775,-0.19725,-0.97326,277.49
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.9547,-0.29204,-0.057122,54.291,-0.27231,-0.93479,0.22806,233.68,-0.12,-0.20217,-0.97197,278.08
> view matrix models
> #10,0.95173,-0.29746,-0.075656,57.315,-0.27693,-0.9385,0.20621,237.11,-0.13234,-0.17531,-0.97558,277.29
> view matrix models
> #10,0.88769,-0.45987,0.022982,68.997,-0.4567,-0.873,0.17115,255.37,-0.058645,-0.16243,-0.98498,268.7
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.88769,-0.45987,0.022982,69.027,-0.4567,-0.873,0.17115,255.43,-0.058645,-0.16243,-0.98498,268.91
> view matrix models
> #10,0.88769,-0.45987,0.022982,69.188,-0.4567,-0.873,0.17115,255.62,-0.058645,-0.16243,-0.98498,268.99
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> select add #10
2 models selected
> view matrix models
> #10,0.88769,-0.45987,0.022982,71.124,-0.4567,-0.873,0.17115,254.25,-0.058645,-0.16243,-0.98498,269.49
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.91356,-0.40236,-0.059297,72.131,-0.38423,-0.90165,0.1985,245.57,-0.13333,-0.15856,-0.97831,276.88
> ui mousemode right select
> fitmap #3 inMap #10
Fit molecule 8u8f (#3) to map emd_42023_8U8F.map (#10) using 4141 atoms
average map value = 0.4117, steps = 48
shifted from previous position = 1.71
rotated from previous position = 1.6 degrees
atoms outside contour = 2121, contour level = 0.36411
Position of 8u8f (#3) relative to emd_42023_8U8F.map (#10) coordinates:
Matrix rotation and translation
0.99999902 0.00120173 0.00071855 -0.19601774
-0.00120458 0.99999135 0.00398280 -0.25695137
-0.00071375 -0.00398366 0.99999181 0.53913177
Axis -0.94341223 0.16961756 -0.28496185
Axis point 0.00000000 134.32444864 64.28382463
Rotation angle (degrees) 0.24191227
Shift along axis -0.01228992
> select clear
> transparency #10.1 50
> select add #3
4141 atoms, 4187 bonds, 1 pseudobond, 266 residues, 2 models selected
> hide sel ribbons
> select subtract #3
Nothing selected
> select add #10
2 models selected
> volume sel style mesh
> volume sel style surface
> select clear
> ui mousemode right "map eraser"
> volume erase #10 center 117.7,116.64,162.97 radius 15.055 outside true
Opened emd_42023_8U8F.map copy as #13, grid size 256,256,256, pixel 0.86,
shown at step 1, values float32
> volume erase #13 center 116.79,102.75,163.3 radius 7.9258
> volume erase #13 center 111.05,106.54,171.81 radius 7.9258
> volume erase #13 center 120.71,106.79,157.7 radius 7.9258
> volume erase #13 center 124.7,110.37,171.04 radius 7.9258
> volume erase #13 center 121.04,110.48,171.92 radius 7.9258
> volume erase #13 center 105.04,115.99,155.78 radius 7.9258
> volume erase #13 center 118.01,100.14,158.41 radius 7.9258
> volume erase #13 center 128.52,108.66,159.84 radius 7.9258
> volume erase #13 center 129.08,114.99,168.53 radius 7.9258
> volume erase #13 center 124.09,121.82,178.56 radius 7.9258
> volume erase #13 center 129.62,124.33,168.57 radius 7.9258
> volume erase #13 center 120.15,112.65,154.11 radius 7.9258
> volume erase #13 center 122.18,114.46,153.45 radius 7.9258
> volume erase #13 center 115.83,112.64,152.98 radius 7.9258
> volume erase #13 center 109.37,106.78,150.6 radius 7.9258
> volume erase #13 center 102.31,103.74,159.66 radius 7.9258
> volume erase #13 center 122.28,123.84,151.67 radius 7.9258
> volume erase #13 center 128.24,123.7,148.61 radius 7.9258
> volume erase #13 center 114.43,125.51,156.94 radius 7.9258
> volume erase #13 center 122.2,126.46,151.3 radius 7.9258
> volume erase #13 center 123.71,127.92,169 radius 7.9258
> volume erase #13 center 117.79,125.27,170.02 radius 7.9258
> volume erase #13 center 126.34,129.99,164.82 radius 7.9258
> volume erase #13 center 128.46,130.55,157.76 radius 7.9258
> volume erase #13 center 126.76,132.97,162.51 radius 7.9258
[Repeated 1 time(s)]
> volume erase #13 center 117.16,121.02,177.7 radius 3.0822
> volume erase #13 center 117.4,115.9,177.67 radius 3.0822
> volume erase #13 center 114.58,116,177.53 radius 3.0822
> volume erase #13 center 114.79,116.29,176.51 radius 3.0822
[Repeated 1 time(s)]
> volume erase #13 center 114.57,114.41,176.24 radius 3.0822
> volume erase #13 center 113.27,118.05,179.54 radius 3.0822
> volume erase #13 center 112.99,120.41,178.61 radius 3.0822
> volume erase #13 center 118.41,130.57,163.6 radius 3.0822
> volume erase #13 center 111.38,119.59,150.76 radius 3.0822
> volume erase #13 center 115.31,118.78,149.01 radius 3.0822
> volume erase #13 center 117.82,118,158.2 radius 3.0822
> volume erase #13 center 112.67,119.09,162.03 radius 3.0822
> volume erase #13 center 114.55,120.02,164.12 radius 3.0822
> volume erase #13 center 112.65,122.72,163.77 radius 3.0822
> volume erase #13 center 109.49,124.56,161.57 radius 3.0822
> volume erase #13 center 110.17,118.4,174.3 radius 3.0822
> volume erase #13 center 111.11,122.43,172.75 radius 3.0822
> volume erase #13 center 102.49,119.55,167.53 radius 3.0822
> volume erase #13 center 100.76,116.59,164.82 radius 3.0822
> volume erase #13 center 106.59,120.53,171.66 radius 3.0822
> volume erase #13 center 105.28,116.39,171.69 radius 3.0822
> volume erase #13 center 108.38,114.95,174.21 radius 3.0822
> volume erase #13 center 106.76,115.57,174.43 radius 3.0822
> hide #!13 models
> ui mousemode right select
Drag select of 2 atoms, 2 bonds
> hide sel atoms
Drag select of 1 atoms, 1 bonds
> hide sel atoms
Drag select of 4 atoms, 3 bonds
> hide sel atoms
> show #!13 models
Drag select of eraser sphere, 183 of 1000 triangles, 1 atoms, 13
emd_42023_8U8F.map copy
> select clear
> ui mousemode right "map eraser"
> volume erase #13 center 108.09,107.52,158.16 radius 3.0822
> volume erase #13 center 114.1,110.88,162.3 radius 1.431
> volume erase #13 center 108.99,109.31,166.7 radius 1.431
> volume erase #13 center 108.51,110.29,165.94 radius 1.431
> volume erase #13 center 107.82,110.35,165.37 radius 1.431
> volume erase #13 center 106.99,111.99,163.41 radius 1.431
> volume erase #13 center 109.81,113.95,164.24 radius 1.431
> volume erase #13 center 110.96,114.2,163.7 radius 1.431
> volume erase #13 center 102.18,117.15,164.89 radius 1.431
> volume erase #13 center 102.46,117.32,163.27 radius 1.431
> volume erase #13 center 104.77,125.58,165.01 radius 1.431
> volume erase #13 center 107.41,124.89,166.86 radius 3.4125
> volume erase #13 center 111.87,121.8,167.47 radius 3.4125
> volume erase #13 center 111.26,119.34,168.42 radius 1.8714
> volume erase #13 center 111.44,120.62,169.64 radius 1.8714
> volume erase #13 center 110.39,121.3,169.78 radius 1.8714
> volume erase #13 center 110.13,119.84,168.41 radius 1.8714
> volume erase #13 center 109.42,118.75,168.38 radius 1.8714
> volume erase #13 center 109.74,122.19,167.63 radius 1.8714
> volume erase #13 center 111.05,123.71,171.01 radius 1.8714
> volume erase #13 center 110.89,123.53,171.84 radius 1.8714
> volume erase #13 center 109.31,123.03,172.58 radius 1.8714
> volume erase #13 center 113.06,110.96,162.71 radius 1.8714
> volume erase #13 center 107.82,121.79,164.28 radius 1.8714
> volume erase #13 center 106.28,121.88,168.51 radius 1.8714
> volume erase #13 center 108.09,121.35,170.06 radius 1.8714
> volume erase #13 center 110.47,119.08,167.21 radius 1.8714
> select add #13
2 models selected
> volume sel style mesh
> ui mousemode right select
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_GPR3_8U8F.cxs"
——— End of log from Mon Sep 23 15:58:13 2024 ———
opened ChimeraX session
> select add #3
4141 atoms, 4187 bonds, 1 pseudobond, 266 residues, 2 models selected
> show sel ribbons
> show #!1 models
> hide #!3 models
> hide #!7 models
> show #!9 models
> select add #1
6062 atoms, 6143 bonds, 4 pseudobonds, 529 residues, 6 models selected
> select subtract #3
1921 atoms, 1956 bonds, 3 pseudobonds, 263 residues, 4 models selected
> show sel ribbons
> hide #!13 models
> show #!4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #4 change image level -0.05594,0 level 0.1762,0.8 level 4.403,1
> volume #4 level 0.5696
> show #!4 models
> hide #!9 models
> hide #7.1 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #1 inMap #4
Fit molecule 8x2k (#1) to map emd_38015_8X2K.map (#4) using 1921 atoms
average map value = 0.907, steps = 28
shifted from previous position = 0.0179
rotated from previous position = 0.0166 degrees
atoms outside contour = 838, contour level = 0.56958
Position of 8x2k (#1) relative to emd_38015_8X2K.map (#4) coordinates:
Matrix rotation and translation
0.99999919 -0.00029728 0.00123779 -0.14813315
0.00029782 0.99999986 -0.00043551 0.03667520
-0.00123766 0.00043588 0.99999914 0.11830230
Axis 0.32381927 0.91991067 0.22114575
Axis point 93.36805511 0.00000000 122.85809050
Rotation angle (degrees) 0.07709056
Shift along axis 0.01193159
> hide #!1 models
> show #!1 models
> show #!6 models
> hide #!6 models
> show #!9 models
> volume #4 level 0.4363
> select subtract #1
Nothing selected
> volume #4 level 0.2497
> volume #4 level 0.3564
> hide #!4 models
> ui mousemode right select
> select #1/A:96@NE2
1 atom, 1 residue, 1 model selected
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hbonds sel color #000000 restrict cross select true reveal true
1 hydrogen bonds found
> hbonds sel color #000000 restrict cross select true reveal true
2 hydrogen bonds found
> hbonds sel color #000000 restrict cross select true reveal true
2 hydrogen bonds found
> hbonds sel color #000000 restrict cross select true reveal true
2 hydrogen bonds found
> select clear
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hbonds sel color #000000 restrict cross distSlop 1.0 angleSlop 25.0 select
> true reveal true
Atom specifier selects no atoms
> select #1/A:280@OH
1 atom, 1 residue, 1 model selected
> select add #1/A:96@NE2
2 atoms, 1 bond, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 restrict cross distSlop 1.0 angleSlop 25.0 select
> true reveal true
5 hydrogen bonds found
> hbonds sel color #000000 restrict cross distSlop 1.0 angleSlop 30.0 select
> true reveal true
8 hydrogen bonds found
> hbonds sel color #000000 restrict cross distSlop 1.0 angleSlop 25.0 select
> true reveal true
6 hydrogen bonds found
> hbonds sel color #000000 restrict cross distSlop 1.0 angleSlop 25.0 select
> true reveal true
7 hydrogen bonds found
> select clear
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 3 days, 13 hours, 9 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 13 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Mac Qt crash in displayConfigFinalizedProc connecting or disconnecting display or waking from sleep.