![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17437 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-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001fb080840 (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, lxml._elementpath, lxml.etree, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix (total: 61)
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{
"uptime" : 220000,
"procRole" : "Background",
"version" : 2,
"userID" : 1195785599,
"deployVersion" : 210,
"modelCode" : "Mac14,5",
"coalitionID" : 3340,
"osVersion" : {
"train" : "macOS 15.3.2",
"build" : "24D81",
"releaseType" : "User"
},
"captureTime" : "2025-04-15 18:00:50.6769 -0400",
"codeSigningMonitor" : 1,
"incident" : "A17AB552-C016-46D3-B3CB-1304B1800468",
"pid" : 84570,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-15 08:57:28.0211 -0400",
"procStartAbsTime" : 4766988439682,
"procExitAbsTime" : 5402549828780,
"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":"0EC3B9EC-4136-540D-AC90-521AA6712099","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "AAE09EAA-E991-08DE-E25C-56BCD904E286",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "0ECD1CCF-EF3D-4D11-9891-619770104F9D",
"wakeTime" : 22917,
"sleepWakeUUID" : "969E71C4-1BB1-479F-9349-3B8CFDCCC13D",
"sip" : "enabled",
"vmRegionInfo" : "0xa38e3fd69f8 is not in any region. Bytes after previous region: 10758423144953 Bytes before following region: 94313656784392\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00008a38e3fd69f8","rawCodes":[1,151976947837432],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00008a38e3fd69f8 -> 0x00000a38e3fd69f8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":84570},
"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\nVM - (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" : "0xa38e3fd69f8 is not in any region. Bytes after previous region: 10758423144953 Bytes before following region: 94313656784392\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00516, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0108, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0128, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0683, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00686, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
level 0.0122, step 1, values float32
Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened rOAT1-R466A.mrc as #46, grid size 480,480,480, pixel 0.553, shown at
level 0.0115, step 1, values float32
Opened rOAT1-Apo.mrc as #48, grid size 240,240,240, pixel 0.553, shown at step
1, values float32
Log from Sat Apr 12 21:31:41 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00516, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0108, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0128, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0683, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00686, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
level 0.0122, step 1, values float32
Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened postprocess_rescaled.mrc as #46, grid size 480,480,480, pixel 0.553,
shown at level 0.0115, step 1, values float32
Log from Thu Apr 10 15:43:35 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs format session
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0116, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00383, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0141, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0546, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Log from Thu Apr 10 14:06:06 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0116, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00383, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0141, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0546, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Log from Tue Mar 11 12:00:09 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0116, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00383, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0141, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0546, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Log from Mon Feb 10 17:46:10 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
shown at level 0.00928, step 1, values float32
Log from Wed Dec 11 13:28:04 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> format session
Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
shown at level 0.00928, step 1, values float32
Log from Tue Dec 10 11:33:02 2024 Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
> hOCT1-VB1_3_real_space_refined_002.pdb"
Chain information for hOCT1-VB1_3_real_space_refined_002.pdb #1
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 1650, resource id:
35652789, major code: 40 (TranslateCoords), minor code: 0
> select ::name="VIB"
18 atoms, 19 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> save
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
> hOCT1-noVB1.pdb" relModel #1
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7992, resource id:
35652794, major code: 40 (TranslateCoords), minor code: 0
> close session
> open
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
> hOCT1-noVB1.pdb"
Chain information for hOCT1-noVB1.pdb #1
---
Chain | Description
A | No description available
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1
Ignored bad PDB record found on line 2
REMARK SMILES IDX 15 1 14 2 10 3 9 4 8 5 7 6 11 7 12 8 13 9 6 11 5 12 4 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 16 14 3 15 18 16 2 17 1 18 17 19
Ignored bad PDB record found on line 4
REMARK H PARENT 13 10 17 20 17 21
Ignored bad PDB record found on line 5
REMARK Flexibility Score: inf
15 messages similar to the above omitted
Opened ligand.pdbqt containing 1 structures (21 atoms, 22 bonds)
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1
Ignored bad PDB record found on line 2
REMARK SMILES IDX 15 1 14 2 10 3 9 4 8 5 7 6 11 7 12 8 13 9 6 11 5 12 4 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 16 14 3 15 18 16 2 17 1 18 17 19
Ignored bad PDB record found on line 4
REMARK H PARENT 13 10 17 20 17 21
Ignored bad PDB record found on line 5
REMARK Flexibility Score: inf
15 messages similar to the above omitted
Opened ligand.pdbqt containing 1 structures (21 atoms, 22 bonds)
QXcbConnection: XCB error: 3 (BadWindow), sequence: 6676, resource id:
35652851, major code: 40 (TranslateCoords), minor code: 0
> hide #3 models
> show #3 models
> hide #3 models
> close #2-3
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/vina_dock.pdbqt
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/vina_dock.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.139 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -8.396
Ignored bad PDB record found on line 4
REMARK INTER: -7.934
Ignored bad PDB record found on line 5
REMARK INTRA: -0.463
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.463
495 messages similar to the above omitted
Opened vina_dock.pdbqt containing 20 structures (420 atoms, 440 bonds)
> viewdockx #2.1-20
> set bgColor white
> select #2.9/?:1@@serial_number=16
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 22 bonds, 1 residue, 1 model selected
> view sel
[deleted to fit within ticket limits]
> select clear
> show #!10 models
> hide #!10 models
> select clear
> volume #11.3 level 0.01081
> select clear
> show #!10 models
> hide #!10 models
> save /Users/dout2/Desktop/rOAT1-PBD_OF_LigandDensity.png supersample 3
> hide #!12 models
> hide #!11 models
> show #!18 models
> show #!19 models
> show #!19.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!18 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-TFV_OF_LigandDensity.png supersample 3
> hide #!19 models
> hide #!18 models
> show #!24 models
> show #!25 models
> show #!25.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!24 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
> hide #!25 models
> hide #!24 models
> show #!35 models
> show #!34 models
> show #!35.3 models
> hide #!35.3 models
> hide #!35 models
> hide #!34 models
> show #!41 models
> show #!42 models
> show #!42.3 models
> save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
> hide #!41 models
> hide #!42 models
> hide #!42.3 models
> show #!25 models
> show #!24 models
> save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
> hide #!24 models
> hide #!25 models
> show #!42.3 models
> show #!41 models
> select clear
[Repeated 1 time(s)]
> ui tool show Distances
> select clear
No distances to delete!
> save /Users/dout2/Desktop/hOAT1-TFV_OF_LigandDensity.png supersample 3
> view
> view orient
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
> facing/postprocess.mrc
Opened postprocess.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
level 0.00432, step 2, values float32
> volume #40 step 1
> volume #40 level 0.008916
> hide #!41 models
> hide #!40 models
> select add #41
4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected
> select subtract #41
Nothing selected
> hide #!42 models
> show #!40 models
> rename #40 rOAT1-AKG_OF.mrc
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
> facing/RealSpaceRefine_1/rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb
Chain information for rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb #43
---
Chain | Description
A | No description available
> select clear
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
> occluded/postprocess.mrc
Opened postprocess.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
level 0.00378, step 2, values float32
> rename #44 rOAT1-AKG_OOC.mrc
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
> occluded/RealSpaceRefine_3/rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb
Chain information for rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb #45
---
Chain | Description
A | No description available
> rename #45 rOAT1-AKG_OOC-coot-4_real_space_refined_003.pdb
> hide #!43 models
> hide #!40 models
> volume #44 step 1
> volume #44 level 0.01023
> select ::name="AKG"
20 atoms, 18 bonds, 2 residues, 2 models selected
> view sel
> color #44 #ffffb24d models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2228 atoms, 2112 bonds, 244 residues, 16 models selected
> show sel & #!45 atoms
> select clear
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> color #44 #ffffb280 models
> color #44 #ffffb266 models
> color #44 #ffffb24d models
> select clear
> save /Users/dout2/Desktop/hOAT1-AKG_OOC_LigandDensity.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> hide #!45 models
> hide #!44 models
> show #!43 models
> show #!40 models
> color #40 #b2b2b24d models
> select clear
> color #40 #ffffb24d models
> select clear
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2228 atoms, 2112 bonds, 244 residues, 16 models selected
> show sel & #!43 atoms
> select clear
[Repeated 1 time(s)]
> volume #40 level 0.009283
> save /Users/dout2/Desktop/rOAT1-AKG_OF_LigandDensity.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> volume #40 level 0.01222
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> hide #!43 models
> hide #!40 models
> open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
> occluded/postprocess_rescaled.mrc
Opened postprocess_rescaled.mrc as #46, grid size 480,480,480, pixel 0.553,
shown at level 0.0038, step 2, values float32
> open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
> occluded/RealSpaceRefine_1/rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb
Chain information for rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb #47
---
Chain | Description
A | No description available
> select #46
4 models selected
> select clear
> view
> volume #46 step 1
> volume #46 level 0.01147
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2367 atoms, 2244 bonds, 259 residues, 17 models selected
> view sel
> color #46 #b2ffff4d models
> select #46
4 models selected
> show #!47 atoms
> select clear
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> close #47
> open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
> occluded/RealSpaceRefine_2/rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb
Chain information for rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb #47
---
Chain | Description
A | No description available
> select add #46
4 models selected
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2361 atoms, 2238 bonds, 259 residues, 17 models selected
> show sel & #!47 atoms
> select clear
> select #46
4 models selected
> select clear
> save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> hide #!46 models
> show #!46 models
> save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> view
> color #46 #b2ffffff models
> color #46 #b2ffffab models
> color #46 #b2ffffff models
> select clear
[Repeated 1 time(s)]
> save /Users/dout2/Desktop/rOAT1-R466A_OF.png supersample 3
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Thu Apr 10 15:43:35 2025 ———
opened ChimeraX session
> hide #!47 models
> hide #!46 models
> rename #46 rOAT1-R466A.mrc
> open
> /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/J12_2.05A_clip-240/cryosparc_P4_J16__localfilter_240.mrc
Opened cryosparc_P4_J16__localfilter_240.mrc as #48, grid size 240,240,240,
pixel 0.553, shown at level 0.238, step 1, values float32
> open
> /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/model/rOAT1-apo-
> coot-4_real_space_refined_004.pdb
Chain information for rOAT1-apo-coot-4_real_space_refined_004.pdb #49
---
Chain | Description
A | No description available
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> rename #48 rOAT1-Apo.mrc
> hide #49 models
> hide #!48 models
> hide #48.1 models
> show #49 models
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> size stickRadius 0.3
Changed 72733 bond radii
> select add #49
3942 atoms, 3966 bonds, 570 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 10 atoms, 11 bonds
Drag select of 6 atoms, 9 bonds
Drag select of 8 atoms, 10 bonds
Drag select of 4 atoms, 4 bonds
> select up
36 atoms, 34 bonds, 4 residues, 1 model selected
> lighting flat
> graphics silhouettes false
> select clear
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> select clear
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color sel orange
> color sel purple
> color sel hot pink
> size stickRadius 0.5
Changed 72733 bond radii
> size stickRadius 0.4
Changed 72733 bond radii
> select clear
> select add #49/A:466@CB
1 atom, 1 residue, 1 model selected
> select add #49/A:382@NZ
2 atoms, 2 residues, 1 model selected
> select up
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color sel lime
> color sel purple
> select clear
> select add #49/A:382@NZ
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
20 atoms, 18 bonds, 2 residues, 1 model selected
> color sel byhetero
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color sel purple
> select clear
> select #49/A:382@NZ
1 atom, 1 residue, 1 model selected
> select add #49/A:466@NH2
2 atoms, 2 residues, 1 model selected
> select add #49/A:466@NH1
3 atoms, 2 residues, 1 model selected
> select add #49/A:466@CZ
4 atoms, 2 residues, 1 model selected
> select add #49/A:466@NE
5 atoms, 2 residues, 1 model selected
> color sel byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-Apo_keyresidue.png supersample 3
> transparentBackground true
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> hide sel atoms
> select add #49
3942 atoms, 3966 bonds, 570 residues, 1 model selected
> show sel cartoons
> select clear
> view
> select add #49
3942 atoms, 3966 bonds, 570 residues, 1 model selected
> color sel gray
> color sel light gray
> color sel dark gray
> surface sel
> select clear
> save /Users/dout2/Desktop/rOAT1-Apo_bg.png supersample 3
> transparentBackground true
> open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif
Summary of feedback from opening
/Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Chain information for model.cif #50
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
> hide #!49 models
> rename #50 rOAT1-AKG_IF_af3.cif
> select add #50
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> select clear
> select #50: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel purple
> size stickRadius 0.4
Changed 77114 bond radii
> select clear
> select add #50
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> select #50/A:354@CG
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #50/B:1@C4
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select #50/A:382@NZ
1 atom, 1 residue, 1 model selected
> select add #50/A:466@NH1
2 atoms, 2 residues, 1 model selected
> select add #50/A:466@NH2
3 atoms, 2 residues, 1 model selected
> select add #50/A:466@NE
4 atoms, 2 residues, 1 model selected
> color sel byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_keyresidue.png supersample 3
> transparentBackground true
> select add #50
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> surface sel
> color (#!50 & sel) dark gray
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_bg.png supersample 3
> transparentBackground true
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> hide #!50 models
> show #!45 models
> show #!44 models
> hide #!44 models
> view
> view orient
> hide #!45 models
> show #!43 models
> show #!45 models
> hide #!45 models
> select add #43
3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected
> color (#!43 & sel) dark gray
> surface (#!43 & sel)
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_OF_bg.png supersample 3
> transparentBackground true
> hide #43.2 models
> hide #43.1 models
> show #43.1 models
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> select subtract #43.2
1 model selected
> select add #43
3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected
> hide sel cartoons
> select clear
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> select add #43
3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 3 models selected
> hide sel atoms
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> select #43: akg
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #43/A:601@C2
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> select #43/A:466@NH2
1 atom, 1 residue, 1 model selected
> select add #43/A:466@NH1
2 atoms, 1 residue, 2 models selected
> select add #43/A:466@NE
3 atoms, 1 residue, 2 models selected
> select add #43/A:382@NZ
4 atoms, 2 residues, 2 models selected
> color (#!43 & sel) byhetero
> select clear
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color (#!43 & sel) purple
> select subtract #43/A:382@NZ
65 atoms, 63 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH2
64 atoms, 62 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH1
63 atoms, 61 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@CD
62 atoms, 59 bonds, 6 residues, 2 models selected
> color (#!43 & sel) byhetero
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color (#!43 & sel) purple
> select subtract #43/A:382@NZ
65 atoms, 63 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH1
64 atoms, 62 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH2
63 atoms, 61 bonds, 6 residues, 2 models selected
> select clear
> select add #43/A:466@NH2
1 atom, 1 residue, 1 model selected
> select add #43/A:466@NH1
2 atoms, 1 residue, 2 models selected
> select add #43/A:382@NZ
3 atoms, 2 residues, 2 models selected
> color (#!43 & sel) byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_OF_residue.png supersample 3
> transparentBackground true
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif
Summary of feedback from opening
/Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Chain information for model.cif #51
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
> hide #!43 models
> hide #43.1 models
> view
> rename #51 rOAT1-AKG_IF_af3_model1.cif
> rename #51 rOAT1-AKG_IF_af3_model1-1.cif
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> color sel dark gray
> surface sel
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_IF_bg.png supersample 3
> transparentBackground true
> hide #51.1 models
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #51: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> color (#!51 & sel) purple
> size stickRadius 0.4
Changed 81495 bond radii
> select clear
> select #51: AKG
Nothing selected
> show #!51 atoms
> undo
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> show sel atoms
> select #51/B:1@C3
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel atoms
> select #51/B
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select clear
> select #51: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> select #51/A:382@NZ
1 atom, 1 residue, 1 model selected
> select add #51/A:466@NH1
2 atoms, 2 residues, 2 models selected
> select add #51/A:466@NH2
3 atoms, 2 residues, 2 models selected
> color (#!51 & sel) byhetero
> select #51/A:466@NE
1 atom, 1 residue, 1 model selected
> color (#!51 & sel) byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_IF_residue.png supersample 3
> transparentBackground true
> close #50
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Sat Apr 12 21:31:41 2025 ———
opened ChimeraX session
> hide #!51 models
> show #!2 models
> show #1 models
> view
> lighting simple
> lighting soft
> lighting simple
> hide #!2 models
> select #1: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> view sel
> cofr sel
> select clear
> show #!2 models
> color #2 #ffffb2ff models
> color #2 #ffffb24f models
> color #2 #ffffb24e models
> color #2 #ffffb24d models
> select clear
[Repeated 1 time(s)]
> color #2 #a5ffb24d models
> color #2 #9effb24d models
> color #2 #9e43b24d models
> color #2 #9effb24d models
> color #2 #9effff4d models
> select clear
> size stickRadius 0.2
Changed 77114 bond radii
> select clear
> color #2 #942192ff models
> color #2 #9421924d models
> select clear
> color #2 #aa7942ff models
> color #2 #00fdffff models
> color #2 #00fdff4e models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> view sel
> ui tool show "Side View"
> volume #2 level 0.01002
> select clear
> select #1/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #1/A:207
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!2 models
> select #1/A:36
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> select clear
> select #1/A:601@C4'
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
3891 atoms, 3986 bonds, 501 residues, 1 model selected
> select down
19 atoms, 20 bonds, 1 residue, 1 model selected
> cofr sel
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie1.mp4
Movie saved to /Users/dout2/Desktop/movie1.mp4
> hide #!2 models
> hide #1 models
> select add #1
3905 atoms, 3986 bonds, 515 residues, 1 model selected
> select subtract #1
Nothing selected
> show #1 models
> hide #1 models
> show #!5 models
> show #!4 models
> select clear
> volume #4 level 0.01053
> color #4 #fffb00ff models
> color #4 #ffffb2ff models
> color #4 #ffffb24d models
> select #4
4 models selected
> select clear
> select #1: 382, 353,438,230,442,466,207
74 atoms, 71 bonds, 7 residues, 1 model selected
> show #!5 atoms
> select add #5
3848 atoms, 3935 bonds, 5 pseudobonds, 493 residues, 3 models selected
> hide sel & #!5 atoms
> select #5: 382, 353,438,230,442,466,207,601
93 atoms, 91 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> show sel atoms
> select clear
> select #5/A:601@O4
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> cofr sel
> select #4
4 models selected
> volume #4 level 0.01089
> volume #4 level 0.01182
> volume #4 level 0.01292
> select clear
> volume #4 level 0.01311
> volume #4 level 0.01274
> volume #4 level 0.01126
> volume #4 level 0.01274
> volume #4 level 0.012
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> view
> hide #!4 models
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> hide sel atoms
> select #5: 382, 353,438,230,442,466,207,601
93 atoms, 91 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #8 models
> show #!7 models
> hide #8 models
> hide #!7 models
> show #!10 models
> show #!12 models
> color #10 darkgrey models
> color #10 silver models
> color #10 #c0c0c04d models
> select clear
> hide #!12 models
> show #!12 models
> hide #!10 models
> show #!10 models
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> volume #10 level 0.0124
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 1 residue, 1 model selected
> select #12: 382, 353,438,230,442,466,207,601
111 atoms, 108 bonds, 8 residues, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select H
117 atoms, 10 residues, 9 models selected
> hide sel & #!12 atoms
> select clear
> select #12: 382, 353,438,230,442,466,207,601
111 atoms, 108 bonds, 8 residues, 1 model selected
> view sel
> cofr sel
> volume #10 level 0.009894
> volume #10 level 0.01073
> select clear
[Repeated 1 time(s)]
> select #12/B:601@C16
1 atom, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 1 residue, 1 model selected
> view sel
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> select #10
4 models selected
> select clear
> hide #!12 models
> hide #!10 models
> show #8 models
> show #!7 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> color #7 #ff2f92ff models
> color #7 #ff2f924d models
> select #7
4 models selected
> select clear
> select #8: 382, 353,438,230,442,466,207,601
93 atoms, 90 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> open
> /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-PBD_20230217/cryosparc_P4_J55__localfilter_160.mrc
Opened cryosparc_P4_J55__localfilter_160.mrc as #50, grid size 160,160,160,
pixel 0.83, shown at level 0.131, step 1, values float32
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie1.mp4
Movie saved to /Users/dout2/Desktop/movie1.mp4
> hide #!7 models
> view
> show #!7 models
> rename #50 rOAT1-PBD_IF.mrc
> select add #50
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #50,1,0,0,82.163,0,1,0,34.821,0,0,1,72.008
> view matrix models #50,1,0,0,78.322,0,1,0,71.965,0,0,1,68.805
> view matrix models #50,1,0,0,68.336,0,1,0,66.309,0,0,1,66.361
> ui tool show "Fit in Map"
> fitmap #50 inMap #7
Fit map rOAT1-PBD_IF.mrc in map rOAT1-PBD_IF.mrc using 40907 points
correlation = 0.9052, correlation about mean = 0.7104, overlap = 318.4
steps = 88, shift = 2.7, angle = 7.48 degrees
Position of rOAT1-PBD_IF.mrc (#50) relative to rOAT1-PBD_IF.mrc (#7)
coordinates:
Matrix rotation and translation
0.99182552 0.09586728 -0.08421166 67.85108178
-0.09362983 0.99515083 0.03013765 73.24636935
0.08669251 -0.02200656 0.99599203 61.03836799
Axis -0.20020488 -0.65617735 -0.72756395
Axis point 63.93693297 -480.82614561 -0.00000000
Rotation angle (degrees) 7.48271681
Shift along axis -106.05604184
> hide #!7 models
> color #50 #b2b2b24d models
> select clear
> ui mousemode right translate
> select #8: 382, 353,438,230,442,466,207,601
93 atoms, 90 bonds, 8 residues, 1 model selected
> view sel
> cofr sel
> volume #50 level 0.2404
> select clear
> select #8: 382, 353,438,230,442,466,207,601
93 atoms, 90 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> volume #50 level 0.2822
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> hide #!50 models
> view
> hide #8 models
> show #!20 models
> show #21 models
> color #20 #ffffb2ff models
> color #20 #ffffb24d models
> select clear
> select #21: 382, 353,438,230,442,466,207,601
109 atoms, 109 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> select H
117 atoms, 10 residues, 9 models selected
> hide sel & #21 atoms
> select clear
> select #21: 382, 353,438,230,442,466,207,601
109 atoms, 109 bonds, 8 residues, 1 model selected
> view sel
> select clear
> color #20 #ffffb280 models
> select clear
> volume #20 level 0.01329
> select #21/A:602@O24
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 38 bonds, 1 residue, 1 model selected
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> select #21: 382, 353,438,230,442,466,207,601,602
144 atoms, 147 bonds, 9 residues, 1 model selected
> select #20
4 models selected
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> hide #!20 models
> view
> hide #21 models
> show #!24 models
> show #!23 models
> color #23 #ffffb2ff models
> select clear
> hide #!23 models
> show #!23 models
> select #24: 382, 353,438,230,442,466,207,601,602
109 atoms, 109 bonds, 8 residues, 1 model selected
> view sel
> color #23 #ffffb280 models
> select clear
> select #24/A:601@O14
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 38 bonds, 1 residue, 1 model selected
> cofr sel
> select #23
4 models selected
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Tue Apr 15 12:09:47 2025 ———
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,5
Model Number: MPHG3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 16 hours, 13 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
R240HY:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 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 , 7 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 , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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