id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17437 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ 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) {""app_name"":""ChimeraX"",""timestamp"":""2025-04-15 18:00:55.00 -0400"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""A17AB552-C016-46D3-B3CB-1304B1800468""} { ""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. 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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 }}} " defect closed normal Window Toolkit duplicate all ChimeraX