id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17446 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 0x00000001eb554840 (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.pdb_lib._load_libs, 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.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 (total: 59) {""app_name"":""ChimeraX"",""timestamp"":""2025-04-20 23:29:03.00 -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"":""852DF0D7-9E2C-4DBA-97E1-3CC885C43FCA""} { ""uptime"" : 60000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 1195785599, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,5"", ""coalitionID"" : 7115, ""osVersion"" : { ""train"" : ""macOS 15.3.2"", ""build"" : ""24D81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-04-20 23:28:56.3174 -0400"", ""codeSigningMonitor"" : 1, ""incident"" : ""852DF0D7-9E2C-4DBA-97E1-3CC885C43FCA"", ""pid"" : 11720, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-04-20 12:19:23.5553 -0400"", ""procStartAbsTime"" : 592545169902, ""procExitAbsTime"" : 1450056072430, ""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"":""27EE72F8-B0D1-53D5-AD81-4CDFF7234557"",""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"" : ""3FC27746-092C-41C1-8812-52D1AB48BB7C"", ""wakeTime"" : 16912, ""sleepWakeUUID"" : ""F4BF2588-1386-4515-8DB3-2EB3188D60ED"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x2c8200002de9 is not in any region. 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240000116 } ], ""experiments"" : [ ] } } ===== 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 0.01, 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 0.012, 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 0.0107, 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 0.0133, 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 Opened rOAT1-PBD_IF.mrc as #50, grid size 160,160,160, pixel 0.83, shown at level 0.282, step 1, values float32 Log from Tue Apr 15 12:09:47 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 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 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/note.txt Unrecognized file suffix '.txt' > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83, shown at level 0.00146, step 2, values float32 > color #3 #b2b2b296 models > volume #3 step 1 > ui tool show ""Side View"" > volume #3 level 0.01472 > select add #1 3482 atoms, 3578 bonds, 1 pseudobond, 448 residues, 3 models selected > show sel atoms JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read properties of undefined (reading 'id') > hide #2.1-20 models > show #2.1 models > select clear > volume #3 level 0.01037 > show #2.2 models > show #2.3 models > hide #2.2 models > hide #2.1 models > volume #3 level 0.009064 > volume #3 level 0.009281 > hide #2.3 models > show #2.4 models > hide #2.4 models > show #2.5 models > close #1 > 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 > select add #1 3461 atoms, 3556 bonds, 1 pseudobond, 447 residues, 2 models selected > show sel atoms > select clear > hide #2.5 models > show #2.6 models > hide #2.6 models > show #2.7 models > hide #2.7 models > show #2.8 models > hide #2.8 models > show #2.9 models > hide #2.9 models > show #2.10 models > hide #2.10 models > show #2.10 models > hide #2.10 models > show #2.11 models > hide #2.11 models > show #2.12 models > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs > includeMaps true > lighting soft > lighting simple > color #3 #b2b2b264 models > hide #2.12 models > show #2.13 models > hide #2.13 models > show #2.14 models > hide #2.14 models > show #2.15 models > hide #2.15 models > show #2.15 models > hide #2.15 models > show #2.16 models > hide #2.16 models > show #2.17 models > hide #2.17 models > show #2.18 models > hide #2.18 models > show #2.19 models > hide #2.19 models > show #2.20 models > hide #2.20 models > show #2.19 models > hide #2.19 models > show #2.20 models > hide #2.20 models > show #2.1 models > hide #2.1 models > show #2.2 models > hide #2.2 models > show #2.1 models > hide #2.1 models > show #2.2 models > hide #2.2 models > show #2.3 models > hide #2.3 models > show #2.3 models > hide #2.3 models > show #2.4 models > hide #2.4 models > show #2.5 models > hide #2.5 models > show #2.6 models > hide #2.6 models > show #2.7 models > hide #2.7 models > show #2.7 models > hide #2.7 models > show #2.8 models > hide #2.8 models > show #2.9 models > hide #2.9 models > show #2.10 models > select down Nothing selected > hide #2.10 models > show #2.10 models > hide #2.10 models > show #2.11 models > hide #2.11 models > show #2.12 models > hide #2.12 models > show #2.13 models > hide #2.13 models > show #2.14 models > hide #2.14 models > show #2.15 models > hide #2.15 models > show #2.15 models > hide #2.15 models > show #2.15 models > hide #2.15 models > show #2.16 models > hide #2.16 models > show #2.16 models > hide #2.16 models > show #2.17 models > hide #2.17 models > show #2.17 models > hide #2.17 models > show #2.18 models > hide #2.18 models > show #2.19 models > hide #2.19 models > show #2.20 models > volume #3 level 0.01124 > hide #2.20 models > show #2.20 models > hide #2.20 models > show #2.20 models > hide #2.20 models > show #2.19 models > hide #2.19 models > show #2.18 models > hide #2.18 models > show #2.19 models > hide #2.19 models > show #2.18 models > volume #3 level 0.008629 > hide #2.18 models > show #2.18 models > hide #2.18 models > show #2.17 models > hide #2.17 models > show #2.16 models > hide #2.16 models > show #2.15 models > hide #2.15 models > show #2.14 models > hide #2.14 models > show #2.13 models > hide #2.13 models > show #2.12 models > hide #2.12 models > show #2.11 models > hide #2.11 models > show #2.10 models > hide #2.10 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.2 models > hide #2.2 models > show #2.3 models > hide #2.3 models > show #2.4 models > hide #2.4 models > show #2.5 models > hide #2.5 models > show #2.6 models > hide #2.6 models > show #2.7 models > hide #2.7 models > show #2.8 models > hide #2.8 models > show #2.9 models > hide #2.9 models > show #2.9 models > hide #2.9 models > show #2.9 models > hide #2.9 models > show #2.10 models > hide #2.10 models > show #2.11 models > hide #2.11 models > show #2.12 models > hide #2.12 models > show #2.13 models > hide #2.13 models > show #2.12 models > hide #2.12 models > show #2.1 models > hide #2.1 models > show #2.2 models > hide #2.2 models > show #2.3 models > hide #2.3 models > show #2.4 models > hide #2.4 models > show #2.5 models > hide #2.5 models > show #2.6 models > hide #2.6 models > show #2.7 models > hide #2.7 models > show #2.8 models > hide #2.8 models > show #2.8 models > hide #2.8 models > show #2.9 models > hide #2.9 models > show #2.10 models > hide #2.10 models > show #2.11 models > hide #2.11 models > show #2.12 models > hide #2.12 models > show #2.1 models > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 35492, resource id: 35652978, major code: 40 (TranslateCoords), minor code: 0 > volume #3 level 0.009281 > hide #2.1 models > show #2.2 models > hide #2.2 models > show #2.3 models > hide #2.3 models > show #2.4 models > show #2.5 models > hide #2.4 models > hide #2.5 models > show #2.18 models > hide #2.18 models > show #2.18 models > hide #2.18 models > show #2.17 models > hide #2.17 models > show #2.16 models > hide #2.16 models > show #2.15 models > hide #2.15 models > show #2.14 models > hide #2.14 models > show #2.13 models > hide #2.13 models > show #2.12 models > hide #2.12 models > show #2.12 models > hide #2.12 models > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 32670, resource id: 35652988, major code: 40 (TranslateCoords), minor code: 0 ——— End of log from Tue Dec 10 11:33:02 2024 ——— opened ChimeraX session JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 7404, resource id: 35653140, major code: 40 (TranslateCoords), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7416, resource id: 35653135, major code: 40 (TranslateCoords), minor code: 0 > show #2.11 models > hide #2.11 models > show #2.12 models > hide #2.12 models > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 60442, resource id: 35653379, major code: 40 (TranslateCoords), minor code: 0 ——— End of log from Wed Dec 11 13:28:04 2024 ——— opened ChimeraX session JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined > show #2.11 models > show #2.12 models > hide #2.11 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_7/hOCT1VB1007.pdb Chain information for hOCT1VB1007.pdb #4 --- Chain | Description A | No description available > open > ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_8/ > hOCT1-VB_Dock2_real_space_refined_008.pdb"" Chain information for hOCT1-VB_Dock2_real_space_refined_008.pdb #5 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 17659, resource id: 35653657, major code: 40 (TranslateCoords), minor code: 0 > close session > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/P3_J149_fsc_iteration_010_after_fsc_mask_auto_tightening.pdf QXcbConnection: XCB error: 3 (BadWindow), sequence: 50929, resource id: 35654568, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240.mrc Opened cryosparc_P3_J154__localfilter_240.mrc as #1, grid size 240,240,240, pixel 0.553, shown at level 0.207, step 1, values float32 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240_VB1.mrc Opened cryosparc_P3_J154__localfilter_240_VB1.mrc as #2, grid size 240,240,240, pixel 0.553, shown at level 0.000117, step 1, values float32 > volume #2 level 0.3318 Drag select of 2 cryosparc_P3_J154__localfilter_240_VB1.mrc > view orient > select clear > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb Summary of feedback from opening /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb --- warnings | Cannot find LINK/SSBOND residue CYS (50 ) Cannot find LINK/SSBOND residue CYS (62 ) Cannot find LINK/SSBOND residue CYS (89 ) [deleted to fit within ticket limits] > select subtract #8 Nothing selected > select #8: 601 19 atoms, 19 bonds, 1 residue, 1 model selected > color sel hot pink > select add #8 3912 atoms, 3985 bonds, 522 residues, 1 model selected > select subtract #8 Nothing selected > color zone #7 near #8 distance 2.5 > volume splitbyzone #7 Opened rOAT1-PBD_IF.mrc 0 as #55.1, grid size 320,320,320, pixel 0.83, shown at level 0.0111, step 1, values float32 Opened rOAT1-PBD_IF.mrc 1 as #55.2, grid size 320,320,320, pixel 0.83, shown at level 0.0111, step 1, values float32 Opened rOAT1-PBD_IF.mrc 2 as #55.3, grid size 320,320,320, pixel 0.83, shown at level 0.0111, step 1, values float32 Opened rOAT1-PBD_IF.mrc 3 as #55.4, grid size 320,320,320, pixel 0.83, shown at level 0.0111, step 1, values float32 > surface dust #55.1 size 4.98 > surface dust #55.2 size 4.98 > surface dust #55.3 size 4.98 > surface dust #55.4 size 4.98 > volume #55.1 level 0.01136 > surface dust #55.4 size 7 > volume #55.1 level 0.01088 > surface dust #55.1 size 4.98 > surface dust #55.1 size 7 [Repeated 2 time(s)] > surface dust #55.1 size 8 [Repeated 1 time(s)] > volume #55.1 level 0.009811 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-PBD_IF.png > width 809 height 738 supersample 3 transparentBackground true > volume #55.1 level 0.009096 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-PBD_IF.png > width 809 height 738 supersample 3 transparentBackground true > hide #!55 models > show #!54 models > hide #!54 models > show #!54 models > hide #!54 models > hide #8 models > show #!54 models > surface dust #54.1 size 6 > volume #54.1 level 0.008735 > volume #54.1 level 0.009565 [Repeated 1 time(s)] > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF.png > width 809 height 738 supersample 3 transparentBackground true > hide #!54 models > show #!52 models > show #!52.1 models > show #!52.2 models > show #!52.3 models > show #!52.4 models > volume #52.1 level 0.007805 > surface dust #50 size 6 > surface dust #52.2 size 6 [Repeated 1 time(s)] > surface dust #52.3 size 4.98 > surface dust #52.3 size 6 [Repeated 1 time(s)] > surface dust #52.4 size 6 > volume #52.1 level 0.008213 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF.png > width 809 height 738 supersample 3 transparentBackground true > hide #8 target m > hide #!52 models > show #!10 models > show #!12 models > show #10.1 models > color #10.1 #e599004d > color #10.1 #e59900ff > select #12: 601 37 atoms, 37 bonds, 1 residue, 1 model selected > color sel hot pink > select #12: 601 37 atoms, 37 bonds, 1 residue, 1 model selected > select clear > color zone #10 near #12 distance 2.5 > volume #52.1 level 0.009419 > volume #10 level 0.01032 > volume #10 level 0.009917 > color zone #10 near #12 distance 2 [Repeated 2 time(s)] > color zone #10 near #12 distance 2.3 [Repeated 1 time(s)] > color zone #10 near #12 distance 2.4 [Repeated 1 time(s)] > color zone #10 near #12 distance 2.5 [Repeated 1 time(s)] > surface dust #10 size 4.98 > volume #10 level 0.01032 > volume #10 level 0.009377 > surface dust #10 size 6 > volume #10 level 0.008296 > surface dust #10 size 7 > surface dust #10 size 8 [Repeated 1 time(s)] > volume #10 level 0.009782 > volume #10 level 0.009647 > color zone #10 near #12 distance 2.5 > volume splitbyzone #10 Opened rOAT1-PBD_OF.mrc 0 as #56.1, grid size 320,320,320, pixel 0.83, shown at level 0.00965, step 1, values float32 Opened rOAT1-PBD_OF.mrc 1 as #56.2, grid size 320,320,320, pixel 0.83, shown at level 0.00965, step 1, values float32 Opened rOAT1-PBD_OF.mrc 2 as #56.3, grid size 320,320,320, pixel 0.83, shown at level 0.00965, step 1, values float32 Opened rOAT1-PBD_OF.mrc 3 as #56.4, grid size 320,320,320, pixel 0.83, shown at level 0.00965, step 1, values float32 > hide #10.1 models > hide #!12 models > surface dust #56.1 size 8 > surface dust #56.1 size 7 > surface dust #56.1 size 6 > surface dust #56.1 size 5 [Repeated 1 time(s)] > surface dust #56.2 size 4.98 > surface dust #56.3 size 4.98 > surface dust #56.4 size 4.98 [Repeated 2 time(s)] > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-PBD_OF.png > width 809 height 738 supersample 3 transparentBackground true > hide #!56 models > show #15 models > show #!14 models > show #14.1 models > color #14.1 #e59900ff > volume #14 step 1 > surface dust #14 size 4.98 > volume #14 level 0.006781 > volume #14 level 0.007273 > hide #14.1 models > show #14.1 models > select #15: 601 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel hot pink > select clear > volume #14 level 0.007929 > color zone #14 near #15 distance 4.98 > color zone #14 near #15 distance 2 > color zone #14 near #15 distance 2.5 [Repeated 1 time(s)] > select clear > volume splitbyzone #14 Opened rOAT1-TFV_IF.mrc 0 as #57.1, grid size 320,320,320, pixel 0.83, shown at level 0.00793, step 1, values float32 Opened rOAT1-TFV_IF.mrc 1 as #57.2, grid size 320,320,320, pixel 0.83, shown at level 0.00793, step 1, values float32 Opened rOAT1-TFV_IF.mrc 2 as #57.3, grid size 320,320,320, pixel 0.83, shown at level 0.00793, step 1, values float32 Opened rOAT1-TFV_IF.mrc 3 as #57.4, grid size 320,320,320, pixel 0.83, shown at level 0.00793, step 1, values float32 > hide #15 models > hide #14.1 models > surface dust #57.1 size 4.98 > surface dust #57.1 size 6 > surface dust #57.1 size 7 > surface dust #57.1 size 8 > volume #57.1 level 0.008027 > surface dust #57.1 size 8 > surface dust #57.2 size 4.98 > surface dust #57.3 size 4.98 > surface dust #57.4 size 4.98 > select clear > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF.png > width 809 height 738 supersample 3 transparentBackground true > hide #!57 models > show #!18 models > show #!17 models > show #17.1 models > color #17.1 #e599004d > color #17.1 #e59900ff > color zone #17 near #18 distance 4.98 > color zone #17 near #18 distance 2 > color zone #17 near #18 distance 2.5 [Repeated 1 time(s)] > color zone #17 near #18 distance 3 > color zone #17 near #18 distance 2 > color zone #17 near #18 distance 2.8 [Repeated 1 time(s)] > color zone #17 near #18 distance 3 > volume splitbyzone #17 Opened rOAT1-TVF_OF.mrc 0 as #58.1, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 1 as #58.2, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 2 as #58.3, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 3 as #58.4, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 > hide #17.1 models > hide #!18 models > close #58 > show #!17 models > show #!18 models > show #17.1 models > select #18: 601 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel hot pink > select clear > color zone #17 near #18 distance 3 > volume splitbyzone #17 Opened rOAT1-TVF_OF.mrc 0 as #58.1, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 1 as #58.2, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 2 as #58.3, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 3 as #58.4, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 > hide #17.1 models > hide #!18 models > surface dust #58.1 size 4.98 > surface dust #58.2 size 4.98 > surface dust #58.3 size 4.98 > surface dust #58.4 size 4.98 > volume #58.2 level 0.004506 > volume #58.1 level 0.008289 > surface dust #58.4 size 7 > surface dust #58.1 size 7 > surface dust #58.1 size 8 > volume #58.1 level 0.008125 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF.png > width 809 height 738 supersample 3 transparentBackground true > hide #!58 models > show #!20 models > show #21 models > show #20.1 models > select #21: 601 35 atoms, 38 bonds, 1 residue, 1 model selected > select #21: 601,602 70 atoms, 76 bonds, 2 residues, 1 model selected > color sel hot pink > select clear > color #20.1 #e5990080 > color #20.1 #e59900ff > select clear > color zone #17 near #18 distance 3.01 > color zone #17 near #18 distance 3.02 > color zone #20 near #21 distance 3 > volume #58.1 level 0.007961 > color zone #20 near #21 distance 2 > color zone #20 near #21 distance 2.8 > color zone #20 near #21 distance 2 > color zone #20 near #21 distance 2.7 [Repeated 1 time(s)] > volume splitbyzone #20 Opened rOAT1-AAI_IF.mrc 0 as #59.1, grid size 320,320,320, pixel 0.83, shown at level 0.0133, step 1, values float32 Opened rOAT1-AAI_IF.mrc 1 as #59.2, grid size 320,320,320, pixel 0.83, shown at level 0.0133, step 1, values float32 Opened rOAT1-AAI_IF.mrc 2 as #59.3, grid size 320,320,320, pixel 0.83, shown at level 0.0133, step 1, values float32 Opened rOAT1-AAI_IF.mrc 3 as #59.4, grid size 320,320,320, pixel 0.83, shown at level 0.0133, step 1, values float32 > hide #21 models > hide #20.1 models > hide #!58.2 models > hide #!58.3 models > hide #!58.4 models > surface dust #59.1 size 4.98 > volume #59.1 level 0.01002 > volume #59.1 level 0.009926 > surface dust #59.2 size 4.98 > select add #59 9 models selected > surface dust #59.3 size 4.98 > select clear > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF.png > width 809 height 738 supersample 3 transparentBackground true > hide #!59 models > show #!24 models > show #!23 models > show #23.1 models > select #24: 601,602 35 atoms, 38 bonds, 1 residue, 1 model selected > color sel hot pink > select clear > color #23.1 #e5990080 > color #23.1 #e59900ff > select clear > volume #23 level 0.009882 > color zone #23 near #24 distance 4.98 > color zone #23 near #24 distance 3 [Repeated 1 time(s)] > volume splitbyzone #23 Opened rOAT1-AAI_OF.mrc 0 as #60.1, grid size 320,320,320, pixel 0.83, shown at level 0.00988, step 1, values float32 Opened rOAT1-AAI_OF.mrc 1 as #60.2, grid size 320,320,320, pixel 0.83, shown at level 0.00988, step 1, values float32 Opened rOAT1-AAI_OF.mrc 2 as #60.3, grid size 320,320,320, pixel 0.83, shown at level 0.00988, step 1, values float32 Opened rOAT1-AAI_OF.mrc 3 as #60.4, grid size 320,320,320, pixel 0.83, shown at level 0.00988, step 1, values float32 > hide #23.1 models > hide #!24 models > select add #60 9 models selected > surface dust #59.3 size 4.98 > surface dust #60.1 size 4.98 > surface dust #60.2 size 4.98 > surface dust #60.3 size 4.98 > surface dust #60.4 size 4.98 > select clear > volume #60.1 level 0.00867 > surface dust #60.4 size 7 > surface dust #60.1 size 4.98 [Repeated 1 time(s)] > surface dust #60.1 size 7 > select clear > surface dust #60.1 size 8 > volume #60.1 level 0.009276 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_OF.png > width 809 height 738 supersample 3 transparentBackground true > hide #!60 models > show #!36 models > show #37 models > select #37: 318-570 1865 atoms, 1903 bonds, 246 residues, 1 model selected > color sel #3ec0c2ff > select clear > show #36.1 models > select #37/A:525 7 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #37: 525-570 316 atoms, 321 bonds, 39 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true > color #36.1 #e59900ff > select clear > select #37: 601-603 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel hot pink > select clear > color zone #36 near #37 distance 3 > select #36 2 models selected > volume splitbyzone #36 Opened hOAT1-TFV_IF.mrc 0 as #61.1, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 Opened hOAT1-TFV_IF.mrc 1 as #61.2, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 Opened hOAT1-TFV_IF.mrc 2 as #61.3, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 Opened hOAT1-TFV_IF.mrc 3 as #61.4, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 > hide #37 models > select subtract #36 Nothing selected > select add #36 2 models selected > select subtract #36 Nothing selected > surface dust #61.1 size 4.98 > surface dust #61.2 size 4.98 > surface dust #61.3 size 4.98 > surface dust #61.4 size 4.98 > select clear [Repeated 1 time(s)] > volume #61.1 level 0.009185 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/hOAT1-TFV_IF.png > width 809 height 738 supersample 3 transparentBackground true > hide #!61 models > show #!39 models > show #!41 models > select #41: 601-603 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel hot pink > select #41: 525-570 316 atoms, 321 bonds, 39 residues, 1 model selected > delete atoms sel > delete bonds sel > open /Volumes/bbc/Lab- > Jiang/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/outward_j68_3.1A/hOAT1-TFV_OF- > coot-5_real_space_refined_007.pdb Chain information for hOAT1-TFV_OF-coot-5_real_space_refined_007.pdb #62 --- Chain | Description A | No description available > close #41 > select #62: 1-317 2454 atoms, 2519 bonds, 315 residues, 1 model selected > select clear > select #62: 1-317 2454 atoms, 2519 bonds, 315 residues, 1 model selected > color sel #a166d1ff > select #62: 318-570 1503 atoms, 1535 bonds, 200 residues, 1 model selected > color sel #3ec0c2ff > select #62: 601-603 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel hot pink > select clear > show #!40 models > hide #!40 models > show #39.1 models > ui tool show ""Fit in Map"" > fitmap #62 inMap #39 Fit molecule hOAT1-TFV_OF-coot-5_real_space_refined_007.pdb (#62) to map hOAT1-TFV_OF.mrc (#39) using 3976 atoms average map value = 0.01786, steps = 124 shifted from previous position = 1.62 rotated from previous position = 13.4 degrees atoms outside contour = 1104, contour level = 0.010555 Position of hOAT1-TFV_OF-coot-5_real_space_refined_007.pdb (#62) relative to hOAT1-TFV_OF.mrc (#39) coordinates: Matrix rotation and translation 0.99999997 0.00013203 0.00020852 -0.03273890 -0.00013199 0.99999997 -0.00020384 0.04132497 -0.00020855 0.00020382 0.99999996 -0.00751800 Axis 0.63678518 0.65147667 -0.41241094 Axis point -17.94306109 -0.00000000 185.02377550 Rotation angle (degrees) 0.01833990 Shift along axis 0.00917511 Drag select of 39 hOAT1-TFV_OF.mrc > select clear > hide #36.1 models > color #39.1 #e59900ff > select clear > color zone #39 near #62 distance 4.98 > color zone #39 near #62 distance 3 [Repeated 1 time(s)] > volume splitbyzone #39 Opened hOAT1-TFV_OF.mrc 0 as #41.1, grid size 320,320,320, pixel 0.83, shown at level 0.0106, step 1, values float32 Opened hOAT1-TFV_OF.mrc 1 as #41.2, grid size 320,320,320, pixel 0.83, shown at level 0.0106, step 1, values float32 Opened hOAT1-TFV_OF.mrc 2 as #41.3, grid size 320,320,320, pixel 0.83, shown at level 0.0106, step 1, values float32 Opened hOAT1-TFV_OF.mrc 3 as #41.4, grid size 320,320,320, pixel 0.83, shown at level 0.0106, step 1, values float32 > hide #39.1 models > surface dust #41.1 size 4.98 > surface dust #41.2 size 4.98 > surface dust #41.3 size 4.98 > surface dust #41.4 size 4.98 [Repeated 1 time(s)] > surface dust #42.3 size 4.98 > surface dust #41.4 size 4.98 > surface dust #41.1 size 4.98 > select clear > volume #41.1 level 0.01048 > hide #!62 models > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/hOAT1-TFV_OF.png > width 809 height 738 supersample 3 transparentBackground true > open /Volumes/bbc/Lab- > Jiang/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1-TVF_IF- > coot-3.pdb Chain information for hOAT1-TVF_IF-coot-3.pdb #63 --- Chain | Description A | No description available > hide #!41 models > show #!36 models > show #36.1 models > ui tool show ""Fit in Map"" > fitmap #63 inMap #36 Fit molecule hOAT1-TVF_IF-coot-3.pdb (#63) to map hOAT1-TFV_IF.mrc (#36) using 3988 atoms average map value = 0.01587, steps = 40 shifted from previous position = 0.013 rotated from previous position = 0.0468 degrees atoms outside contour = 1071, contour level = 0.008515 Position of hOAT1-TVF_IF-coot-3.pdb (#63) relative to hOAT1-TFV_IF.mrc (#36) coordinates: Matrix rotation and translation 0.99999982 0.00052001 0.00028819 -0.09949069 -0.00052017 0.99999971 0.00056108 -0.00480012 -0.00028790 -0.00056123 0.99999980 0.10326003 Axis -0.68640011 0.35233129 -0.63617415 Axis point 0.00000000 185.01527828 9.22177002 Rotation angle (degrees) 0.04684105 Shift along axis 0.00090783 > fitmap #63 inMap #36 Fit molecule hOAT1-TVF_IF-coot-3.pdb (#63) to map hOAT1-TFV_IF.mrc (#36) using 3988 atoms average map value = 0.01587, steps = 44 shifted from previous position = 0.00151 rotated from previous position = 0.00338 degrees atoms outside contour = 1071, contour level = 0.008515 Position of hOAT1-TVF_IF-coot-3.pdb (#63) relative to hOAT1-TFV_IF.mrc (#36) coordinates: Matrix rotation and translation 0.99999984 0.00047947 0.00028576 -0.09335598 -0.00047961 0.99999975 0.00051832 -0.00591563 -0.00028551 -0.00051846 0.99999982 0.09657995 Axis -0.68052069 0.37496589 -0.62951741 Axis point 0.00000000 186.90180615 11.87456849 Rotation angle (degrees) 0.04364555 Shift along axis 0.00051376 > close #37 > fitmap #63 inMap #36 Fit molecule hOAT1-TVF_IF-coot-3.pdb (#63) to map hOAT1-TFV_IF.mrc (#36) using 3988 atoms average map value = 0.01587, steps = 40 shifted from previous position = 0.00938 rotated from previous position = 0.00367 degrees atoms outside contour = 1072, contour level = 0.008515 Position of hOAT1-TVF_IF-coot-3.pdb (#63) relative to hOAT1-TFV_IF.mrc (#36) coordinates: Matrix rotation and translation 0.99999986 0.00047777 0.00024709 -0.09234265 -0.00047791 0.99999972 0.00056927 -0.01315730 -0.00024682 -0.00056939 0.99999981 0.10649613 Axis -0.72689618 0.31530566 -0.61008548 Axis point 0.00000000 184.88987693 22.09640694 Rotation angle (degrees) 0.04487577 Shift along axis -0.00199679 > color zone #36 near #63 distance 3 > select add #63 3988 atoms, 4085 bonds, 1 pseudobond, 517 residues, 2 models selected > select #63: 601-603 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel hot pink > select #63: 1-317 2471 atoms, 2537 bonds, 316 residues, 1 model selected > color sel #a166d1ff [Repeated 2 time(s)] > select #63: 318-570 1498 atoms, 1528 bonds, 200 residues, 1 model selected > color sel #3ec0c2ff [Repeated 2 time(s)] > hide #!63 models > show #!63 models > color zone #36 near #63 distance 3 > volume splitbyzone #36 Opened hOAT1-TFV_IF.mrc 0 as #37.1, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 Opened hOAT1-TFV_IF.mrc 1 as #37.2, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 Opened hOAT1-TFV_IF.mrc 2 as #37.3, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 Opened hOAT1-TFV_IF.mrc 3 as #37.4, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 > close #61 > hide #!63 models > select add #63 3988 atoms, 4085 bonds, 1 pseudobond, 517 residues, 2 models selected > select subtract #63 Nothing selected > surface dust #37.1 size 4.98 > surface dust #37.2 size 4.98 [Repeated 1 time(s)] > surface dust #37.3 size 4.98 > surface dust #37.4 size 4.98 > surface dust #38.3 size 4.98 > volume #37.1 level 0.009315 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/hOAT1-TFV_IF.png > width 809 height 738 supersample 3 transparentBackground true > hide #!41.1 models > hide #36.1 models > hide #!37 models > show #!40 models > show #40.1 models > show #!43 models > select add #43 3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected > show sel cartoons > color #40 #e599004d models > color #40 #e59900ff models > select #43: 601-603 10 atoms, 9 bonds, 1 residue, 1 model selected > color sel hot pink > select clear > select #43: 1-317 2332 atoms, 2392 bonds, 2 pseudobonds, 297 residues, 2 models selected > color (#!43 & sel) #a166d1ff > select #43: 318-570 1465 atoms, 1498 bonds, 194 residues, 1 model selected > color (#!43 & sel) #3ec0c2ff [Repeated 2 time(s)] > select clear > color zone #40 near #43 distance 3 > color zone #40 near #43 distance 2 > color zone #40 near #43 distance 2.8 [Repeated 2 time(s)] > volume splitbyzone #40 Opened rOAT1-AKG_OF.mrc 0 as #61.1, grid size 320,320,320, pixel 0.83, shown at level 0.0122, step 1, values float32 Opened rOAT1-AKG_OF.mrc 1 as #61.2, grid size 320,320,320, pixel 0.83, shown at level 0.0122, step 1, values float32 Opened rOAT1-AKG_OF.mrc 2 as #61.3, grid size 320,320,320, pixel 0.83, shown at level 0.0122, step 1, values float32 Opened rOAT1-AKG_OF.mrc 3 as #61.4, grid size 320,320,320, pixel 0.83, shown at level 0.0122, step 1, values float32 > hide #!43 models > surface dust #61.1 size 4.98 > surface dust #61.2 size 4.98 > surface dust #61.3 size 4.98 > surface dust #61.4 size 4.98 > volume #37.1 level 0.007221 > volume #61.1 level 0.01166 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AKG_OF.png > width 809 height 738 supersample 3 transparentBackground true > hide #!61 models > show #!44 models > show #!45 models > select #45: 601-603 10 atoms, 9 bonds, 1 residue, 1 model selected > color sel hot pink > select clear > show #!43 models > hide #!43 models > show #44.1 models > color #44.1 #e599004d > color #44.1 #e59900ff > color zone #44 near #45 distance 2.8 > volume splitbyzone #44 Opened rOAT1-AKG_OOC.mrc 0 as #64.1, grid size 320,320,320, pixel 0.83, shown at level 0.0102, step 1, values float32 Opened rOAT1-AKG_OOC.mrc 1 as #64.2, grid size 320,320,320, pixel 0.83, shown at level 0.0102, step 1, values float32 Opened rOAT1-AKG_OOC.mrc 2 as #64.3, grid size 320,320,320, pixel 0.83, shown at level 0.0102, step 1, values float32 Opened rOAT1-AKG_OOC.mrc 3 as #64.4, grid size 320,320,320, pixel 0.83, shown at level 0.0102, step 1, values float32 > hide #44.1 models > hide #!45 models > surface dust #64.1 size 4.98 > surface dust #64.2 size 4.98 > surface dust #64.3 size 4.98 > surface dust #64.4 size 4.98 > volume #64.1 level 0.01073 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AKG_OO.png > width 809 height 738 supersample 3 transparentBackground true [Repeated 1 time(s)] > hide #!64 models > show #!47 models > show #!46 models > show #46.1 models > color #46.1 #e59900ff > select clear > color zone #46 near #47 distance 2.8 > volume splitbyzone #46 Opened rOAT1-R466A.mrc 0 as #65.1, grid size 480,480,480, pixel 0.553, shown at level 0.0115, step 1, values float32 Opened rOAT1-R466A.mrc 1 as #65.2, grid size 480,480,480, pixel 0.553, shown at level 0.0115, step 1, values float32 Opened rOAT1-R466A.mrc 2 as #65.3, grid size 480,480,480, pixel 0.553, shown at level 0.0115, step 1, values float32 > hide #46.1 models > hide #!47 models > surface dust #65.1 size 3.32 > surface dust #65.2 size 3.32 > surface dust #65.3 size 3.32 > select clear > volume #65.1 level 0.0121 > surface dust #65.3 size 6 > volume #65.1 level 0.009936 > surface dust #65.1 size 6 > surface dust #65.1 size 7 > volume #65.1 level 0.008672 > surface dust #65.1 size 8 > volume #65.1 level 0.008943 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-R466A_OO.png > width 809 height 738 supersample 3 transparentBackground true > hide #!65 models > show #!59 models > volume #59.2 level 0.008094 > volume #59.3 level 0.006974 > volume #59.2 level 0.00901 > select ~sel & ##selected Nothing selected > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF.png > width 809 height 738 supersample 3 transparentBackground true > volume #59.3 level 0.0102 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF.png > width 809 height 738 supersample 3 transparentBackground true > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true > hide #!59 models > show #!58 models > hide #!58 models > show #!34 models > show #!35 models > show #!35.3 models > color #35 #b2b2b2ff models > select add #35 3 models selected > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 5 models selected > hide sel atoms > color #35 #b2b2b2ff models > color #35.3 #b2b2b2ff models > hide #!34 models > select subtract #34 3 models selected > select subtract #35 Nothing selected > select add #35 3 models selected > view sel No displayed objects specified. > hide #!35 models > show #!35 models > hide #!35 models > hide #!35.3 models > select subtract #35.3 1 model selected > select add #35 3 models selected > select subtract #35 Nothing selected > show #!34 models > show #!17 models > show #17.1 models > hide #17.1 models > hide #!17 models > select ::name=""CL"" 5 atoms, 5 residues, 5 models selected > show sel & #!34 atoms > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > color sel lime > select clear > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected > show #!19 models > show #!19.3 models > hide #!19.3 models > hide #!19 models > show #!17 models > show #17.1 models > color zone #17 near #34 distance 3.02 > volume splitbyzone #17 Opened rOAT1-TVF_OF.mrc 0 as #66.1, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 1 as #66.2, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 2 as #66.3, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 3 as #66.4, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 4 as #66.5, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 > select clear > show #!17 models > hide #!66 models > show #!66 models > hide #!66 models > show #33 models > hide #33 models > color #17 #b2b2b2ff models > select clear > hide #!17 models > select #34/B 1 atom, 1 residue, 1 model selected > select ::name=""HOH"" 240 atoms, 240 residues, 10 models selected > show #!34 atoms > select #34: h2o Nothing selected > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected > hide sel atoms > select #34/B 1 atom, 1 residue, 1 model selected > open /Volumes/bbc/Lab- > Jiang/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF- > coot-4_real_space_refined_009.pdb Chain information for rOAT1-TFV_OF-coot-4_real_space_refined_009.pdb #67 --- Chain | Description A | No description available > rename #67 rOAT1-TFV-Cl_OF-coot-4_real_space_refined_009.pdb > select add #67 3829 atoms, 3910 bonds, 3 pseudobonds, 505 residues, 3 models selected > show sel atoms > select #67/B:1@CL 1 atom, 1 residue, 1 model selected > style sel ball Changed 1 atom style > hide #!34 models > select #67:1-317 2344 atoms, 2392 bonds, 2 pseudobonds, 309 residues, 2 models selected > color (#!67 & sel) #a166d1ff > select #67:318-570 1465 atoms, 1498 bonds, 194 residues, 1 model selected > color sel #3dc0c2ff > select #67/B:1@CL 1 atom, 1 residue, 1 model selected > select clear > select #67/B:1@CL 1 atom, 1 residue, 1 model selected > color sel lime > select #67/D:4@O 1 atom, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select #67/D:4@O 1 atom, 1 residue, 1 model selected > color sel red > select clear > show #!17 models > color zone #17 near #67 distance 3.02 Drag select of 17 rOAT1-TVF_OF.mrc , 3 residues, 2 bonds > select clear > hide #17.1 models > hide #!17 models > hide #!66.1 models > show #!47 models > show #!46 models > hide #!67 models > select #47/B 1 atom, 1 residue, 1 model selected > show sel atoms > show #46.1 models > select #47/B 1 atom, 1 residue, 1 model selected > color sel lime > style sel ball Changed 1 atom style > hide #!46 models > hide #46.1 models > hide #!47 models > select add #47 3795 atoms, 3884 bonds, 3 pseudobonds, 495 residues, 2 models selected > select subtract #47 Nothing selected > show #!67 models > select add #67 3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected > show #!17 models > show #17.1 models > volume splitbyzone #17 Opened rOAT1-TVF_OF.mrc 0 as #68.1, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 1 as #68.2, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 2 as #68.3, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 3 as #68.4, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 4 as #68.5, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 5 as #68.6, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 6 as #68.7, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 7 as #68.8, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 8 as #68.9, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 > hide #!68.9 models > hide #!68.7 models > hide #!68.6 models > hide #!68.5 models > hide #!68.4 models > hide #!68.3 models > hide #!68.2 models > hide #!68.1 models > color #68.8 #b2b2b2ff models > color #68.8 #b2b2b276 models > color #68.8 #b2b2b249 models > color #68.8 #b2b2b24c models > select clear [Repeated 1 time(s)] > select add #67 3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected > hide sel cartoons > hide sel atoms > select #67/B 1 atom, 1 residue, 1 model selected > show sel atoms > select clear [Repeated 2 time(s)] > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV- > Cl_OF.png width 809 height 738 supersample 3 transparentBackground true > hide #!67 models > hide #!68 models > show #!19 models > show #!19.3 models > show #!18 models > color #19.3 #b2b2b29f models > close #19 > show #!68 models > show #!68.1 models > hide #!68.1 models > show #!68.7 models > close #68 > select add #67 3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected > show #!67 models > hide #!18 models > hide #17.1 models > show sel cartoons > show sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel hot pink > select clear > color zone #17 near #67 distance 3.02 > show #!66 models > select add #66 11 models selected > close #66 > show #!35 models > close #35 > show #!17 models > show #17.1 models > color zone #17 near #67 distance 3.02 > volume splitbyzone #17 Opened rOAT1-TVF_OF.mrc 0 as #19.1, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 1 as #19.2, 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-TVF_OF.mrc 3 as #19.4, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 4 as #19.5, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 5 as #19.6, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 > hide #!19.2 models > hide #!19.1 models > hide #!19.3 models > hide #!19.6 models > show #!19.6 models > hide #!19.6 models > select add #67 3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected > hide sel atoms > hide sel cartoons > select #67:601 19 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > color #67 #b2b2b2ff > color #19.4 #b2b2b2ff models > color #19.4 #b2b2b280 models > select #67:601 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel lime > color sel hot pink > color sel byhetero > select clear > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF- > TFV.png width 809 height 738 supersample 3 transparentBackground true > color #19.4 #b2b2b29b models > color #19.4 #b2b2b29a models > color #19.4 #b2b2b280 models > select clear > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat > graphics silhouettes false > graphics silhouettes true > select clear > lighting flat [Repeated 1 time(s)] > lighting simple > lighting soft > lighting flat [Repeated 2 time(s)] > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat > graphics silhouettes false > lighting flat > select clear > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF- > TFV.png width 809 height 738 supersample 3 transparentBackground true > color #19.4 black models > color #19.4 #00000008 models > color #19.4 #0000000a models > color #19.4 transparent models > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat > graphics silhouettes false > graphics silhouettes true > select clear > color #19.4 #929292ff models > color #19.4 #797979ff models > color #19.4 #79797980 models > color #19.4 silver models > color #19.4 #c0c0c080 models > lighting flat > lighting shadows true intensity 0.5 > lighting flat > graphics silhouettes false > lighting flat > color #19.4 #929292ff models > color #19.4 #9292927e models > color #19.4 darkgrey models > color #19.4 silver models > select clear > volume #19.4 level 0.009812 > surface dust #19.4 size 4.98 > volume #19.4 level 0.008153 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF- > TFV.png width 809 height 738 supersample 3 transparentBackground true > volume #19.4 level 0.005723 > surface dust #19.4 size 8 [Repeated 1 time(s)] > volume #19.4 level 0.007027 > surface dust #19.4 size 8 > volume #19.4 level 0.007797 > surface dust #19.4 size 8 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF- > TFV.png width 809 height 738 supersample 3 transparentBackground true > hide #!19 models > hide #!19.4 models > hide #!19.5 models > show #!58 models > hide #!58 models > show #!58 models > close #58 > show #!57 models > hide #!57.1 models > hide #!57.2 models > hide #!57.3 models > show #!57.1 models > show #!57.2 models > show #!57.3 models > hide #!57.2 models > hide #!57.1 models > hide #!57.3 models > show #15 models > hide #15 models > show #15 models > hide #15 models > select #67/A:601@C08 1 atom, 1 residue, 1 model selected > select up 19 atoms, 20 bonds, 1 residue, 1 model selected > hide #!67 models > hide #67.1 models > select add #67 3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected > select subtract #67 Nothing selected > select #15:601 31 atoms, 32 bonds, 1 residue, 1 model selected > select clear > color #57.4 #ff69b481 models > color #57.4 #ff69b480 models > select #15:601 31 atoms, 32 bonds, 1 residue, 1 model selected > show #15 models > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #15:601 31 atoms, 32 bonds, 1 residue, 1 model selected > show sel atoms > hide #17.1 models > volume #57.4 level 0.006742 > select #15:601 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel hot pink > color sel byhetero > select clear > select H 93 atoms, 8 residues, 7 models selected > hide sel & #15 atoms > color #57.4 #b2b2b280 models > volume #57.4 level 0.007863 > volume #57.4 level 0.007995 > volume #57.4 level 0.007863 > volume #57.4 level 0.007995 > volume #57.4 level 0.007797 > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF- > TFV.png width 809 height 738 supersample 3 transparentBackground true > show #!63 models > hide #!57.4 models > hide #!57 models > hide #15 models > select add #15 3998 atoms, 3998 bonds, 522 residues, 7 models selected > select subtract #15 81 atoms, 7 residues, 6 models selected > select add #18 3855 atoms, 3876 bonds, 5 pseudobonds, 492 residues, 7 models selected > select subtract #18 69 atoms, 6 residues, 5 models selected > hide #!63 models > hide #63.1 models > open /Volumes/bbc/Lab- > Jiang/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/inward_j152_2.7A/rOAT1-TFV_IF- > coot-1_real_space_refined_001_real_space_refined_002.pdb Chain information for rOAT1-TFV_IF- coot-1_real_space_refined_001_real_space_refined_002.pdb #35 --- Chain | Description A | No description available > show #!57.4 models > select #35:601 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel hot pink > color sel byhetero > select clear > select add #35 3905 atoms, 3986 bonds, 515 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #35:601 19 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF- > TFV.png width 809 height 738 supersample 3 transparentBackground true > hide #35 models > hide #!57.4 models > show #!59 models > hide #!59.3 models > hide #!59.2 models > hide #!59.1 models > show #21 models > select #21: 601-603 70 atoms, 76 bonds, 2 residues, 1 model selected > color sel forest green > color sel byhetero > color sel orange > color sel byhetero > select add #21 3956 atoms, 4042 bonds, 516 residues, 1 model selected > hide sel cartoons > hide sel atoms > select #21: 601-603 70 atoms, 76 bonds, 2 residues, 1 model selected > show sel atoms > select H 93 atoms, 8 residues, 7 models selected > hide sel & #21 atoms > color #59.4 #b2b2b2ff models > color #59.4 #b2b2b200 models > color #59.4 #b2b2b280 models > surface dust #59.4 size 4.98 > volume #59.4 level 0.01251 > select clear > save > /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF- > AAI.png width 809 height 738 supersample 3 transparentBackground true > save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true ——— End of log from Sun Apr 20 23:23:04 2025 ——— opened ChimeraX session 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: 1 day, 16 hours, 18 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 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: 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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 assigned normal Window Toolkit all ChimeraX