id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17437 ChimeraX bug report submission chimerax-bug-report@… "{{{ 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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""com.apple.CoreFoundation"", ""size"" : 5197824, ""uuid"" : ""190e6a36-fcaa-3ea3-94bb-7009c44653da"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""3302.1.400"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6925164544, ""CFBundleShortVersionString"" : ""2.1.1"", ""CFBundleIdentifier"" : ""com.apple.HIToolbox"", ""size"" : 3178496, ""uuid"" : ""950f1236-acaf-379d-819f-6c6b0b5deabd"", ""path"" : ""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"", ""name"" : ""HIToolbox"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6731374592, ""size"" : 532288, ""uuid"" : ""398a133c-9bcb-317f-a064-a40d3cea3c0f"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6734106624, ""size"" : 581628, ""uuid"" : ""bbab286c-2e51-3d64-9ae3-a4102935fe32"", ""path"" : ""\/usr\/lib\/libc++.1.dylib"", ""name"" : ""libc++.1.dylib"" } ], ""sharedCache"" : { ""base"" : 6730563584, ""size"" : 4865835008, ""uuid"" : ""5700d77a-6190-36e0-884d-fee6d586d62f"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=18.4G written=9959K(0%) resident=9959K(0%) swapped_out=0K(0%) unallocated=18.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1232K 58 \nColorSync 736K 38 \nCoreAnimation 4416K 214 \nCoreGraphics 48K 3 \nCoreImage 128K 4 \nCoreServices 624K 2 \nCoreUI image data 5552K 43 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 17.5G 300 \nMALLOC guard page 288K 18 \nMALLOC_LARGE (reserved) 122.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 752K 47 \nStack 160.2M 48 \nStack Guard 56.0M 1 \nVM_ALLOCATE 328.1M 332 \nVM_ALLOCATE (reserved) 256.0M 3 reserved VM address space (unallocated)\n__AUTH 5288K 672 \n__AUTH_CONST 70.9M 920 \n__CTF 824 1 \n__DATA 33.5M 1068 \n__DATA_CONST 34.2M 1083 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 638.0M 157 \n__OBJC_RW 2374K 1 \n__TEXT 1.3G 1103 \n__TPRO_CONST 272K 2 \ndyld private memory 32K 1 \nmapped file 580.0M 95 \nowned unmapped memory 100.6M 1 \npage table in kernel 9959K 1 \nshared memory 3184K 23 \n=========== ======= ======= \nTOTAL 21.1G 6597 \nTOTAL, minus reserved VM space 20.7G 6597 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""f911532e1b8949a51df4d8aa97dafc9c5b5adf57"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""658361a603dc58766bab2d2a"", ""factorPackIds"" : { ""SIRI_TTS_DEVICE_TRAINING"" : ""6736733a26c1270f5a9ef53d"" }, ""deploymentId"" : 240000045 }, { ""rolloutId"" : ""648cada15dbc71671bb3aa1b"", ""factorPackIds"" : { ""SIRI_EXPERIENCE_CAM"" : ""65a81173096f6a1f1ba46525"" }, ""deploymentId"" : 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 0.0151, 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 ) > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/RealSpaceRefine_6/mOCT1-VB1-coot-11_real_space_refined_006.pdb Chain information for mOCT1-VB1-coot-11_real_space_refined_006.pdb #4 --- Chain | Description A | No description available > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_real_space_refined_014.pdb Chain information for mOCT1-VB1_real_space_refined_014.pdb #5 --- Chain | Description A | No description available > close #3#4 > volume #2 color #ffffb296 > volume #2 color #ffffb2c8 > volume #2 level 0.4304 > volume #2 level 0.3677 > select /A:601@C15 1 atom, 1 residue, 1 model selected > select up 18 atoms, 19 bonds, 1 residue, 1 model selected > view sel > select clear > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_Model/mOCT1-ABC_real_space_refined_009.pdb Chain information for mOCT1-ABC_real_space_refined_009.pdb #3 --- Chain | Description A | No description available > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_20220411_cryoSPARC/J142_2.25A_clip-240/cryosparc_P3_J150__localfilter_240.mrc Opened cryosparc_P3_J150__localfilter_240.mrc as #4, grid size 240,240,240, pixel 0.553, shown at level 0.229, step 1, values float32 > volume #4 level 0.7041 > hide #!2 models > hide #!3 models > hide #!5 models > show #!3 models > select ::name=""ABC"" 42 atoms, 48 bonds, 2 residues, 1 model selected > view sel > volume #4 level 0.5273 > hide #!4 models > show #!4 models > show #!1 models > hide #!3 models > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 57982, resource id: 35654641, major code: 40 (TranslateCoords), minor code: 0 > hide #!1 models > rename #1 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc > rename #2 mOCT1-VB1_cryosparc_P3_J154__localfilter_240_VB1.mrc > rename #4 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc > show #!3 models > select clear > hide #!4 models > select ::name=""ABC"" 42 atoms, 48 bonds, 2 residues, 1 model selected > select add #3 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected > color (#!3 & sel) white > select clear > select ::name=""ABC"" 42 atoms, 48 bonds, 2 residues, 1 model selected > color sel red > show #!4 models > ui tool show ""Color Zone"" > color zone #4 near #3 distance 3.32 > volume splitbyzone #4 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 0 as #6.1, grid size 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 1 as #6.2, grid size 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 as #6.3, grid size 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 > hide #!3 models > select add #3 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected > select subtract #3 Nothing selected > hide #!6.1 models > hide #!6.3 models > show #!6.3 models > hide #!6.2 models > close #6.1-2 > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 18121, resource id: 35654647, major code: 40 (TranslateCoords), minor code: 0 > show #!3 models > color #3 #fffffbff > color #3 #ddddaaff > color #3 #dda0deff > color #3 plum > select add #3 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected > color (#!3 & sel) byhetero > color #6.3 #ddddaaff models > color #6.3 plum models > color #6.3 #ffffb2ff models Drag select of 6.3 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 , 5 atoms, 5 residues, 5 bonds > select clear > color #6.3 #ffffb2c8 models > select ::name=""ABC"" 42 atoms, 48 bonds, 2 residues, 1 model selected > view sel > select #3/A:234 11 atoms, 10 bonds, 1 residue, 1 model selected > color #6.3 #ffffb296 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!6 models > hide #!6.3 models > show #!4 models > hide #!4 models > show #!5 models > show #!3 models > hide #!3 models > select #5/A:36 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > hide #!5 models > hide #!2 models > show #!1 models > view > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 5156, resource id: 35654673, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_20240411/job207/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #7, grid size 320,320,320, pixel 0.83, shown at level 0.00144, step 2, values float32 > volume #7 level 0.01204 > select add #7 12 atoms, 12 bonds, 1 residue, 3 models selected > select add #5 3526 atoms, 3584 bonds, 1 pseudobond, 489 residues, 4 models selected > select subtract #5 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,-67.025,0,1,0,-62.171,0,0,1,-62.016 > view matrix models #7,1,0,0,-65.422,0,1,0,-60.829,0,0,1,-69.057 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.44906,0.62428,0.63923,-47.882,-0.83076,-0.55508,-0.041522,263.31,0.32891,-0.5497,0.76789,-6.0495 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.44906,0.62428,0.63923,-43.112,-0.83076,-0.55508,-0.041522,259.52,0.32891,-0.5497,0.76789,-3.3226 > view matrix models > #7,-0.44906,0.62428,0.63923,-46.691,-0.83076,-0.55508,-0.041522,257.64,0.32891,-0.5497,0.76789,-5.4256 > view matrix models > #7,-0.44906,0.62428,0.63923,-43.086,-0.83076,-0.55508,-0.041522,254.57,0.32891,-0.5497,0.76789,-5.2175 > ui tool show ""Fit in Map"" > fitmap #7 inMap #1 Fit map relion_locres_filtered.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 3812 points correlation = 0.2373, correlation about mean = 0.07089, overlap = 11.07 steps = 116, shift = 1.21, angle = 8.84 degrees Position of relion_locres_filtered.mrc (#7) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.36461695 0.73265397 0.57469351 -59.14787422 -0.87490183 -0.48082660 0.05790126 236.29988230 0.31874951 -0.48168862 0.81631784 -18.80617873 Axis -0.31464704 0.14924672 -0.93740208 Axis point 41.71559551 127.71968026 0.00000000 Rotation angle (degrees) 120.96824033 Shift along axis 71.50663710 > rename #7 mOCT1-3TC > select clear [Repeated 1 time(s)] > rename #7 mOCT1-3TC.mrc > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_Model/RealSpaceRefine_6/mOCT1-3TC- > coot-14_real_space_refined_006.pdb Chain information for mOCT1-3TC-coot-14_real_space_refined_006.pdb #8 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!8 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1-3TC- coot-14_real_space_refined_006.pdb, chain A (#8), sequence alignment score = 2352.2 RMSD between 450 pruned atom pairs is 0.409 angstroms; (across all 450 pairs: 0.409) > hide #!1 models > hide #!7 models > show #!1 models > hide #!8 models > show #!7 models > select add #7 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.49719,-0.57211,-0.6523,173.98,0.80196,0.58997,0.093813,-133.23,0.33116,-0.56976,0.75214,0.34956 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.49719,-0.57211,-0.6523,164.87,0.80196,0.58997,0.093813,-137.47,0.33116,-0.56976,0.75214,-2.3096 > fitmap #7 inMap #1 Fit map mOCT1-3TC.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 3812 points correlation = 0.9181, correlation about mean = 0.7496, overlap = 65.08 steps = 160, shift = 6.4, angle = 20.1 degrees Position of mOCT1-3TC.mrc (#7) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.27009123 -0.75134279 -0.60210857 210.67160095 0.83888334 0.49056205 -0.23584655 -78.20606144 0.47257322 -0.44139877 0.76278546 -39.17036140 Axis -0.10648785 -0.55674686 0.82382842 Axis point 169.78551241 113.86943556 0.00000000 Rotation angle (degrees) 74.82789173 Shift along axis -11.16264322 > fitmap #8 inMap #7 Fit molecule mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) to map mOCT1-3TC.mrc (#7) using 7048 atoms average map value = 0.01706, steps = 60 shifted from previous position = 0.0823 rotated from previous position = 0.357 degrees atoms outside contour = 4146, contour level = 0.012041 Position of mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) relative to mOCT1-3TC.mrc (#7) coordinates: Matrix rotation and translation 0.99999991 -0.00005602 -0.00043067 0.07339565 0.00005621 0.99999991 0.00043709 -0.06044298 0.00043064 -0.00043712 0.99999982 0.02180230 Axis -0.70938425 -0.69891365 0.09106970 Axis point 0.00000000 51.44490735 150.82453668 Rotation angle (degrees) 0.03530433 Shift along axis -0.00783577 > show #!8 models > hide #!8 models > select subtract #7 Nothing selected > hide #!1 models > show #!8 models > select ::name=""3TC"" 26 atoms, 27 bonds, 1 residue, 1 model selected > select add #8 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected > color (#!8 & sel) white > select ::name=""3TC"" 26 atoms, 27 bonds, 1 residue, 1 model selected > color sel red > view sel > volume #7 step 1 > color zone #7 near #8 distance 4.98 > volume splitbyzone #7 Opened mOCT1-3TC.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at level 0.012, step 1, values float32 Opened mOCT1-3TC.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at level 0.012, step 1, values float32 Opened mOCT1-3TC.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at level 0.012, step 1, values float32 > close #9.2 > close #9.1 > color #9.3 white models > color #9.3 #ffffb2ff models > color #9.3 #ffffb296 models > select #8/A:447 19 atoms, 18 bonds, 1 residue, 1 model selected > select add #8 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected > color #8 #bb22ffff > color #8 #b2fffbff > color #8 #b2ffb2ff > color (#!8 & sel) byhetero > select clear [Repeated 1 time(s)] > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true > hide #!9.3 models > hide #!9 models > hide #!8 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_20240413/job307/relion_locres_filtered_flipz.mrc Opened relion_locres_filtered_flipz.mrc as #10, grid size 320,320,320, pixel 0.83, shown at level 0.00125, step 2, values float32 > show #!1 models > view > volume #1 level 0.3063 > volume #10 step 1 > volume #10 level 0.01019 > rename #10 mOCT1-AZT.mrc > select add #10 2 models selected > view matrix models #10,1,0,0,-48.383,0,1,0,-77.671,0,0,1,-67.093 > view matrix models #10,1,0,0,-54.836,0,1,0,-59.483,0,0,1,-63.826 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.55307,0.83192,0.044939,-108.96,-0.78881,0.54024,-0.29312,148.24,-0.26813,0.12666,0.95502,-37.718 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.55307,0.83192,0.044939,-120.39,-0.78881,0.54024,-0.29312,136.85,-0.26813,0.12666,0.95502,-39.969 > view matrix models > #10,0.55307,0.83192,0.044939,-121.53,-0.78881,0.54024,-0.29312,137.41,-0.26813,0.12666,0.95502,-39.609 > fitmap #10 inMap #1 Fit map mOCT1-AZT.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 33175 points correlation = 0.9169, correlation about mean = 0.7611, overlap = 495.2 steps = 172, shift = 3.01, angle = 24.4 degrees Position of mOCT1-AZT.mrc (#10) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.17958596 0.98366820 0.01207312 -89.49221412 -0.89232990 0.16805236 -0.41893408 218.60375344 -0.41412105 0.06446147 0.90793639 -7.62218964 Axis 0.24369569 0.21485858 -0.94575272 Axis point 81.50821029 166.97786454 0.00000000 Rotation angle (degrees) 82.65824965 Shift along axis 32.36873253 > view > view orient > ui tool show ""Side View"" > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_Model/RealSpaceRefine_4/mOCT1-AZT_14_real_space_refined_004.pdb Chain information for mOCT1-AZT_14_real_space_refined_004.pdb #11 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!11 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1-AZT_14_real_space_refined_004.pdb, chain A (#11), sequence alignment score = 2367.3 RMSD between 449 pruned atom pairs is 0.415 angstroms; (across all 449 pairs: 0.415) > fitmap #11 inMap #10 Fit molecule mOCT1-AZT_14_real_space_refined_004.pdb (#11) to map mOCT1-AZT.mrc (#10) using 7017 atoms average map value = 0.01592, steps = 48 shifted from previous position = 0.0651 rotated from previous position = 0.278 degrees atoms outside contour = 3029, contour level = 0.010186 Position of mOCT1-AZT_14_real_space_refined_004.pdb (#11) relative to mOCT1-AZT.mrc (#10) coordinates: Matrix rotation and translation -0.89530533 -0.39092164 -0.21356179 331.89133766 0.43778783 -0.68362766 -0.58394781 243.21431714 0.08228108 -0.61630634 0.78319622 99.39179726 Axis -0.03674901 -0.33598352 0.94115067 Axis point 137.92729950 180.24940846 0.00000000 Rotation angle (degrees) 153.87927506 Shift along axis -0.37002346 > hide #!1 models > select ::name=""AZZ"" 19 atoms, 20 bonds, 1 residue, 1 model selected > hide #!10 models > select add #11 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected > select subtract #11 Nothing selected > select add #11 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected > color (#!11 & sel) white > color #11 #aaaaffff > color (#!11 & sel) white > select ::name=""AZZ"" 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel red > color zone #10 near #11 distance 4.98 > show #!10 models > volume splitbyzone #10 Opened mOCT1-AZT.mrc 0 as #12.1, grid size 320,320,320, pixel 0.83, shown at level 0.0102, step 1, values float32 Opened mOCT1-AZT.mrc 1 as #12.2, grid size 320,320,320, pixel 0.83, shown at level 0.0102, step 1, values float32 Opened mOCT1-AZT.mrc 2 as #12.3, grid size 320,320,320, pixel 0.83, shown at level 0.0102, step 1, values float32 > close #12.2 > close #12.1 > color #12.3 #ff0000fe models > color #12.3 #ff000096 models > color #12.3 #ffffff96 models > color #12.3 #ffffb296 models > color #11 #aaffffff > color #11 #aaaaffff > select add #11 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected > color (#!11 & sel) byhetero > select clear > show #!3 models > hide #!3 models > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true > hide #!12.3 models > hide #!12 models > hide #!11 models > show #!1 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240702/job350/postprocess.mrc Opened postprocess.mrc as #13, grid size 320,320,320, pixel 0.83, shown at level 0.00595, step 2, values float32 > volume #13 step 1 > volume #13 level 0.02012 > select add #13 2 models selected > view matrix models #13,1,0,0,-56.643,0,1,0,-72.238,0,0,1,-68.565 > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.02465,-0.61986,0.78433,49.618,-0.43145,0.70114,0.56768,-50.105,-0.9018,-0.35239,-0.25015,252.26 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.02465,-0.61986,0.78433,42.91,-0.43145,0.70114,0.56768,-47.812,-0.9018,-0.35239,-0.25015,260.75 > view matrix models > #13,0.02465,-0.61986,0.78433,45.137,-0.43145,0.70114,0.56768,-48.218,-0.9018,-0.35239,-0.25015,267.86 > rename #13 mOCT1-MTF.mrc > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240603/RealSpaceRefine_3/mOCT1_MTF- > coot-9_real_space_refined_003.pdb Chain information for mOCT1_MTF-coot-9_real_space_refined_003.pdb #14 --- Chain | Description A | No description available > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.2983, correlation about mean = 0.07385, overlap = 82.29 steps = 200, shift = 2.4, angle = 7.61 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.05771312 -0.64461025 0.76232987 59.74942259 -0.34050237 0.73052504 0.59193860 -66.21901607 -0.93847075 -0.22541250 -0.26165220 256.68697920 Axis -0.42762978 0.88984156 0.15910615 Axis point 123.33045199 0.00000000 117.21732044 Rotation angle (degrees) 107.12276965 Shift along axis -43.63458901 > select subtract #13 Nothing selected > select add #13 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.50114,0.40107,-0.76681,42.081,-0.045209,-0.87277,-0.48604,255.79,-0.86419,0.27824,-0.41924,198.29 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.50114,0.40107,-0.76681,41.903,-0.045209,-0.87277,-0.48604,247.49,-0.86419,0.27824,-0.41924,198.18 > view matrix models > #13,0.50114,0.40107,-0.76681,53.046,-0.045209,-0.87277,-0.48604,251.12,-0.86419,0.27824,-0.41924,198.38 > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.2273, correlation about mean = 0.06656, overlap = 59.06 steps = 120, shift = 2.59, angle = 4.72 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.43566959 0.38627366 -0.81300964 69.55864121 -0.07375796 -0.88487887 -0.45994473 251.91510217 -0.89707959 0.26034986 -0.35702406 194.41028021 Axis 0.83873143 0.09789343 -0.53567385 Axis point 0.00000000 97.27212052 153.57991582 Rotation angle (degrees) 154.57081238 Shift along axis -21.13865268 > view matrix models > #13,0.43567,0.38627,-0.81301,67.4,-0.073758,-0.88488,-0.45994,259.27,-0.89708,0.26035,-0.35702,197.15 > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.3307,0.47313,-0.81657,68.962,0.20831,-0.88051,-0.42581,219.2,-0.92046,-0.029281,-0.38974,244.12 > view matrix models > #13,0.3796,0.48184,-0.78977,58.246,0.18592,-0.87598,-0.44507,223.83,-0.90628,0.022112,-0.42211,239.42 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.3796,0.48184,-0.78977,53.846,0.18592,-0.87598,-0.44507,217.81,-0.90628,0.022112,-0.42211,235.11 > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.2652, correlation about mean = 0.06679, overlap = 73.72 steps = 92, shift = 1.81, angle = 5.01 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.31415893 0.53789144 -0.78228958 53.81386032 0.19698588 -0.84300825 -0.50053338 220.95415625 -0.92870918 0.00314703 -0.37079559 234.49017112 Axis 0.80514260 0.23405449 -0.54494394 Axis point 0.00000000 81.07236056 158.23174632 Rotation angle (degrees) 161.77257653 Shift along axis -32.74085292 > view matrix models > #13,0.31416,0.53789,-0.78229,60.198,0.19699,-0.84301,-0.50053,217.39,-0.92871,0.003147,-0.3708,234.22 > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.2449, correlation about mean = 0.05515, overlap = 65.5 steps = 80, shift = 1.45, angle = 5.73 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.28419679 0.60053681 -0.74738728 50.81854511 0.27816291 -0.79764719 -0.53514891 205.19579930 -0.91752798 -0.05580782 -0.39373584 245.12613641 Axis 0.79598780 0.28253351 -0.53533003 Axis point 0.00000000 71.54715698 160.41463451 Rotation angle (degrees) 162.47642045 Shift along axis -32.79775064 > view matrix models > #13,0.2842,0.60054,-0.74739,49.177,0.27816,-0.79765,-0.53515,206.5,-0.91753,-0.055808,-0.39374,243.99 > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.3559, correlation about mean = 0.151, overlap = 107.2 steps = 88, shift = 2.33, angle = 2.34 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.29378487 0.57675594 -0.76226180 52.65591556 0.29516509 -0.81321822 -0.50155130 203.18767751 -0.90915787 -0.07764488 -0.40914943 245.95334709 Axis 0.80029578 0.27732609 -0.53161726 Axis point 0.00000000 73.19686532 158.33534093 Rotation angle (degrees) 164.64234082 Shift along axis -32.26349399 > view matrix models > #13,0.29378,0.57676,-0.76226,50.19,0.29517,-0.81322,-0.50155,203.5,-0.90916,-0.077645,-0.40915,251.78 > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.9033, correlation about mean = 0.6277, overlap = 419.6 steps = 52, shift = 1.52, angle = 1.92 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.29574252 0.60146473 -0.74214321 45.38180479 0.29484975 -0.79643687 -0.52796964 204.44935424 -0.90862533 -0.06267767 -0.41288198 249.74597785 Axis 0.80005949 0.28626242 -0.52721784 Axis point 0.00000000 72.71544700 159.79227740 Rotation angle (degrees) 163.09499009 Shift along axis -36.83622428 > ui tool show Matchmaker > matchmaker #!14 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1_MTF- coot-9_real_space_refined_003.pdb, chain A (#14), sequence alignment score = 2355.8 RMSD between 450 pruned atom pairs is 0.377 angstroms; (across all 450 pairs: 0.377) > select add #14 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected > select subtract #13 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > hide #!1 models > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 5891, resource id: 35654810, major code: 40 (TranslateCoords), minor code: 0 > color #14 #95cacdff > select ::name=""MF8"" 22 atoms, 21 bonds, 1 residue, 1 model selected > select add #14 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > select subtract #14 Nothing selected > select add #14 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > color (#!14 & sel) white > select ::name=""MF8"" 22 atoms, 21 bonds, 1 residue, 1 model selected > color sel red > color zone #10 near #11 distance 4.98 > color zone #13 near #14 distance 4.98 > hide #!14 models > show #!14 models > volume #13 level 0.0238 > volume #13 level 0.02122 > volume #13 level 0.01423 > volume splitbyzone #13 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 > close #15.1 > close #15.2 > volume #15.3 level 0.009273 > volume #15.3 level 0.01703 > close #15#15.3 > select add #14 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > show #!13 models > color zone #13 near #14 distance 4.88 > color zone #13 near #14 distance 4.78 > color zone #13 near #14 distance 4.68 > color zone #13 near #14 distance 4.58 > color zone #13 near #14 distance 4.48 > color zone #13 near #14 distance 4.38 > color zone #13 near #14 distance 4.28 > color zone #13 near #14 distance 4.18 > color zone #13 near #14 distance 4.08 > color zone #13 near #14 distance 3.98 > color zone #13 near #14 distance 3.88 > color zone #13 near #14 distance 3.78 > color zone #13 near #14 distance 3.68 > color zone #13 near #14 distance 3.58 > color zone #13 near #14 distance 3.48 > color zone #13 near #14 distance 3.38 [Repeated 1 time(s)] > volume splitbyzone #13 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 > close #15.1-2 > volume #15.3 level 0.009634 > color zone #13 near #14 distance 3.28 > color zone #13 near #14 distance 3.18 > color zone #13 near #14 distance 3.08 > close #15#15.3 > show #!13 models > select add #13 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected > select subtract #13 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > color zone #13 near #14 distance 2.98 > color zone #13 near #14 distance 2.88 > color zone #13 near #14 distance 2.78 > color zone #13 near #14 distance 2.68 > color zone #13 near #14 distance 2.58 > color zone #13 near #14 distance 2.48 > volume #13 level 0.01681 > fitmap #14 inMap #13 Fit molecule mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) to map mOCT1-MTF.mrc (#13) using 7044 atoms average map value = 0.01572, steps = 48 shifted from previous position = 0.0765 rotated from previous position = 0.266 degrees atoms outside contour = 4386, contour level = 0.016807 Position of mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) relative to mOCT1-MTF.mrc (#13) coordinates: Matrix rotation and translation 0.99946408 0.01781074 -0.02746495 0.87693504 -0.01720783 0.99960910 0.02203450 -1.16466203 0.02784666 -0.02155008 0.99937988 -1.14535630 Axis -0.55418255 -0.70329295 -0.44526478 Axis point 28.72708736 -0.00000000 48.38067452 Rotation angle (degrees) 2.25364092 Shift along axis 0.84310332 > color zone #13 near #14 distance 2.48 [Repeated 1 time(s)] > color single #13 > color zone #13 near #14 distance 2.48 > color zone #13 near #14 distance 2.38 > color zone #13 near #14 distance 2.28 > color zone #13 near #14 distance 2.18 > color zone #13 near #14 distance 2.08 > color zone #13 near #14 distance 1.98 > color zone #13 near #14 distance 1.88 > color zone #13 near #14 distance 1.78 > color zone #13 near #14 distance 1.68 > color zone #13 near #14 distance 1.58 > color zone #13 near #14 distance 1.48 > color zone #13 near #14 distance 1.38 > color zone #13 near #14 distance 1.48 > color zone #13 near #14 distance 1.58 > color zone #13 near #14 distance 1.68 > color zone #13 near #14 distance 1.78 > color zone #13 near #14 distance 1.88 > color zone #13 near #14 distance 1.98 > volume #13 level 0.01957 > color zone #13 near #14 distance 1.98 > volume splitbyzone #13 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at level 0.0196, step 1, values float32 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at level 0.0196, step 1, values float32 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at level 0.0196, step 1, values float32 > close #15.1-2 > color #15.3 yellow models > color #15.3 white models > color #15.3 #ffffb2ff models > color #15.3 #ffffb296 models > volume #15.3 level 0.01524 > volume #15.3 level 0.0119 > select subtract #14 Nothing selected > select add #14 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > color #14 #55dd44ff > color #14 #5d42cdff > color #14 #5858cdff > color #14 #7d76cdff > color #14 #9d7bcdff > color #14 #cd75baff > color #14 #9381cdff > color (#!14 & sel) byhetero > select clear > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true > hide #!15.3 models > hide #!15 models > hide #!14 models > show #!1 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job321/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #16, grid size 320,320,320, pixel 0.83, shown at level 0.00147, step 2, values float32 > volume #13 level 0.01846 > volume #16 step 1 > volume #16 level 0.01137 > select add #16 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #16,0.91726,-0.046522,0.39555,-35.801,-0.13266,0.90075,0.41357,-25.02,-0.37554,-0.43183,0.82006,127.4 > view matrix models > #16,0.97308,0.0084656,-0.23031,32.94,-0.035652,0.99283,-0.11414,20.659,0.2277,0.11927,0.9664,-40.203 > view matrix models > #16,0.95291,-0.013325,0.30296,-32.366,-0.094841,0.93583,0.33946,-24.554,-0.28805,-0.35221,0.89049,96.605 > view matrix models > #16,0.68405,0.72927,0.015283,-53.826,0.65561,-0.6055,-0.45117,179.02,-0.31977,0.31864,-0.89231,251.74 > view matrix models > #16,-0.14871,0.82898,-0.53915,114.85,0.43367,-0.43531,-0.78894,230.9,-0.88872,-0.35114,-0.29476,331.38 > view matrix models > #16,-0.59154,0.6904,-0.41646,173.56,0.69281,0.17103,-0.70054,108.52,-0.41243,-0.70292,-0.57948,352.16 > ui mousemode right ""translate selected models"" > view matrix models > #16,-0.59154,0.6904,-0.41646,98.473,0.69281,0.17103,-0.70054,82.195,-0.41243,-0.70292,-0.57948,295.09 > view matrix models > #16,-0.59154,0.6904,-0.41646,115.7,0.69281,0.17103,-0.70054,51.467,-0.41243,-0.70292,-0.57948,297.87 > view matrix models > #16,-0.59154,0.6904,-0.41646,109.24,0.69281,0.17103,-0.70054,49.803,-0.41243,-0.70292,-0.57948,297.08 > view matrix models > #16,-0.59154,0.6904,-0.41646,112.5,0.69281,0.17103,-0.70054,41.909,-0.41243,-0.70292,-0.57948,292.69 > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.52634,0.62911,-0.57201,132.47,0.46428,-0.35094,-0.81319,152.81,-0.71233,-0.69359,-0.10737,267.76 > view matrix models > #16,-0.56071,0.74447,-0.36245,94.475,0.40226,-0.13769,-0.90511,145.91,-0.72373,-0.6533,-0.22227,279.35 > ui mousemode right ""translate selected models"" > view matrix models > #16,-0.56071,0.74447,-0.36245,91.988,0.40226,-0.13769,-0.90511,152.84,-0.72373,-0.6533,-0.22227,276.37 > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.69312,0.68147,-0.23491,100.24,0.41746,0.11382,-0.90154,118.42,-0.58764,-0.72294,-0.36338,286.3 > rename #16 hOCT1-VB1.mrc > fitmap #16 inMap #1 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 29501 points correlation = 0.336, correlation about mean = 0.1558, overlap = 114.4 steps = 148, shift = 3.34, angle = 5.64 degrees Position of hOCT1-VB1.mrc (#16) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.66774800 0.66848229 -0.32748134 111.59775010 0.47076725 0.03845367 -0.88141903 115.78397104 -0.57662015 -0.74273329 -0.34037693 282.67572866 Axis 0.39969377 0.71802066 -0.56981683 Axis point 39.62225841 0.00000000 179.67701786 Rotation angle (degrees) 170.00920250 Shift along axis -33.33317846 > ui mousemode right ""translate selected models"" > view matrix models > #16,-0.66775,0.66848,-0.32748,111.72,0.47077,0.038454,-0.88142,115.95,-0.57662,-0.74273,-0.34038,288.9 > fitmap #16 inMap #1 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 29501 points correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 steps = 60, shift = 1.34, angle = 1.92 degrees Position of hOCT1-VB1.mrc (#16) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.68896253 0.65809895 -0.30370448 111.90845021 0.45027206 0.06027049 -0.89085495 116.65862228 -0.56796628 -0.75051532 -0.33784768 287.44343290 Axis 0.38522072 0.72537689 -0.57046767 Axis point 41.86637964 0.00000000 181.62562393 Rotation angle (degrees) 169.50470225 Shift along axis -36.24626372 > view matrix models > #16,-0.68896,0.6581,-0.3037,110.15,0.45027,0.06027,-0.89085,119.19,-0.56797,-0.75052,-0.33785,287.46 > fitmap #16 inMap #1 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 29501 points correlation = 0.7772, correlation about mean = 0.5327, overlap = 352.7 steps = 72, shift = 3.09, angle = 0.0182 degrees Position of hOCT1-VB1.mrc (#16) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.68902052 0.65795875 -0.30387662 111.96278841 0.45022908 0.06002731 -0.89089309 116.69902951 -0.56793001 -0.75065771 -0.33759222 287.41226501 Axis 0.38519550 0.72529614 -0.57058737 Axis point 41.87016659 0.00000000 181.64241189 Rotation angle (degrees) 169.51189271 Shift along axis -36.22489055 > fitmap #16 inMap #1 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 29501 points correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 steps = 36, shift = 0.00448, angle = 0.00722 degrees Position of hOCT1-VB1.mrc (#16) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.68898476 0.65802671 -0.30381055 111.93916561 0.45024501 0.06010903 -0.89087953 116.68451889 -0.56796077 -0.75059160 -0.33768744 287.42460080 Axis 0.38521270 0.72532270 -0.57054198 Axis point 41.86758112 0.00000000 181.63640339 Rotation angle (degrees) 169.50839167 Shift along axis -36.23348002 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_10/hOCT1-VB_Dock2_real_space_refined_010.pdb Chain information for hOCT1-VB_Dock2_real_space_refined_010.pdb #17 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!17 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with hOCT1-VB_Dock2_real_space_refined_010.pdb, chain A (#17), sequence alignment score = 1980 RMSD between 416 pruned atom pairs is 0.792 angstroms; (across all 446 pairs: 1.346) > fitmap #17 inMap #16 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map hOCT1-VB1.mrc (#16) using 3479 atoms average map value = 0.02025, steps = 64 shifted from previous position = 0.153 rotated from previous position = 0.521 degrees atoms outside contour = 1063, contour level = 0.011373 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to hOCT1-VB1.mrc (#16) coordinates: Matrix rotation and translation 0.99999651 0.00186028 0.00187897 -0.40239474 -0.00185675 0.99999652 -0.00187607 0.55801929 -0.00188246 0.00187257 0.99999648 0.09469763 Axis 0.57831092 0.58028383 -0.57343453 Axis point 61.09212114 0.00000000 225.59585813 Rotation angle (degrees) 0.18569746 Shift along axis 0.03679741 > fitmap #17 inMap #16 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map hOCT1-VB1.mrc (#16) using 3479 atoms average map value = 0.02025, steps = 28 shifted from previous position = 0.0153 rotated from previous position = 0.0146 degrees atoms outside contour = 1064, contour level = 0.011373 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to hOCT1-VB1.mrc (#16) coordinates: Matrix rotation and translation 0.99999599 0.00211002 0.00188874 -0.43726655 -0.00210638 0.99999592 -0.00192887 0.59237860 -0.00189280 0.00192488 0.99999636 0.07510223 Axis 0.56254941 0.55200867 -0.61548727 Axis point 271.69369003 217.02489508 0.00000000 Rotation angle (degrees) 0.19625280 Shift along axis 0.03478962 > hide #!1 models > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected > select subtract #16 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected > color (#!17 & sel) white > select clear > select ::name=""VIB"" 18 atoms, 19 bonds, 1 residue, 1 model selected > color sel red > color zone #16 near #17 distance 4.98 > color zone #16 near #17 distance 4.88 > color zone #16 near #17 distance 4.78 > color zone #16 near #17 distance 4.68 > color zone #16 near #17 distance 4.58 > color zone #16 near #17 distance 4.48 > color zone #16 near #17 distance 4.38 > color zone #16 near #17 distance 4.28 > color zone #16 near #17 distance 4.18 > color zone #16 near #17 distance 4.08 > color zone #16 near #17 distance 3.98 > color zone #16 near #17 distance 3.88 > color zone #16 near #17 distance 3.78 > color zone #16 near #17 distance 3.68 > color zone #16 near #17 distance 3.58 > color zone #16 near #17 distance 3.48 > color zone #16 near #17 distance 3.38 > color zone #16 near #17 distance 3.28 > color sel white > select ::name=""VIB"" 18 atoms, 19 bonds, 1 residue, 1 model selected > color sel red > select add #16 18 atoms, 19 bonds, 1 residue, 3 models selected > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected > select subtract #17 2 models selected > color #16.1 white > color zone #16 near #17 distance 3.28 > color zone #16 near #17 distance 3.18 > color zone #16 near #17 distance 3.08 > color zone #16 near #17 distance 2.98 > color zone #16 near #17 distance 2.88 > color zone #16 near #17 distance 2.98 > color zone #16 near #17 distance 3.08 > color zone #16 near #17 distance 3.18 > color zone #16 near #17 distance 3.28 > color zone #16 near #17 distance 3.38 [Repeated 1 time(s)] > volume splitbyzone #16 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 > close #18.1-2 > color #18.3 yellow models > color #18.3 white models > color #18.3 #ffffb2ff models > color #18.3 #ffffb296 models > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected > select subtract #16 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected > color #17 #6622bbff > color #17 #62be40ff > color (#!17 & sel) byhetero Drag select of 1 atoms, 1 bonds > volume #18.3 level 0.006511 > volume #18.3 level 0.01112 > close #18#18.3 > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected > color (#!17 & sel) white > select ::name=""VIB"" 18 atoms, 19 bonds, 1 residue, 1 model selected > color sel red > show #!16 models > color zone #16 near #17 distance 3.28 > color zone #16 near #17 distance 3.18 > color zone #16 near #17 distance 3.08 > color zone #16 near #17 distance 2.98 > color zone #16 near #17 distance 2.88 > color zone #16 near #17 distance 2.78 > color zone #16 near #17 distance 2.68 > color zone #16 near #17 distance 2.58 > color zone #16 near #17 distance 2.48 > color zone #16 near #17 distance 2.38 > color zone #16 near #17 distance 2.28 > color zone #16 near #17 distance 2.18 > color zone #16 near #17 distance 2.08 > color zone #16 near #17 distance 1.98 > color zone #16 near #17 distance 1.88 > color zone #16 near #17 distance 1.78 > color zone #16 near #17 distance 1.68 > color zone #16 near #17 distance 1.78 > color zone #16 near #17 distance 1.88 > color zone #16 near #17 distance 1.98 > color zone #16 near #17 distance 2.08 > volume splitbyzone #16 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 > close #18.1-2 > color #18.3 white models > color #18.3 #ffffb2ff models > select add #18.3 18 atoms, 19 bonds, 1 residue, 3 models selected > color #18.3 #ffffb296 models > select subtract #18.3 18 atoms, 19 bonds, 1 residue, 1 model selected > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected > select subtract #17 Nothing selected > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected > color #17 #6622bbff > color #17 #62be40ff > color (#!17 & sel) byhetero > view > hide #!18.3 models > hide #!18 models > hide #!17 models > select subtract #17 Nothing selected > show #!1 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/job154/postprocess_masked.mrc Opened postprocess_masked.mrc as #19, grid size 320,320,320, pixel 0.83, shown at level 2.83e-06, step 2, values float32 > volume #19 step 1 > volume #19 level 0.0131 > select add #19 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #19,-0.93986,0.28611,-0.18654,253.04,-0.10485,-0.76147,-0.63967,340.05,-0.32506,-0.58164,0.74567,158.04 > ui mousemode right ""translate selected models"" > view matrix models > #19,-0.93986,0.28611,-0.18654,175.89,-0.10485,-0.76147,-0.63967,293,-0.32506,-0.58164,0.74567,91.801 > view matrix models > #19,-0.93986,0.28611,-0.18654,185.27,-0.10485,-0.76147,-0.63967,269.77,-0.32506,-0.58164,0.74567,91.027 > view matrix models > #19,-0.93986,0.28611,-0.18654,178.6,-0.10485,-0.76147,-0.63967,268.3,-0.32506,-0.58164,0.74567,89.593 > rename #19 hOCT1-AZT.mrc > fitmap #19 inMap #16 Fit map hOCT1-AZT.mrc in map hOCT1-VB1.mrc using 23475 points correlation = 0.9652, correlation about mean = 0.8232, overlap = 14.07 steps = 112, shift = 2.59, angle = 19.3 degrees Position of hOCT1-AZT.mrc (#19) relative to hOCT1-VB1.mrc (#16) coordinates: Matrix rotation and translation 0.86934918 -0.02079803 -0.49376051 87.20318527 -0.45396874 0.36123943 -0.81450504 253.58267245 0.19530587 0.93224113 0.30460154 -57.13169181 Axis 0.90642923 -0.35757337 -0.22478286 Axis point 0.00000000 185.25380563 166.58335969 Rotation angle (degrees) 74.47879004 Shift along axis 1.21133072 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/RealSpaceRefine_6/hOCT1_AZT- > coot-2_real_space_refined_006.pdb Chain information for hOCT1_AZT-coot-2_real_space_refined_006.pdb #20 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!20 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with hOCT1_AZT- coot-2_real_space_refined_006.pdb, chain A (#20), sequence alignment score = 1978 RMSD between 414 pruned atom pairs is 0.849 angstroms; (across all 446 pairs: 1.482) > hide #!1 models > color #19 white models > select add #20 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 4 models selected > color #20 white > hide #!19 models > select subtract #19 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel red > color zone #19 near #20 distance 4.98 > show #!19 models > select add #19 19 atoms, 20 bonds, 1 residue, 3 models selected > select subtract #19 19 atoms, 20 bonds, 1 residue, 1 model selected > color zone #19 near #20 distance 4.88 > color zone #19 near #20 distance 4.78 > color zone #19 near #20 distance 4.68 > color zone #19 near #20 distance 4.58 > color zone #19 near #20 distance 4.48 > color zone #19 near #20 distance 4.38 > color zone #19 near #20 distance 4.28 > color zone #19 near #20 distance 4.18 > color zone #19 near #20 distance 4.08 > color zone #19 near #20 distance 3.98 > color zone #19 near #20 distance 3.88 > color zone #19 near #20 distance 3.78 > color zone #19 near #20 distance 3.68 > color zone #19 near #20 distance 3.58 > color zone #19 near #20 distance 3.48 > volume #19 level 0.01039 > color zone #19 near #20 distance 3.38 > color zone #19 near #20 distance 3.28 > color zone #19 near #20 distance 3.18 > color zone #19 near #20 distance 3.08 > color zone #19 near #20 distance 2.98 > color zone #19 near #20 distance 2.88 > color zone #19 near #20 distance 2.78 > color zone #19 near #20 distance 2.68 > color zone #19 near #20 distance 2.58 > color zone #19 near #20 distance 2.48 > color zone #19 near #20 distance 2.38 > color zone #19 near #20 distance 2.28 > color zone #19 near #20 distance 2.18 > color zone #19 near #20 distance 2.08 > color zone #19 near #20 distance 1.98 > color zone #19 near #20 distance 1.88 > color zone #19 near #20 distance 1.78 > color zone #19 near #20 distance 1.88 > color zone #19 near #20 distance 1.98 > color zone #19 near #20 distance 2.08 [Repeated 1 time(s)] > volume splitbyzone #19 Opened hOCT1-AZT.mrc 0 as #21.1, grid size 320,320,320, pixel 0.83, shown at level 0.0104, step 1, values float32 Opened hOCT1-AZT.mrc 1 as #21.2, grid size 320,320,320, pixel 0.83, shown at level 0.0104, step 1, values float32 Opened hOCT1-AZT.mrc 2 as #21.3, grid size 320,320,320, pixel 0.83, shown at level 0.0104, step 1, values float32 > close #21.1-2 > select add #20 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected > select subtract #20 Nothing selected > select add #20 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected > color #20 #773333ff > color #20 #733551ff > color (#!20 & sel) byhetero > select clear > color #21.3 #ff000096 models > color #21.3 #ffffff96 models > color #21.3 #ffffb296 models > volume #21.3 level 0.008896 > hide #!21.3 models > hide #!21 models > hide #!20 models > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 59019, resource id: 35654939, major code: 40 (TranslateCoords), minor code: 0 > show #!3 models > show #!6.3 models > select ::name=""ABC"" 42 atoms, 48 bonds, 2 residues, 1 model selected > view sel > select clear > hide #!6.3 models > hide #!6 models > hide #!3 models > show #!2 models > show #!5 models > hide #!5 models > hide #!2 models > show #!8 models > show #!9.3 models > hide #!9.3 models > hide #!9 models > hide #!8 models > show #!11 models > show #!12.3 models > hide #!12.3 models > hide #!12 models > hide #!11 models > show #!14 models > show #!15 models > hide #!15 models > show #!15.3 models > hide #!14 models > hide #!15 models > hide #!15.3 models > show #!17 models > show #!18.3 models > hide #!18.3 models > hide #!18 models > hide #!17 models > show #!20 models > show #!21.3 models > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1_structures_ligand_density.cxs > includeMaps true [Repeated 1 time(s)] > close session > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/0-coot- > history.scm Unrecognized file suffix '.scm' > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif Summary of feedback from opening /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 187 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""3"" near line 98 Bad residue range for struct_conf ""4"" near line 99 Bad residue range for struct_conf ""5"" near line 100 Bad residue range for struct_conf ""6"" near line 101 Bad residue range for struct_conf ""7"" near line 102 15 messages similar to the above omitted Invalid sheet range for struct_sheet_range ""2 1"" near line 183 Invalid sheet range for struct_sheet_range ""3 1"" near line 184 Invalid sheet range for struct_sheet_range ""4 1"" near line 186 Missing or incomplete sequence information. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' near line 4361 Chain information for rOAT1-AZT_coot-4_real_space_refined_002.cif #1 --- Chain | Description A | No description available > close session > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.pdb Chain information for rOAT1-AZT_coot-4_real_space_refined_002.pdb #1 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 10568, resource id: 35655077, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/postprocess.mrc Opened postprocess.mrc as #2, grid size 320,320,320, pixel 0.83, shown at level 0.00421, step 2, values float32 > rename #2 rOAT1-AZT.mrc > volume #2 step 1 > volume #2 level 0.01415 > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > select add #1 3905 atoms, 3986 bonds, 515 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.81264,-0.025153,-0.58222,300.85,0.24435,0.8923,-0.37961,31.685,0.52906,-0.45075,-0.71897,210.07 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.81264,-0.025153,-0.58222,320.11,0.24435,0.8923,-0.37961,31.387,0.52906,-0.45075,-0.71897,214.5 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.62181,-0.74054,-0.25487,347.35,-0.028985,0.34697,-0.93743,205.98,0.78263,-0.57551,-0.23722,138.33 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.62181,-0.74054,-0.25487,344.94,-0.028985,0.34697,-0.93743,211.72,0.78263,-0.57551,-0.23722,135.34 > view matrix models > #1,-0.62181,-0.74054,-0.25487,347.37,-0.028985,0.34697,-0.93743,211.37,0.78263,-0.57551,-0.23722,136.41 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) to map rOAT1-AZT.mrc (#2) using 3905 atoms average map value = 0.01965, steps = 108 shifted from previous position = 2.32 rotated from previous position = 12.8 degrees atoms outside contour = 1436, contour level = 0.014154 Position of rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) relative to rOAT1-AZT.mrc (#2) coordinates: Matrix rotation and translation -0.62427498 -0.78041245 -0.03517318 323.27181278 -0.15760640 0.16991691 -0.97277359 257.26632447 0.76514114 -0.60173470 -0.22907287 142.60270901 Axis 0.34360458 -0.74113973 0.57675627 Axis point 193.37147122 0.00000000 235.15956508 Rotation angle (degrees) 147.32171525 Shift along axis 2.65438788 > select subtract #1 Nothing selected > select add #1 3905 atoms, 3986 bonds, 515 residues, 1 model selected > color sel white > select ::name=""AZZ"" 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel red > ui tool show ""Color Zone"" > color zone #2 near #1 distance 4.98 > volume #2 level 0.0105 > color zone #2 near #1 distance 4.88 > color zone #2 near #1 distance 4.78 > color zone #2 near #1 distance 4.68 > color zone #2 near #1 distance 4.58 > color zone #2 near #1 distance 4.48 > color zone #2 near #1 distance 4.38 > color zone #2 near #1 distance 4.28 > color zone #2 near #1 distance 4.18 > color zone #2 near #1 distance 4.08 > color zone #2 near #1 distance 3.98 > color zone #2 near #1 distance 3.88 > color zone #2 near #1 distance 3.78 > color zone #2 near #1 distance 3.68 > color zone #2 near #1 distance 3.58 > color zone #2 near #1 distance 3.48 > color zone #2 near #1 distance 3.38 > color zone #2 near #1 distance 3.28 > color zone #2 near #1 distance 3.18 > color zone #2 near #1 distance 3.08 > color zone #2 near #1 distance 2.98 > color zone #2 near #1 distance 2.88 > color zone #2 near #1 distance 2.78 > color zone #2 near #1 distance 2.68 > color zone #2 near #1 distance 2.58 > color zone #2 near #1 distance 2.48 > color zone #2 near #1 distance 2.38 > color zone #2 near #1 distance 2.28 > color zone #2 near #1 distance 2.18 > color zone #2 near #1 distance 2.08 > color zone #2 near #1 distance 1.98 > color zone #2 near #1 distance 1.88 > color zone #2 near #1 distance 1.78 > volume #2 level 0.008069 > volume splitbyzone #2 Opened rOAT1-AZT.mrc 0 as #3.1, grid size 320,320,320, pixel 0.83, shown at level 0.00807, step 1, values float32 Opened rOAT1-AZT.mrc 1 as #3.2, grid size 320,320,320, pixel 0.83, shown at level 0.00807, step 1, values float32 Opened rOAT1-AZT.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at level 0.00807, step 1, values float32 > close #3.1-2 > color #3.3 white models > color #3.3 #ffffb2ff models > select add #1 3905 atoms, 3986 bonds, 515 residues, 1 model selected > color #1 #dd22bbff > color #1 tan > color sel byhetero > color #3.3 #ffffb296 models > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 355, resource id: 35655128, major code: 40 (TranslateCoords), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 366, resource id: 35655123, major code: 40 (TranslateCoords), minor code: 0 > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 14345, resource id: 35655133, major code: 40 (TranslateCoords), minor code: 0 > rename #1 rOAT1-AZT_IF.pdb > rename #2 rOAT1-AZT_IF.mrc > rename #3 ""rOAT1-AZT_IF.mrc split"" > rename #3.3 ""rOAT1-AZT_IF.mrc 2"" > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 23455, resource id: 35655148, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/run_class001.mrc Opened run_class001.mrc as #4, grid size 320,320,320, pixel 0.83, shown at level 0.00134, step 2, values float32 > close #4 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc Opened postprocess.mrc as #4, grid size 320,320,320, pixel 0.83, shown at level 0.00459, step 2, values float32 > volume #4 step 1 > volume #4 level 0.01366 > rename #4 rOAT1-AZT_OF.mrc > open > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF- > coot-7_real_space_refined_008.pdb Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #5 --- Chain | Description A | No description available > select subtract #1 Nothing selected > select add #5 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected > hide #!3 models > hide #!3.3 models > hide #1 models > view matrix models #5,1,0,0,68.569,0,1,0,64.41,0,0,1,67.632 > view matrix models #5,1,0,0,67.083,0,1,0,66.14,0,0,1,66.95 > fitmap #5 inMap #4 Fit molecule rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) to map rOAT1-AZT_OF.mrc (#4) using 3792 atoms average map value = 0.01938, steps = 84 shifted from previous position = 0.803 rotated from previous position = 4.35 degrees atoms outside contour = 1323, contour level = 0.013659 Position of rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) relative to rOAT1-AZT_OF.mrc (#4) coordinates: Matrix rotation and translation 0.99822969 -0.04531644 -0.03852150 72.45731875 0.04345449 0.99790785 -0.04787105 67.21065914 0.04061025 0.04611237 0.99811044 61.32293455 Axis 0.62004547 -0.52206316 0.58565662 Axis point 0.00000000 -669.59173064 1932.22009801 Rotation angle (degrees) 4.34647273 Shift along axis 45.75280586 > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF.pdb > models #5 relModel #4 > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/rOAT1-AZT_IF.pdb > models #1 > close #5 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc Opened rOAT1-AZT_OF.mrc as #5, grid size 320,320,320, pixel 0.83, shown at level 0.00459, step 2, values float32 > close #5 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF- > coot-0_real_space_refined_003.pdb Chain information for rOAT1-AZT_OF-coot-0_real_space_refined_003.pdb #5 --- Chain | Description A | No description available > select add #4 2 models selected > select subtract #4 Nothing selected > select add #5 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected > select clear > select add #5 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #5 white > color #4 white models > color #2 white models > select #5/A:601@O4 1 atom, 1 residue, 1 model selected > select up 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel red > color zone #4 near #5 distance 4.98 > color zone #4 near #5 distance 4.88 > color zone #4 near #5 distance 4.78 > color zone #4 near #5 distance 4.68 > color zone #4 near #5 distance 4.58 > color zone #4 near #5 distance 4.48 > color zone #4 near #5 distance 4.38 > color zone #4 near #5 distance 4.28 > color zone #4 near #5 distance 4.18 > color zone #4 near #5 distance 4.08 > color zone #4 near #5 distance 3.98 > color zone #4 near #5 distance 3.88 > color zone #4 near #5 distance 3.78 > color zone #4 near #5 distance 3.68 > color zone #4 near #5 distance 3.58 > color zone #4 near #5 distance 3.48 > color zone #4 near #5 distance 3.38 > color zone #4 near #5 distance 3.28 > color zone #4 near #5 distance 3.18 > color zone #4 near #5 distance 3.08 > color zone #4 near #5 distance 2.98 > color zone #4 near #5 distance 2.88 > color zone #4 near #5 distance 2.78 > color zone #4 near #5 distance 2.68 > color zone #4 near #5 distance 2.58 > color zone #4 near #5 distance 2.48 > color zone #4 near #5 distance 2.38 > color zone #4 near #5 distance 2.28 > color zone #4 near #5 distance 2.18 > color zone #4 near #5 distance 2.08 > color zone #4 near #5 distance 1.98 > color zone #4 near #5 distance 1.88 > color zone #4 near #5 distance 1.78 > color zone #4 near #5 distance 1.68 > color zone #4 near #5 distance 1.58 > color zone #4 near #5 distance 1.48 > color zone #4 near #5 distance 1.58 > color zone #4 near #5 distance 1.68 > color zone #4 near #5 distance 1.78 > color zone #4 near #5 distance 1.88 > volume splitbyzone #4 Opened rOAT1-AZT_OF.mrc 0 as #6.1, grid size 320,320,320, pixel 0.83, shown at level 0.0137, step 1, values float32 Opened rOAT1-AZT_OF.mrc 1 as #6.2, 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 0.0137, step 1, values float32 > close #6.1-2 > volume #6.3 level 0.0116 > select add #5 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected > select subtract #5 Nothing selected > color #6.3 yellow models > color #6.3 white models > color #6.3 #ffffb2ff models > select add #5 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #5 #ffaa88ff > color #5 salmon > color (#!5 & sel) byhetero > color #6.3 #ffffb296 models > select clear > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > show #!2 models > hide #!5 models > hide #!6 models > hide #!6.3 models > volume #2 level 0.01456 > color #2 #a5a5a5ff models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/postprocess.mrc Opened postprocess.mrc as #7, grid size 320,320,320, pixel 0.83, shown at level 0.00408, step 2, values float32 > rename #7 rOAT1-PBD_IF.mrc > volume #2 level 0.01983 > volume #2 level 0.0151 > hide #!7 models > volume #7 level 0.01185 > volume #7 step 1 > volume #7 level 0.01094 > hide #!2 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/rOAT1-PBD- > coot-6.pdb Chain information for rOAT1-PBD-coot-6.pdb #8 --- Chain | Description A | No description available > select add #8 3912 atoms, 3985 bonds, 522 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,55.004,0,1,0,73.737,0,0,1,58.702 > view matrix models #8,1,0,0,66.378,0,1,0,64.897,0,0,1,63.973 > fitmap #8 inMap #7 Fit molecule rOAT1-PBD-coot-6.pdb (#8) to map rOAT1-PBD_IF.mrc (#7) using 3912 atoms average map value = 0.02737, steps = 56 shifted from previous position = 2.6 rotated from previous position = 0.396 degrees atoms outside contour = 571, contour level = 0.010939 Position of rOAT1-PBD-coot-6.pdb (#8) relative to rOAT1-PBD_IF.mrc (#7) coordinates: Matrix rotation and translation 0.99998387 0.00531886 -0.00199304 66.36205660 -0.00532668 0.99997806 -0.00393867 67.06308709 0.00197205 0.00394922 0.99999026 65.65327743 Axis 0.57034742 -0.28670293 -0.76974363 Axis point 10937.66555565 -15865.74627304 0.00000000 Rotation angle (degrees) 0.39620277 Shift along axis -31.91394767 > rename #8 rOAT1-PBD_IF.pdb > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 51376, resource id: 35655645, major code: 40 (TranslateCoords), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 51388, resource id: 35655640, major code: 40 (TranslateCoords), minor code: 0 > color #8 white > hide #!7 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 19 atoms, 19 bonds, 1 residue, 1 model selected > color sel red > show #!7 models > color zone #7 near #8 distance 4.98 > color zone #7 near #8 distance 4.88 > color zone #7 near #8 distance 4.78 > color zone #7 near #8 distance 4.68 > color zone #7 near #8 distance 4.58 > color zone #7 near #8 distance 4.48 > color zone #7 near #8 distance 4.38 > color zone #7 near #8 distance 4.28 > color zone #7 near #8 distance 4.18 > color zone #7 near #8 distance 4.08 > color zone #7 near #8 distance 3.98 > color zone #7 near #8 distance 3.88 > color zone #7 near #8 distance 3.78 > color zone #7 near #8 distance 3.68 > volume #7 level 0.02515 > volume #7 level 0.01677 > volume #7 level 0.0124 > volume #7 level 0.01476 > color zone #7 near #8 distance 3.58 > color zone #7 near #8 distance 3.48 > color zone #7 near #8 distance 3.38 > color zone #7 near #8 distance 3.28 > color zone #7 near #8 distance 3.18 > color zone #7 near #8 distance 3.08 > color zone #7 near #8 distance 2.98 > color zone #7 near #8 distance 2.88 > color zone #7 near #8 distance 2.78 > color zone #7 near #8 distance 2.68 > color zone #7 near #8 distance 2.58 > color zone #7 near #8 distance 2.48 > color zone #7 near #8 distance 2.38 > color zone #7 near #8 distance 2.28 > volume #7 level 0.01112 > color zone #7 near #8 distance 2.18 > color zone #7 near #8 distance 2.08 > color zone #7 near #8 distance 1.98 > color zone #7 near #8 distance 1.88 > color zone #7 near #8 distance 1.98 > color zone #7 near #8 distance 2.08 > volume splitbyzone #7 Opened rOAT1-PBD_IF.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at level 0.0111, step 1, values float32 Opened rOAT1-PBD_IF.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at level 0.0111, step 1, values float32 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at level 0.0111, step 1, values float32 > close #9.1-2 > color #9.3 #ff000096 models > color #9.3 #ffff0096 models > color #9.3 #ffffff96 models > color #9.3 #ffffb296 models > select add #8 3912 atoms, 3985 bonds, 522 residues, 1 model selected > color #8 #ffffddff > color #8 gold > select clear > select add #8 3912 atoms, 3985 bonds, 522 residues, 1 model selected > color sel byhetero > select clear > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 19133, resource id: 35655670, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/postprocess.mrc Opened postprocess.mrc as #10, grid size 320,320,320, pixel 0.83, shown at level 0.00409, step 2, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 23804, resource id: 35655680, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/rOAT1-PBD_OF- > coot-0.pdb Chain information for rOAT1-PBD_OF-coot-0.pdb #11 --- Chain | Description A | No description available > hide #!9 models > hide #8 models > rename #10 rOAT1-PBD_OF > rename #10 rOAT1-PBD_OF.mrc > show #!2 models > volume #10 level 0.004712 > volume #10 step 1 > volume #10 level 0.01128 > hide #!2 models > select add #11 3872 atoms, 3966 bonds, 500 residues, 1 model selected > view matrix models #11,1,0,0,65.11,0,1,0,69.986,0,0,1,61.035 > view matrix models #11,1,0,0,68.61,0,1,0,68.058,0,0,1,65.073 > view matrix models #11,1,0,0,67.516,0,1,0,68.105,0,0,1,67.386 > fitmap #11 inMap #10 Fit molecule rOAT1-PBD_OF-coot-0.pdb (#11) to map rOAT1-PBD_OF.mrc (#10) using 3872 atoms average map value = 0.01531, steps = 56 shifted from previous position = 2.42 rotated from previous position = 0.764 degrees atoms outside contour = 1505, contour level = 0.011277 Position of rOAT1-PBD_OF-coot-0.pdb (#11) relative to rOAT1-PBD_OF.mrc (#10) coordinates: Matrix rotation and translation 0.99995211 0.00939248 0.00274947 65.65298070 -0.00936721 0.99991506 -0.00906240 67.47749964 -0.00283436 0.00903621 0.99995516 65.83404461 Axis 0.67891074 0.20945939 -0.70370943 Axis point 6981.74049553 -6059.62250131 0.00000000 Rotation angle (degrees) 0.76372650 Shift along axis 12.37827175 > show sel atoms > hide #!10 models > show #!10 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF- > coot-7_real_space_refined_008.pdb Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #12 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!12 to #11 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rOAT1-PBD_OF-coot-0.pdb, chain A (#11) with rOAT1-PBD_OF- coot-7_real_space_refined_008.pdb, chain A (#12), sequence alignment score = 2423.1 RMSD between 470 pruned atom pairs is 0.696 angstroms; (across all 485 pairs: 1.080) > hide #11 models > select subtract #11 Nothing selected > show #11 models > hide #!12 models > hide #!10 models > show #!12 models > close #11 > color #12 #bb4455ff > color #12 #b4503bff QXcbConnection: XCB error: 3 (BadWindow), sequence: 15705, resource id: 35655708, major code: 40 (TranslateCoords), minor code: 0 > show #!10 models > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 19760, resource id: 35655718, major code: 40 (TranslateCoords), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19772, resource id: 35655713, major code: 40 (TranslateCoords), minor code: 0 > color #10 #ffb2ff96 models > volume #10 level 0.009218 > volume #10 level 0.008059 > color #10 #ffb2ffff models > select add #12 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected > hide #!10 models > color #12 white > select clear > select #12/B:601@C11 1 atom, 1 residue, 1 model selected > select up 37 atoms, 37 bonds, 1 residue, 1 model selected > color sel red > color #10 white models > select add #10 37 atoms, 37 bonds, 1 residue, 3 models selected > select subtract #10 37 atoms, 37 bonds, 1 residue, 1 model selected > show #!10 models > color zone #10 near #12 distance 2 > color zone #10 near #12 distance 1.9 > color zone #10 near #12 distance 1.8 > color zone #10 near #12 distance 1.7 > color zone #10 near #12 distance 1.8 > color zone #10 near #12 distance 1.9 > color zone #10 near #12 distance 2 [Repeated 1 time(s)] > volume splitbyzone #10 Opened rOAT1-PBD_OF.mrc 0 as #11.1, grid size 320,320,320, pixel 0.83, shown at level 0.00806, step 1, values float32 Opened rOAT1-PBD_OF.mrc 1 as #11.2, 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 > volume splitbyzone #10 Opened rOAT1-PBD_OF.mrc 0 as #13.1, grid size 320,320,320, pixel 0.83, shown at level 0.00806, step 1, values float32 Opened rOAT1-PBD_OF.mrc 1 as #13.2, 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 > close #11.1-2 > hide #!12 models > hide #!11.3 models > hide #!11 models > select add #12 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected > select subtract #12 Nothing selected > close #13.1-2 > show #!12 models > color #11.3 white models > color #11.3 #ffffb2ff models > color #13.3 white models > color #13.3 #ffffb2ff models > select add #12 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #12 #bb4455ff > color #12 #b4503bff > color (#!12 & sel) byhetero > select #12/A:440 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #12 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected > select subtract #12 Nothing selected > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > hide #!13 models > hide #!13.3 models > hide #!12 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/inward_j152_2.7A/postprocess.mrc Opened postprocess.mrc as #14, grid size 320,320,320, pixel 0.83, shown at level 0.00408, step 2, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 27239, resource id: 35655778, major code: 40 (TranslateCoords), minor code: 0 > show #!2 models > hide #!2 models > rename #14 rOAT1-TFV_IF.mrc > show #1 models > hide #!14 models > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF.pdb > models #1 relModel #14 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_5/rOAT1-TFV_IF- > coot-2_real_space_refined_005.pdb Chain information for rOAT1-TFV_IF-coot-2_real_space_refined_005.pdb #15 --- Chain | Description A | No description available > hide #1 models > show #!14 models > color #15 white > color #14 white models > select ::name=""TFV"" 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > color zone #14 near #15 distance 4.68 > color zone #14 near #15 distance 4.58 > color zone #14 near #15 distance 4.48 > color zone #14 near #15 distance 4.38 > color zone #14 near #15 distance 4.28 > color zone #14 near #15 distance 4.18 > color zone #14 near #15 distance 4.08 > color zone #14 near #15 distance 3.98 > color zone #14 near #15 distance 3.88 > color zone #14 near #15 distance 3.78 > color zone #14 near #15 distance 3.68 > color zone #14 near #15 distance 3.58 > color zone #14 near #15 distance 3.48 > color zone #14 near #15 distance 3.38 > color zone #14 near #15 distance 3.28 > color zone #14 near #15 distance 3.18 > color zone #14 near #15 distance 3.08 > color zone #14 near #15 distance 2.98 > color zone #14 near #15 distance 2.88 > color zone #14 near #15 distance 2.78 > color zone #14 near #15 distance 2.68 > volume #14 level 0.007613 > color zone #14 near #15 distance 2.78 > color zone #14 near #15 distance 2.88 > color zone #14 near #15 distance 2.98 > color zone #14 near #15 distance 2.88 > color zone #14 near #15 distance 2.78 > color zone #14 near #15 distance 2.68 > color zone #14 near #15 distance 2.58 > color zone #14 near #15 distance 2.48 > color zone #14 near #15 distance 2.38 > volume #14 level 0.005915 > volume #14 level 0.005632 > volume splitbyzone #14 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, values float32 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, 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 > close #16.1-2 > color zone #14 near #15 distance 2.09 > close #16#16.3 > show #!14 models > color zone #14 near #15 distance 1.99 > color zone #14 near #15 distance 2.09 > color zone #14 near #15 distance 2.19 > color zone #14 near #15 distance 2.29 > color zone #14 near #15 distance 2.39 > color zone #14 near #15 distance 2.29 > volume splitbyzone #14 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, values float32 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, 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 > close #16.1-2 > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > color #16.3 #ff5500ff models > color #16.3 #aa0000ff models > color #16.3 #ff5500ff models > color #16.3 #ff557fff models > color #15 #ff557fff > color #16.3 white models > color #16.3 #ffffb2ff models > color #16.3 #ffffb296 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF- > coot-3.pdb Chain information for rOAT1-TFV_IF-coot-3.pdb #17 --- Chain | Description A | No description available > close #17#16#16.3 > close #15 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF- > coot-3.pdb Chain information for rOAT1-TFV_IF-coot-3.pdb #15 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 28850, resource id: 35656402, major code: 40 (TranslateCoords), minor code: 0 > show #!14 models > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > select subtract #15 Nothing selected > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > color #15 white > color zone #14 near #15 distance 2.29 > select ::name=""TFV"" 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > color zone #14 near #15 distance 2.29 > color zone #14 near #15 distance 2.19 > color zone #14 near #15 distance 2.09 > color zone #14 near #15 distance 1.99 > color zone #14 near #15 distance 1.89 > color zone #14 near #15 distance 1.79 > color zone #14 near #15 distance 1.69 > color zone #14 near #15 distance 1.59 > color zone #14 near #15 distance 1.49 > color zone #14 near #15 distance 1.39 > color zone #14 near #15 distance 1.29 > color zone #14 near #15 distance 1.19 > color zone #14 near #15 distance 1.09 > color zone #14 near #15 distance 1.19 > color zone #14 near #15 distance 1.29 > color zone #14 near #15 distance 1.39 > color zone #14 near #15 distance 1.49 > color zone #14 near #15 distance 1.59 > color zone #14 near #15 distance 1.69 > color zone #14 near #15 distance 1.79 > color zone #14 near #15 distance 1.89 > color zone #14 near #15 distance 1.99 > color zone #14 near #15 distance 2.09 [Repeated 1 time(s)] > volume splitbyzone #14 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, values float32 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, 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 > close #16.1-2 > color #16.3 white models > color #16.3 #ffffb2ff models > color #16.3 #ffffb296 models > color #15 #ff5500ff > color #15 #ff557fff > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > color sel byhetero > select clear > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/postprocess.mrc Opened postprocess.mrc as #17, grid size 320,320,320, pixel 0.83, shown at level 0.00401, step 2, values float32 > rename #17 rOAT1-TVF_OF.mrc > hide #15 models > hide #!16 models > show #8 models > hide #8 models > show #!11.3 models > hide #!11 models > hide #!11.3 models > show #!12 models > volume #17 step 1 > volume #17 level 0.01305 > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb > models #12 relModel #17 > hide #!16.3 models > hide #!12 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb Chain information for rOAT1-TFV_OF.pdb #18 --- Chain | Description A | No description available > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > close #18 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV_OF- > coot-1_real_space_refined_007.pdb Chain information for rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb #18 --- Chain | Description A | No description available > select add #18 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #18 white > color #17 white models > select #18/A:601@H131 1 atom, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > volume #17 level 0.011 > color zone #17 near #18 distance 4.98 > color zone #17 near #18 distance 4.88 > color zone #17 near #18 distance 4.78 > color zone #17 near #18 distance 4.68 > color zone #17 near #18 distance 4.58 > color zone #17 near #18 distance 4.48 > color zone #17 near #18 distance 4.38 > color zone #17 near #18 distance 4.28 > color zone #17 near #18 distance 4.18 > color zone #17 near #18 distance 4.08 > color zone #17 near #18 distance 3.98 > color zone #17 near #18 distance 3.88 > color zone #17 near #18 distance 3.78 > color zone #17 near #18 distance 3.68 > color zone #17 near #18 distance 3.58 > color zone #17 near #18 distance 3.48 > color zone #17 near #18 distance 3.38 > color zone #17 near #18 distance 3.28 > color zone #17 near #18 distance 3.18 > color zone #17 near #18 distance 3.08 > color zone #17 near #18 distance 2.98 > 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 > close #19.1-2 > color #19.3 white models > color #19.3 #ffffb2ff models > select add #18 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #18 #337744ff > color #18 #374c02ff > color (#!18 & sel) byhetero > select clear > color #19.3 #ffffb296 models > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/inward_j112_2.6A/postprocess.mrc Opened postprocess.mrc as #20, grid size 320,320,320, pixel 0.83, shown at level 0.00494, step 2, values float32 > volume #20 step 1 > hide #!19 models > hide #!18 models > rename #20 rOAT1-AAI_IF.mrc > volume #20 level 0.0194 QXcbConnection: XCB error: 3 (BadWindow), sequence: 35473, resource id: 35656688, major code: 40 (TranslateCoords), minor code: 0 > show #!2 models > hide #!2 models > show #1 models > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb > models #1 relModel #20 > hide #1 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb Chain information for rOAT1-AAI_IF.pdb #21 --- Chain | Description A | No description available > close #21 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_1/rOAT1-AAI_IF_real_space_refined_001.pdb Chain information for rOAT1-AAI_IF_real_space_refined_001.pdb #21 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 12758, resource id: 35656914, major code: 40 (TranslateCoords), minor code: 0 > close #21 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF- > coot-1_real_space_refined_003_initial.geo Unrecognized file suffix '.geo' > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF- > coot-1_real_space_refined_003.pdb Chain information for rOAT1-AAI_IF-coot-1_real_space_refined_003.pdb #21 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 49188, resource id: 35657106, major code: 40 (TranslateCoords), minor code: 0 > select add #21 3956 atoms, 4042 bonds, 516 residues, 1 model selected > color #21 white > color #20 white models > select clear > select #21/A:602@O24 1 atom, 1 residue, 1 model selected > select up 35 atoms, 38 bonds, 1 residue, 1 model selected > select #21/A:601@O20 1 atom, 1 residue, 1 model selected > select add #21/A:602@C23 2 atoms, 2 residues, 1 model selected > select up 70 atoms, 76 bonds, 2 residues, 1 model selected > color sel red > color zone #20 near #21 distance 4.98 > color zone #20 near #21 distance 4.88 > color zone #20 near #21 distance 4.78 > color zone #20 near #21 distance 4.68 > color zone #20 near #21 distance 4.58 > color zone #20 near #21 distance 4.48 > color zone #20 near #21 distance 4.38 > color zone #20 near #21 distance 4.28 > color zone #20 near #21 distance 4.18 > color zone #20 near #21 distance 4.08 > color zone #20 near #21 distance 3.98 > color zone #20 near #21 distance 3.88 > color zone #20 near #21 distance 3.78 > color zone #20 near #21 distance 3.68 > color zone #20 near #21 distance 3.58 > color zone #20 near #21 distance 3.48 > color zone #20 near #21 distance 3.38 > color zone #20 near #21 distance 3.28 > color zone #20 near #21 distance 3.18 > color zone #20 near #21 distance 3.08 > color zone #20 near #21 distance 2.98 > color zone #20 near #21 distance 2.88 > volume splitbyzone #20 Opened rOAT1-AAI_IF.mrc 0 as #22.1, grid size 320,320,320, pixel 0.83, shown at level 0.0194, step 1, values float32 Opened rOAT1-AAI_IF.mrc 1 as #22.2, 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 0.0194, step 1, values float32 > close #22.1-2 > color #22.3 yellow models > color #22.3 white models > color #22.3 #ffffb2ff models > color #22.3 #ffffb296 models > select add #21 3956 atoms, 4042 bonds, 516 residues, 1 model selected > color #21 #668855ff > color #21 #685d73ff > color sel byhetero > select clear [Repeated 1 time(s)] > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 7603, resource id: 35657141, major code: 40 (TranslateCoords), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7615, resource id: 35657136, major code: 40 (TranslateCoords), minor code: 0 > hide #!22.3 models > hide #!22 models > hide #21 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/postprocess.mrc Opened postprocess.mrc as #23, grid size 320,320,320, pixel 0.83, shown at level 0.00494, step 2, values float32 > volume #23 level 0.01307 > volume #23 step 1 > volume #23 level 0.01684 > show #1 models > hide #1 models > show #!5 models > rename #23 rOAT1-AAI_OF.mrc > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/rOAT1-AAI_OF.pdb > models #5 relModel #23 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_4/rOAT1-AAI_OF- > coot-1_real_space_refined_004.pdb Chain information for rOAT1-AAI_OF-coot-1_real_space_refined_004.pdb #24 --- Chain | Description A | No description available > color #23 white models > color #24 white > hide #!5 models > select add #24/A:601@O24 1 atom, 1 residue, 1 model selected > select add #24/A:230@OH 2 atoms, 2 residues, 1 model selected > select clear > select add #24/A:601@O24 1 atom, 1 residue, 1 model selected > select up 35 atoms, 38 bonds, 1 residue, 1 model selected > color sel red > color zone #23 near #24 distance 4.98 > volume splitbyzone #23 Opened rOAT1-AAI_OF.mrc 0 as #25.1, grid size 320,320,320, pixel 0.83, shown at level 0.0168, step 1, values float32 Opened rOAT1-AAI_OF.mrc 1 as #25.2, 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 > close #25.1-2 > select add #24 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected > select subtract #24 Nothing selected > color #25.3 white models > color #25.3 #ffffb2ff models > select add #24 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #24 #1177ccff > color #24 #17c127ff > color (#!24 & sel) byhetero > select #24/A:438@CE2 1 atom, 1 residue, 1 model selected Drag select of 1 atoms, 1 bonds > select clear > color #25.3 #ffffb296 models > select clear > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > open > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/rOAT1-PAH- > coot-7_real_space_refined_007.pdb Chain information for rOAT1-PAH-coot-7_real_space_refined_007.pdb #26 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 7338, resource id: 35657291, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/cryosparc_P4_J89__localfilter_160.mrc Opened cryosparc_P4_J89__localfilter_160.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level 0.134, step 1, values float32 > hide #!24 models > hide #!25.3 models > hide #!25 models > view > show #!2 models > select add #26 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected > select add #27 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 4 models selected > view matrix models > #26,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865,#27,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865 > view matrix models > #26,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563,#27,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563 > rename #27 rOAT1-PAH > rename #27 rOAT1-PAH.mrc > view > fitmap #26 inMap #27 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map rOAT1-PAH.mrc (#27) using 3865 atoms average map value = 0.3441, steps = 44 shifted from previous position = 0.0131 rotated from previous position = 0.0158 degrees atoms outside contour = 699, contour level = 0.13428 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to rOAT1-PAH.mrc (#27) coordinates: Matrix rotation and translation 0.99999996 -0.00021122 0.00016567 0.00535685 0.00021123 0.99999998 -0.00006568 0.00053709 -0.00016566 0.00006571 0.99999998 -0.00148379 Axis 0.23771757 0.59945172 0.76429575 Axis point -1.23064203 24.84299856 0.00000000 Rotation angle (degrees) 0.01583428 Shift along axis 0.00046132 > hide #!2 models > color #27 white models > color #26 white > hide #!26 models > select subtract #27 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected > select subtract #26 Nothing selected > hide #!27 models > show #!26 models > select #26/B:601@C07 1 atom, 1 residue, 1 model selected > select up 23 atoms, 23 bonds, 1 residue, 1 model selected > color sel red > show #!27 models > color zone #27 near #26 distance 4.98 > color zone #27 near #26 distance 4.88 > color zone #27 near #26 distance 4.78 > color zone #27 near #26 distance 4.68 > color zone #27 near #26 distance 4.58 > color zone #27 near #26 distance 4.48 > color zone #27 near #26 distance 4.38 > color zone #27 near #26 distance 4.28 > color zone #27 near #26 distance 4.18 > color zone #27 near #26 distance 4.08 > color zone #27 near #26 distance 3.98 > color zone #27 near #26 distance 3.88 > color zone #27 near #26 distance 3.78 > color zone #27 near #26 distance 3.68 > color zone #27 near #26 distance 3.58 > color zone #27 near #26 distance 3.48 > color zone #27 near #26 distance 3.38 > color zone #27 near #26 distance 3.28 > color zone #27 near #26 distance 3.18 > color zone #27 near #26 distance 3.08 > color zone #27 near #26 distance 2.98 > color zone #27 near #26 distance 2.88 > color zone #27 near #26 distance 2.78 > color zone #27 near #26 distance 2.68 > color zone #27 near #26 distance 2.58 > color zone #27 near #26 distance 2.48 > color zone #27 near #26 distance 2.38 > color zone #27 near #26 distance 2.28 > volume #27 level 0.1207 > color zone #27 near #26 distance 2.18 > color zone #27 near #26 distance 2.08 > hide #!27 models > show #!27 models > fitmap #26 inMap #27 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map rOAT1-PAH.mrc (#27) using 3865 atoms average map value = 0.3441, steps = 44 shifted from previous position = 0.00509 rotated from previous position = 0.0145 degrees atoms outside contour = 605, contour level = 0.12073 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to rOAT1-PAH.mrc (#27) coordinates: Matrix rotation and translation 1.00000000 -0.00003177 0.00004592 0.00408484 0.00003177 1.00000000 0.00006809 -0.00110606 -0.00004592 -0.00006809 1.00000000 0.00040828 Axis -0.77323345 0.52146975 0.36080373 Axis point 0.00000000 25.00840435 -11.23310139 Rotation angle (degrees) 0.00504562 Shift along axis -0.00358800 > fitmap #26 inMap #27 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map rOAT1-PAH.mrc (#27) using 3865 atoms average map value = 0.3441, steps = 40 shifted from previous position = 0.0153 rotated from previous position = 0.0197 degrees atoms outside contour = 607, contour level = 0.12073 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to rOAT1-PAH.mrc (#27) coordinates: Matrix rotation and translation 0.99999998 -0.00017402 -0.00004728 0.01145050 0.00017401 0.99999996 -0.00023139 -0.00012574 0.00004732 0.00023138 0.99999997 -0.01696563 Axis 0.78875519 -0.16123857 0.59318410 Axis point 0.00000000 70.72803400 -1.26127659 Rotation angle (degrees) 0.01680827 Shift along axis -0.00101183 > volume splitbyzone #27 Opened rOAT1-PAH.mrc 0 as #28.1, grid size 160,160,160, pixel 0.83, shown at level 0.121, step 1, values float32 Opened rOAT1-PAH.mrc 1 as #28.2, 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 0.121, step 1, values float32 > close #28.1-2 > volume #28.3 level 0.05463 > color #28.3 white models > color #28.3 #ffffb2ff models > color #28.3 #ffffb296 models > select add #26 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected > color #26 #bf3434ff > select subtract #26 Nothing selected > hide #!26 models > hide #!28 models > hide #!28.3 models > show #!28 models > show #!28.3 models > hide #!28 models > show #!28 models > show #!26 models > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 59852, resource id: 35657337, major code: 40 (TranslateCoords), minor code: 0 > hide #!26 models > hide #!28 models > hide #!28.3 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220525_rOAT1-FBP/inward_j46_2.8A/postprocess.mrc Opened postprocess.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level 0.0068, step 2, values float32 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-FBP_model/rOAT1-FBP_Model04_RSR_004.pdb Chain information for rOAT1-FBP_Model04_RSR_004.pdb #30 --- Chain | Description A | No description available > show #!2 models > volume #29 step 1 > volume #29 level 0.01695 > select add #30 4327 atoms, 4393 bonds, 591 residues, 1 model selected > view matrix models #30,1,0,0,75.395,0,1,0,59.328,0,0,1,65.467 > view matrix models #30,1,0,0,69.37,0,1,0,69.752,0,0,1,66.8 > view matrix models #30,1,0,0,64.899,0,1,0,72.303,0,0,1,66.211 > view matrix models #30,1,0,0,67.675,0,1,0,68.154,0,0,1,64.823 > rename #29 rOAT1-FBP.mrc > fitmap #30 inMap #29 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29) using 4327 atoms average map value = 0.02366, steps = 64 shifted from previous position = 2.15 rotated from previous position = 1.57 degrees atoms outside contour = 1497, contour level = 0.016951 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc (#29) coordinates: Matrix rotation and translation 0.99965949 -0.01809184 -0.01880406 69.16631575 0.01825291 0.99979787 0.00842953 64.90387685 0.01864775 -0.00876989 0.99978765 65.39100171 Axis -0.31300664 -0.68157330 0.66142625 Axis point -4271.01743380 0.00000000 3378.83285764 Rotation angle (degrees) 1.57437238 Shift along axis -22.63494048 > fitmap #29 inMap #28.3 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points correlation = 0.04397, correlation about mean = 0.03331, overlap = 0.1449 steps = 2000, shift = 8.88, angle = 34.9 degrees Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3) coordinates: Matrix rotation and translation 0.83021101 -0.04922054 -0.55527201 36.70411652 0.13130357 0.98533433 0.10897540 -101.23145590 0.54176475 -0.16338178 0.82449824 -98.97434819 Axis -0.23793623 -0.95839145 0.15770918 Axis point 214.13564799 0.00000000 31.76591481 Rotation angle (degrees) 34.91302477 Shift along axis 72.67695975 > fitmap #29 inMap #28.3 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points correlation = 0.06352, correlation about mean = 0.0448, overlap = 0.3215 steps = 1976, shift = 9.79, angle = 47.5 degrees Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3) coordinates: Matrix rotation and translation 0.44591506 0.03168285 -0.89451437 128.47676238 -0.42572042 0.88660402 -0.18081879 31.25418163 0.78735118 0.46144286 0.40883812 -156.17744024 Axis 0.34576253 -0.90543486 -0.24624374 Axis point 186.53313716 0.00000000 6.98625710 Rotation angle (degrees) 68.24252592 Shift along axis 54.58154231 > fitmap #29 inMap #2 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points correlation = 0.2561, correlation about mean = 0.04268, overlap = 2.051 steps = 232, shift = 3.32, angle = 8.56 degrees Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: Matrix rotation and translation 0.54964589 -0.00012465 -0.83539774 175.75622877 -0.44507129 0.84621907 -0.29295875 119.06565669 0.70696602 0.53283512 0.46506536 -99.09845418 Axis 0.45744920 -0.85439368 -0.24647856 Axis point 210.95352936 0.00000000 94.96801349 Rotation angle (degrees) 64.50291620 Shift along axis 3.09624573 > select add #29 4327 atoms, 4393 bonds, 591 residues, 3 models selected > hide #!2 models > show #!2 models > hide #!2 models > show #!27 models > view matrix models > #29,0.54965,-0.00012465,-0.8354,176.85,-0.44507,0.84622,-0.29296,120.37,0.70697,0.53284,0.46507,-99.177,#30,0.99966,-0.018092,-0.018804,70.259,0.018253,0.9998,0.0084295,66.206,0.018648,-0.0087699,0.99979,65.312 > select subtract #30 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #29,0.93603,-0.13155,0.32642,-36.684,0.29946,0.78494,-0.54239,70.054,-0.18487,0.60545,0.77412,-40.4 > view matrix models > #29,0.99097,-0.1328,0.018694,4.0787,0.13411,0.98118,-0.13891,3.4116,0.00010362,0.14016,0.99013,-37.407 > ui mousemode right ""translate selected models"" > view matrix models > #29,0.99097,-0.1328,0.018694,17.811,0.13411,0.98118,-0.13891,8.06,0.00010362,0.14016,0.99013,-17.751 > view matrix models > #29,0.99097,-0.1328,0.018694,18.852,0.13411,0.98118,-0.13891,3.5023,0.00010362,0.14016,0.99013,-19.331 > fitmap #29 inMap #2 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points correlation = 0.937, correlation about mean = 0.7119, overlap = 14.98 steps = 260, shift = 2.93, angle = 16.7 degrees Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: Matrix rotation and translation 0.99338416 0.10541244 -0.04556454 -5.89234048 -0.10461957 0.99432199 0.01945563 14.33237930 0.04735669 -0.01455997 0.99877192 -4.89753719 Axis -0.14650897 -0.40022199 -0.90463113 Axis point 131.78683646 64.78395429 0.00000000 Rotation angle (degrees) 6.66633138 Shift along axis -0.44238796 > fitmap #30 inMap #29 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29) using 4327 atoms average map value = 0.02366, steps = 84 shifted from previous position = 1.18 rotated from previous position = 6.66 degrees atoms outside contour = 1496, contour level = 0.016951 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc (#29) coordinates: Matrix rotation and translation 0.99966027 -0.01808767 -0.01876641 69.16021058 0.01824668 0.99979876 0.00833662 64.90031908 0.01861185 -0.00867622 0.99978914 65.39198117 Axis -0.31026139 -0.68166338 0.66262576 Axis point -4271.35731029 0.00000000 3392.84555643 Rotation angle (degrees) 1.57107230 Shift along axis -22.36750269 > select subtract #29 Nothing selected > hide #!27 models > color #29 white models > color #30 white > select ::name=""FBP"" 18 atoms, 19 bonds, 1 residue, 1 model selected > color sel red > color zone #29 near #30 distance 4.98 > volume #29 level 0.01043 > volume splitbyzone #29 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at level 0.0104, step 1, values float32 Opened rOAT1-FBP.mrc 1 as #31.2, 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 0.0104, step 1, values float32 > close #31.1-2 > volume #31.3 level 0.002491 > volume #31.3 level 0.005476 > close #31#31.3 > show #!29 models > color zone #29 near #30 distance 2 [Repeated 1 time(s)] > volume splitbyzone #29 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at level 0.0104, step 1, values float32 Opened rOAT1-FBP.mrc 1 as #31.2, 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 0.0104, step 1, values float32 > close #31.1-2 > volume #31.3 level 0.003802 > color #31.3 white models > color #31.3 #ffffb2ff models > color #31.3 #ffffb20f models > color #31.3 #ffffb296 models > select add #30 4327 atoms, 4393 bonds, 591 residues, 1 model selected > color #30 #889944ff > color #30 #894a08ff > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > hide #!31.3 models > hide #!31 models > select subtract #30 Nothing selected > hide #30 models > show #!2 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220609_rOAT1-CFM/inward_j194_2.7A/postprocess.mrc Opened postprocess.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level 0.00396, step 2, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 4668, resource id: 35657387, major code: 40 (TranslateCoords), minor code: 0 > volume #32 step 1 > volume #32 level 0.01186 > rename #32 rOAT1-CFM.mrc > fitmap #31.3 inMap #32 Fit map rOAT1-FBP.mrc 2 in map rOAT1-CFM.mrc using 186 points correlation = 0.7788, correlation about mean = 0.1794, overlap = 0.008643 steps = 80, shift = 1.06, angle = 39.7 degrees Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-CFM.mrc (#32) coordinates: Matrix rotation and translation 0.74404465 0.65679786 0.12253212 -67.09990326 -0.66239846 0.70118044 0.26376935 89.56606533 0.08732602 -0.27742126 0.95677145 29.93219993 Axis -0.37942983 0.02468307 -0.92489121 Axis point 75.79903236 131.70903838 0.00000000 Rotation angle (degrees) 45.49284979 Shift along axis -0.01355792 > fitmap #31.3 inMap #2 Fit map rOAT1-FBP.mrc 2 in map rOAT1-AZT_IF.mrc using 186 points correlation = 0.8514, correlation about mean = 0.3895, overlap = 0.01295 steps = 76, shift = 0.987, angle = 35 degrees Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-AZT_IF.mrc (#2) coordinates: Matrix rotation and translation 0.98357109 0.17790518 -0.03062105 -15.98050765 -0.17592201 0.98266732 0.05844983 19.75924781 0.04048883 -0.05210265 0.99782061 1.12732183 Axis -0.29288928 -0.18839308 -0.93740275 Axis point 102.41456930 99.44616144 0.00000000 Rotation angle (degrees) 10.87852675 Shift along axis -0.09874061 > fitmap #32 inMap #2 Fit map rOAT1-CFM.mrc in map rOAT1-AZT_IF.mrc using 30016 points correlation = 0.9542, correlation about mean = 0.7898, overlap = 13.57 steps = 72, shift = 2.43, angle = 7.06 degrees Position of rOAT1-CFM.mrc (#32) relative to rOAT1-AZT_IF.mrc (#2) coordinates: Matrix rotation and translation 0.99240829 0.11776796 -0.03544703 -8.88787383 -0.11778889 0.99303752 0.00150464 18.44106769 0.03537743 0.00268205 0.99937042 -5.69387210 Axis 0.00478670 -0.28793162 -0.95763901 Axis point 151.76616064 85.25679566 0.00000000 Rotation angle (degrees) 7.06459913 Shift along axis 0.10036409 > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb > models #30 relModel #32 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb Chain information for rOAT1-CFM_IF.pdb #33 --- Chain | Description A | No description available > color #33 #ffff7fff > color #33 #55aaffff > select add #33 4327 atoms, 4393 bonds, 591 residues, 1 model selected > view matrix models #33,1,0,0,-3.2206,0,1,0,10.827,0,0,1,-3.1224 > view matrix models #33,1,0,0,-4.4307,0,1,0,11.668,0,0,1,-3.5924 > view matrix models #33,1,0,0,-4.3326,0,1,0,9.3726,0,0,1,-2.8036 > fitmap #33 inMap #32 Fit molecule rOAT1-CFM_IF.pdb (#33) to map rOAT1-CFM.mrc (#32) using 4327 atoms average map value = 0.0191, steps = 80 shifted from previous position = 1.1 rotated from previous position = 7.12 degrees atoms outside contour = 1362, contour level = 0.01186 Position of rOAT1-CFM_IF.pdb (#33) relative to rOAT1-CFM.mrc (#32) coordinates: Matrix rotation and translation 0.99999299 -0.00023005 -0.00373680 -4.70643521 0.00021365 0.99999035 -0.00438786 8.58155234 0.00373777 0.00438703 0.99998339 -3.97966882 Axis 0.76069466 -0.64796926 0.03846397 Axis point 0.00000000 827.85989235 581.48051316 Rotation angle (degrees) 0.33046593 Shift along axis -9.29381608 > save /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM.pdb > models #33 relModel #32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 60371, resource id: 35657459, major code: 40 (TranslateCoords), minor code: 0 > hide #33 models > hide #!32 models > select subtract #33 Nothing selected > show #!17 models > hide #!17 models > show #!17 models > hide #!2 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV- > Cl_OF-coot-2.pdb Chain information for rOAT1-TFV-Cl_OF-coot-2.pdb #34 --- Chain | Description A | No description available > select ::name=""CL"" 1 atom, 1 residue, 1 model selected > hide #!17 models > show sel atoms > show #!17 models > style sel stick Changed 1 atom style > color zone #17 near #34 distance 2.98 > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected > color #34 white > color zone #17 near #34 distance 2.98 > select ::name=""CL"" 1 atom, 1 residue, 1 model selected > color sel red > color zone #17 near #34 distance 2.98 > volume splitbyzone #17 Opened rOAT1-TVF_OF.mrc 0 as #35.1, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 1 as #35.2, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 > rename #35 ""rOAT1-TVF-Cl_OF.mrc split"" > close #35.1-2 > rename #35.3 ""rOAT1-TVF-Cl_OF.mrc 2"" > hide #!35.3 models > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > ui tool show Contacts > contacts sel interModel false ignoreHiddenModels true select true 6 contacts > ui tool show Contacts > contacts sel intraRes true ignoreHiddenModels true select true 15 contacts > show sel atoms > color #34 yellow > show sel atoms > close #36 > select add #34 3787 atoms, 3876 bonds, 11 pseudobonds, 487 residues, 3 models selected > color #34 white > hide sel atoms > select ::name=""CL"" 1 atom, 1 residue, 1 model selected > show sel atoms > hide #35.3.1 models > show #35.3.1 models > close #34.2 > hide #!35.3 models > hide #35.3.1 models > hide #!35 models > hide #34.1 models > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > select #34/A:216 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #34/A:511 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #34: 219 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #34: 273 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #34/A:4 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select add #34/A:511 15 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > select add #34/A:512 23 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > color sel lime > color #35.3.1 white > color #35.3.1 #ffffb2ff > color #35.3.1 #ffffb296 > 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 > color #34 #374c02ff > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > color sel lime > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected > color (#!34 & sel) byhetero > select #34/A:2 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select #34/A:3 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select add #34/A:215 18 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > show #35.3.1 models > view sel > hide #35.3.1 models > hide #!35.3 models > hide #!35 models > hide #!34 models > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected > select subtract #34 Nothing selected > show #1 models > view > hide #1 models > show #21 models > select add #21/A:602@C12 1 atom, 1 residue, 1 model selected > select up 3 atoms, 1 bond, 2 residues, 1 model selected > select up 44 atoms, 46 bonds, 2 residues, 1 model selected > select clear > select #21/A:602@O14 1 atom, 1 residue, 1 model selected > select add #21/A:601@C04 2 atoms, 2 residues, 1 model selected > select up 70 atoms, 76 bonds, 2 residues, 1 model selected > view sel > show #!22.3 models > hide #!22.3 models > hide #!22 models > hide #21 models > select add #21 3956 atoms, 4042 bonds, 516 residues, 1 model selected > select subtract #21 Nothing selected > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 40781, resource id: 35657669, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/postprocess.mrc Opened postprocess.mrc as #36, grid size 320,320,320, pixel 0.83, shown at level 0.00418, step 2, values float32 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for solute carrier family 22 member 6 (Q4U2R8) [more info...] Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #37 --- Chain | Description | UniProt A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 > rename #36 hOAT1-TFV.mrc > volume #36 step 1 > volume #36 level 0.008515 > rename #37 hOAT1-TFV_IF.pdb > view > show #!2 models > hide #!2 models > ui tool show Matchmaker > matchmaker #37 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A (#37), sequence alignment score = 2359.6 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs: 0.862) > matchmaker #37 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A (#37), sequence alignment score = 2359.6 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs: 0.862) > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1-TVF_IF.pdb > models #37 relModel #36 > rename #36 hOAT1-TFV_IF.mrc > hide #37 models > hide #!36 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for solute carrier family 22 member 6 (Q4U2R8) [more info...] Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #38 --- Chain | Description | UniProt A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 > close #38 > close #37 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/RealSpaceRefine_2/hOAT1-TVF_IF- > coot-1_real_space_refined_002.pdb Chain information for hOAT1-TVF_IF-coot-1_real_space_refined_002.pdb #37 --- Chain | Description A | No description available > show #!36 models > color #36 white models > color #37 white > hide #!36 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select #37/A:601@C08 1 atom, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > show #!36 models > color zone #36 near #37 distance 4.98 > color zone #36 near #37 distance 2 [Repeated 1 time(s)] > color zone #36 near #37 distance 1.9 > color zone #36 near #37 distance 1.8 > color zone #36 near #37 distance 1.7 > volume splitbyzone #36 Opened hOAT1-TFV_IF.mrc 0 as #38.1, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 Opened hOAT1-TFV_IF.mrc 1 as #38.2, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 > close #38.1-2 > color #38.3 white models > color #38.3 #ffffb2ff models > color #38.3 #ffffb296 models > color #37 #aaff7fff > select add #37 4375 atoms, 4481 bonds, 564 residues, 1 model selected > color sel byhetero > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 48690, resource id: 35657985, major code: 40 (TranslateCoords), minor code: 0 > hide #!38.3 models > hide #!38 models > select subtract #37 Nothing selected > show #!34 models Drag select of 25 atoms, 383 residues, 24 bonds > select up 2906 atoms, 2958 bonds, 383 residues, 2 models selected > select clear > select add #37/A:326 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > hide #!34 models > select add #37 4375 atoms, 4481 bonds, 564 residues, 1 model selected > select subtract #37 Nothing selected > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb > models #37 relModel #36 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16970, resource id: 35658005, major code: 40 (TranslateCoords), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16981, resource id: 35657995, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/outward_j68_3.1A/postprocess.mrc Opened postprocess.mrc as #39, grid size 320,320,320, pixel 0.83, shown at level 0.00436, step 2, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 18302, resource id: 35658010, major code: 40 (TranslateCoords), minor code: 0 > rename #39 hOAT1-TFV_OF.mrc > volume #39 step 1 > volume #39 level 0.01031 > hide #!39 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb Chain information for hOAT1-TFV_OF.pdb #40 --- Chain | Description A | No description available > hide #37 models > select #40: 320-600 1850 atoms, 1888 bonds, 244 residues, 1 model selected > hide sel cartoons [Repeated 1 time(s)] > show sel cartoons > ui tool show Matchmaker > matchmaker #40 & sel to #18 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb, chain A (#18) with hOAT1-TFV_OF.pdb, chain A (#40), sequence alignment score = 866.1 RMSD between 164 pruned atom pairs is 0.748 angstroms; (across all 200 pairs: 7.198) > matchmaker #40 to #15 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rOAT1-TFV_IF-coot-3.pdb, chain A (#15) with hOAT1-TFV_OF.pdb, chain A (#40), sequence alignment score = 2368.6 RMSD between 493 pruned atom pairs is 0.665 angstroms; (across all 500 pairs: 0.719) > show #!18 models > ui mousemode right ""translate selected atoms"" > ui mousemode right ""rotate selected models"" > view matrix models > #40,0.99727,-0.025813,-0.069217,13.221,0.025375,0.99965,-0.0072002,-1.7643,0.069379,0.0054242,0.99758,-8.8122 > undo > ui mousemode right ""move picked models"" > view matrix models #18,1,0,0,0.019269,0,1,0,-0.04277,0,0,1,0.28987 > undo > ui mousemode right pivot > ui tool show Matchmaker > matchmaker #40 & sel to #5 & sel No 'to' model specified > select clear > hide #!18 models > show #!18 models > select #18,40: 320-600 3274 atoms, 3340 bonds, 2 pseudobonds, 433 residues, 3 models selected > ui tool show Matchmaker > matchmaker #40 & sel to #5 & sel No 'to' model specified > matchmaker #40 & sel to #5 & sel No 'to' model specified > matchmaker #40 & sel to #5 & sel No 'to' model specified > ui mousemode right ""translate selected atoms"" > select #40: 320-600 1850 atoms, 1888 bonds, 244 residues, 1 model selected > hide #!18 models > show #!18 models > hide #40 models > hide #!18 models > show #40 models > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb > models #40 relModel #39 QXcbConnection: XCB error: 3 (BadWindow), sequence: 34583, resource id: 35658147, major code: 40 (TranslateCoords), minor code: 0 > fitmap #40 inMap #39 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375 atoms average map value = 0.007219, steps = 88 shifted from previous position = 0.909 rotated from previous position = 8.49 degrees atoms outside contour = 2887, contour level = 0.010308 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39) coordinates: Matrix rotation and translation 0.99019825 -0.07829950 -0.11565728 27.38037598 0.07892080 0.99688057 0.00079533 -10.70816731 0.11523422 -0.00991530 0.99328886 -13.08861468 Axis -0.03831490 -0.82596303 0.56242070 Axis point 128.86145300 0.00000000 225.96021530 Rotation angle (degrees) 8.03460025 Shift along axis 0.43416611 > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb > models #40 relModel #39 > undo > select clear > show #!39 models > fitmap #40 inMap #39 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375 atoms average map value = 0.007218, steps = 28 shifted from previous position = 0.0175 rotated from previous position = 0.016 degrees atoms outside contour = 2888, contour level = 0.010308 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39) coordinates: Matrix rotation and translation 0.99020256 -0.07845145 -0.11551732 27.36683659 0.07909202 0.99686685 0.00096497 -10.76110579 0.11507968 -0.01009202 0.99330500 -13.04322773 Axis -0.03956067 -0.82505023 0.56367284 Axis point 128.67057833 0.00000000 226.14572082 Rotation angle (degrees) 8.03322105 Shift along axis 0.44368911 > fitmap #40 inMap #39 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375 atoms average map value = 0.007219, steps = 44 shifted from previous position = 0.00455 rotated from previous position = 0.00258 degrees atoms outside contour = 2889, contour level = 0.010308 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39) coordinates: Matrix rotation and translation 0.99020340 -0.07846932 -0.11549800 27.37049731 0.07911379 0.99686509 0.00099928 -10.76639922 0.11505751 -0.01012698 0.99330721 -13.03687370 Axis -0.03980982 -0.82492871 0.56383314 Axis point 128.62890621 0.00000000 226.21984207 Rotation angle (degrees) 8.03295687 Shift along axis 0.44127588 > select add #40 4375 atoms, 4481 bonds, 564 residues, 1 model selected > fitmap #40 inMap #39 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375 atoms average map value = 0.007219, steps = 60 shifted from previous position = 2.24 rotated from previous position = 0.00666 degrees atoms outside contour = 2889, contour level = 0.010308 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39) coordinates: Matrix rotation and translation 0.99020164 -0.07840067 -0.11555975 25.97288245 0.07903810 0.99687116 0.00093711 -9.32824593 0.11512471 -0.01006155 0.99330009 -12.03377088 Axis -0.03935047 -0.82533103 0.56327634 Axis point 116.53468443 0.00000000 214.84157931 Rotation angle (degrees) 8.03353574 Shift along axis -0.10149276 > show #!17 models > fitmap #39 inMap #19.3 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points correlation = 0.03002, correlation about mean = -0.02439, overlap = 0.01206 steps = 936, shift = 1.08, angle = 13.4 degrees Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3) coordinates: Matrix rotation and translation 0.98280665 -0.13043667 -0.13068041 37.39205996 0.11063752 0.98266445 -0.14876125 8.18112237 0.14781892 0.13174539 0.98020035 -34.01816129 Axis 0.60585490 -0.60151939 0.52068635 Axis point 0.00000000 261.98069292 24.54762139 Rotation angle (degrees) 13.38519605 Shift along axis 0.02026683 > fitmap #39 inMap #19.3 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points correlation = 0.03002, correlation about mean = -0.0244, overlap = 0.01206 steps = 48, shift = 0.0138, angle = 0.161 degrees Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3) coordinates: Matrix rotation and translation 0.98301413 -0.12857767 -0.13096186 37.15798588 0.10847145 0.98263409 -0.15054633 8.70610140 0.14804449 0.13378355 0.97989019 -34.26954280 Axis 0.61337235 -0.60188813 0.51137563 Axis point -0.00000000 260.45263984 27.89398858 Rotation angle (degrees) 13.40165031 Shift along axis 0.02697294 > fitmap #40 inMap #39 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375 atoms average map value = 0.007219, steps = 132 shifted from previous position = 0.778 rotated from previous position = 13.4 degrees atoms outside contour = 2889, contour level = 0.010308 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39) coordinates: Matrix rotation and translation 0.99020454 -0.07852899 -0.11544767 25.97319443 0.07917768 0.99685998 0.00103677 -9.35919916 0.11500374 -0.01016749 0.99331302 -12.00484753 Axis -0.04009077 -0.82459474 0.56430155 Axis point 116.41047661 0.00000000 215.06686153 Rotation angle (degrees) 8.03257950 Shift along axis -0.09809308 > hide #!17 models > hide #!39 models > close #40 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF- > coot-1.pdb Chain information for hOAT1-TFV_OF-coot-1.pdb #40 --- Chain | Description A | No description available > show #!39 models > color #39 white models > color #40 white > hide #!39 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > color sel red > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > show #!39 models > color zone #39 near #40 distance 4.98 > color zone #39 near #40 distance 2 [Repeated 1 time(s)] > volume #39 level 0.01241 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF- > coot-2.pdb Chain information for hOAT1-TFV_OF-coot-2.pdb #41 --- Chain | Description A | No description available > hide #!40 models > color #41 white > color zone #39 near #41 distance 2 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > color zone #39 near #41 distance 2 > volume #39 level 0.01056 > color zone #39 near #41 distance 2.1 > color zone #39 near #41 distance 2.2 > color zone #39 near #41 distance 2.3 > color zone #39 near #41 distance 2.4 > color zone #39 near #41 distance 2.5 > color zone #39 near #41 distance 2.6 > color zone #39 near #41 distance 2.7 > color zone #39 near #41 distance 2.8 > color zone #39 near #41 distance 2.9 > color zone #39 near #41 distance 3 > color zone #39 near #41 distance 2.9 > color zone #39 near #41 distance 2.8 > color zone #39 near #41 distance 2.7 > color zone #39 near #41 distance 2.6 > color zone #39 near #41 distance 2.5 > color zone #39 near #41 distance 2.4 > color zone #39 near #41 distance 2.3 > color zone #39 near #41 distance 2.2 > color zone #39 near #41 distance 2.1 > color zone #39 near #41 distance 2 > color zone #39 near #41 distance 1.9 > color zone #39 near #41 distance 2 > color zone #39 near #41 distance 2.1 > color zone #39 near #41 distance 2.2 > color zone #39 near #41 distance 2.3 > color zone #39 near #41 distance 2.4 > color zone #39 near #41 distance 2.5 > volume splitbyzone #39 Opened hOAT1-TFV_OF.mrc 0 as #42.1, grid size 320,320,320, pixel 0.83, shown at level 0.0106, step 1, values float32 Opened hOAT1-TFV_OF.mrc 1 as #42.2, grid size 320,320,320, pixel 0.83, shown at level 0.0106, step 1, values float32 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown at level 0.0106, step 1, values float32 > close #42.1-2 > color #42.3 white models > color #42.3 #ffffb2ff models > color #42.3 #ffffb296 models > volume #42.3 level 0.006989 > select add #41 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected > color #41 #aaffffff > color #41 blue > color #41 red > color #41 #aa00ffff > color #41 #0055ffff > color #41 #55557fff > color #41 #ff557fff > color #41 #ffaaffff > color (#!41 & sel) byhetero > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > show #!34 models > hide #!41 models > hide #!42 models > hide #!42.3 models > select subtract #41 Nothing selected > hide #!34 models > show #1 models > show #!3.3 models > hide #!3.3 models > hide #!3 models > hide #1 models > show #!22.3 models > show #21 models > select add #21/A:601@O25 1 atom, 1 bond, 1 residue, 1 model selected > select up 3 atoms, 1 bond, 2 residues, 1 model selected > view sel > volume #22.3 level 0.01409 > hide #!22.3 models > hide #!22 models > hide #21 models > show #!22.3 models > hide #!22.3 models > hide #!22 models > show #!23 models > hide #!23 models > show #!25.3 models > show #!24 models > hide #!25.3 models > hide #!25 models > hide #!24 models > show #1 models > show #!3.3 models > hide #!3.3 models > hide #!3 models > hide #1 models > show #!5 models > show #!6.3 models > hide #!6.3 models > hide #!6 models > hide #!5 models > show #8 models > show #!9.3 models > volume #9.3 level 0.003826 > select #8/A:230 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #8/A:227 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select clear > hide #!9.3 models > hide #!9 models > hide #8 models > show #!12 models > show #!11.3 models > color #11.3 #ffffb296 models > hide #!12 models > hide #!11.3 models > hide #!11 models > show #15 models > show #!16.3 models > hide #!16.3 models > hide #!16 models > hide #15 models > show #!18 models > show #!19.3 models > hide #!18 models > hide #!19 models > hide #!19.3 models > show #37 models > show #!38.3 models > hide #!38.3 models > hide #!38 models > hide #37 models > close #40 > show #!41 models > show #!42.3 models > hide #!42.3 models > hide #!42 models > hide #!41 models > show #!26 models > show #!28.3 models > select #26/A:230 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:200 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select add #26 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected > color (#!26 & sel) byhetero > select clear > select #26/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:227 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:200 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:226 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:204 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > hide #!28.3 models > hide #!28 models > hide #!26 models > show #!31.3 models > show #30 models > select add #30 4327 atoms, 4393 bonds, 591 residues, 1 model selected > color sel byhetero > select clear > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true ——— End of log from Mon Feb 10 17:46:10 2025 ——— opened ChimeraX session > hide #!31.3 models > hide #!31 models > hide #30 models > show #!34 models > show #!35 models > show #!35.3 models > volume #35.3 level 0.01175 > select #35.3 2 models selected > view sel > color #34 tan > ui tool show ""Side View"" > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 4 models selected > color (#!34 & sel) byhetero > select clear > select #34/A:447 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #34/A:507 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true ——— End of log from Tue Mar 11 12:00:09 2025 ——— opened ChimeraX session > hide #!35.3 models > hide #!35 models > show #!17 models > color #17 #ffffb2ff models > color #17 #ffffb280 models > ui tool show ""Side View"" > color #17 #ffffb24d models > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true ——— End of log from Thu Apr 10 14:06:06 2025 ——— opened ChimeraX session > movie record > turn y 2 180 > wait 180 > movie encode /Users/dout2/Desktop/movie1.mp4 Movie saved to /Users/dout2/Desktop/movie1.mp4 > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected > show sel atoms > select clear > hide #!34 models > hide #!17 models > show #!6 models > show #1 models > view > select #1/A:463 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:466 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:228 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:230 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:231 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:377 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:381 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:225 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:382 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide #!6 models > show #!6 models > hide #1 models > show #1 models > select add #1 3905 atoms, 3986 bonds, 515 residues, 1 model selected > select subtract #1 Nothing selected > hide #1 models > hide #!6 models > show #!18 models > hide #!18 models > show #1 models > select #1/A:228 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:199 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:257 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:145 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:466 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A:149 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:146 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:204 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:150 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:149 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:203 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:146 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:149 5 atoms, 4 bonds, 1 residue, 1 model selected Drag select of 13 residues > select #1/A:463 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A:466@CZ 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Contacts > contacts sel intraRes true ignoreHiddenModels true select true > makePseudobonds false reveal true 26 contacts > select clear > select : 382 126 atoms, 112 bonds, 14 residues, 14 models selected > select : 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 & #1 atoms > hide #!6 target m [Repeated 1 time(s)] > hide #!4 target m > select add #1 5716 atoms, 5702 bonds, 714 residues, 14 models selected > select subtract #1 1811 atoms, 1716 bonds, 199 residues, 13 models selected > select add #5 5446 atoms, 5448 bonds, 5 pseudobonds, 670 residues, 14 models selected > select subtract #5 1672 atoms, 1584 bonds, 184 residues, 12 models selected > select add #8 5445 atoms, 5437 bonds, 691 residues, 12 models selected > select subtract #8 1533 atoms, 1452 bonds, 169 residues, 11 models selected > select add #12 5186 atoms, 5201 bonds, 5 pseudobonds, 640 residues, 12 models selected > select subtract #12 1394 atoms, 1320 bonds, 154 residues, 10 models selected > hide #1 models > show #1 models > select add #15 5172 atoms, 5186 bonds, 654 residues, 10 models selected > select subtract #15 1255 atoms, 1188 bonds, 139 residues, 9 models selected > select add #18 4902 atoms, 4932 bonds, 5 pseudobonds, 610 residues, 10 models selected > select subtract #18 1116 atoms, 1056 bonds, 124 residues, 8 models selected > select add #21 4933 atoms, 4966 bonds, 625 residues, 8 models selected > select subtract #21 977 atoms, 924 bonds, 109 residues, 7 models selected > select add #24 4628 atoms, 4674 bonds, 5 pseudobonds, 580 residues, 8 models selected > select subtract #24 838 atoms, 792 bonds, 94 residues, 6 models selected > select add #26 4564 atoms, 4607 bonds, 1 pseudobond, 585 residues, 7 models selected > select subtract #26 699 atoms, 660 bonds, 79 residues, 5 models selected > select add #30 4885 atoms, 4921 bonds, 653 residues, 5 models selected > select subtract #30 558 atoms, 528 bonds, 62 residues, 4 models selected > select add #33 4744 atoms, 4789 bonds, 636 residues, 4 models selected > select subtract #33 417 atoms, 396 bonds, 45 residues, 3 models selected > select add #34 4065 atoms, 4140 bonds, 5 pseudobonds, 517 residues, 4 models selected > select subtract #34 278 atoms, 264 bonds, 30 residues, 2 models selected > select add #37 4514 atoms, 4613 bonds, 579 residues, 2 models selected > select subtract #37 139 atoms, 132 bonds, 15 residues, 1 model selected > select add #41 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected > select subtract #41 Nothing selected > show #!2 models > hide #!2 models > show #!3 models > show #!3.3 models > ui tool show ""Side View"" > select #1/A:35@CG 1 atom, 1 residue, 1 model selected > select : 35 112 atoms, 98 bonds, 14 residues, 14 models selected > hide sel & #1 atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select : 35 112 atoms, 98 bonds, 14 residues, 14 models selected > show sel & #1 atoms > select clear > select : 35 112 atoms, 98 bonds, 14 residues, 14 models selected > hide sel & #1 atoms > save /Users/dout2/Desktop/image1.png supersample 3 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3 > select add #1 4009 atoms, 4077 bonds, 528 residues, 14 models selected > select subtract #1 104 atoms, 91 bonds, 13 residues, 13 models selected > select add #5 3870 atoms, 3948 bonds, 5 pseudobonds, 498 residues, 14 models selected > select subtract #5 96 atoms, 84 bonds, 12 residues, 12 models selected > select add #8 4000 atoms, 4062 bonds, 533 residues, 12 models selected > select subtract #8 88 atoms, 77 bonds, 11 residues, 11 models selected > select add #12 3872 atoms, 3951 bonds, 5 pseudobonds, 496 residues, 12 models selected > select subtract #12 80 atoms, 70 bonds, 10 residues, 10 models selected > select add #21 4028 atoms, 4105 bonds, 525 residues, 10 models selected > select subtract #21 72 atoms, 63 bonds, 9 residues, 9 models selected > select add #18 3850 atoms, 3932 bonds, 5 pseudobonds, 494 residues, 10 models selected > select subtract #18 64 atoms, 56 bonds, 8 residues, 8 models selected > select add #24 3846 atoms, 3931 bonds, 5 pseudobonds, 493 residues, 9 models selected > select subtract #24 56 atoms, 49 bonds, 7 residues, 7 models selected > select add #26 3913 atoms, 3989 bonds, 1 pseudobond, 512 residues, 8 models selected > select subtract #26 48 atoms, 42 bonds, 6 residues, 6 models selected > select add #30 4367 atoms, 4428 bonds, 596 residues, 6 models selected > select subtract #30 40 atoms, 35 bonds, 5 residues, 5 models selected > select add #33 4359 atoms, 4421 bonds, 595 residues, 5 models selected > select subtract #33 32 atoms, 28 bonds, 4 residues, 4 models selected > select add #34 3811 atoms, 3897 bonds, 5 pseudobonds, 490 residues, 5 models selected > select subtract #34 24 atoms, 21 bonds, 3 residues, 3 models selected > select add #37 4391 atoms, 4495 bonds, 566 residues, 3 models selected > select subtract #37 16 atoms, 14 bonds, 2 residues, 2 models selected > select add #41 4383 atoms, 4488 bonds, 1 pseudobond, 565 residues, 3 models selected > select subtract #41 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #!3.3 models > hide #!3 models > hide #1 models > show #!5 models > show #!6.3 models > hide #!6.3 models > hide #!6 models > hide #!5 models > show #8 models > show #!9 models > show #!9.3 models > select : 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 & #8 atoms > select: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234 Unknown command: select: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234 > select : 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 & #8 atoms > 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 & #8 atoms > select clear > volume #9.3 level 0.00516 > save /Users/dout2/Desktop/rOAT1-PBD_IF_LigandDensity.png supersample 3 > hide #!9.3 models > hide #!9 models > hide #8 models > show #15 models > show #!16 models > show #!16.3 models > select #15/A:442 11 atoms, 11 bonds, 1 residue, 1 model selected > 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 & #15 atoms > select #1-50: 438 154 atoms, 154 bonds, 14 residues, 14 models selected > select clear > save /Users/dout2/Desktop/rOAT1-TFV_IF_LigandDensity.png supersample 3 > hide #!16.3 models > hide #!16 models > hide #15 models > show #21 models > show #!22 models > show #!22.3 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 & #21 atoms > select clear > save /Users/dout2/Desktop/rOAT1-AAI_IF_LigandDensity.png supersample 3 > volume #22.3 level 0.0128 > hide #!22.3 models > hide #!22 models > hide #21 models > show #!27 models > show #!28 models > hide #!27 models > show #!26 models > show #!28.3 models > volume #28.3 level 0.06828 > 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 & #!26 atoms > select clear > save /Users/dout2/Desktop/rOAT1-PAH_IF_LigandDensity.png supersample 3 > hide #!28.3 models > hide #!28 models > hide #!26 models > show #30 models > show #!31 models > show #!31.3 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 & #30 atoms > select clear > save /Users/dout2/Desktop/rOAT1-FBP_IF_LigandDensity.png supersample 3 > hide #!31.3 models > hide #!31 models > hide #30 models > show #37 models > show #!38 models > show #!38.3 models > select clear > 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 & #37 atoms > select clear > show #!36 models > hide #!36 models > show #!36 models > hide #!36 models > volume #38.3 level 0.006101 > volume #38.3 level 0.006864 > save /Users/dout2/Desktop/hOAT1-TFV_IF_LigandDensity.png supersample 3 > hide #!38.3 models > hide #!38 models > hide #37 models > show #!2 models > hide #!2 models > show #1 models > show #!3 models > show #!3.3 models > hide #!3.3 models > hide #!3 models > hide #1 models > show #!5 models > show #!6.3 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 & #!5 atoms > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select clear [Repeated 1 time(s)] > 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 & #!5 atoms > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > hide sel atoms > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > volume #6.3 level 0.0106 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3 > hide #!5 models > hide #!6 models > hide #!6.3 models > show #!11 models > show #!12 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 & #!12 atoms > select clear > show #!11.3 models > select clear > volume #11.3 level 0.009777 > 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 > 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 > 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 > 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 > close session > open /Users/dout2/Downloads/OAT1_ligand_Keyresidue.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 opened ChimeraX session > hide #15 models > select subtract #15 Nothing selected > show #!49 models > hide #49.1 models > select #49: 382, 353,438,230,442,466,207,601,602 74 atoms, 71 bonds, 7 residues, 1 model selected > show sel atoms > select add #49 3942 atoms, 3966 bonds, 570 residues, 2 models selected > hide sel cartoons > select clear > size stickRadius 0.4 Changed 77114 bond radii > select add #49 3942 atoms, 3966 bonds, 570 residues, 1 model selected > show sel cartoons > hide sel cartoons > show sel atoms > hide sel atoms > show sel cartoons > select #49: 382, 353,438,230,442,466,207,601,602 74 atoms, 71 bonds, 7 residues, 1 model selected > show sel atoms > view > hide sel cartoons > select add #49 3942 atoms, 3966 bonds, 570 residues, 2 models selected > hide sel cartoons > color (#!49 & sel) purple > select clear > select add #49 3942 atoms, 3966 bonds, 570 residues, 1 model selected > show sel cartoons > select #49/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select #49: 382, 353,438,230,442,466,207,601,602,203 79 atoms, 75 bonds, 8 residues, 1 model selected > hide sel cartoons > select add #49 3942 atoms, 3966 bonds, 570 residues, 2 models selected > hide sel cartoons > select #49/A:223@CA 1 atom, 1 residue, 1 model selected > select up 4 atoms, 3 bonds, 1 residue, 2 models selected > hide sel atoms > select add #49 3942 atoms, 3966 bonds, 570 residues, 2 models selected > show sel cartoons > select #49/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > select #49/A:224 7 atoms, 6 bonds, 1 residue, 1 model selected > select #49/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel cartoons > select add #49 3942 atoms, 3966 bonds, 570 residues, 2 models selected > hide sel cartoons > select #49/A:382@NZ 1 atom, 1 residue, 1 model selected > select add #49/A:466@NH2 2 atoms, 2 residues, 2 models selected > select add #49/A:466@NH1 3 atoms, 2 residues, 2 models selected > select add #49/A:466@NE 4 atoms, 2 residues, 2 models selected > color (#!49 & sel) byhetero > select clear > save /Users/dout2/Desktop/rOAT1-Apo_residues.png supersample 3 > transparentBackground true > select clear > save /Users/dout2/Desktop/rOAT1-Apo_residues.png supersample 3 > transparentBackground true > hide #!49 models > show #!51 models > view > show #!51 atoms > select add #51 4280 atoms, 4381 bonds, 552 residues, 1 model selected > undo > select add #51 4280 atoms, 4381 bonds, 552 residues, 1 model selected > show sel atoms > select #51/A:207@CE 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 2 models selected > undo > show sel cartoons > select #51/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > select #51/A:208 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select #51/A:211 7 atoms, 6 bonds, 1 residue, 1 model selected > select #51/A:207 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color (#!51 & sel) purple > select #51: 382, 353,438,230,442,466,207,601,602,203 79 atoms, 75 bonds, 8 residues, 1 model selected > select add #51 4280 atoms, 4381 bonds, 552 residues, 2 models selected > hide sel cartoons > select clear > save /Users/dout2/Desktop/rOAT1-AKG_IF_residues.png supersample 3 > transparentBackground true > save /Users/dout2/Downloads/OAT1_ligand_Keyresidue.cxs includeMaps true > hide #!51 models > show #!43 models > view > select #43: 382, 353,438,230,442,466,207,601,602 84 atoms, 80 bonds, 8 residues, 1 model selected > show sel atoms > select clear > select #43/A:207@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 2 models selected > color (#!43 & sel) purple > select clear > save /Users/dout2/Desktop/rOAT1-AKG_OF_residues.png supersample 3 > transparentBackground true > hide #!43 models > show #!18 models > select #18: 382, 353,438,230,442,466,207,601,602 105 atoms, 103 bonds, 8 residues, 1 model selected > show sel atoms > select clear > select #18/A:601@C05 1 atom, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > hide sel atoms > select #18/A:207@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 2 models selected > color (#!18 & sel) purple > select clear > save /Users/dout2/Desktop/rOAT1-Apo_OF_residues.png supersample 3 > transparentBackground true > select #18: 382, 353,438,230,442,466,207,601,602 105 atoms, 103 bonds, 8 residues, 1 model selected > show sel atoms > select #18/A:601@C05 1 atom, 1 residue, 1 model selected > select #18/A:601@H051 1 atom, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > select H 117 atoms, 10 residues, 9 models selected > hide sel & #!18 atoms > select clear > save /Users/dout2/Desktop/rOAT1-TFV_OF_residues.png supersample 3 > transparentBackground true > hide #!18 models > show #15 models > select #15: 382, 353,438,230,442,466,207,601,602 105 atoms, 103 bonds, 8 residues, 1 model selected > show sel atoms > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > hide sel cartoons > select clear > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > hide sel atoms > select #15: 382, 353,438,230,442,466,207,601,602 105 atoms, 103 bonds, 8 residues, 1 model selected > show sel atoms > select #15/A:601@C07 1 atom, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > select H 117 atoms, 10 residues, 9 models selected > hide sel & #15 atoms > select clear > select #15/A:601@O19 1 atom, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > select up 3903 atoms, 3998 bonds, 501 residues, 1 model selected > select down 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > select #15: 382, 353,438,230,442,466,207 74 atoms, 71 bonds, 7 residues, 1 model selected > color sel purple > select clear > select #15/A:382@NZ 1 atom, 1 residue, 1 model selected > select add #15/A:466@NH2 2 atoms, 2 residues, 1 model selected > select add #15/A:466@NH1 3 atoms, 2 residues, 1 model selected > select add #15/A:466@NE 4 atoms, 2 residues, 1 model selected > color sel byhetero > select clear > select #15/A:601@N13 1 atom, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel cyan > color sel byhetero > select clear > save /Users/dout2/Desktop/rOAT1-TFV_IF_residues.png supersample 3 > transparentBackground true > save /Users/dout2/Downloads/OAT1_ligand_Keyresidue.cxs includeMaps true > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > show sel cartoons > select #15/A:227 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select #15/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > hide sel cartoons > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > hide sel cartoons > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 4 atoms, 3 bonds, 1 residue, 1 model selected > hide sel atoms > undo > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > show sel cartoons > select #15/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > select clear > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > hide sel cartoons > show sel cartoons > select #15/A:203 5 atoms, 4 bonds, 1 residue, 1 model selected > select #15/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > hide sel cartoons > select clear ===== Log before crash end ===== Log: 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 ) > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/RealSpaceRefine_6/mOCT1-VB1-coot-11_real_space_refined_006.pdb Chain information for mOCT1-VB1-coot-11_real_space_refined_006.pdb #4 --- Chain | Description A | No description available > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_real_space_refined_014.pdb Chain information for mOCT1-VB1_real_space_refined_014.pdb #5 --- Chain | Description A | No description available > close #3#4 > volume #2 color #ffffb296 > volume #2 color #ffffb2c8 > volume #2 level 0.4304 > volume #2 level 0.3677 > select /A:601@C15 1 atom, 1 residue, 1 model selected > select up 18 atoms, 19 bonds, 1 residue, 1 model selected > view sel > select clear > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_Model/mOCT1-ABC_real_space_refined_009.pdb Chain information for mOCT1-ABC_real_space_refined_009.pdb #3 --- Chain | Description A | No description available > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_20220411_cryoSPARC/J142_2.25A_clip-240/cryosparc_P3_J150__localfilter_240.mrc Opened cryosparc_P3_J150__localfilter_240.mrc as #4, grid size 240,240,240, pixel 0.553, shown at level 0.229, step 1, values float32 > volume #4 level 0.7041 > hide #!2 models > hide #!3 models > hide #!5 models > show #!3 models > select ::name=""ABC"" 42 atoms, 48 bonds, 2 residues, 1 model selected > view sel > volume #4 level 0.5273 > hide #!4 models > show #!4 models > show #!1 models > hide #!3 models > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 57982, resource id: 35654641, major code: 40 (TranslateCoords), minor code: 0 > hide #!1 models > rename #1 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc > rename #2 mOCT1-VB1_cryosparc_P3_J154__localfilter_240_VB1.mrc > rename #4 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc > show #!3 models > select clear > hide #!4 models > select ::name=""ABC"" 42 atoms, 48 bonds, 2 residues, 1 model selected > select add #3 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected > color (#!3 & sel) white > select clear > select ::name=""ABC"" 42 atoms, 48 bonds, 2 residues, 1 model selected > color sel red > show #!4 models > ui tool show ""Color Zone"" > color zone #4 near #3 distance 3.32 > volume splitbyzone #4 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 0 as #6.1, grid size 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 1 as #6.2, grid size 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 as #6.3, grid size 240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32 > hide #!3 models > select add #3 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected > select subtract #3 Nothing selected > hide #!6.1 models > hide #!6.3 models > show #!6.3 models > hide #!6.2 models > close #6.1-2 > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 18121, resource id: 35654647, major code: 40 (TranslateCoords), minor code: 0 > show #!3 models > color #3 #fffffbff > color #3 #ddddaaff > color #3 #dda0deff > color #3 plum > select add #3 3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected > color (#!3 & sel) byhetero > color #6.3 #ddddaaff models > color #6.3 plum models > color #6.3 #ffffb2ff models Drag select of 6.3 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 , 5 atoms, 5 residues, 5 bonds > select clear > color #6.3 #ffffb2c8 models > select ::name=""ABC"" 42 atoms, 48 bonds, 2 residues, 1 model selected > view sel > select #3/A:234 11 atoms, 10 bonds, 1 residue, 1 model selected > color #6.3 #ffffb296 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!6 models > hide #!6.3 models > show #!4 models > hide #!4 models > show #!5 models > show #!3 models > hide #!3 models > select #5/A:36 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > hide #!5 models > hide #!2 models > show #!1 models > view > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 5156, resource id: 35654673, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_20240411/job207/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #7, grid size 320,320,320, pixel 0.83, shown at level 0.00144, step 2, values float32 > volume #7 level 0.01204 > select add #7 12 atoms, 12 bonds, 1 residue, 3 models selected > select add #5 3526 atoms, 3584 bonds, 1 pseudobond, 489 residues, 4 models selected > select subtract #5 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,-67.025,0,1,0,-62.171,0,0,1,-62.016 > view matrix models #7,1,0,0,-65.422,0,1,0,-60.829,0,0,1,-69.057 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.44906,0.62428,0.63923,-47.882,-0.83076,-0.55508,-0.041522,263.31,0.32891,-0.5497,0.76789,-6.0495 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.44906,0.62428,0.63923,-43.112,-0.83076,-0.55508,-0.041522,259.52,0.32891,-0.5497,0.76789,-3.3226 > view matrix models > #7,-0.44906,0.62428,0.63923,-46.691,-0.83076,-0.55508,-0.041522,257.64,0.32891,-0.5497,0.76789,-5.4256 > view matrix models > #7,-0.44906,0.62428,0.63923,-43.086,-0.83076,-0.55508,-0.041522,254.57,0.32891,-0.5497,0.76789,-5.2175 > ui tool show ""Fit in Map"" > fitmap #7 inMap #1 Fit map relion_locres_filtered.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 3812 points correlation = 0.2373, correlation about mean = 0.07089, overlap = 11.07 steps = 116, shift = 1.21, angle = 8.84 degrees Position of relion_locres_filtered.mrc (#7) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.36461695 0.73265397 0.57469351 -59.14787422 -0.87490183 -0.48082660 0.05790126 236.29988230 0.31874951 -0.48168862 0.81631784 -18.80617873 Axis -0.31464704 0.14924672 -0.93740208 Axis point 41.71559551 127.71968026 0.00000000 Rotation angle (degrees) 120.96824033 Shift along axis 71.50663710 > rename #7 mOCT1-3TC > select clear [Repeated 1 time(s)] > rename #7 mOCT1-3TC.mrc > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_Model/RealSpaceRefine_6/mOCT1-3TC- > coot-14_real_space_refined_006.pdb Chain information for mOCT1-3TC-coot-14_real_space_refined_006.pdb #8 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!8 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1-3TC- coot-14_real_space_refined_006.pdb, chain A (#8), sequence alignment score = 2352.2 RMSD between 450 pruned atom pairs is 0.409 angstroms; (across all 450 pairs: 0.409) > hide #!1 models > hide #!7 models > show #!1 models > hide #!8 models > show #!7 models > select add #7 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.49719,-0.57211,-0.6523,173.98,0.80196,0.58997,0.093813,-133.23,0.33116,-0.56976,0.75214,0.34956 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.49719,-0.57211,-0.6523,164.87,0.80196,0.58997,0.093813,-137.47,0.33116,-0.56976,0.75214,-2.3096 > fitmap #7 inMap #1 Fit map mOCT1-3TC.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 3812 points correlation = 0.9181, correlation about mean = 0.7496, overlap = 65.08 steps = 160, shift = 6.4, angle = 20.1 degrees Position of mOCT1-3TC.mrc (#7) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.27009123 -0.75134279 -0.60210857 210.67160095 0.83888334 0.49056205 -0.23584655 -78.20606144 0.47257322 -0.44139877 0.76278546 -39.17036140 Axis -0.10648785 -0.55674686 0.82382842 Axis point 169.78551241 113.86943556 0.00000000 Rotation angle (degrees) 74.82789173 Shift along axis -11.16264322 > fitmap #8 inMap #7 Fit molecule mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) to map mOCT1-3TC.mrc (#7) using 7048 atoms average map value = 0.01706, steps = 60 shifted from previous position = 0.0823 rotated from previous position = 0.357 degrees atoms outside contour = 4146, contour level = 0.012041 Position of mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) relative to mOCT1-3TC.mrc (#7) coordinates: Matrix rotation and translation 0.99999991 -0.00005602 -0.00043067 0.07339565 0.00005621 0.99999991 0.00043709 -0.06044298 0.00043064 -0.00043712 0.99999982 0.02180230 Axis -0.70938425 -0.69891365 0.09106970 Axis point 0.00000000 51.44490735 150.82453668 Rotation angle (degrees) 0.03530433 Shift along axis -0.00783577 > show #!8 models > hide #!8 models > select subtract #7 Nothing selected > hide #!1 models > show #!8 models > select ::name=""3TC"" 26 atoms, 27 bonds, 1 residue, 1 model selected > select add #8 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected > color (#!8 & sel) white > select ::name=""3TC"" 26 atoms, 27 bonds, 1 residue, 1 model selected > color sel red > view sel > volume #7 step 1 > color zone #7 near #8 distance 4.98 > volume splitbyzone #7 Opened mOCT1-3TC.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at level 0.012, step 1, values float32 Opened mOCT1-3TC.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at level 0.012, step 1, values float32 Opened mOCT1-3TC.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at level 0.012, step 1, values float32 > close #9.2 > close #9.1 > color #9.3 white models > color #9.3 #ffffb2ff models > color #9.3 #ffffb296 models > select #8/A:447 19 atoms, 18 bonds, 1 residue, 1 model selected > select add #8 7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected > color #8 #bb22ffff > color #8 #b2fffbff > color #8 #b2ffb2ff > color (#!8 & sel) byhetero > select clear [Repeated 1 time(s)] > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true > hide #!9.3 models > hide #!9 models > hide #!8 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_20240413/job307/relion_locres_filtered_flipz.mrc Opened relion_locres_filtered_flipz.mrc as #10, grid size 320,320,320, pixel 0.83, shown at level 0.00125, step 2, values float32 > show #!1 models > view > volume #1 level 0.3063 > volume #10 step 1 > volume #10 level 0.01019 > rename #10 mOCT1-AZT.mrc > select add #10 2 models selected > view matrix models #10,1,0,0,-48.383,0,1,0,-77.671,0,0,1,-67.093 > view matrix models #10,1,0,0,-54.836,0,1,0,-59.483,0,0,1,-63.826 > ui mousemode right ""rotate selected models"" > view matrix models > #10,0.55307,0.83192,0.044939,-108.96,-0.78881,0.54024,-0.29312,148.24,-0.26813,0.12666,0.95502,-37.718 > ui mousemode right ""translate selected models"" > view matrix models > #10,0.55307,0.83192,0.044939,-120.39,-0.78881,0.54024,-0.29312,136.85,-0.26813,0.12666,0.95502,-39.969 > view matrix models > #10,0.55307,0.83192,0.044939,-121.53,-0.78881,0.54024,-0.29312,137.41,-0.26813,0.12666,0.95502,-39.609 > fitmap #10 inMap #1 Fit map mOCT1-AZT.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 33175 points correlation = 0.9169, correlation about mean = 0.7611, overlap = 495.2 steps = 172, shift = 3.01, angle = 24.4 degrees Position of mOCT1-AZT.mrc (#10) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.17958596 0.98366820 0.01207312 -89.49221412 -0.89232990 0.16805236 -0.41893408 218.60375344 -0.41412105 0.06446147 0.90793639 -7.62218964 Axis 0.24369569 0.21485858 -0.94575272 Axis point 81.50821029 166.97786454 0.00000000 Rotation angle (degrees) 82.65824965 Shift along axis 32.36873253 > view > view orient > ui tool show ""Side View"" > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_Model/RealSpaceRefine_4/mOCT1-AZT_14_real_space_refined_004.pdb Chain information for mOCT1-AZT_14_real_space_refined_004.pdb #11 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!11 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1-AZT_14_real_space_refined_004.pdb, chain A (#11), sequence alignment score = 2367.3 RMSD between 449 pruned atom pairs is 0.415 angstroms; (across all 449 pairs: 0.415) > fitmap #11 inMap #10 Fit molecule mOCT1-AZT_14_real_space_refined_004.pdb (#11) to map mOCT1-AZT.mrc (#10) using 7017 atoms average map value = 0.01592, steps = 48 shifted from previous position = 0.0651 rotated from previous position = 0.278 degrees atoms outside contour = 3029, contour level = 0.010186 Position of mOCT1-AZT_14_real_space_refined_004.pdb (#11) relative to mOCT1-AZT.mrc (#10) coordinates: Matrix rotation and translation -0.89530533 -0.39092164 -0.21356179 331.89133766 0.43778783 -0.68362766 -0.58394781 243.21431714 0.08228108 -0.61630634 0.78319622 99.39179726 Axis -0.03674901 -0.33598352 0.94115067 Axis point 137.92729950 180.24940846 0.00000000 Rotation angle (degrees) 153.87927506 Shift along axis -0.37002346 > hide #!1 models > select ::name=""AZZ"" 19 atoms, 20 bonds, 1 residue, 1 model selected > hide #!10 models > select add #11 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected > select subtract #11 Nothing selected > select add #11 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected > color (#!11 & sel) white > color #11 #aaaaffff > color (#!11 & sel) white > select ::name=""AZZ"" 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel red > color zone #10 near #11 distance 4.98 > show #!10 models > volume splitbyzone #10 Opened mOCT1-AZT.mrc 0 as #12.1, grid size 320,320,320, pixel 0.83, shown at level 0.0102, step 1, values float32 Opened mOCT1-AZT.mrc 1 as #12.2, grid size 320,320,320, pixel 0.83, shown at level 0.0102, step 1, values float32 Opened mOCT1-AZT.mrc 2 as #12.3, grid size 320,320,320, pixel 0.83, shown at level 0.0102, step 1, values float32 > close #12.2 > close #12.1 > color #12.3 #ff0000fe models > color #12.3 #ff000096 models > color #12.3 #ffffff96 models > color #12.3 #ffffb296 models > color #11 #aaffffff > color #11 #aaaaffff > select add #11 7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected > color (#!11 & sel) byhetero > select clear > show #!3 models > hide #!3 models > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true > hide #!12.3 models > hide #!12 models > hide #!11 models > show #!1 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240702/job350/postprocess.mrc Opened postprocess.mrc as #13, grid size 320,320,320, pixel 0.83, shown at level 0.00595, step 2, values float32 > volume #13 step 1 > volume #13 level 0.02012 > select add #13 2 models selected > view matrix models #13,1,0,0,-56.643,0,1,0,-72.238,0,0,1,-68.565 > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.02465,-0.61986,0.78433,49.618,-0.43145,0.70114,0.56768,-50.105,-0.9018,-0.35239,-0.25015,252.26 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.02465,-0.61986,0.78433,42.91,-0.43145,0.70114,0.56768,-47.812,-0.9018,-0.35239,-0.25015,260.75 > view matrix models > #13,0.02465,-0.61986,0.78433,45.137,-0.43145,0.70114,0.56768,-48.218,-0.9018,-0.35239,-0.25015,267.86 > rename #13 mOCT1-MTF.mrc > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240603/RealSpaceRefine_3/mOCT1_MTF- > coot-9_real_space_refined_003.pdb Chain information for mOCT1_MTF-coot-9_real_space_refined_003.pdb #14 --- Chain | Description A | No description available > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.2983, correlation about mean = 0.07385, overlap = 82.29 steps = 200, shift = 2.4, angle = 7.61 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.05771312 -0.64461025 0.76232987 59.74942259 -0.34050237 0.73052504 0.59193860 -66.21901607 -0.93847075 -0.22541250 -0.26165220 256.68697920 Axis -0.42762978 0.88984156 0.15910615 Axis point 123.33045199 0.00000000 117.21732044 Rotation angle (degrees) 107.12276965 Shift along axis -43.63458901 > select subtract #13 Nothing selected > select add #13 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.50114,0.40107,-0.76681,42.081,-0.045209,-0.87277,-0.48604,255.79,-0.86419,0.27824,-0.41924,198.29 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.50114,0.40107,-0.76681,41.903,-0.045209,-0.87277,-0.48604,247.49,-0.86419,0.27824,-0.41924,198.18 > view matrix models > #13,0.50114,0.40107,-0.76681,53.046,-0.045209,-0.87277,-0.48604,251.12,-0.86419,0.27824,-0.41924,198.38 > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.2273, correlation about mean = 0.06656, overlap = 59.06 steps = 120, shift = 2.59, angle = 4.72 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.43566959 0.38627366 -0.81300964 69.55864121 -0.07375796 -0.88487887 -0.45994473 251.91510217 -0.89707959 0.26034986 -0.35702406 194.41028021 Axis 0.83873143 0.09789343 -0.53567385 Axis point 0.00000000 97.27212052 153.57991582 Rotation angle (degrees) 154.57081238 Shift along axis -21.13865268 > view matrix models > #13,0.43567,0.38627,-0.81301,67.4,-0.073758,-0.88488,-0.45994,259.27,-0.89708,0.26035,-0.35702,197.15 > ui mousemode right ""rotate selected models"" > view matrix models > #13,0.3307,0.47313,-0.81657,68.962,0.20831,-0.88051,-0.42581,219.2,-0.92046,-0.029281,-0.38974,244.12 > view matrix models > #13,0.3796,0.48184,-0.78977,58.246,0.18592,-0.87598,-0.44507,223.83,-0.90628,0.022112,-0.42211,239.42 > ui mousemode right ""translate selected models"" > view matrix models > #13,0.3796,0.48184,-0.78977,53.846,0.18592,-0.87598,-0.44507,217.81,-0.90628,0.022112,-0.42211,235.11 > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.2652, correlation about mean = 0.06679, overlap = 73.72 steps = 92, shift = 1.81, angle = 5.01 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.31415893 0.53789144 -0.78228958 53.81386032 0.19698588 -0.84300825 -0.50053338 220.95415625 -0.92870918 0.00314703 -0.37079559 234.49017112 Axis 0.80514260 0.23405449 -0.54494394 Axis point 0.00000000 81.07236056 158.23174632 Rotation angle (degrees) 161.77257653 Shift along axis -32.74085292 > view matrix models > #13,0.31416,0.53789,-0.78229,60.198,0.19699,-0.84301,-0.50053,217.39,-0.92871,0.003147,-0.3708,234.22 > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.2449, correlation about mean = 0.05515, overlap = 65.5 steps = 80, shift = 1.45, angle = 5.73 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.28419679 0.60053681 -0.74738728 50.81854511 0.27816291 -0.79764719 -0.53514891 205.19579930 -0.91752798 -0.05580782 -0.39373584 245.12613641 Axis 0.79598780 0.28253351 -0.53533003 Axis point 0.00000000 71.54715698 160.41463451 Rotation angle (degrees) 162.47642045 Shift along axis -32.79775064 > view matrix models > #13,0.2842,0.60054,-0.74739,49.177,0.27816,-0.79765,-0.53515,206.5,-0.91753,-0.055808,-0.39374,243.99 > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.3559, correlation about mean = 0.151, overlap = 107.2 steps = 88, shift = 2.33, angle = 2.34 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.29378487 0.57675594 -0.76226180 52.65591556 0.29516509 -0.81321822 -0.50155130 203.18767751 -0.90915787 -0.07764488 -0.40914943 245.95334709 Axis 0.80029578 0.27732609 -0.53161726 Axis point 0.00000000 73.19686532 158.33534093 Rotation angle (degrees) 164.64234082 Shift along axis -32.26349399 > view matrix models > #13,0.29378,0.57676,-0.76226,50.19,0.29517,-0.81322,-0.50155,203.5,-0.90916,-0.077645,-0.40915,251.78 > fitmap #13 inMap #1 Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 17817 points correlation = 0.9033, correlation about mean = 0.6277, overlap = 419.6 steps = 52, shift = 1.52, angle = 1.92 degrees Position of mOCT1-MTF.mrc (#13) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation 0.29574252 0.60146473 -0.74214321 45.38180479 0.29484975 -0.79643687 -0.52796964 204.44935424 -0.90862533 -0.06267767 -0.41288198 249.74597785 Axis 0.80005949 0.28626242 -0.52721784 Axis point 0.00000000 72.71544700 159.79227740 Rotation angle (degrees) 163.09499009 Shift along axis -36.83622428 > ui tool show Matchmaker > matchmaker #!14 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1_MTF- coot-9_real_space_refined_003.pdb, chain A (#14), sequence alignment score = 2355.8 RMSD between 450 pruned atom pairs is 0.377 angstroms; (across all 450 pairs: 0.377) > select add #14 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected > select subtract #13 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > hide #!1 models > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 5891, resource id: 35654810, major code: 40 (TranslateCoords), minor code: 0 > color #14 #95cacdff > select ::name=""MF8"" 22 atoms, 21 bonds, 1 residue, 1 model selected > select add #14 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > select subtract #14 Nothing selected > select add #14 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > color (#!14 & sel) white > select ::name=""MF8"" 22 atoms, 21 bonds, 1 residue, 1 model selected > color sel red > color zone #10 near #11 distance 4.98 > color zone #13 near #14 distance 4.98 > hide #!14 models > show #!14 models > volume #13 level 0.0238 > volume #13 level 0.02122 > volume #13 level 0.01423 > volume splitbyzone #13 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 > close #15.1 > close #15.2 > volume #15.3 level 0.009273 > volume #15.3 level 0.01703 > close #15#15.3 > select add #14 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > show #!13 models > color zone #13 near #14 distance 4.88 > color zone #13 near #14 distance 4.78 > color zone #13 near #14 distance 4.68 > color zone #13 near #14 distance 4.58 > color zone #13 near #14 distance 4.48 > color zone #13 near #14 distance 4.38 > color zone #13 near #14 distance 4.28 > color zone #13 near #14 distance 4.18 > color zone #13 near #14 distance 4.08 > color zone #13 near #14 distance 3.98 > color zone #13 near #14 distance 3.88 > color zone #13 near #14 distance 3.78 > color zone #13 near #14 distance 3.68 > color zone #13 near #14 distance 3.58 > color zone #13 near #14 distance 3.48 > color zone #13 near #14 distance 3.38 [Repeated 1 time(s)] > volume splitbyzone #13 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at level 0.0142, step 1, values float32 > close #15.1-2 > volume #15.3 level 0.009634 > color zone #13 near #14 distance 3.28 > color zone #13 near #14 distance 3.18 > color zone #13 near #14 distance 3.08 > close #15#15.3 > show #!13 models > select add #13 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected > select subtract #13 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > color zone #13 near #14 distance 2.98 > color zone #13 near #14 distance 2.88 > color zone #13 near #14 distance 2.78 > color zone #13 near #14 distance 2.68 > color zone #13 near #14 distance 2.58 > color zone #13 near #14 distance 2.48 > volume #13 level 0.01681 > fitmap #14 inMap #13 Fit molecule mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) to map mOCT1-MTF.mrc (#13) using 7044 atoms average map value = 0.01572, steps = 48 shifted from previous position = 0.0765 rotated from previous position = 0.266 degrees atoms outside contour = 4386, contour level = 0.016807 Position of mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) relative to mOCT1-MTF.mrc (#13) coordinates: Matrix rotation and translation 0.99946408 0.01781074 -0.02746495 0.87693504 -0.01720783 0.99960910 0.02203450 -1.16466203 0.02784666 -0.02155008 0.99937988 -1.14535630 Axis -0.55418255 -0.70329295 -0.44526478 Axis point 28.72708736 -0.00000000 48.38067452 Rotation angle (degrees) 2.25364092 Shift along axis 0.84310332 > color zone #13 near #14 distance 2.48 [Repeated 1 time(s)] > color single #13 > color zone #13 near #14 distance 2.48 > color zone #13 near #14 distance 2.38 > color zone #13 near #14 distance 2.28 > color zone #13 near #14 distance 2.18 > color zone #13 near #14 distance 2.08 > color zone #13 near #14 distance 1.98 > color zone #13 near #14 distance 1.88 > color zone #13 near #14 distance 1.78 > color zone #13 near #14 distance 1.68 > color zone #13 near #14 distance 1.58 > color zone #13 near #14 distance 1.48 > color zone #13 near #14 distance 1.38 > color zone #13 near #14 distance 1.48 > color zone #13 near #14 distance 1.58 > color zone #13 near #14 distance 1.68 > color zone #13 near #14 distance 1.78 > color zone #13 near #14 distance 1.88 > color zone #13 near #14 distance 1.98 > volume #13 level 0.01957 > color zone #13 near #14 distance 1.98 > volume splitbyzone #13 Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at level 0.0196, step 1, values float32 Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at level 0.0196, step 1, values float32 Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at level 0.0196, step 1, values float32 > close #15.1-2 > color #15.3 yellow models > color #15.3 white models > color #15.3 #ffffb2ff models > color #15.3 #ffffb296 models > volume #15.3 level 0.01524 > volume #15.3 level 0.0119 > select subtract #14 Nothing selected > select add #14 7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected > color #14 #55dd44ff > color #14 #5d42cdff > color #14 #5858cdff > color #14 #7d76cdff > color #14 #9d7bcdff > color #14 #cd75baff > color #14 #9381cdff > color (#!14 & sel) byhetero > select clear > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true > hide #!15.3 models > hide #!15 models > hide #!14 models > show #!1 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job321/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #16, grid size 320,320,320, pixel 0.83, shown at level 0.00147, step 2, values float32 > volume #13 level 0.01846 > volume #16 step 1 > volume #16 level 0.01137 > select add #16 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #16,0.91726,-0.046522,0.39555,-35.801,-0.13266,0.90075,0.41357,-25.02,-0.37554,-0.43183,0.82006,127.4 > view matrix models > #16,0.97308,0.0084656,-0.23031,32.94,-0.035652,0.99283,-0.11414,20.659,0.2277,0.11927,0.9664,-40.203 > view matrix models > #16,0.95291,-0.013325,0.30296,-32.366,-0.094841,0.93583,0.33946,-24.554,-0.28805,-0.35221,0.89049,96.605 > view matrix models > #16,0.68405,0.72927,0.015283,-53.826,0.65561,-0.6055,-0.45117,179.02,-0.31977,0.31864,-0.89231,251.74 > view matrix models > #16,-0.14871,0.82898,-0.53915,114.85,0.43367,-0.43531,-0.78894,230.9,-0.88872,-0.35114,-0.29476,331.38 > view matrix models > #16,-0.59154,0.6904,-0.41646,173.56,0.69281,0.17103,-0.70054,108.52,-0.41243,-0.70292,-0.57948,352.16 > ui mousemode right ""translate selected models"" > view matrix models > #16,-0.59154,0.6904,-0.41646,98.473,0.69281,0.17103,-0.70054,82.195,-0.41243,-0.70292,-0.57948,295.09 > view matrix models > #16,-0.59154,0.6904,-0.41646,115.7,0.69281,0.17103,-0.70054,51.467,-0.41243,-0.70292,-0.57948,297.87 > view matrix models > #16,-0.59154,0.6904,-0.41646,109.24,0.69281,0.17103,-0.70054,49.803,-0.41243,-0.70292,-0.57948,297.08 > view matrix models > #16,-0.59154,0.6904,-0.41646,112.5,0.69281,0.17103,-0.70054,41.909,-0.41243,-0.70292,-0.57948,292.69 > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.52634,0.62911,-0.57201,132.47,0.46428,-0.35094,-0.81319,152.81,-0.71233,-0.69359,-0.10737,267.76 > view matrix models > #16,-0.56071,0.74447,-0.36245,94.475,0.40226,-0.13769,-0.90511,145.91,-0.72373,-0.6533,-0.22227,279.35 > ui mousemode right ""translate selected models"" > view matrix models > #16,-0.56071,0.74447,-0.36245,91.988,0.40226,-0.13769,-0.90511,152.84,-0.72373,-0.6533,-0.22227,276.37 > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.69312,0.68147,-0.23491,100.24,0.41746,0.11382,-0.90154,118.42,-0.58764,-0.72294,-0.36338,286.3 > rename #16 hOCT1-VB1.mrc > fitmap #16 inMap #1 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 29501 points correlation = 0.336, correlation about mean = 0.1558, overlap = 114.4 steps = 148, shift = 3.34, angle = 5.64 degrees Position of hOCT1-VB1.mrc (#16) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.66774800 0.66848229 -0.32748134 111.59775010 0.47076725 0.03845367 -0.88141903 115.78397104 -0.57662015 -0.74273329 -0.34037693 282.67572866 Axis 0.39969377 0.71802066 -0.56981683 Axis point 39.62225841 0.00000000 179.67701786 Rotation angle (degrees) 170.00920250 Shift along axis -33.33317846 > ui mousemode right ""translate selected models"" > view matrix models > #16,-0.66775,0.66848,-0.32748,111.72,0.47077,0.038454,-0.88142,115.95,-0.57662,-0.74273,-0.34038,288.9 > fitmap #16 inMap #1 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 29501 points correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 steps = 60, shift = 1.34, angle = 1.92 degrees Position of hOCT1-VB1.mrc (#16) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.68896253 0.65809895 -0.30370448 111.90845021 0.45027206 0.06027049 -0.89085495 116.65862228 -0.56796628 -0.75051532 -0.33784768 287.44343290 Axis 0.38522072 0.72537689 -0.57046767 Axis point 41.86637964 0.00000000 181.62562393 Rotation angle (degrees) 169.50470225 Shift along axis -36.24626372 > view matrix models > #16,-0.68896,0.6581,-0.3037,110.15,0.45027,0.06027,-0.89085,119.19,-0.56797,-0.75052,-0.33785,287.46 > fitmap #16 inMap #1 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 29501 points correlation = 0.7772, correlation about mean = 0.5327, overlap = 352.7 steps = 72, shift = 3.09, angle = 0.0182 degrees Position of hOCT1-VB1.mrc (#16) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.68902052 0.65795875 -0.30387662 111.96278841 0.45022908 0.06002731 -0.89089309 116.69902951 -0.56793001 -0.75065771 -0.33759222 287.41226501 Axis 0.38519550 0.72529614 -0.57058737 Axis point 41.87016659 0.00000000 181.64241189 Rotation angle (degrees) 169.51189271 Shift along axis -36.22489055 > fitmap #16 inMap #1 Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 29501 points correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7 steps = 36, shift = 0.00448, angle = 0.00722 degrees Position of hOCT1-VB1.mrc (#16) relative to mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates: Matrix rotation and translation -0.68898476 0.65802671 -0.30381055 111.93916561 0.45024501 0.06010903 -0.89087953 116.68451889 -0.56796077 -0.75059160 -0.33768744 287.42460080 Axis 0.38521270 0.72532270 -0.57054198 Axis point 41.86758112 0.00000000 181.63640339 Rotation angle (degrees) 169.50839167 Shift along axis -36.23348002 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_10/hOCT1-VB_Dock2_real_space_refined_010.pdb Chain information for hOCT1-VB_Dock2_real_space_refined_010.pdb #17 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!17 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with hOCT1-VB_Dock2_real_space_refined_010.pdb, chain A (#17), sequence alignment score = 1980 RMSD between 416 pruned atom pairs is 0.792 angstroms; (across all 446 pairs: 1.346) > fitmap #17 inMap #16 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map hOCT1-VB1.mrc (#16) using 3479 atoms average map value = 0.02025, steps = 64 shifted from previous position = 0.153 rotated from previous position = 0.521 degrees atoms outside contour = 1063, contour level = 0.011373 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to hOCT1-VB1.mrc (#16) coordinates: Matrix rotation and translation 0.99999651 0.00186028 0.00187897 -0.40239474 -0.00185675 0.99999652 -0.00187607 0.55801929 -0.00188246 0.00187257 0.99999648 0.09469763 Axis 0.57831092 0.58028383 -0.57343453 Axis point 61.09212114 0.00000000 225.59585813 Rotation angle (degrees) 0.18569746 Shift along axis 0.03679741 > fitmap #17 inMap #16 Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map hOCT1-VB1.mrc (#16) using 3479 atoms average map value = 0.02025, steps = 28 shifted from previous position = 0.0153 rotated from previous position = 0.0146 degrees atoms outside contour = 1064, contour level = 0.011373 Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to hOCT1-VB1.mrc (#16) coordinates: Matrix rotation and translation 0.99999599 0.00211002 0.00188874 -0.43726655 -0.00210638 0.99999592 -0.00192887 0.59237860 -0.00189280 0.00192488 0.99999636 0.07510223 Axis 0.56254941 0.55200867 -0.61548727 Axis point 271.69369003 217.02489508 0.00000000 Rotation angle (degrees) 0.19625280 Shift along axis 0.03478962 > hide #!1 models > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected > select subtract #16 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected > color (#!17 & sel) white > select clear > select ::name=""VIB"" 18 atoms, 19 bonds, 1 residue, 1 model selected > color sel red > color zone #16 near #17 distance 4.98 > color zone #16 near #17 distance 4.88 > color zone #16 near #17 distance 4.78 > color zone #16 near #17 distance 4.68 > color zone #16 near #17 distance 4.58 > color zone #16 near #17 distance 4.48 > color zone #16 near #17 distance 4.38 > color zone #16 near #17 distance 4.28 > color zone #16 near #17 distance 4.18 > color zone #16 near #17 distance 4.08 > color zone #16 near #17 distance 3.98 > color zone #16 near #17 distance 3.88 > color zone #16 near #17 distance 3.78 > color zone #16 near #17 distance 3.68 > color zone #16 near #17 distance 3.58 > color zone #16 near #17 distance 3.48 > color zone #16 near #17 distance 3.38 > color zone #16 near #17 distance 3.28 > color sel white > select ::name=""VIB"" 18 atoms, 19 bonds, 1 residue, 1 model selected > color sel red > select add #16 18 atoms, 19 bonds, 1 residue, 3 models selected > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected > select subtract #17 2 models selected > color #16.1 white > color zone #16 near #17 distance 3.28 > color zone #16 near #17 distance 3.18 > color zone #16 near #17 distance 3.08 > color zone #16 near #17 distance 2.98 > color zone #16 near #17 distance 2.88 > color zone #16 near #17 distance 2.98 > color zone #16 near #17 distance 3.08 > color zone #16 near #17 distance 3.18 > color zone #16 near #17 distance 3.28 > color zone #16 near #17 distance 3.38 [Repeated 1 time(s)] > volume splitbyzone #16 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 > close #18.1-2 > color #18.3 yellow models > color #18.3 white models > color #18.3 #ffffb2ff models > color #18.3 #ffffb296 models > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected > select subtract #16 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected > color #17 #6622bbff > color #17 #62be40ff > color (#!17 & sel) byhetero Drag select of 1 atoms, 1 bonds > volume #18.3 level 0.006511 > volume #18.3 level 0.01112 > close #18#18.3 > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected > color (#!17 & sel) white > select ::name=""VIB"" 18 atoms, 19 bonds, 1 residue, 1 model selected > color sel red > show #!16 models > color zone #16 near #17 distance 3.28 > color zone #16 near #17 distance 3.18 > color zone #16 near #17 distance 3.08 > color zone #16 near #17 distance 2.98 > color zone #16 near #17 distance 2.88 > color zone #16 near #17 distance 2.78 > color zone #16 near #17 distance 2.68 > color zone #16 near #17 distance 2.58 > color zone #16 near #17 distance 2.48 > color zone #16 near #17 distance 2.38 > color zone #16 near #17 distance 2.28 > color zone #16 near #17 distance 2.18 > color zone #16 near #17 distance 2.08 > color zone #16 near #17 distance 1.98 > color zone #16 near #17 distance 1.88 > color zone #16 near #17 distance 1.78 > color zone #16 near #17 distance 1.68 > color zone #16 near #17 distance 1.78 > color zone #16 near #17 distance 1.88 > color zone #16 near #17 distance 1.98 > color zone #16 near #17 distance 2.08 > volume splitbyzone #16 Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at level 0.0114, step 1, values float32 > close #18.1-2 > color #18.3 white models > color #18.3 #ffffb2ff models > select add #18.3 18 atoms, 19 bonds, 1 residue, 3 models selected > color #18.3 #ffffb296 models > select subtract #18.3 18 atoms, 19 bonds, 1 residue, 1 model selected > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected > select subtract #17 Nothing selected > select add #17 3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected > color #17 #6622bbff > color #17 #62be40ff > color (#!17 & sel) byhetero > view > hide #!18.3 models > hide #!18 models > hide #!17 models > select subtract #17 Nothing selected > show #!1 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/job154/postprocess_masked.mrc Opened postprocess_masked.mrc as #19, grid size 320,320,320, pixel 0.83, shown at level 2.83e-06, step 2, values float32 > volume #19 step 1 > volume #19 level 0.0131 > select add #19 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #19,-0.93986,0.28611,-0.18654,253.04,-0.10485,-0.76147,-0.63967,340.05,-0.32506,-0.58164,0.74567,158.04 > ui mousemode right ""translate selected models"" > view matrix models > #19,-0.93986,0.28611,-0.18654,175.89,-0.10485,-0.76147,-0.63967,293,-0.32506,-0.58164,0.74567,91.801 > view matrix models > #19,-0.93986,0.28611,-0.18654,185.27,-0.10485,-0.76147,-0.63967,269.77,-0.32506,-0.58164,0.74567,91.027 > view matrix models > #19,-0.93986,0.28611,-0.18654,178.6,-0.10485,-0.76147,-0.63967,268.3,-0.32506,-0.58164,0.74567,89.593 > rename #19 hOCT1-AZT.mrc > fitmap #19 inMap #16 Fit map hOCT1-AZT.mrc in map hOCT1-VB1.mrc using 23475 points correlation = 0.9652, correlation about mean = 0.8232, overlap = 14.07 steps = 112, shift = 2.59, angle = 19.3 degrees Position of hOCT1-AZT.mrc (#19) relative to hOCT1-VB1.mrc (#16) coordinates: Matrix rotation and translation 0.86934918 -0.02079803 -0.49376051 87.20318527 -0.45396874 0.36123943 -0.81450504 253.58267245 0.19530587 0.93224113 0.30460154 -57.13169181 Axis 0.90642923 -0.35757337 -0.22478286 Axis point 0.00000000 185.25380563 166.58335969 Rotation angle (degrees) 74.47879004 Shift along axis 1.21133072 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/RealSpaceRefine_6/hOCT1_AZT- > coot-2_real_space_refined_006.pdb Chain information for hOCT1_AZT-coot-2_real_space_refined_006.pdb #20 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!20 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with hOCT1_AZT- coot-2_real_space_refined_006.pdb, chain A (#20), sequence alignment score = 1978 RMSD between 414 pruned atom pairs is 0.849 angstroms; (across all 446 pairs: 1.482) > hide #!1 models > color #19 white models > select add #20 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 4 models selected > color #20 white > hide #!19 models > select subtract #19 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel red > color zone #19 near #20 distance 4.98 > show #!19 models > select add #19 19 atoms, 20 bonds, 1 residue, 3 models selected > select subtract #19 19 atoms, 20 bonds, 1 residue, 1 model selected > color zone #19 near #20 distance 4.88 > color zone #19 near #20 distance 4.78 > color zone #19 near #20 distance 4.68 > color zone #19 near #20 distance 4.58 > color zone #19 near #20 distance 4.48 > color zone #19 near #20 distance 4.38 > color zone #19 near #20 distance 4.28 > color zone #19 near #20 distance 4.18 > color zone #19 near #20 distance 4.08 > color zone #19 near #20 distance 3.98 > color zone #19 near #20 distance 3.88 > color zone #19 near #20 distance 3.78 > color zone #19 near #20 distance 3.68 > color zone #19 near #20 distance 3.58 > color zone #19 near #20 distance 3.48 > volume #19 level 0.01039 > color zone #19 near #20 distance 3.38 > color zone #19 near #20 distance 3.28 > color zone #19 near #20 distance 3.18 > color zone #19 near #20 distance 3.08 > color zone #19 near #20 distance 2.98 > color zone #19 near #20 distance 2.88 > color zone #19 near #20 distance 2.78 > color zone #19 near #20 distance 2.68 > color zone #19 near #20 distance 2.58 > color zone #19 near #20 distance 2.48 > color zone #19 near #20 distance 2.38 > color zone #19 near #20 distance 2.28 > color zone #19 near #20 distance 2.18 > color zone #19 near #20 distance 2.08 > color zone #19 near #20 distance 1.98 > color zone #19 near #20 distance 1.88 > color zone #19 near #20 distance 1.78 > color zone #19 near #20 distance 1.88 > color zone #19 near #20 distance 1.98 > color zone #19 near #20 distance 2.08 [Repeated 1 time(s)] > volume splitbyzone #19 Opened hOCT1-AZT.mrc 0 as #21.1, grid size 320,320,320, pixel 0.83, shown at level 0.0104, step 1, values float32 Opened hOCT1-AZT.mrc 1 as #21.2, grid size 320,320,320, pixel 0.83, shown at level 0.0104, step 1, values float32 Opened hOCT1-AZT.mrc 2 as #21.3, grid size 320,320,320, pixel 0.83, shown at level 0.0104, step 1, values float32 > close #21.1-2 > select add #20 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected > select subtract #20 Nothing selected > select add #20 3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected > color #20 #773333ff > color #20 #733551ff > color (#!20 & sel) byhetero > select clear > color #21.3 #ff000096 models > color #21.3 #ffffff96 models > color #21.3 #ffffb296 models > volume #21.3 level 0.008896 > hide #!21.3 models > hide #!21 models > hide #!20 models > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 59019, resource id: 35654939, major code: 40 (TranslateCoords), minor code: 0 > show #!3 models > show #!6.3 models > select ::name=""ABC"" 42 atoms, 48 bonds, 2 residues, 1 model selected > view sel > select clear > hide #!6.3 models > hide #!6 models > hide #!3 models > show #!2 models > show #!5 models > hide #!5 models > hide #!2 models > show #!8 models > show #!9.3 models > hide #!9.3 models > hide #!9 models > hide #!8 models > show #!11 models > show #!12.3 models > hide #!12.3 models > hide #!12 models > hide #!11 models > show #!14 models > show #!15 models > hide #!15 models > show #!15.3 models > hide #!14 models > hide #!15 models > hide #!15.3 models > show #!17 models > show #!18.3 models > hide #!18.3 models > hide #!18 models > hide #!17 models > show #!20 models > show #!21.3 models > save ""/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand > density.cxs"" includeMaps true > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1_structures_ligand_density.cxs > includeMaps true [Repeated 1 time(s)] > close session > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/0-coot- > history.scm Unrecognized file suffix '.scm' > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif Summary of feedback from opening /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 187 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""3"" near line 98 Bad residue range for struct_conf ""4"" near line 99 Bad residue range for struct_conf ""5"" near line 100 Bad residue range for struct_conf ""6"" near line 101 Bad residue range for struct_conf ""7"" near line 102 15 messages similar to the above omitted Invalid sheet range for struct_sheet_range ""2 1"" near line 183 Invalid sheet range for struct_sheet_range ""3 1"" near line 184 Invalid sheet range for struct_sheet_range ""4 1"" near line 186 Missing or incomplete sequence information. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' near line 4361 Chain information for rOAT1-AZT_coot-4_real_space_refined_002.cif #1 --- Chain | Description A | No description available > close session > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.pdb Chain information for rOAT1-AZT_coot-4_real_space_refined_002.pdb #1 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 10568, resource id: 35655077, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/postprocess.mrc Opened postprocess.mrc as #2, grid size 320,320,320, pixel 0.83, shown at level 0.00421, step 2, values float32 > rename #2 rOAT1-AZT.mrc > volume #2 step 1 > volume #2 level 0.01415 > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > select add #1 3905 atoms, 3986 bonds, 515 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.81264,-0.025153,-0.58222,300.85,0.24435,0.8923,-0.37961,31.685,0.52906,-0.45075,-0.71897,210.07 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.81264,-0.025153,-0.58222,320.11,0.24435,0.8923,-0.37961,31.387,0.52906,-0.45075,-0.71897,214.5 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.62181,-0.74054,-0.25487,347.35,-0.028985,0.34697,-0.93743,205.98,0.78263,-0.57551,-0.23722,138.33 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.62181,-0.74054,-0.25487,344.94,-0.028985,0.34697,-0.93743,211.72,0.78263,-0.57551,-0.23722,135.34 > view matrix models > #1,-0.62181,-0.74054,-0.25487,347.37,-0.028985,0.34697,-0.93743,211.37,0.78263,-0.57551,-0.23722,136.41 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) to map rOAT1-AZT.mrc (#2) using 3905 atoms average map value = 0.01965, steps = 108 shifted from previous position = 2.32 rotated from previous position = 12.8 degrees atoms outside contour = 1436, contour level = 0.014154 Position of rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) relative to rOAT1-AZT.mrc (#2) coordinates: Matrix rotation and translation -0.62427498 -0.78041245 -0.03517318 323.27181278 -0.15760640 0.16991691 -0.97277359 257.26632447 0.76514114 -0.60173470 -0.22907287 142.60270901 Axis 0.34360458 -0.74113973 0.57675627 Axis point 193.37147122 0.00000000 235.15956508 Rotation angle (degrees) 147.32171525 Shift along axis 2.65438788 > select subtract #1 Nothing selected > select add #1 3905 atoms, 3986 bonds, 515 residues, 1 model selected > color sel white > select ::name=""AZZ"" 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel red > ui tool show ""Color Zone"" > color zone #2 near #1 distance 4.98 > volume #2 level 0.0105 > color zone #2 near #1 distance 4.88 > color zone #2 near #1 distance 4.78 > color zone #2 near #1 distance 4.68 > color zone #2 near #1 distance 4.58 > color zone #2 near #1 distance 4.48 > color zone #2 near #1 distance 4.38 > color zone #2 near #1 distance 4.28 > color zone #2 near #1 distance 4.18 > color zone #2 near #1 distance 4.08 > color zone #2 near #1 distance 3.98 > color zone #2 near #1 distance 3.88 > color zone #2 near #1 distance 3.78 > color zone #2 near #1 distance 3.68 > color zone #2 near #1 distance 3.58 > color zone #2 near #1 distance 3.48 > color zone #2 near #1 distance 3.38 > color zone #2 near #1 distance 3.28 > color zone #2 near #1 distance 3.18 > color zone #2 near #1 distance 3.08 > color zone #2 near #1 distance 2.98 > color zone #2 near #1 distance 2.88 > color zone #2 near #1 distance 2.78 > color zone #2 near #1 distance 2.68 > color zone #2 near #1 distance 2.58 > color zone #2 near #1 distance 2.48 > color zone #2 near #1 distance 2.38 > color zone #2 near #1 distance 2.28 > color zone #2 near #1 distance 2.18 > color zone #2 near #1 distance 2.08 > color zone #2 near #1 distance 1.98 > color zone #2 near #1 distance 1.88 > color zone #2 near #1 distance 1.78 > volume #2 level 0.008069 > volume splitbyzone #2 Opened rOAT1-AZT.mrc 0 as #3.1, grid size 320,320,320, pixel 0.83, shown at level 0.00807, step 1, values float32 Opened rOAT1-AZT.mrc 1 as #3.2, grid size 320,320,320, pixel 0.83, shown at level 0.00807, step 1, values float32 Opened rOAT1-AZT.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at level 0.00807, step 1, values float32 > close #3.1-2 > color #3.3 white models > color #3.3 #ffffb2ff models > select add #1 3905 atoms, 3986 bonds, 515 residues, 1 model selected > color #1 #dd22bbff > color #1 tan > color sel byhetero > color #3.3 #ffffb296 models > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 355, resource id: 35655128, major code: 40 (TranslateCoords), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 366, resource id: 35655123, major code: 40 (TranslateCoords), minor code: 0 > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 14345, resource id: 35655133, major code: 40 (TranslateCoords), minor code: 0 > rename #1 rOAT1-AZT_IF.pdb > rename #2 rOAT1-AZT_IF.mrc > rename #3 ""rOAT1-AZT_IF.mrc split"" > rename #3.3 ""rOAT1-AZT_IF.mrc 2"" > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 23455, resource id: 35655148, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/run_class001.mrc Opened run_class001.mrc as #4, grid size 320,320,320, pixel 0.83, shown at level 0.00134, step 2, values float32 > close #4 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc Opened postprocess.mrc as #4, grid size 320,320,320, pixel 0.83, shown at level 0.00459, step 2, values float32 > volume #4 step 1 > volume #4 level 0.01366 > rename #4 rOAT1-AZT_OF.mrc > open > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF- > coot-7_real_space_refined_008.pdb Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #5 --- Chain | Description A | No description available > select subtract #1 Nothing selected > select add #5 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected > hide #!3 models > hide #!3.3 models > hide #1 models > view matrix models #5,1,0,0,68.569,0,1,0,64.41,0,0,1,67.632 > view matrix models #5,1,0,0,67.083,0,1,0,66.14,0,0,1,66.95 > fitmap #5 inMap #4 Fit molecule rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) to map rOAT1-AZT_OF.mrc (#4) using 3792 atoms average map value = 0.01938, steps = 84 shifted from previous position = 0.803 rotated from previous position = 4.35 degrees atoms outside contour = 1323, contour level = 0.013659 Position of rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) relative to rOAT1-AZT_OF.mrc (#4) coordinates: Matrix rotation and translation 0.99822969 -0.04531644 -0.03852150 72.45731875 0.04345449 0.99790785 -0.04787105 67.21065914 0.04061025 0.04611237 0.99811044 61.32293455 Axis 0.62004547 -0.52206316 0.58565662 Axis point 0.00000000 -669.59173064 1932.22009801 Rotation angle (degrees) 4.34647273 Shift along axis 45.75280586 > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF.pdb > models #5 relModel #4 > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/rOAT1-AZT_IF.pdb > models #1 > close #5 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc Opened rOAT1-AZT_OF.mrc as #5, grid size 320,320,320, pixel 0.83, shown at level 0.00459, step 2, values float32 > close #5 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF- > coot-0_real_space_refined_003.pdb Chain information for rOAT1-AZT_OF-coot-0_real_space_refined_003.pdb #5 --- Chain | Description A | No description available > select add #4 2 models selected > select subtract #4 Nothing selected > select add #5 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected > select clear > select add #5 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #5 white > color #4 white models > color #2 white models > select #5/A:601@O4 1 atom, 1 residue, 1 model selected > select up 19 atoms, 20 bonds, 1 residue, 1 model selected > color sel red > color zone #4 near #5 distance 4.98 > color zone #4 near #5 distance 4.88 > color zone #4 near #5 distance 4.78 > color zone #4 near #5 distance 4.68 > color zone #4 near #5 distance 4.58 > color zone #4 near #5 distance 4.48 > color zone #4 near #5 distance 4.38 > color zone #4 near #5 distance 4.28 > color zone #4 near #5 distance 4.18 > color zone #4 near #5 distance 4.08 > color zone #4 near #5 distance 3.98 > color zone #4 near #5 distance 3.88 > color zone #4 near #5 distance 3.78 > color zone #4 near #5 distance 3.68 > color zone #4 near #5 distance 3.58 > color zone #4 near #5 distance 3.48 > color zone #4 near #5 distance 3.38 > color zone #4 near #5 distance 3.28 > color zone #4 near #5 distance 3.18 > color zone #4 near #5 distance 3.08 > color zone #4 near #5 distance 2.98 > color zone #4 near #5 distance 2.88 > color zone #4 near #5 distance 2.78 > color zone #4 near #5 distance 2.68 > color zone #4 near #5 distance 2.58 > color zone #4 near #5 distance 2.48 > color zone #4 near #5 distance 2.38 > color zone #4 near #5 distance 2.28 > color zone #4 near #5 distance 2.18 > color zone #4 near #5 distance 2.08 > color zone #4 near #5 distance 1.98 > color zone #4 near #5 distance 1.88 > color zone #4 near #5 distance 1.78 > color zone #4 near #5 distance 1.68 > color zone #4 near #5 distance 1.58 > color zone #4 near #5 distance 1.48 > color zone #4 near #5 distance 1.58 > color zone #4 near #5 distance 1.68 > color zone #4 near #5 distance 1.78 > color zone #4 near #5 distance 1.88 > volume splitbyzone #4 Opened rOAT1-AZT_OF.mrc 0 as #6.1, grid size 320,320,320, pixel 0.83, shown at level 0.0137, step 1, values float32 Opened rOAT1-AZT_OF.mrc 1 as #6.2, 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 0.0137, step 1, values float32 > close #6.1-2 > volume #6.3 level 0.0116 > select add #5 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected > select subtract #5 Nothing selected > color #6.3 yellow models > color #6.3 white models > color #6.3 #ffffb2ff models > select add #5 3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #5 #ffaa88ff > color #5 salmon > color (#!5 & sel) byhetero > color #6.3 #ffffb296 models > select clear > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > show #!2 models > hide #!5 models > hide #!6 models > hide #!6.3 models > volume #2 level 0.01456 > color #2 #a5a5a5ff models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/postprocess.mrc Opened postprocess.mrc as #7, grid size 320,320,320, pixel 0.83, shown at level 0.00408, step 2, values float32 > rename #7 rOAT1-PBD_IF.mrc > volume #2 level 0.01983 > volume #2 level 0.0151 > hide #!7 models > volume #7 level 0.01185 > volume #7 step 1 > volume #7 level 0.01094 > hide #!2 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/rOAT1-PBD- > coot-6.pdb Chain information for rOAT1-PBD-coot-6.pdb #8 --- Chain | Description A | No description available > select add #8 3912 atoms, 3985 bonds, 522 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,55.004,0,1,0,73.737,0,0,1,58.702 > view matrix models #8,1,0,0,66.378,0,1,0,64.897,0,0,1,63.973 > fitmap #8 inMap #7 Fit molecule rOAT1-PBD-coot-6.pdb (#8) to map rOAT1-PBD_IF.mrc (#7) using 3912 atoms average map value = 0.02737, steps = 56 shifted from previous position = 2.6 rotated from previous position = 0.396 degrees atoms outside contour = 571, contour level = 0.010939 Position of rOAT1-PBD-coot-6.pdb (#8) relative to rOAT1-PBD_IF.mrc (#7) coordinates: Matrix rotation and translation 0.99998387 0.00531886 -0.00199304 66.36205660 -0.00532668 0.99997806 -0.00393867 67.06308709 0.00197205 0.00394922 0.99999026 65.65327743 Axis 0.57034742 -0.28670293 -0.76974363 Axis point 10937.66555565 -15865.74627304 0.00000000 Rotation angle (degrees) 0.39620277 Shift along axis -31.91394767 > rename #8 rOAT1-PBD_IF.pdb > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 51376, resource id: 35655645, major code: 40 (TranslateCoords), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 51388, resource id: 35655640, major code: 40 (TranslateCoords), minor code: 0 > color #8 white > hide #!7 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 19 atoms, 19 bonds, 1 residue, 1 model selected > color sel red > show #!7 models > color zone #7 near #8 distance 4.98 > color zone #7 near #8 distance 4.88 > color zone #7 near #8 distance 4.78 > color zone #7 near #8 distance 4.68 > color zone #7 near #8 distance 4.58 > color zone #7 near #8 distance 4.48 > color zone #7 near #8 distance 4.38 > color zone #7 near #8 distance 4.28 > color zone #7 near #8 distance 4.18 > color zone #7 near #8 distance 4.08 > color zone #7 near #8 distance 3.98 > color zone #7 near #8 distance 3.88 > color zone #7 near #8 distance 3.78 > color zone #7 near #8 distance 3.68 > volume #7 level 0.02515 > volume #7 level 0.01677 > volume #7 level 0.0124 > volume #7 level 0.01476 > color zone #7 near #8 distance 3.58 > color zone #7 near #8 distance 3.48 > color zone #7 near #8 distance 3.38 > color zone #7 near #8 distance 3.28 > color zone #7 near #8 distance 3.18 > color zone #7 near #8 distance 3.08 > color zone #7 near #8 distance 2.98 > color zone #7 near #8 distance 2.88 > color zone #7 near #8 distance 2.78 > color zone #7 near #8 distance 2.68 > color zone #7 near #8 distance 2.58 > color zone #7 near #8 distance 2.48 > color zone #7 near #8 distance 2.38 > color zone #7 near #8 distance 2.28 > volume #7 level 0.01112 > color zone #7 near #8 distance 2.18 > color zone #7 near #8 distance 2.08 > color zone #7 near #8 distance 1.98 > color zone #7 near #8 distance 1.88 > color zone #7 near #8 distance 1.98 > color zone #7 near #8 distance 2.08 > volume splitbyzone #7 Opened rOAT1-PBD_IF.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at level 0.0111, step 1, values float32 Opened rOAT1-PBD_IF.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at level 0.0111, step 1, values float32 Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at level 0.0111, step 1, values float32 > close #9.1-2 > color #9.3 #ff000096 models > color #9.3 #ffff0096 models > color #9.3 #ffffff96 models > color #9.3 #ffffb296 models > select add #8 3912 atoms, 3985 bonds, 522 residues, 1 model selected > color #8 #ffffddff > color #8 gold > select clear > select add #8 3912 atoms, 3985 bonds, 522 residues, 1 model selected > color sel byhetero > select clear > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 19133, resource id: 35655670, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/postprocess.mrc Opened postprocess.mrc as #10, grid size 320,320,320, pixel 0.83, shown at level 0.00409, step 2, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 23804, resource id: 35655680, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/rOAT1-PBD_OF- > coot-0.pdb Chain information for rOAT1-PBD_OF-coot-0.pdb #11 --- Chain | Description A | No description available > hide #!9 models > hide #8 models > rename #10 rOAT1-PBD_OF > rename #10 rOAT1-PBD_OF.mrc > show #!2 models > volume #10 level 0.004712 > volume #10 step 1 > volume #10 level 0.01128 > hide #!2 models > select add #11 3872 atoms, 3966 bonds, 500 residues, 1 model selected > view matrix models #11,1,0,0,65.11,0,1,0,69.986,0,0,1,61.035 > view matrix models #11,1,0,0,68.61,0,1,0,68.058,0,0,1,65.073 > view matrix models #11,1,0,0,67.516,0,1,0,68.105,0,0,1,67.386 > fitmap #11 inMap #10 Fit molecule rOAT1-PBD_OF-coot-0.pdb (#11) to map rOAT1-PBD_OF.mrc (#10) using 3872 atoms average map value = 0.01531, steps = 56 shifted from previous position = 2.42 rotated from previous position = 0.764 degrees atoms outside contour = 1505, contour level = 0.011277 Position of rOAT1-PBD_OF-coot-0.pdb (#11) relative to rOAT1-PBD_OF.mrc (#10) coordinates: Matrix rotation and translation 0.99995211 0.00939248 0.00274947 65.65298070 -0.00936721 0.99991506 -0.00906240 67.47749964 -0.00283436 0.00903621 0.99995516 65.83404461 Axis 0.67891074 0.20945939 -0.70370943 Axis point 6981.74049553 -6059.62250131 0.00000000 Rotation angle (degrees) 0.76372650 Shift along axis 12.37827175 > show sel atoms > hide #!10 models > show #!10 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF- > coot-7_real_space_refined_008.pdb Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #12 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!12 to #11 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rOAT1-PBD_OF-coot-0.pdb, chain A (#11) with rOAT1-PBD_OF- coot-7_real_space_refined_008.pdb, chain A (#12), sequence alignment score = 2423.1 RMSD between 470 pruned atom pairs is 0.696 angstroms; (across all 485 pairs: 1.080) > hide #11 models > select subtract #11 Nothing selected > show #11 models > hide #!12 models > hide #!10 models > show #!12 models > close #11 > color #12 #bb4455ff > color #12 #b4503bff QXcbConnection: XCB error: 3 (BadWindow), sequence: 15705, resource id: 35655708, major code: 40 (TranslateCoords), minor code: 0 > show #!10 models > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 19760, resource id: 35655718, major code: 40 (TranslateCoords), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 19772, resource id: 35655713, major code: 40 (TranslateCoords), minor code: 0 > color #10 #ffb2ff96 models > volume #10 level 0.009218 > volume #10 level 0.008059 > color #10 #ffb2ffff models > select add #12 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected > hide #!10 models > color #12 white > select clear > select #12/B:601@C11 1 atom, 1 residue, 1 model selected > select up 37 atoms, 37 bonds, 1 residue, 1 model selected > color sel red > color #10 white models > select add #10 37 atoms, 37 bonds, 1 residue, 3 models selected > select subtract #10 37 atoms, 37 bonds, 1 residue, 1 model selected > show #!10 models > color zone #10 near #12 distance 2 > color zone #10 near #12 distance 1.9 > color zone #10 near #12 distance 1.8 > color zone #10 near #12 distance 1.7 > color zone #10 near #12 distance 1.8 > color zone #10 near #12 distance 1.9 > color zone #10 near #12 distance 2 [Repeated 1 time(s)] > volume splitbyzone #10 Opened rOAT1-PBD_OF.mrc 0 as #11.1, grid size 320,320,320, pixel 0.83, shown at level 0.00806, step 1, values float32 Opened rOAT1-PBD_OF.mrc 1 as #11.2, 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 > volume splitbyzone #10 Opened rOAT1-PBD_OF.mrc 0 as #13.1, grid size 320,320,320, pixel 0.83, shown at level 0.00806, step 1, values float32 Opened rOAT1-PBD_OF.mrc 1 as #13.2, 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 > close #11.1-2 > hide #!12 models > hide #!11.3 models > hide #!11 models > select add #12 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected > select subtract #12 Nothing selected > close #13.1-2 > show #!12 models > color #11.3 white models > color #11.3 #ffffb2ff models > color #13.3 white models > color #13.3 #ffffb2ff models > select add #12 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #12 #bb4455ff > color #12 #b4503bff > color (#!12 & sel) byhetero > select #12/A:440 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #12 3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected > select subtract #12 Nothing selected > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > hide #!13 models > hide #!13.3 models > hide #!12 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/inward_j152_2.7A/postprocess.mrc Opened postprocess.mrc as #14, grid size 320,320,320, pixel 0.83, shown at level 0.00408, step 2, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 27239, resource id: 35655778, major code: 40 (TranslateCoords), minor code: 0 > show #!2 models > hide #!2 models > rename #14 rOAT1-TFV_IF.mrc > show #1 models > hide #!14 models > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF.pdb > models #1 relModel #14 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_5/rOAT1-TFV_IF- > coot-2_real_space_refined_005.pdb Chain information for rOAT1-TFV_IF-coot-2_real_space_refined_005.pdb #15 --- Chain | Description A | No description available > hide #1 models > show #!14 models > color #15 white > color #14 white models > select ::name=""TFV"" 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > color zone #14 near #15 distance 4.68 > color zone #14 near #15 distance 4.58 > color zone #14 near #15 distance 4.48 > color zone #14 near #15 distance 4.38 > color zone #14 near #15 distance 4.28 > color zone #14 near #15 distance 4.18 > color zone #14 near #15 distance 4.08 > color zone #14 near #15 distance 3.98 > color zone #14 near #15 distance 3.88 > color zone #14 near #15 distance 3.78 > color zone #14 near #15 distance 3.68 > color zone #14 near #15 distance 3.58 > color zone #14 near #15 distance 3.48 > color zone #14 near #15 distance 3.38 > color zone #14 near #15 distance 3.28 > color zone #14 near #15 distance 3.18 > color zone #14 near #15 distance 3.08 > color zone #14 near #15 distance 2.98 > color zone #14 near #15 distance 2.88 > color zone #14 near #15 distance 2.78 > color zone #14 near #15 distance 2.68 > volume #14 level 0.007613 > color zone #14 near #15 distance 2.78 > color zone #14 near #15 distance 2.88 > color zone #14 near #15 distance 2.98 > color zone #14 near #15 distance 2.88 > color zone #14 near #15 distance 2.78 > color zone #14 near #15 distance 2.68 > color zone #14 near #15 distance 2.58 > color zone #14 near #15 distance 2.48 > color zone #14 near #15 distance 2.38 > volume #14 level 0.005915 > volume #14 level 0.005632 > volume splitbyzone #14 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, values float32 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, 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 > close #16.1-2 > color zone #14 near #15 distance 2.09 > close #16#16.3 > show #!14 models > color zone #14 near #15 distance 1.99 > color zone #14 near #15 distance 2.09 > color zone #14 near #15 distance 2.19 > color zone #14 near #15 distance 2.29 > color zone #14 near #15 distance 2.39 > color zone #14 near #15 distance 2.29 > volume splitbyzone #14 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, values float32 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, 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 > close #16.1-2 > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > color #16.3 #ff5500ff models > color #16.3 #aa0000ff models > color #16.3 #ff5500ff models > color #16.3 #ff557fff models > color #15 #ff557fff > color #16.3 white models > color #16.3 #ffffb2ff models > color #16.3 #ffffb296 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF- > coot-3.pdb Chain information for rOAT1-TFV_IF-coot-3.pdb #17 --- Chain | Description A | No description available > close #17#16#16.3 > close #15 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF- > coot-3.pdb Chain information for rOAT1-TFV_IF-coot-3.pdb #15 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 28850, resource id: 35656402, major code: 40 (TranslateCoords), minor code: 0 > show #!14 models > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > select subtract #15 Nothing selected > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > color #15 white > color zone #14 near #15 distance 2.29 > select ::name=""TFV"" 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > color zone #14 near #15 distance 2.29 > color zone #14 near #15 distance 2.19 > color zone #14 near #15 distance 2.09 > color zone #14 near #15 distance 1.99 > color zone #14 near #15 distance 1.89 > color zone #14 near #15 distance 1.79 > color zone #14 near #15 distance 1.69 > color zone #14 near #15 distance 1.59 > color zone #14 near #15 distance 1.49 > color zone #14 near #15 distance 1.39 > color zone #14 near #15 distance 1.29 > color zone #14 near #15 distance 1.19 > color zone #14 near #15 distance 1.09 > color zone #14 near #15 distance 1.19 > color zone #14 near #15 distance 1.29 > color zone #14 near #15 distance 1.39 > color zone #14 near #15 distance 1.49 > color zone #14 near #15 distance 1.59 > color zone #14 near #15 distance 1.69 > color zone #14 near #15 distance 1.79 > color zone #14 near #15 distance 1.89 > color zone #14 near #15 distance 1.99 > color zone #14 near #15 distance 2.09 [Repeated 1 time(s)] > volume splitbyzone #14 Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, values float32 Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown at level 0.00563, step 1, 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 > close #16.1-2 > color #16.3 white models > color #16.3 #ffffb2ff models > color #16.3 #ffffb296 models > color #15 #ff5500ff > color #15 #ff557fff > select add #15 3917 atoms, 3998 bonds, 515 residues, 1 model selected > color sel byhetero > select clear > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/postprocess.mrc Opened postprocess.mrc as #17, grid size 320,320,320, pixel 0.83, shown at level 0.00401, step 2, values float32 > rename #17 rOAT1-TVF_OF.mrc > hide #15 models > hide #!16 models > show #8 models > hide #8 models > show #!11.3 models > hide #!11 models > hide #!11.3 models > show #!12 models > volume #17 step 1 > volume #17 level 0.01305 > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb > models #12 relModel #17 > hide #!16.3 models > hide #!12 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb Chain information for rOAT1-TFV_OF.pdb #18 --- Chain | Description A | No description available > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > close #18 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV_OF- > coot-1_real_space_refined_007.pdb Chain information for rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb #18 --- Chain | Description A | No description available > select add #18 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #18 white > color #17 white models > select #18/A:601@H131 1 atom, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > volume #17 level 0.011 > color zone #17 near #18 distance 4.98 > color zone #17 near #18 distance 4.88 > color zone #17 near #18 distance 4.78 > color zone #17 near #18 distance 4.68 > color zone #17 near #18 distance 4.58 > color zone #17 near #18 distance 4.48 > color zone #17 near #18 distance 4.38 > color zone #17 near #18 distance 4.28 > color zone #17 near #18 distance 4.18 > color zone #17 near #18 distance 4.08 > color zone #17 near #18 distance 3.98 > color zone #17 near #18 distance 3.88 > color zone #17 near #18 distance 3.78 > color zone #17 near #18 distance 3.68 > color zone #17 near #18 distance 3.58 > color zone #17 near #18 distance 3.48 > color zone #17 near #18 distance 3.38 > color zone #17 near #18 distance 3.28 > color zone #17 near #18 distance 3.18 > color zone #17 near #18 distance 3.08 > color zone #17 near #18 distance 2.98 > 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 > close #19.1-2 > color #19.3 white models > color #19.3 #ffffb2ff models > select add #18 3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #18 #337744ff > color #18 #374c02ff > color (#!18 & sel) byhetero > select clear > color #19.3 #ffffb296 models > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/inward_j112_2.6A/postprocess.mrc Opened postprocess.mrc as #20, grid size 320,320,320, pixel 0.83, shown at level 0.00494, step 2, values float32 > volume #20 step 1 > hide #!19 models > hide #!18 models > rename #20 rOAT1-AAI_IF.mrc > volume #20 level 0.0194 QXcbConnection: XCB error: 3 (BadWindow), sequence: 35473, resource id: 35656688, major code: 40 (TranslateCoords), minor code: 0 > show #!2 models > hide #!2 models > show #1 models > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb > models #1 relModel #20 > hide #1 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb Chain information for rOAT1-AAI_IF.pdb #21 --- Chain | Description A | No description available > close #21 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_1/rOAT1-AAI_IF_real_space_refined_001.pdb Chain information for rOAT1-AAI_IF_real_space_refined_001.pdb #21 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 12758, resource id: 35656914, major code: 40 (TranslateCoords), minor code: 0 > close #21 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF- > coot-1_real_space_refined_003_initial.geo Unrecognized file suffix '.geo' > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF- > coot-1_real_space_refined_003.pdb Chain information for rOAT1-AAI_IF-coot-1_real_space_refined_003.pdb #21 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 49188, resource id: 35657106, major code: 40 (TranslateCoords), minor code: 0 > select add #21 3956 atoms, 4042 bonds, 516 residues, 1 model selected > color #21 white > color #20 white models > select clear > select #21/A:602@O24 1 atom, 1 residue, 1 model selected > select up 35 atoms, 38 bonds, 1 residue, 1 model selected > select #21/A:601@O20 1 atom, 1 residue, 1 model selected > select add #21/A:602@C23 2 atoms, 2 residues, 1 model selected > select up 70 atoms, 76 bonds, 2 residues, 1 model selected > color sel red > color zone #20 near #21 distance 4.98 > color zone #20 near #21 distance 4.88 > color zone #20 near #21 distance 4.78 > color zone #20 near #21 distance 4.68 > color zone #20 near #21 distance 4.58 > color zone #20 near #21 distance 4.48 > color zone #20 near #21 distance 4.38 > color zone #20 near #21 distance 4.28 > color zone #20 near #21 distance 4.18 > color zone #20 near #21 distance 4.08 > color zone #20 near #21 distance 3.98 > color zone #20 near #21 distance 3.88 > color zone #20 near #21 distance 3.78 > color zone #20 near #21 distance 3.68 > color zone #20 near #21 distance 3.58 > color zone #20 near #21 distance 3.48 > color zone #20 near #21 distance 3.38 > color zone #20 near #21 distance 3.28 > color zone #20 near #21 distance 3.18 > color zone #20 near #21 distance 3.08 > color zone #20 near #21 distance 2.98 > color zone #20 near #21 distance 2.88 > volume splitbyzone #20 Opened rOAT1-AAI_IF.mrc 0 as #22.1, grid size 320,320,320, pixel 0.83, shown at level 0.0194, step 1, values float32 Opened rOAT1-AAI_IF.mrc 1 as #22.2, 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 0.0194, step 1, values float32 > close #22.1-2 > color #22.3 yellow models > color #22.3 white models > color #22.3 #ffffb2ff models > color #22.3 #ffffb296 models > select add #21 3956 atoms, 4042 bonds, 516 residues, 1 model selected > color #21 #668855ff > color #21 #685d73ff > color sel byhetero > select clear [Repeated 1 time(s)] > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 7603, resource id: 35657141, major code: 40 (TranslateCoords), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 7615, resource id: 35657136, major code: 40 (TranslateCoords), minor code: 0 > hide #!22.3 models > hide #!22 models > hide #21 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/postprocess.mrc Opened postprocess.mrc as #23, grid size 320,320,320, pixel 0.83, shown at level 0.00494, step 2, values float32 > volume #23 level 0.01307 > volume #23 step 1 > volume #23 level 0.01684 > show #1 models > hide #1 models > show #!5 models > rename #23 rOAT1-AAI_OF.mrc > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/rOAT1-AAI_OF.pdb > models #5 relModel #23 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_4/rOAT1-AAI_OF- > coot-1_real_space_refined_004.pdb Chain information for rOAT1-AAI_OF-coot-1_real_space_refined_004.pdb #24 --- Chain | Description A | No description available > color #23 white models > color #24 white > hide #!5 models > select add #24/A:601@O24 1 atom, 1 residue, 1 model selected > select add #24/A:230@OH 2 atoms, 2 residues, 1 model selected > select clear > select add #24/A:601@O24 1 atom, 1 residue, 1 model selected > select up 35 atoms, 38 bonds, 1 residue, 1 model selected > color sel red > color zone #23 near #24 distance 4.98 > volume splitbyzone #23 Opened rOAT1-AAI_OF.mrc 0 as #25.1, grid size 320,320,320, pixel 0.83, shown at level 0.0168, step 1, values float32 Opened rOAT1-AAI_OF.mrc 1 as #25.2, 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 > close #25.1-2 > select add #24 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected > select subtract #24 Nothing selected > color #25.3 white models > color #25.3 #ffffb2ff models > select add #24 3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected > color #24 #1177ccff > color #24 #17c127ff > color (#!24 & sel) byhetero > select #24/A:438@CE2 1 atom, 1 residue, 1 model selected Drag select of 1 atoms, 1 bonds > select clear > color #25.3 #ffffb296 models > select clear > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > open > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/rOAT1-PAH- > coot-7_real_space_refined_007.pdb Chain information for rOAT1-PAH-coot-7_real_space_refined_007.pdb #26 --- Chain | Description A | No description available QXcbConnection: XCB error: 3 (BadWindow), sequence: 7338, resource id: 35657291, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/cryosparc_P4_J89__localfilter_160.mrc Opened cryosparc_P4_J89__localfilter_160.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level 0.134, step 1, values float32 > hide #!24 models > hide #!25.3 models > hide #!25 models > view > show #!2 models > select add #26 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected > select add #27 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 4 models selected > view matrix models > #26,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865,#27,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865 > view matrix models > #26,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563,#27,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563 > rename #27 rOAT1-PAH > rename #27 rOAT1-PAH.mrc > view > fitmap #26 inMap #27 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map rOAT1-PAH.mrc (#27) using 3865 atoms average map value = 0.3441, steps = 44 shifted from previous position = 0.0131 rotated from previous position = 0.0158 degrees atoms outside contour = 699, contour level = 0.13428 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to rOAT1-PAH.mrc (#27) coordinates: Matrix rotation and translation 0.99999996 -0.00021122 0.00016567 0.00535685 0.00021123 0.99999998 -0.00006568 0.00053709 -0.00016566 0.00006571 0.99999998 -0.00148379 Axis 0.23771757 0.59945172 0.76429575 Axis point -1.23064203 24.84299856 0.00000000 Rotation angle (degrees) 0.01583428 Shift along axis 0.00046132 > hide #!2 models > color #27 white models > color #26 white > hide #!26 models > select subtract #27 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected > select subtract #26 Nothing selected > hide #!27 models > show #!26 models > select #26/B:601@C07 1 atom, 1 residue, 1 model selected > select up 23 atoms, 23 bonds, 1 residue, 1 model selected > color sel red > show #!27 models > color zone #27 near #26 distance 4.98 > color zone #27 near #26 distance 4.88 > color zone #27 near #26 distance 4.78 > color zone #27 near #26 distance 4.68 > color zone #27 near #26 distance 4.58 > color zone #27 near #26 distance 4.48 > color zone #27 near #26 distance 4.38 > color zone #27 near #26 distance 4.28 > color zone #27 near #26 distance 4.18 > color zone #27 near #26 distance 4.08 > color zone #27 near #26 distance 3.98 > color zone #27 near #26 distance 3.88 > color zone #27 near #26 distance 3.78 > color zone #27 near #26 distance 3.68 > color zone #27 near #26 distance 3.58 > color zone #27 near #26 distance 3.48 > color zone #27 near #26 distance 3.38 > color zone #27 near #26 distance 3.28 > color zone #27 near #26 distance 3.18 > color zone #27 near #26 distance 3.08 > color zone #27 near #26 distance 2.98 > color zone #27 near #26 distance 2.88 > color zone #27 near #26 distance 2.78 > color zone #27 near #26 distance 2.68 > color zone #27 near #26 distance 2.58 > color zone #27 near #26 distance 2.48 > color zone #27 near #26 distance 2.38 > color zone #27 near #26 distance 2.28 > volume #27 level 0.1207 > color zone #27 near #26 distance 2.18 > color zone #27 near #26 distance 2.08 > hide #!27 models > show #!27 models > fitmap #26 inMap #27 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map rOAT1-PAH.mrc (#27) using 3865 atoms average map value = 0.3441, steps = 44 shifted from previous position = 0.00509 rotated from previous position = 0.0145 degrees atoms outside contour = 605, contour level = 0.12073 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to rOAT1-PAH.mrc (#27) coordinates: Matrix rotation and translation 1.00000000 -0.00003177 0.00004592 0.00408484 0.00003177 1.00000000 0.00006809 -0.00110606 -0.00004592 -0.00006809 1.00000000 0.00040828 Axis -0.77323345 0.52146975 0.36080373 Axis point 0.00000000 25.00840435 -11.23310139 Rotation angle (degrees) 0.00504562 Shift along axis -0.00358800 > fitmap #26 inMap #27 Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map rOAT1-PAH.mrc (#27) using 3865 atoms average map value = 0.3441, steps = 40 shifted from previous position = 0.0153 rotated from previous position = 0.0197 degrees atoms outside contour = 607, contour level = 0.12073 Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to rOAT1-PAH.mrc (#27) coordinates: Matrix rotation and translation 0.99999998 -0.00017402 -0.00004728 0.01145050 0.00017401 0.99999996 -0.00023139 -0.00012574 0.00004732 0.00023138 0.99999997 -0.01696563 Axis 0.78875519 -0.16123857 0.59318410 Axis point 0.00000000 70.72803400 -1.26127659 Rotation angle (degrees) 0.01680827 Shift along axis -0.00101183 > volume splitbyzone #27 Opened rOAT1-PAH.mrc 0 as #28.1, grid size 160,160,160, pixel 0.83, shown at level 0.121, step 1, values float32 Opened rOAT1-PAH.mrc 1 as #28.2, 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 0.121, step 1, values float32 > close #28.1-2 > volume #28.3 level 0.05463 > color #28.3 white models > color #28.3 #ffffb2ff models > color #28.3 #ffffb296 models > select add #26 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected > color #26 #bf3434ff > select subtract #26 Nothing selected > hide #!26 models > hide #!28 models > hide #!28.3 models > show #!28 models > show #!28.3 models > hide #!28 models > show #!28 models > show #!26 models > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 59852, resource id: 35657337, major code: 40 (TranslateCoords), minor code: 0 > hide #!26 models > hide #!28 models > hide #!28.3 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220525_rOAT1-FBP/inward_j46_2.8A/postprocess.mrc Opened postprocess.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level 0.0068, step 2, values float32 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-FBP_model/rOAT1-FBP_Model04_RSR_004.pdb Chain information for rOAT1-FBP_Model04_RSR_004.pdb #30 --- Chain | Description A | No description available > show #!2 models > volume #29 step 1 > volume #29 level 0.01695 > select add #30 4327 atoms, 4393 bonds, 591 residues, 1 model selected > view matrix models #30,1,0,0,75.395,0,1,0,59.328,0,0,1,65.467 > view matrix models #30,1,0,0,69.37,0,1,0,69.752,0,0,1,66.8 > view matrix models #30,1,0,0,64.899,0,1,0,72.303,0,0,1,66.211 > view matrix models #30,1,0,0,67.675,0,1,0,68.154,0,0,1,64.823 > rename #29 rOAT1-FBP.mrc > fitmap #30 inMap #29 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29) using 4327 atoms average map value = 0.02366, steps = 64 shifted from previous position = 2.15 rotated from previous position = 1.57 degrees atoms outside contour = 1497, contour level = 0.016951 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc (#29) coordinates: Matrix rotation and translation 0.99965949 -0.01809184 -0.01880406 69.16631575 0.01825291 0.99979787 0.00842953 64.90387685 0.01864775 -0.00876989 0.99978765 65.39100171 Axis -0.31300664 -0.68157330 0.66142625 Axis point -4271.01743380 0.00000000 3378.83285764 Rotation angle (degrees) 1.57437238 Shift along axis -22.63494048 > fitmap #29 inMap #28.3 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points correlation = 0.04397, correlation about mean = 0.03331, overlap = 0.1449 steps = 2000, shift = 8.88, angle = 34.9 degrees Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3) coordinates: Matrix rotation and translation 0.83021101 -0.04922054 -0.55527201 36.70411652 0.13130357 0.98533433 0.10897540 -101.23145590 0.54176475 -0.16338178 0.82449824 -98.97434819 Axis -0.23793623 -0.95839145 0.15770918 Axis point 214.13564799 0.00000000 31.76591481 Rotation angle (degrees) 34.91302477 Shift along axis 72.67695975 > fitmap #29 inMap #28.3 Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points correlation = 0.06352, correlation about mean = 0.0448, overlap = 0.3215 steps = 1976, shift = 9.79, angle = 47.5 degrees Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3) coordinates: Matrix rotation and translation 0.44591506 0.03168285 -0.89451437 128.47676238 -0.42572042 0.88660402 -0.18081879 31.25418163 0.78735118 0.46144286 0.40883812 -156.17744024 Axis 0.34576253 -0.90543486 -0.24624374 Axis point 186.53313716 0.00000000 6.98625710 Rotation angle (degrees) 68.24252592 Shift along axis 54.58154231 > fitmap #29 inMap #2 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points correlation = 0.2561, correlation about mean = 0.04268, overlap = 2.051 steps = 232, shift = 3.32, angle = 8.56 degrees Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: Matrix rotation and translation 0.54964589 -0.00012465 -0.83539774 175.75622877 -0.44507129 0.84621907 -0.29295875 119.06565669 0.70696602 0.53283512 0.46506536 -99.09845418 Axis 0.45744920 -0.85439368 -0.24647856 Axis point 210.95352936 0.00000000 94.96801349 Rotation angle (degrees) 64.50291620 Shift along axis 3.09624573 > select add #29 4327 atoms, 4393 bonds, 591 residues, 3 models selected > hide #!2 models > show #!2 models > hide #!2 models > show #!27 models > view matrix models > #29,0.54965,-0.00012465,-0.8354,176.85,-0.44507,0.84622,-0.29296,120.37,0.70697,0.53284,0.46507,-99.177,#30,0.99966,-0.018092,-0.018804,70.259,0.018253,0.9998,0.0084295,66.206,0.018648,-0.0087699,0.99979,65.312 > select subtract #30 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #29,0.93603,-0.13155,0.32642,-36.684,0.29946,0.78494,-0.54239,70.054,-0.18487,0.60545,0.77412,-40.4 > view matrix models > #29,0.99097,-0.1328,0.018694,4.0787,0.13411,0.98118,-0.13891,3.4116,0.00010362,0.14016,0.99013,-37.407 > ui mousemode right ""translate selected models"" > view matrix models > #29,0.99097,-0.1328,0.018694,17.811,0.13411,0.98118,-0.13891,8.06,0.00010362,0.14016,0.99013,-17.751 > view matrix models > #29,0.99097,-0.1328,0.018694,18.852,0.13411,0.98118,-0.13891,3.5023,0.00010362,0.14016,0.99013,-19.331 > fitmap #29 inMap #2 Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points correlation = 0.937, correlation about mean = 0.7119, overlap = 14.98 steps = 260, shift = 2.93, angle = 16.7 degrees Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates: Matrix rotation and translation 0.99338416 0.10541244 -0.04556454 -5.89234048 -0.10461957 0.99432199 0.01945563 14.33237930 0.04735669 -0.01455997 0.99877192 -4.89753719 Axis -0.14650897 -0.40022199 -0.90463113 Axis point 131.78683646 64.78395429 0.00000000 Rotation angle (degrees) 6.66633138 Shift along axis -0.44238796 > fitmap #30 inMap #29 Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29) using 4327 atoms average map value = 0.02366, steps = 84 shifted from previous position = 1.18 rotated from previous position = 6.66 degrees atoms outside contour = 1496, contour level = 0.016951 Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc (#29) coordinates: Matrix rotation and translation 0.99966027 -0.01808767 -0.01876641 69.16021058 0.01824668 0.99979876 0.00833662 64.90031908 0.01861185 -0.00867622 0.99978914 65.39198117 Axis -0.31026139 -0.68166338 0.66262576 Axis point -4271.35731029 0.00000000 3392.84555643 Rotation angle (degrees) 1.57107230 Shift along axis -22.36750269 > select subtract #29 Nothing selected > hide #!27 models > color #29 white models > color #30 white > select ::name=""FBP"" 18 atoms, 19 bonds, 1 residue, 1 model selected > color sel red > color zone #29 near #30 distance 4.98 > volume #29 level 0.01043 > volume splitbyzone #29 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at level 0.0104, step 1, values float32 Opened rOAT1-FBP.mrc 1 as #31.2, 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 0.0104, step 1, values float32 > close #31.1-2 > volume #31.3 level 0.002491 > volume #31.3 level 0.005476 > close #31#31.3 > show #!29 models > color zone #29 near #30 distance 2 [Repeated 1 time(s)] > volume splitbyzone #29 Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at level 0.0104, step 1, values float32 Opened rOAT1-FBP.mrc 1 as #31.2, 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 0.0104, step 1, values float32 > close #31.1-2 > volume #31.3 level 0.003802 > color #31.3 white models > color #31.3 #ffffb2ff models > color #31.3 #ffffb20f models > color #31.3 #ffffb296 models > select add #30 4327 atoms, 4393 bonds, 591 residues, 1 model selected > color #30 #889944ff > color #30 #894a08ff > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > hide #!31.3 models > hide #!31 models > select subtract #30 Nothing selected > hide #30 models > show #!2 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220609_rOAT1-CFM/inward_j194_2.7A/postprocess.mrc Opened postprocess.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level 0.00396, step 2, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 4668, resource id: 35657387, major code: 40 (TranslateCoords), minor code: 0 > volume #32 step 1 > volume #32 level 0.01186 > rename #32 rOAT1-CFM.mrc > fitmap #31.3 inMap #32 Fit map rOAT1-FBP.mrc 2 in map rOAT1-CFM.mrc using 186 points correlation = 0.7788, correlation about mean = 0.1794, overlap = 0.008643 steps = 80, shift = 1.06, angle = 39.7 degrees Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-CFM.mrc (#32) coordinates: Matrix rotation and translation 0.74404465 0.65679786 0.12253212 -67.09990326 -0.66239846 0.70118044 0.26376935 89.56606533 0.08732602 -0.27742126 0.95677145 29.93219993 Axis -0.37942983 0.02468307 -0.92489121 Axis point 75.79903236 131.70903838 0.00000000 Rotation angle (degrees) 45.49284979 Shift along axis -0.01355792 > fitmap #31.3 inMap #2 Fit map rOAT1-FBP.mrc 2 in map rOAT1-AZT_IF.mrc using 186 points correlation = 0.8514, correlation about mean = 0.3895, overlap = 0.01295 steps = 76, shift = 0.987, angle = 35 degrees Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-AZT_IF.mrc (#2) coordinates: Matrix rotation and translation 0.98357109 0.17790518 -0.03062105 -15.98050765 -0.17592201 0.98266732 0.05844983 19.75924781 0.04048883 -0.05210265 0.99782061 1.12732183 Axis -0.29288928 -0.18839308 -0.93740275 Axis point 102.41456930 99.44616144 0.00000000 Rotation angle (degrees) 10.87852675 Shift along axis -0.09874061 > fitmap #32 inMap #2 Fit map rOAT1-CFM.mrc in map rOAT1-AZT_IF.mrc using 30016 points correlation = 0.9542, correlation about mean = 0.7898, overlap = 13.57 steps = 72, shift = 2.43, angle = 7.06 degrees Position of rOAT1-CFM.mrc (#32) relative to rOAT1-AZT_IF.mrc (#2) coordinates: Matrix rotation and translation 0.99240829 0.11776796 -0.03544703 -8.88787383 -0.11778889 0.99303752 0.00150464 18.44106769 0.03537743 0.00268205 0.99937042 -5.69387210 Axis 0.00478670 -0.28793162 -0.95763901 Axis point 151.76616064 85.25679566 0.00000000 Rotation angle (degrees) 7.06459913 Shift along axis 0.10036409 > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb > models #30 relModel #32 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb Chain information for rOAT1-CFM_IF.pdb #33 --- Chain | Description A | No description available > color #33 #ffff7fff > color #33 #55aaffff > select add #33 4327 atoms, 4393 bonds, 591 residues, 1 model selected > view matrix models #33,1,0,0,-3.2206,0,1,0,10.827,0,0,1,-3.1224 > view matrix models #33,1,0,0,-4.4307,0,1,0,11.668,0,0,1,-3.5924 > view matrix models #33,1,0,0,-4.3326,0,1,0,9.3726,0,0,1,-2.8036 > fitmap #33 inMap #32 Fit molecule rOAT1-CFM_IF.pdb (#33) to map rOAT1-CFM.mrc (#32) using 4327 atoms average map value = 0.0191, steps = 80 shifted from previous position = 1.1 rotated from previous position = 7.12 degrees atoms outside contour = 1362, contour level = 0.01186 Position of rOAT1-CFM_IF.pdb (#33) relative to rOAT1-CFM.mrc (#32) coordinates: Matrix rotation and translation 0.99999299 -0.00023005 -0.00373680 -4.70643521 0.00021365 0.99999035 -0.00438786 8.58155234 0.00373777 0.00438703 0.99998339 -3.97966882 Axis 0.76069466 -0.64796926 0.03846397 Axis point 0.00000000 827.85989235 581.48051316 Rotation angle (degrees) 0.33046593 Shift along axis -9.29381608 > save /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM.pdb > models #33 relModel #32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 60371, resource id: 35657459, major code: 40 (TranslateCoords), minor code: 0 > hide #33 models > hide #!32 models > select subtract #33 Nothing selected > show #!17 models > hide #!17 models > show #!17 models > hide #!2 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV- > Cl_OF-coot-2.pdb Chain information for rOAT1-TFV-Cl_OF-coot-2.pdb #34 --- Chain | Description A | No description available > select ::name=""CL"" 1 atom, 1 residue, 1 model selected > hide #!17 models > show sel atoms > show #!17 models > style sel stick Changed 1 atom style > color zone #17 near #34 distance 2.98 > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected > color #34 white > color zone #17 near #34 distance 2.98 > select ::name=""CL"" 1 atom, 1 residue, 1 model selected > color sel red > color zone #17 near #34 distance 2.98 > volume splitbyzone #17 Opened rOAT1-TVF_OF.mrc 0 as #35.1, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 1 as #35.2, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 Opened rOAT1-TVF_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83, shown at level 0.011, step 1, values float32 > rename #35 ""rOAT1-TVF-Cl_OF.mrc split"" > close #35.1-2 > rename #35.3 ""rOAT1-TVF-Cl_OF.mrc 2"" > hide #!35.3 models > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > ui tool show Contacts > contacts sel interModel false ignoreHiddenModels true select true 6 contacts > ui tool show Contacts > contacts sel intraRes true ignoreHiddenModels true select true 15 contacts > show sel atoms > color #34 yellow > show sel atoms > close #36 > select add #34 3787 atoms, 3876 bonds, 11 pseudobonds, 487 residues, 3 models selected > color #34 white > hide sel atoms > select ::name=""CL"" 1 atom, 1 residue, 1 model selected > show sel atoms > hide #35.3.1 models > show #35.3.1 models > close #34.2 > hide #!35.3 models > hide #35.3.1 models > hide #!35 models > hide #34.1 models > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > select #34/A:216 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #34/A:511 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #34: 219 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #34: 273 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #34/A:4 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select add #34/A:511 15 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > select add #34/A:512 23 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > color sel lime > color #35.3.1 white > color #35.3.1 #ffffb2ff > color #35.3.1 #ffffb296 > 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 > color #34 #374c02ff > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > color sel lime > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected > color (#!34 & sel) byhetero > select #34/A:2 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select #34/A:3 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select add #34/A:215 18 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > select #34/B:1@CL 1 atom, 1 residue, 1 model selected > show #35.3.1 models > view sel > hide #35.3.1 models > hide #!35.3 models > hide #!35 models > hide #!34 models > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected > select subtract #34 Nothing selected > show #1 models > view > hide #1 models > show #21 models > select add #21/A:602@C12 1 atom, 1 residue, 1 model selected > select up 3 atoms, 1 bond, 2 residues, 1 model selected > select up 44 atoms, 46 bonds, 2 residues, 1 model selected > select clear > select #21/A:602@O14 1 atom, 1 residue, 1 model selected > select add #21/A:601@C04 2 atoms, 2 residues, 1 model selected > select up 70 atoms, 76 bonds, 2 residues, 1 model selected > view sel > show #!22.3 models > hide #!22.3 models > hide #!22 models > hide #21 models > select add #21 3956 atoms, 4042 bonds, 516 residues, 1 model selected > select subtract #21 Nothing selected > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 40781, resource id: 35657669, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/postprocess.mrc Opened postprocess.mrc as #36, grid size 320,320,320, pixel 0.83, shown at level 0.00418, step 2, values float32 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for solute carrier family 22 member 6 (Q4U2R8) [more info...] Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #37 --- Chain | Description | UniProt A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 > rename #36 hOAT1-TFV.mrc > volume #36 step 1 > volume #36 level 0.008515 > rename #37 hOAT1-TFV_IF.pdb > view > show #!2 models > hide #!2 models > ui tool show Matchmaker > matchmaker #37 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A (#37), sequence alignment score = 2359.6 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs: 0.862) > matchmaker #37 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A (#37), sequence alignment score = 2359.6 RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs: 0.862) > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1-TVF_IF.pdb > models #37 relModel #36 > rename #36 hOAT1-TFV_IF.mrc > hide #37 models > hide #!36 models > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb hOAT1_AF-Q4U2R8-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for solute carrier family 22 member 6 (Q4U2R8) [more info...] Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #38 --- Chain | Description | UniProt A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563 > close #38 > close #37 > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/RealSpaceRefine_2/hOAT1-TVF_IF- > coot-1_real_space_refined_002.pdb Chain information for hOAT1-TVF_IF-coot-1_real_space_refined_002.pdb #37 --- Chain | Description A | No description available > show #!36 models > color #36 white models > color #37 white > hide #!36 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select #37/A:601@C08 1 atom, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > show #!36 models > color zone #36 near #37 distance 4.98 > color zone #36 near #37 distance 2 [Repeated 1 time(s)] > color zone #36 near #37 distance 1.9 > color zone #36 near #37 distance 1.8 > color zone #36 near #37 distance 1.7 > volume splitbyzone #36 Opened hOAT1-TFV_IF.mrc 0 as #38.1, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 Opened hOAT1-TFV_IF.mrc 1 as #38.2, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown at level 0.00852, step 1, values float32 > close #38.1-2 > color #38.3 white models > color #38.3 #ffffb2ff models > color #38.3 #ffffb296 models > color #37 #aaff7fff > select add #37 4375 atoms, 4481 bonds, 564 residues, 1 model selected > color sel byhetero > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true QXcbConnection: XCB error: 3 (BadWindow), sequence: 48690, resource id: 35657985, major code: 40 (TranslateCoords), minor code: 0 > hide #!38.3 models > hide #!38 models > select subtract #37 Nothing selected > show #!34 models Drag select of 25 atoms, 383 residues, 24 bonds > select up 2906 atoms, 2958 bonds, 383 residues, 2 models selected > select clear > select add #37/A:326 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > hide #!34 models > select add #37 4375 atoms, 4481 bonds, 564 residues, 1 model selected > select subtract #37 Nothing selected > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb > models #37 relModel #36 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16970, resource id: 35658005, major code: 40 (TranslateCoords), minor code: 0 QXcbConnection: XCB error: 3 (BadWindow), sequence: 16981, resource id: 35657995, major code: 40 (TranslateCoords), minor code: 0 > open > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/outward_j68_3.1A/postprocess.mrc Opened postprocess.mrc as #39, grid size 320,320,320, pixel 0.83, shown at level 0.00436, step 2, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 18302, resource id: 35658010, major code: 40 (TranslateCoords), minor code: 0 > rename #39 hOAT1-TFV_OF.mrc > volume #39 step 1 > volume #39 level 0.01031 > hide #!39 models > open > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb Chain information for hOAT1-TFV_OF.pdb #40 --- Chain | Description A | No description available > hide #37 models > select #40: 320-600 1850 atoms, 1888 bonds, 244 residues, 1 model selected > hide sel cartoons [Repeated 1 time(s)] > show sel cartoons > ui tool show Matchmaker > matchmaker #40 & sel to #18 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb, chain A (#18) with hOAT1-TFV_OF.pdb, chain A (#40), sequence alignment score = 866.1 RMSD between 164 pruned atom pairs is 0.748 angstroms; (across all 200 pairs: 7.198) > matchmaker #40 to #15 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rOAT1-TFV_IF-coot-3.pdb, chain A (#15) with hOAT1-TFV_OF.pdb, chain A (#40), sequence alignment score = 2368.6 RMSD between 493 pruned atom pairs is 0.665 angstroms; (across all 500 pairs: 0.719) > show #!18 models > ui mousemode right ""translate selected atoms"" > ui mousemode right ""rotate selected models"" > view matrix models > #40,0.99727,-0.025813,-0.069217,13.221,0.025375,0.99965,-0.0072002,-1.7643,0.069379,0.0054242,0.99758,-8.8122 > undo > ui mousemode right ""move picked models"" > view matrix models #18,1,0,0,0.019269,0,1,0,-0.04277,0,0,1,0.28987 > undo > ui mousemode right pivot > ui tool show Matchmaker > matchmaker #40 & sel to #5 & sel No 'to' model specified > select clear > hide #!18 models > show #!18 models > select #18,40: 320-600 3274 atoms, 3340 bonds, 2 pseudobonds, 433 residues, 3 models selected > ui tool show Matchmaker > matchmaker #40 & sel to #5 & sel No 'to' model specified > matchmaker #40 & sel to #5 & sel No 'to' model specified > matchmaker #40 & sel to #5 & sel No 'to' model specified > ui mousemode right ""translate selected atoms"" > select #40: 320-600 1850 atoms, 1888 bonds, 244 residues, 1 model selected > hide #!18 models > show #!18 models > hide #40 models > hide #!18 models > show #40 models > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb > models #40 relModel #39 QXcbConnection: XCB error: 3 (BadWindow), sequence: 34583, resource id: 35658147, major code: 40 (TranslateCoords), minor code: 0 > fitmap #40 inMap #39 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375 atoms average map value = 0.007219, steps = 88 shifted from previous position = 0.909 rotated from previous position = 8.49 degrees atoms outside contour = 2887, contour level = 0.010308 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39) coordinates: Matrix rotation and translation 0.99019825 -0.07829950 -0.11565728 27.38037598 0.07892080 0.99688057 0.00079533 -10.70816731 0.11523422 -0.00991530 0.99328886 -13.08861468 Axis -0.03831490 -0.82596303 0.56242070 Axis point 128.86145300 0.00000000 225.96021530 Rotation angle (degrees) 8.03460025 Shift along axis 0.43416611 > save > /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb > models #40 relModel #39 > undo > select clear > show #!39 models > fitmap #40 inMap #39 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375 atoms average map value = 0.007218, steps = 28 shifted from previous position = 0.0175 rotated from previous position = 0.016 degrees atoms outside contour = 2888, contour level = 0.010308 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39) coordinates: Matrix rotation and translation 0.99020256 -0.07845145 -0.11551732 27.36683659 0.07909202 0.99686685 0.00096497 -10.76110579 0.11507968 -0.01009202 0.99330500 -13.04322773 Axis -0.03956067 -0.82505023 0.56367284 Axis point 128.67057833 0.00000000 226.14572082 Rotation angle (degrees) 8.03322105 Shift along axis 0.44368911 > fitmap #40 inMap #39 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375 atoms average map value = 0.007219, steps = 44 shifted from previous position = 0.00455 rotated from previous position = 0.00258 degrees atoms outside contour = 2889, contour level = 0.010308 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39) coordinates: Matrix rotation and translation 0.99020340 -0.07846932 -0.11549800 27.37049731 0.07911379 0.99686509 0.00099928 -10.76639922 0.11505751 -0.01012698 0.99330721 -13.03687370 Axis -0.03980982 -0.82492871 0.56383314 Axis point 128.62890621 0.00000000 226.21984207 Rotation angle (degrees) 8.03295687 Shift along axis 0.44127588 > select add #40 4375 atoms, 4481 bonds, 564 residues, 1 model selected > fitmap #40 inMap #39 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375 atoms average map value = 0.007219, steps = 60 shifted from previous position = 2.24 rotated from previous position = 0.00666 degrees atoms outside contour = 2889, contour level = 0.010308 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39) coordinates: Matrix rotation and translation 0.99020164 -0.07840067 -0.11555975 25.97288245 0.07903810 0.99687116 0.00093711 -9.32824593 0.11512471 -0.01006155 0.99330009 -12.03377088 Axis -0.03935047 -0.82533103 0.56327634 Axis point 116.53468443 0.00000000 214.84157931 Rotation angle (degrees) 8.03353574 Shift along axis -0.10149276 > show #!17 models > fitmap #39 inMap #19.3 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points correlation = 0.03002, correlation about mean = -0.02439, overlap = 0.01206 steps = 936, shift = 1.08, angle = 13.4 degrees Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3) coordinates: Matrix rotation and translation 0.98280665 -0.13043667 -0.13068041 37.39205996 0.11063752 0.98266445 -0.14876125 8.18112237 0.14781892 0.13174539 0.98020035 -34.01816129 Axis 0.60585490 -0.60151939 0.52068635 Axis point 0.00000000 261.98069292 24.54762139 Rotation angle (degrees) 13.38519605 Shift along axis 0.02026683 > fitmap #39 inMap #19.3 Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points correlation = 0.03002, correlation about mean = -0.0244, overlap = 0.01206 steps = 48, shift = 0.0138, angle = 0.161 degrees Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3) coordinates: Matrix rotation and translation 0.98301413 -0.12857767 -0.13096186 37.15798588 0.10847145 0.98263409 -0.15054633 8.70610140 0.14804449 0.13378355 0.97989019 -34.26954280 Axis 0.61337235 -0.60188813 0.51137563 Axis point -0.00000000 260.45263984 27.89398858 Rotation angle (degrees) 13.40165031 Shift along axis 0.02697294 > fitmap #40 inMap #39 Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375 atoms average map value = 0.007219, steps = 132 shifted from previous position = 0.778 rotated from previous position = 13.4 degrees atoms outside contour = 2889, contour level = 0.010308 Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39) coordinates: Matrix rotation and translation 0.99020454 -0.07852899 -0.11544767 25.97319443 0.07917768 0.99685998 0.00103677 -9.35919916 0.11500374 -0.01016749 0.99331302 -12.00484753 Axis -0.04009077 -0.82459474 0.56430155 Axis point 116.41047661 0.00000000 215.06686153 Rotation angle (degrees) 8.03257950 Shift along axis -0.09809308 > hide #!17 models > hide #!39 models > close #40 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF- > coot-1.pdb Chain information for hOAT1-TFV_OF-coot-1.pdb #40 --- Chain | Description A | No description available > show #!39 models > color #39 white models > color #40 white > hide #!39 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > color sel red > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > show #!39 models > color zone #39 near #40 distance 4.98 > color zone #39 near #40 distance 2 [Repeated 1 time(s)] > volume #39 level 0.01241 > open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF- > coot-2.pdb Chain information for hOAT1-TFV_OF-coot-2.pdb #41 --- Chain | Description A | No description available > hide #!40 models > color #41 white > color zone #39 near #41 distance 2 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 31 atoms, 32 bonds, 1 residue, 1 model selected > color sel red > color zone #39 near #41 distance 2 > volume #39 level 0.01056 > color zone #39 near #41 distance 2.1 > color zone #39 near #41 distance 2.2 > color zone #39 near #41 distance 2.3 > color zone #39 near #41 distance 2.4 > color zone #39 near #41 distance 2.5 > color zone #39 near #41 distance 2.6 > color zone #39 near #41 distance 2.7 > color zone #39 near #41 distance 2.8 > color zone #39 near #41 distance 2.9 > color zone #39 near #41 distance 3 > color zone #39 near #41 distance 2.9 > color zone #39 near #41 distance 2.8 > color zone #39 near #41 distance 2.7 > color zone #39 near #41 distance 2.6 > color zone #39 near #41 distance 2.5 > color zone #39 near #41 distance 2.4 > color zone #39 near #41 distance 2.3 > color zone #39 near #41 distance 2.2 > color zone #39 near #41 distance 2.1 > color zone #39 near #41 distance 2 > color zone #39 near #41 distance 1.9 > color zone #39 near #41 distance 2 > color zone #39 near #41 distance 2.1 > color zone #39 near #41 distance 2.2 > color zone #39 near #41 distance 2.3 > color zone #39 near #41 distance 2.4 > color zone #39 near #41 distance 2.5 > volume splitbyzone #39 Opened hOAT1-TFV_OF.mrc 0 as #42.1, grid size 320,320,320, pixel 0.83, shown at level 0.0106, step 1, values float32 Opened hOAT1-TFV_OF.mrc 1 as #42.2, grid size 320,320,320, pixel 0.83, shown at level 0.0106, step 1, values float32 Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown at level 0.0106, step 1, values float32 > close #42.1-2 > color #42.3 white models > color #42.3 #ffffb2ff models > color #42.3 #ffffb296 models > volume #42.3 level 0.006989 > select add #41 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected > color #41 #aaffffff > color #41 blue > color #41 red > color #41 #aa00ffff > color #41 #0055ffff > color #41 #55557fff > color #41 #ff557fff > color #41 #ffaaffff > color (#!41 & sel) byhetero > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true > show #!34 models > hide #!41 models > hide #!42 models > hide #!42.3 models > select subtract #41 Nothing selected > hide #!34 models > show #1 models > show #!3.3 models > hide #!3.3 models > hide #!3 models > hide #1 models > show #!22.3 models > show #21 models > select add #21/A:601@O25 1 atom, 1 bond, 1 residue, 1 model selected > select up 3 atoms, 1 bond, 2 residues, 1 model selected > view sel > volume #22.3 level 0.01409 > hide #!22.3 models > hide #!22 models > hide #21 models > show #!22.3 models > hide #!22.3 models > hide #!22 models > show #!23 models > hide #!23 models > show #!25.3 models > show #!24 models > hide #!25.3 models > hide #!25 models > hide #!24 models > show #1 models > show #!3.3 models > hide #!3.3 models > hide #!3 models > hide #1 models > show #!5 models > show #!6.3 models > hide #!6.3 models > hide #!6 models > hide #!5 models > show #8 models > show #!9.3 models > volume #9.3 level 0.003826 > select #8/A:230 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #8/A:227 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select clear > hide #!9.3 models > hide #!9 models > hide #8 models > show #!12 models > show #!11.3 models > color #11.3 #ffffb296 models > hide #!12 models > hide #!11.3 models > hide #!11 models > show #15 models > show #!16.3 models > hide #!16.3 models > hide #!16 models > hide #15 models > show #!18 models > show #!19.3 models > hide #!18 models > hide #!19 models > hide #!19.3 models > show #37 models > show #!38.3 models > hide #!38.3 models > hide #!38 models > hide #37 models > close #40 > show #!41 models > show #!42.3 models > hide #!42.3 models > hide #!42 models > hide #!41 models > show #!26 models > show #!28.3 models > select #26/A:230 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:200 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select add #26 3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected > color (#!26 & sel) byhetero > select clear > select #26/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:227 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:223 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:200 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:226 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #26/A:204 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > hide #!28.3 models > hide #!28 models > hide #!26 models > show #!31.3 models > show #30 models > select add #30 4327 atoms, 4393 bonds, 591 residues, 1 model selected > color sel byhetero > select clear > save > /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs > includeMaps true ——— End of log from Mon Feb 10 17:46:10 2025 ——— opened ChimeraX session > hide #!31.3 models > hide #!31 models > hide #30 models > show #!34 models > show #!35 models > show #!35.3 models > volume #35.3 level 0.01175 > select #35.3 2 models selected > view sel > color #34 tan > ui tool show ""Side View"" > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 4 models selected > color (#!34 & sel) byhetero > select clear > select #34/A:447 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #34/A:507 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true ——— End of log from Tue Mar 11 12:00:09 2025 ——— opened ChimeraX session > hide #!35.3 models > hide #!35 models > show #!17 models > color #17 #ffffb2ff models > color #17 #ffffb280 models > ui tool show ""Side View"" > color #17 #ffffb24d models > save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true ——— End of log from Thu Apr 10 14:06:06 2025 ——— opened ChimeraX session > movie record > turn y 2 180 > wait 180 > movie encode /Users/dout2/Desktop/movie1.mp4 Movie saved to /Users/dout2/Desktop/movie1.mp4 > select add #34 3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected > show sel atoms > select clear > hide #!34 models > hide #!17 models > show #!6 models > show #1 models > view > select #1/A:463 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:466 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:228 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:230 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:231 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:377 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:378 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:381 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:225 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:382 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide #!6 models > show #!6 models > hide #1 models > show #1 models > select add #1 3905 atoms, 3986 bonds, 515 residues, 1 model selected > select subtract #1 Nothing selected > hide #1 models > hide #!6 models > show #!18 models > hide #!18 models > show #1 models > select #1/A:228 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:199 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:257 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:145 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:466 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A:149 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:146 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:204 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:150 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:149 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:203 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:146 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:149 5 atoms, 4 bonds, 1 residue, 1 model selected Drag select of 13 residues > select #1/A:463 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A:466@CZ 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Contacts > contacts sel intraRes true ignoreHiddenModels true select true > makePseudobonds false reveal true 26 contacts > select clear > select : 382 126 atoms, 112 bonds, 14 residues, 14 models selected > select : 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 & #1 atoms > hide #!6 target m [Repeated 1 time(s)] > hide #!4 target m > select add #1 5716 atoms, 5702 bonds, 714 residues, 14 models selected > select subtract #1 1811 atoms, 1716 bonds, 199 residues, 13 models selected > select add #5 5446 atoms, 5448 bonds, 5 pseudobonds, 670 residues, 14 models selected > select subtract #5 1672 atoms, 1584 bonds, 184 residues, 12 models selected > select add #8 5445 atoms, 5437 bonds, 691 residues, 12 models selected > select subtract #8 1533 atoms, 1452 bonds, 169 residues, 11 models selected > select add #12 5186 atoms, 5201 bonds, 5 pseudobonds, 640 residues, 12 models selected > select subtract #12 1394 atoms, 1320 bonds, 154 residues, 10 models selected > hide #1 models > show #1 models > select add #15 5172 atoms, 5186 bonds, 654 residues, 10 models selected > select subtract #15 1255 atoms, 1188 bonds, 139 residues, 9 models selected > select add #18 4902 atoms, 4932 bonds, 5 pseudobonds, 610 residues, 10 models selected > select subtract #18 1116 atoms, 1056 bonds, 124 residues, 8 models selected > select add #21 4933 atoms, 4966 bonds, 625 residues, 8 models selected > select subtract #21 977 atoms, 924 bonds, 109 residues, 7 models selected > select add #24 4628 atoms, 4674 bonds, 5 pseudobonds, 580 residues, 8 models selected > select subtract #24 838 atoms, 792 bonds, 94 residues, 6 models selected > select add #26 4564 atoms, 4607 bonds, 1 pseudobond, 585 residues, 7 models selected > select subtract #26 699 atoms, 660 bonds, 79 residues, 5 models selected > select add #30 4885 atoms, 4921 bonds, 653 residues, 5 models selected > select subtract #30 558 atoms, 528 bonds, 62 residues, 4 models selected > select add #33 4744 atoms, 4789 bonds, 636 residues, 4 models selected > select subtract #33 417 atoms, 396 bonds, 45 residues, 3 models selected > select add #34 4065 atoms, 4140 bonds, 5 pseudobonds, 517 residues, 4 models selected > select subtract #34 278 atoms, 264 bonds, 30 residues, 2 models selected > select add #37 4514 atoms, 4613 bonds, 579 residues, 2 models selected > select subtract #37 139 atoms, 132 bonds, 15 residues, 1 model selected > select add #41 4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected > select subtract #41 Nothing selected > show #!2 models > hide #!2 models > show #!3 models > show #!3.3 models > ui tool show ""Side View"" > select #1/A:35@CG 1 atom, 1 residue, 1 model selected > select : 35 112 atoms, 98 bonds, 14 residues, 14 models selected > hide sel & #1 atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select : 35 112 atoms, 98 bonds, 14 residues, 14 models selected > show sel & #1 atoms > select clear > select : 35 112 atoms, 98 bonds, 14 residues, 14 models selected > hide sel & #1 atoms > save /Users/dout2/Desktop/image1.png supersample 3 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3 > select add #1 4009 atoms, 4077 bonds, 528 residues, 14 models selected > select subtract #1 104 atoms, 91 bonds, 13 residues, 13 models selected > select add #5 3870 atoms, 3948 bonds, 5 pseudobonds, 498 residues, 14 models selected > select subtract #5 96 atoms, 84 bonds, 12 residues, 12 models selected > select add #8 4000 atoms, 4062 bonds, 533 residues, 12 models selected > select subtract #8 88 atoms, 77 bonds, 11 residues, 11 models selected > select add #12 3872 atoms, 3951 bonds, 5 pseudobonds, 496 residues, 12 models selected > select subtract #12 80 atoms, 70 bonds, 10 residues, 10 models selected > select add #21 4028 atoms, 4105 bonds, 525 residues, 10 models selected > select subtract #21 72 atoms, 63 bonds, 9 residues, 9 models selected > select add #18 3850 atoms, 3932 bonds, 5 pseudobonds, 494 residues, 10 models selected > select subtract #18 64 atoms, 56 bonds, 8 residues, 8 models selected > select add #24 3846 atoms, 3931 bonds, 5 pseudobonds, 493 residues, 9 models selected > select subtract #24 56 atoms, 49 bonds, 7 residues, 7 models selected > select add #26 3913 atoms, 3989 bonds, 1 pseudobond, 512 residues, 8 models selected > select subtract #26 48 atoms, 42 bonds, 6 residues, 6 models selected > select add #30 4367 atoms, 4428 bonds, 596 residues, 6 models selected > select subtract #30 40 atoms, 35 bonds, 5 residues, 5 models selected > select add #33 4359 atoms, 4421 bonds, 595 residues, 5 models selected > select subtract #33 32 atoms, 28 bonds, 4 residues, 4 models selected > select add #34 3811 atoms, 3897 bonds, 5 pseudobonds, 490 residues, 5 models selected > select subtract #34 24 atoms, 21 bonds, 3 residues, 3 models selected > select add #37 4391 atoms, 4495 bonds, 566 residues, 3 models selected > select subtract #37 16 atoms, 14 bonds, 2 residues, 2 models selected > select add #41 4383 atoms, 4488 bonds, 1 pseudobond, 565 residues, 3 models selected > select subtract #41 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #!3.3 models > hide #!3 models > hide #1 models > show #!5 models > show #!6.3 models > hide #!6.3 models > hide #!6 models > hide #!5 models > show #8 models > show #!9 models > show #!9.3 models > select : 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 & #8 atoms > select: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234 Unknown command: select: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234 > select : 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 & #8 atoms > 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 & #8 atoms > select clear > volume #9.3 level 0.00516 > save /Users/dout2/Desktop/rOAT1-PBD_IF_LigandDensity.png supersample 3 > hide #!9.3 models > hide #!9 models > hide #8 models > show #15 models > show #!16 models > show #!16.3 models > select #15/A:442 11 atoms, 11 bonds, 1 residue, 1 model selected > 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 & #15 atoms > select #1-50: 438 154 atoms, 154 bonds, 14 residues, 14 models selected > select clear > save /Users/dout2/Desktop/rOAT1-TFV_IF_LigandDensity.png supersample 3 > hide #!16.3 models > hide #!16 models > hide #15 models > show #21 models > show #!22 models > show #!22.3 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 & #21 atoms > select clear > save /Users/dout2/Desktop/rOAT1-AAI_IF_LigandDensity.png supersample 3 > volume #22.3 level 0.0128 > hide #!22.3 models > hide #!22 models > hide #21 models > show #!27 models > show #!28 models > hide #!27 models > show #!26 models > show #!28.3 models > volume #28.3 level 0.06828 > 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 & #!26 atoms > select clear > save /Users/dout2/Desktop/rOAT1-PAH_IF_LigandDensity.png supersample 3 > hide #!28.3 models > hide #!28 models > hide #!26 models > show #30 models > show #!31 models > show #!31.3 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 & #30 atoms > select clear > save /Users/dout2/Desktop/rOAT1-FBP_IF_LigandDensity.png supersample 3 > hide #!31.3 models > hide #!31 models > hide #30 models > show #37 models > show #!38 models > show #!38.3 models > select clear > 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 & #37 atoms > select clear > show #!36 models > hide #!36 models > show #!36 models > hide #!36 models > volume #38.3 level 0.006101 > volume #38.3 level 0.006864 > save /Users/dout2/Desktop/hOAT1-TFV_IF_LigandDensity.png supersample 3 > hide #!38.3 models > hide #!38 models > hide #37 models > show #!2 models > hide #!2 models > show #1 models > show #!3 models > show #!3.3 models > hide #!3.3 models > hide #!3 models > hide #1 models > show #!5 models > show #!6.3 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 & #!5 atoms > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select clear [Repeated 1 time(s)] > 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 & #!5 atoms > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > hide sel atoms > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > volume #6.3 level 0.0106 > save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3 > hide #!5 models > hide #!6 models > hide #!6.3 models > show #!11 models > show #!12 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 & #!12 atoms > select clear > show #!11.3 models > select clear > volume #11.3 level 0.009777 > 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 new normal Unassigned