Opened 6 months ago

Closed 6 months ago

#17446 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

The following bug report has been submitted:
Platform:        macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00000001eb554840 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 59)


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{
  "uptime" : 60000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 1195785599,
  "deployVersion" : 210,
  "modelCode" : "Mac14,5",
  "coalitionID" : 7115,
  "osVersion" : {
    "train" : "macOS 15.3.2",
    "build" : "24D81",
    "releaseType" : "User"
  },
  "captureTime" : "2025-04-20 23:28:56.3174 -0400",
  "codeSigningMonitor" : 1,
  "incident" : "852DF0D7-9E2C-4DBA-97E1-3CC885C43FCA",
  "pid" : 11720,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-04-20 12:19:23.5553 -0400",
  "procStartAbsTime" : 592545169902,
  "procExitAbsTime" : 1450056072430,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"27EE72F8-B0D1-53D5-AD81-4CDFF7234557","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "AAE09EAA-E991-08DE-E25C-56BCD904E286",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "3FC27746-092C-41C1-8812-52D1AB48BB7C",
  "wakeTime" : 16912,
  "sleepWakeUUID" : "F4BF2588-1386-4515-8DB3-2EB3188D60ED",
  "sip" : "enabled",
  "vmRegionInfo" : "0x2c8200002de9 is not in any region.  Bytes after previous region: 48455821045226  Bytes before following region: 56616258884119\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x00002c8200002de9","rawCodes":[1,48936857382377],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00002c8200002de9"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":11720},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0x2c8200002de9 is not in any region.  Bytes after previous region: 48455821045226  Bytes before following region: 56616258884119\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/dout2/Downloads/OAT1_ligand_density.cxs

Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.01, 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

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> show #2.17 models

> hide #2.17 models

> show #2.17 models

> hide #2.17 models

> show #2.18 models

> hide #2.18 models

> show #2.19 models

> hide #2.19 models

> show #2.20 models

> volume #3 level 0.01124

> hide #2.20 models

> show #2.20 models

> hide #2.20 models

> show #2.20 models

> hide #2.20 models

> show #2.19 models

> hide #2.19 models

> show #2.18 models

> hide #2.18 models

> show #2.19 models

> hide #2.19 models

> show #2.18 models

> volume #3 level 0.008629

> hide #2.18 models

> show #2.18 models

> hide #2.18 models

> show #2.17 models

> hide #2.17 models

> show #2.16 models

> hide #2.16 models

> show #2.15 models

> hide #2.15 models

> show #2.14 models

> hide #2.14 models

> show #2.13 models

> hide #2.13 models

> show #2.12 models

> hide #2.12 models

> show #2.11 models

> hide #2.11 models

> show #2.10 models

> hide #2.10 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.2 models

> hide #2.2 models

> show #2.3 models

> hide #2.3 models

> show #2.4 models

> hide #2.4 models

> show #2.5 models

> hide #2.5 models

> show #2.6 models

> hide #2.6 models

> show #2.7 models

> hide #2.7 models

> show #2.8 models

> hide #2.8 models

> show #2.9 models

> hide #2.9 models

> show #2.9 models

> hide #2.9 models

> show #2.9 models

> hide #2.9 models

> show #2.10 models

> hide #2.10 models

> show #2.11 models

> hide #2.11 models

> show #2.12 models

> hide #2.12 models

> show #2.13 models

> hide #2.13 models

> show #2.12 models

> hide #2.12 models

> show #2.1 models

> hide #2.1 models

> show #2.2 models

> hide #2.2 models

> show #2.3 models

> hide #2.3 models

> show #2.4 models

> hide #2.4 models

> show #2.5 models

> hide #2.5 models

> show #2.6 models

> hide #2.6 models

> show #2.7 models

> hide #2.7 models

> show #2.8 models

> hide #2.8 models

> show #2.8 models

> hide #2.8 models

> show #2.9 models

> hide #2.9 models

> show #2.10 models

> hide #2.10 models

> show #2.11 models

> hide #2.11 models

> show #2.12 models

> hide #2.12 models

> show #2.1 models

> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true

QXcbConnection: XCB error: 3 (BadWindow), sequence: 35492, resource id:
35652978, major code: 40 (TranslateCoords), minor code: 0  

> volume #3 level 0.009281

> hide #2.1 models

> show #2.2 models

> hide #2.2 models

> show #2.3 models

> hide #2.3 models

> show #2.4 models

> show #2.5 models

> hide #2.4 models

> hide #2.5 models

> show #2.18 models

> hide #2.18 models

> show #2.18 models

> hide #2.18 models

> show #2.17 models

> hide #2.17 models

> show #2.16 models

> hide #2.16 models

> show #2.15 models

> hide #2.15 models

> show #2.14 models

> hide #2.14 models

> show #2.13 models

> hide #2.13 models

> show #2.12 models

> hide #2.12 models

> show #2.12 models

> hide #2.12 models

> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true

QXcbConnection: XCB error: 3 (BadWindow), sequence: 32670, resource id:
35652988, major code: 40 (TranslateCoords), minor code: 0  

——— End of log from Tue Dec 10 11:33:02 2024 ———

opened ChimeraX session  
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined  
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined  

> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true

QXcbConnection: XCB error: 3 (BadWindow), sequence: 7404, resource id:
35653140, major code: 40 (TranslateCoords), minor code: 0  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 7416, resource id:
35653135, major code: 40 (TranslateCoords), minor code: 0  

> show #2.11 models

> hide #2.11 models

> show #2.12 models

> hide #2.12 models

> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true

QXcbConnection: XCB error: 3 (BadWindow), sequence: 60442, resource id:
35653379, major code: 40 (TranslateCoords), minor code: 0  

——— End of log from Wed Dec 11 13:28:04 2024 ———

opened ChimeraX session  
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined  
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined  

> show #2.11 models

> show #2.12 models

> hide #2.11 models

> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_7/hOCT1VB1007.pdb

Chain information for hOCT1VB1007.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_8/
> hOCT1-VB_Dock2_real_space_refined_008.pdb"

Chain information for hOCT1-VB_Dock2_real_space_refined_008.pdb #5  
---  
Chain | Description  
A | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 17659, resource id:
35653657, major code: 40 (TranslateCoords), minor code: 0  

> close session

> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/P3_J149_fsc_iteration_010_after_fsc_mask_auto_tightening.pdf

QXcbConnection: XCB error: 3 (BadWindow), sequence: 50929, resource id:
35654568, major code: 40 (TranslateCoords), minor code: 0  

> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240.mrc

Opened cryosparc_P3_J154__localfilter_240.mrc as #1, grid size 240,240,240,
pixel 0.553, shown at level 0.207, step 1, values float32  

> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240_VB1.mrc

Opened cryosparc_P3_J154__localfilter_240_VB1.mrc as #2, grid size
240,240,240, pixel 0.553, shown at level 0.000117, step 1, values float32  

> volume #2 level 0.3318

Drag select of 2 cryosparc_P3_J154__localfilter_240_VB1.mrc  

> view orient

> select clear

> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb

Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb  
---  
warnings | Cannot find LINK/SSBOND residue CYS (50 )  
Cannot find LINK/SSBOND residue CYS (62 )  
Cannot find LINK/SSBOND residue CYS (89 )  
  

[deleted to fit within ticket limits]


> select subtract #8

Nothing selected  

> select #8: 601

19 atoms, 19 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select add #8

3912 atoms, 3985 bonds, 522 residues, 1 model selected  

> select subtract #8

Nothing selected  

> color zone #7 near #8 distance 2.5

> volume splitbyzone #7

Opened rOAT1-PBD_IF.mrc 0 as #55.1, grid size 320,320,320, pixel 0.83, shown
at level 0.0111, step 1, values float32  
Opened rOAT1-PBD_IF.mrc 1 as #55.2, grid size 320,320,320, pixel 0.83, shown
at level 0.0111, step 1, values float32  
Opened rOAT1-PBD_IF.mrc 2 as #55.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0111, step 1, values float32  
Opened rOAT1-PBD_IF.mrc 3 as #55.4, grid size 320,320,320, pixel 0.83, shown
at level 0.0111, step 1, values float32  

> surface dust #55.1 size 4.98

> surface dust #55.2 size 4.98

> surface dust #55.3 size 4.98

> surface dust #55.4 size 4.98

> volume #55.1 level 0.01136

> surface dust #55.4 size 7

> volume #55.1 level 0.01088

> surface dust #55.1 size 4.98

> surface dust #55.1 size 7

[Repeated 2 time(s)]

> surface dust #55.1 size 8

[Repeated 1 time(s)]

> volume #55.1 level 0.009811

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-PBD_IF.png
> width 809 height 738 supersample 3 transparentBackground true

> volume #55.1 level 0.009096

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-PBD_IF.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #!55 models

> show #!54 models

> hide #!54 models

> show #!54 models

> hide #!54 models

> hide #8 models

> show #!54 models

> surface dust #54.1 size 6

> volume #54.1 level 0.008735

> volume #54.1 level 0.009565

[Repeated 1 time(s)]

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #!54 models

> show #!52 models

> show #!52.1 models

> show #!52.2 models

> show #!52.3 models

> show #!52.4 models

> volume #52.1 level 0.007805

> surface dust #50 size 6

> surface dust #52.2 size 6

[Repeated 1 time(s)]

> surface dust #52.3 size 4.98

> surface dust #52.3 size 6

[Repeated 1 time(s)]

> surface dust #52.4 size 6

> volume #52.1 level 0.008213

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #8 target m

> hide #!52 models

> show #!10 models

> show #!12 models

> show #10.1 models

> color #10.1 #e599004d

> color #10.1 #e59900ff

> select #12: 601

37 atoms, 37 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select #12: 601

37 atoms, 37 bonds, 1 residue, 1 model selected  

> select clear

> color zone #10 near #12 distance 2.5

> volume #52.1 level 0.009419

> volume #10 level 0.01032

> volume #10 level 0.009917

> color zone #10 near #12 distance 2

[Repeated 2 time(s)]

> color zone #10 near #12 distance 2.3

[Repeated 1 time(s)]

> color zone #10 near #12 distance 2.4

[Repeated 1 time(s)]

> color zone #10 near #12 distance 2.5

[Repeated 1 time(s)]

> surface dust #10 size 4.98

> volume #10 level 0.01032

> volume #10 level 0.009377

> surface dust #10 size 6

> volume #10 level 0.008296

> surface dust #10 size 7

> surface dust #10 size 8

[Repeated 1 time(s)]

> volume #10 level 0.009782

> volume #10 level 0.009647

> color zone #10 near #12 distance 2.5

> volume splitbyzone #10

Opened rOAT1-PBD_OF.mrc 0 as #56.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00965, step 1, values float32  
Opened rOAT1-PBD_OF.mrc 1 as #56.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00965, step 1, values float32  
Opened rOAT1-PBD_OF.mrc 2 as #56.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00965, step 1, values float32  
Opened rOAT1-PBD_OF.mrc 3 as #56.4, grid size 320,320,320, pixel 0.83, shown
at level 0.00965, step 1, values float32  

> hide #10.1 models

> hide #!12 models

> surface dust #56.1 size 8

> surface dust #56.1 size 7

> surface dust #56.1 size 6

> surface dust #56.1 size 5

[Repeated 1 time(s)]

> surface dust #56.2 size 4.98

> surface dust #56.3 size 4.98

> surface dust #56.4 size 4.98

[Repeated 2 time(s)]

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-PBD_OF.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #!56 models

> show #15 models

> show #!14 models

> show #14.1 models

> color #14.1 #e59900ff

> volume #14 step 1

> surface dust #14 size 4.98

> volume #14 level 0.006781

> volume #14 level 0.007273

> hide #14.1 models

> show #14.1 models

> select #15: 601

31 atoms, 32 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select clear

> volume #14 level 0.007929

> color zone #14 near #15 distance 4.98

> color zone #14 near #15 distance 2

> color zone #14 near #15 distance 2.5

[Repeated 1 time(s)]

> select clear

> volume splitbyzone #14

Opened rOAT1-TFV_IF.mrc 0 as #57.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00793, step 1, values float32  
Opened rOAT1-TFV_IF.mrc 1 as #57.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00793, step 1, values float32  
Opened rOAT1-TFV_IF.mrc 2 as #57.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00793, step 1, values float32  
Opened rOAT1-TFV_IF.mrc 3 as #57.4, grid size 320,320,320, pixel 0.83, shown
at level 0.00793, step 1, values float32  

> hide #15 models

> hide #14.1 models

> surface dust #57.1 size 4.98

> surface dust #57.1 size 6

> surface dust #57.1 size 7

> surface dust #57.1 size 8

> volume #57.1 level 0.008027

> surface dust #57.1 size 8

> surface dust #57.2 size 4.98

> surface dust #57.3 size 4.98

> surface dust #57.4 size 4.98

> select clear

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #!57 models

> show #!18 models

> show #!17 models

> show #17.1 models

> color #17.1 #e599004d

> color #17.1 #e59900ff

> color zone #17 near #18 distance 4.98

> color zone #17 near #18 distance 2

> color zone #17 near #18 distance 2.5

[Repeated 1 time(s)]

> color zone #17 near #18 distance 3

> color zone #17 near #18 distance 2

> color zone #17 near #18 distance 2.8

[Repeated 1 time(s)]

> color zone #17 near #18 distance 3

> volume splitbyzone #17

Opened rOAT1-TVF_OF.mrc 0 as #58.1, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 1 as #58.2, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 2 as #58.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 3 as #58.4, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  

> hide #17.1 models

> hide #!18 models

> close #58

> show #!17 models

> show #!18 models

> show #17.1 models

> select #18: 601

31 atoms, 32 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select clear

> color zone #17 near #18 distance 3

> volume splitbyzone #17

Opened rOAT1-TVF_OF.mrc 0 as #58.1, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 1 as #58.2, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 2 as #58.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 3 as #58.4, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  

> hide #17.1 models

> hide #!18 models

> surface dust #58.1 size 4.98

> surface dust #58.2 size 4.98

> surface dust #58.3 size 4.98

> surface dust #58.4 size 4.98

> volume #58.2 level 0.004506

> volume #58.1 level 0.008289

> surface dust #58.4 size 7

> surface dust #58.1 size 7

> surface dust #58.1 size 8

> volume #58.1 level 0.008125

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #!58 models

> show #!20 models

> show #21 models

> show #20.1 models

> select #21: 601

35 atoms, 38 bonds, 1 residue, 1 model selected  

> select #21: 601,602

70 atoms, 76 bonds, 2 residues, 1 model selected  

> color sel hot pink

> select clear

> color #20.1 #e5990080

> color #20.1 #e59900ff

> select clear

> color zone #17 near #18 distance 3.01

> color zone #17 near #18 distance 3.02

> color zone #20 near #21 distance 3

> volume #58.1 level 0.007961

> color zone #20 near #21 distance 2

> color zone #20 near #21 distance 2.8

> color zone #20 near #21 distance 2

> color zone #20 near #21 distance 2.7

[Repeated 1 time(s)]

> volume splitbyzone #20

Opened rOAT1-AAI_IF.mrc 0 as #59.1, grid size 320,320,320, pixel 0.83, shown
at level 0.0133, step 1, values float32  
Opened rOAT1-AAI_IF.mrc 1 as #59.2, grid size 320,320,320, pixel 0.83, shown
at level 0.0133, step 1, values float32  
Opened rOAT1-AAI_IF.mrc 2 as #59.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0133, step 1, values float32  
Opened rOAT1-AAI_IF.mrc 3 as #59.4, grid size 320,320,320, pixel 0.83, shown
at level 0.0133, step 1, values float32  

> hide #21 models

> hide #20.1 models

> hide #!58.2 models

> hide #!58.3 models

> hide #!58.4 models

> surface dust #59.1 size 4.98

> volume #59.1 level 0.01002

> volume #59.1 level 0.009926

> surface dust #59.2 size 4.98

> select add #59

9 models selected  

> surface dust #59.3 size 4.98

> select clear

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #!59 models

> show #!24 models

> show #!23 models

> show #23.1 models

> select #24: 601,602

35 atoms, 38 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select clear

> color #23.1 #e5990080

> color #23.1 #e59900ff

> select clear

> volume #23 level 0.009882

> color zone #23 near #24 distance 4.98

> color zone #23 near #24 distance 3

[Repeated 1 time(s)]

> volume splitbyzone #23

Opened rOAT1-AAI_OF.mrc 0 as #60.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00988, step 1, values float32  
Opened rOAT1-AAI_OF.mrc 1 as #60.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00988, step 1, values float32  
Opened rOAT1-AAI_OF.mrc 2 as #60.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00988, step 1, values float32  
Opened rOAT1-AAI_OF.mrc 3 as #60.4, grid size 320,320,320, pixel 0.83, shown
at level 0.00988, step 1, values float32  

> hide #23.1 models

> hide #!24 models

> select add #60

9 models selected  

> surface dust #59.3 size 4.98

> surface dust #60.1 size 4.98

> surface dust #60.2 size 4.98

> surface dust #60.3 size 4.98

> surface dust #60.4 size 4.98

> select clear

> volume #60.1 level 0.00867

> surface dust #60.4 size 7

> surface dust #60.1 size 4.98

[Repeated 1 time(s)]

> surface dust #60.1 size 7

> select clear

> surface dust #60.1 size 8

> volume #60.1 level 0.009276

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_OF.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #!60 models

> show #!36 models

> show #37 models

> select #37: 318-570

1865 atoms, 1903 bonds, 246 residues, 1 model selected  

> color sel #3ec0c2ff

> select clear

> show #36.1 models

> select #37/A:525

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select #37: 525-570

316 atoms, 321 bonds, 39 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true

> color #36.1 #e59900ff

> select clear

> select #37: 601-603

31 atoms, 32 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select clear

> color zone #36 near #37 distance 3

> select #36

2 models selected  

> volume splitbyzone #36

Opened hOAT1-TFV_IF.mrc 0 as #61.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32  
Opened hOAT1-TFV_IF.mrc 1 as #61.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32  
Opened hOAT1-TFV_IF.mrc 2 as #61.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32  
Opened hOAT1-TFV_IF.mrc 3 as #61.4, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32  

> hide #37 models

> select subtract #36

Nothing selected  

> select add #36

2 models selected  

> select subtract #36

Nothing selected  

> surface dust #61.1 size 4.98

> surface dust #61.2 size 4.98

> surface dust #61.3 size 4.98

> surface dust #61.4 size 4.98

> select clear

[Repeated 1 time(s)]

> volume #61.1 level 0.009185

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/hOAT1-TFV_IF.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #!61 models

> show #!39 models

> show #!41 models

> select #41: 601-603

31 atoms, 32 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select #41: 525-570

316 atoms, 321 bonds, 39 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> open /Volumes/bbc/Lab-
> Jiang/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/outward_j68_3.1A/hOAT1-TFV_OF-
> coot-5_real_space_refined_007.pdb

Chain information for hOAT1-TFV_OF-coot-5_real_space_refined_007.pdb #62  
---  
Chain | Description  
A | No description available  
  

> close #41

> select #62: 1-317

2454 atoms, 2519 bonds, 315 residues, 1 model selected  

> select clear

> select #62: 1-317

2454 atoms, 2519 bonds, 315 residues, 1 model selected  

> color sel #a166d1ff

> select #62: 318-570

1503 atoms, 1535 bonds, 200 residues, 1 model selected  

> color sel #3ec0c2ff

> select #62: 601-603

19 atoms, 20 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select clear

> show #!40 models

> hide #!40 models

> show #39.1 models

> ui tool show "Fit in Map"

> fitmap #62 inMap #39

Fit molecule hOAT1-TFV_OF-coot-5_real_space_refined_007.pdb (#62) to map
hOAT1-TFV_OF.mrc (#39) using 3976 atoms  
average map value = 0.01786, steps = 124  
shifted from previous position = 1.62  
rotated from previous position = 13.4 degrees  
atoms outside contour = 1104, contour level = 0.010555  
  
Position of hOAT1-TFV_OF-coot-5_real_space_refined_007.pdb (#62) relative to
hOAT1-TFV_OF.mrc (#39) coordinates:  
Matrix rotation and translation  
0.99999997 0.00013203 0.00020852 -0.03273890  
-0.00013199 0.99999997 -0.00020384 0.04132497  
-0.00020855 0.00020382 0.99999996 -0.00751800  
Axis 0.63678518 0.65147667 -0.41241094  
Axis point -17.94306109 -0.00000000 185.02377550  
Rotation angle (degrees) 0.01833990  
Shift along axis 0.00917511  
  
Drag select of 39 hOAT1-TFV_OF.mrc  

> select clear

> hide #36.1 models

> color #39.1 #e59900ff

> select clear

> color zone #39 near #62 distance 4.98

> color zone #39 near #62 distance 3

[Repeated 1 time(s)]

> volume splitbyzone #39

Opened hOAT1-TFV_OF.mrc 0 as #41.1, grid size 320,320,320, pixel 0.83, shown
at level 0.0106, step 1, values float32  
Opened hOAT1-TFV_OF.mrc 1 as #41.2, grid size 320,320,320, pixel 0.83, shown
at level 0.0106, step 1, values float32  
Opened hOAT1-TFV_OF.mrc 2 as #41.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0106, step 1, values float32  
Opened hOAT1-TFV_OF.mrc 3 as #41.4, grid size 320,320,320, pixel 0.83, shown
at level 0.0106, step 1, values float32  

> hide #39.1 models

> surface dust #41.1 size 4.98

> surface dust #41.2 size 4.98

> surface dust #41.3 size 4.98

> surface dust #41.4 size 4.98

[Repeated 1 time(s)]

> surface dust #42.3 size 4.98

> surface dust #41.4 size 4.98

> surface dust #41.1 size 4.98

> select clear

> volume #41.1 level 0.01048

> hide #!62 models

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/hOAT1-TFV_OF.png
> width 809 height 738 supersample 3 transparentBackground true

> open /Volumes/bbc/Lab-
> Jiang/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1-TVF_IF-
> coot-3.pdb

Chain information for hOAT1-TVF_IF-coot-3.pdb #63  
---  
Chain | Description  
A | No description available  
  

> hide #!41 models

> show #!36 models

> show #36.1 models

> ui tool show "Fit in Map"

> fitmap #63 inMap #36

Fit molecule hOAT1-TVF_IF-coot-3.pdb (#63) to map hOAT1-TFV_IF.mrc (#36) using
3988 atoms  
average map value = 0.01587, steps = 40  
shifted from previous position = 0.013  
rotated from previous position = 0.0468 degrees  
atoms outside contour = 1071, contour level = 0.008515  
  
Position of hOAT1-TVF_IF-coot-3.pdb (#63) relative to hOAT1-TFV_IF.mrc (#36)
coordinates:  
Matrix rotation and translation  
0.99999982 0.00052001 0.00028819 -0.09949069  
-0.00052017 0.99999971 0.00056108 -0.00480012  
-0.00028790 -0.00056123 0.99999980 0.10326003  
Axis -0.68640011 0.35233129 -0.63617415  
Axis point 0.00000000 185.01527828 9.22177002  
Rotation angle (degrees) 0.04684105  
Shift along axis 0.00090783  
  

> fitmap #63 inMap #36

Fit molecule hOAT1-TVF_IF-coot-3.pdb (#63) to map hOAT1-TFV_IF.mrc (#36) using
3988 atoms  
average map value = 0.01587, steps = 44  
shifted from previous position = 0.00151  
rotated from previous position = 0.00338 degrees  
atoms outside contour = 1071, contour level = 0.008515  
  
Position of hOAT1-TVF_IF-coot-3.pdb (#63) relative to hOAT1-TFV_IF.mrc (#36)
coordinates:  
Matrix rotation and translation  
0.99999984 0.00047947 0.00028576 -0.09335598  
-0.00047961 0.99999975 0.00051832 -0.00591563  
-0.00028551 -0.00051846 0.99999982 0.09657995  
Axis -0.68052069 0.37496589 -0.62951741  
Axis point 0.00000000 186.90180615 11.87456849  
Rotation angle (degrees) 0.04364555  
Shift along axis 0.00051376  
  

> close #37

> fitmap #63 inMap #36

Fit molecule hOAT1-TVF_IF-coot-3.pdb (#63) to map hOAT1-TFV_IF.mrc (#36) using
3988 atoms  
average map value = 0.01587, steps = 40  
shifted from previous position = 0.00938  
rotated from previous position = 0.00367 degrees  
atoms outside contour = 1072, contour level = 0.008515  
  
Position of hOAT1-TVF_IF-coot-3.pdb (#63) relative to hOAT1-TFV_IF.mrc (#36)
coordinates:  
Matrix rotation and translation  
0.99999986 0.00047777 0.00024709 -0.09234265  
-0.00047791 0.99999972 0.00056927 -0.01315730  
-0.00024682 -0.00056939 0.99999981 0.10649613  
Axis -0.72689618 0.31530566 -0.61008548  
Axis point 0.00000000 184.88987693 22.09640694  
Rotation angle (degrees) 0.04487577  
Shift along axis -0.00199679  
  

> color zone #36 near #63 distance 3

> select add #63

3988 atoms, 4085 bonds, 1 pseudobond, 517 residues, 2 models selected  

> select #63: 601-603

19 atoms, 20 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select #63: 1-317

2471 atoms, 2537 bonds, 316 residues, 1 model selected  

> color sel #a166d1ff

[Repeated 2 time(s)]

> select #63: 318-570

1498 atoms, 1528 bonds, 200 residues, 1 model selected  

> color sel #3ec0c2ff

[Repeated 2 time(s)]

> hide #!63 models

> show #!63 models

> color zone #36 near #63 distance 3

> volume splitbyzone #36

Opened hOAT1-TFV_IF.mrc 0 as #37.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32  
Opened hOAT1-TFV_IF.mrc 1 as #37.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32  
Opened hOAT1-TFV_IF.mrc 2 as #37.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32  
Opened hOAT1-TFV_IF.mrc 3 as #37.4, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32  

> close #61

> hide #!63 models

> select add #63

3988 atoms, 4085 bonds, 1 pseudobond, 517 residues, 2 models selected  

> select subtract #63

Nothing selected  

> surface dust #37.1 size 4.98

> surface dust #37.2 size 4.98

[Repeated 1 time(s)]

> surface dust #37.3 size 4.98

> surface dust #37.4 size 4.98

> surface dust #38.3 size 4.98

> volume #37.1 level 0.009315

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/hOAT1-TFV_IF.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #!41.1 models

> hide #36.1 models

> hide #!37 models

> show #!40 models

> show #40.1 models

> show #!43 models

> select add #43

3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected  

> show sel cartoons

> color #40 #e599004d models

> color #40 #e59900ff models

> select #43: 601-603

10 atoms, 9 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select clear

> select #43: 1-317

2332 atoms, 2392 bonds, 2 pseudobonds, 297 residues, 2 models selected  

> color (#!43 & sel) #a166d1ff

> select #43: 318-570

1465 atoms, 1498 bonds, 194 residues, 1 model selected  

> color (#!43 & sel) #3ec0c2ff

[Repeated 2 time(s)]

> select clear

> color zone #40 near #43 distance 3

> color zone #40 near #43 distance 2

> color zone #40 near #43 distance 2.8

[Repeated 2 time(s)]

> volume splitbyzone #40

Opened rOAT1-AKG_OF.mrc 0 as #61.1, grid size 320,320,320, pixel 0.83, shown
at level 0.0122, step 1, values float32  
Opened rOAT1-AKG_OF.mrc 1 as #61.2, grid size 320,320,320, pixel 0.83, shown
at level 0.0122, step 1, values float32  
Opened rOAT1-AKG_OF.mrc 2 as #61.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0122, step 1, values float32  
Opened rOAT1-AKG_OF.mrc 3 as #61.4, grid size 320,320,320, pixel 0.83, shown
at level 0.0122, step 1, values float32  

> hide #!43 models

> surface dust #61.1 size 4.98

> surface dust #61.2 size 4.98

> surface dust #61.3 size 4.98

> surface dust #61.4 size 4.98

> volume #37.1 level 0.007221

> volume #61.1 level 0.01166

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AKG_OF.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #!61 models

> show #!44 models

> show #!45 models

> select #45: 601-603

10 atoms, 9 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select clear

> show #!43 models

> hide #!43 models

> show #44.1 models

> color #44.1 #e599004d

> color #44.1 #e59900ff

> color zone #44 near #45 distance 2.8

> volume splitbyzone #44

Opened rOAT1-AKG_OOC.mrc 0 as #64.1, grid size 320,320,320, pixel 0.83, shown
at level 0.0102, step 1, values float32  
Opened rOAT1-AKG_OOC.mrc 1 as #64.2, grid size 320,320,320, pixel 0.83, shown
at level 0.0102, step 1, values float32  
Opened rOAT1-AKG_OOC.mrc 2 as #64.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0102, step 1, values float32  
Opened rOAT1-AKG_OOC.mrc 3 as #64.4, grid size 320,320,320, pixel 0.83, shown
at level 0.0102, step 1, values float32  

> hide #44.1 models

> hide #!45 models

> surface dust #64.1 size 4.98

> surface dust #64.2 size 4.98

> surface dust #64.3 size 4.98

> surface dust #64.4 size 4.98

> volume #64.1 level 0.01073

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AKG_OO.png
> width 809 height 738 supersample 3 transparentBackground true

[Repeated 1 time(s)]

> hide #!64 models

> show #!47 models

> show #!46 models

> show #46.1 models

> color #46.1 #e59900ff

> select clear

> color zone #46 near #47 distance 2.8

> volume splitbyzone #46

Opened rOAT1-R466A.mrc 0 as #65.1, grid size 480,480,480, pixel 0.553, shown
at level 0.0115, step 1, values float32  
Opened rOAT1-R466A.mrc 1 as #65.2, grid size 480,480,480, pixel 0.553, shown
at level 0.0115, step 1, values float32  
Opened rOAT1-R466A.mrc 2 as #65.3, grid size 480,480,480, pixel 0.553, shown
at level 0.0115, step 1, values float32  

> hide #46.1 models

> hide #!47 models

> surface dust #65.1 size 3.32

> surface dust #65.2 size 3.32

> surface dust #65.3 size 3.32

> select clear

> volume #65.1 level 0.0121

> surface dust #65.3 size 6

> volume #65.1 level 0.009936

> surface dust #65.1 size 6

> surface dust #65.1 size 7

> volume #65.1 level 0.008672

> surface dust #65.1 size 8

> volume #65.1 level 0.008943

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-R466A_OO.png
> width 809 height 738 supersample 3 transparentBackground true

> hide #!65 models

> show #!59 models

> volume #59.2 level 0.008094

> volume #59.3 level 0.006974

> volume #59.2 level 0.00901

> select ~sel & ##selected

Nothing selected  

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF.png
> width 809 height 738 supersample 3 transparentBackground true

> volume #59.3 level 0.0102

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF.png
> width 809 height 738 supersample 3 transparentBackground true

> save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true

> hide #!59 models

> show #!58 models

> hide #!58 models

> show #!34 models

> show #!35 models

> show #!35.3 models

> color #35 #b2b2b2ff models

> select add #35

3 models selected  

> select add #34

3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 5 models selected  

> hide sel atoms

> color #35 #b2b2b2ff models

> color #35.3 #b2b2b2ff models

> hide #!34 models

> select subtract #34

3 models selected  

> select subtract #35

Nothing selected  

> select add #35

3 models selected  

> view sel

No displayed objects specified.  

> hide #!35 models

> show #!35 models

> hide #!35 models

> hide #!35.3 models

> select subtract #35.3

1 model selected  

> select add #35

3 models selected  

> select subtract #35

Nothing selected  

> show #!34 models

> show #!17 models

> show #17.1 models

> hide #17.1 models

> hide #!17 models

> select ::name="CL"

5 atoms, 5 residues, 5 models selected  

> show sel & #!34 atoms

> select #34/B:1@CL

1 atom, 1 residue, 1 model selected  

> color sel lime

> select clear

> select #34/B:1@CL

1 atom, 1 residue, 1 model selected  

> select add #34

3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected  

> show #!19 models

> show #!19.3 models

> hide #!19.3 models

> hide #!19 models

> show #!17 models

> show #17.1 models

> color zone #17 near #34 distance 3.02

> volume splitbyzone #17

Opened rOAT1-TVF_OF.mrc 0 as #66.1, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 1 as #66.2, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 2 as #66.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 3 as #66.4, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 4 as #66.5, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  

> select clear

> show #!17 models

> hide #!66 models

> show #!66 models

> hide #!66 models

> show #33 models

> hide #33 models

> color #17 #b2b2b2ff models

> select clear

> hide #!17 models

> select #34/B

1 atom, 1 residue, 1 model selected  

> select ::name="HOH"

240 atoms, 240 residues, 10 models selected  

> show #!34 atoms

> select #34: h2o

Nothing selected  

> select add #34

3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected  

> hide sel atoms

> select #34/B

1 atom, 1 residue, 1 model selected  

> open /Volumes/bbc/Lab-
> Jiang/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF-
> coot-4_real_space_refined_009.pdb

Chain information for rOAT1-TFV_OF-coot-4_real_space_refined_009.pdb #67  
---  
Chain | Description  
A | No description available  
  

> rename #67 rOAT1-TFV-Cl_OF-coot-4_real_space_refined_009.pdb

> select add #67

3829 atoms, 3910 bonds, 3 pseudobonds, 505 residues, 3 models selected  

> show sel atoms

> select #67/B:1@CL

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> hide #!34 models

> select #67:1-317

2344 atoms, 2392 bonds, 2 pseudobonds, 309 residues, 2 models selected  

> color (#!67 & sel) #a166d1ff

> select #67:318-570

1465 atoms, 1498 bonds, 194 residues, 1 model selected  

> color sel #3dc0c2ff

> select #67/B:1@CL

1 atom, 1 residue, 1 model selected  

> select clear

> select #67/B:1@CL

1 atom, 1 residue, 1 model selected  

> color sel lime

> select #67/D:4@O

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #67/D:4@O

1 atom, 1 residue, 1 model selected  

> color sel red

> select clear

> show #!17 models

> color zone #17 near #67 distance 3.02

Drag select of 17 rOAT1-TVF_OF.mrc , 3 residues, 2 bonds  

> select clear

> hide #17.1 models

> hide #!17 models

> hide #!66.1 models

> show #!47 models

> show #!46 models

> hide #!67 models

> select #47/B

1 atom, 1 residue, 1 model selected  

> show sel atoms

> show #46.1 models

> select #47/B

1 atom, 1 residue, 1 model selected  

> color sel lime

> style sel ball

Changed 1 atom style  

> hide #!46 models

> hide #46.1 models

> hide #!47 models

> select add #47

3795 atoms, 3884 bonds, 3 pseudobonds, 495 residues, 2 models selected  

> select subtract #47

Nothing selected  

> show #!67 models

> select add #67

3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected  

> show #!17 models

> show #17.1 models

> volume splitbyzone #17

Opened rOAT1-TVF_OF.mrc 0 as #68.1, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 1 as #68.2, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 2 as #68.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 3 as #68.4, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 4 as #68.5, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 5 as #68.6, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 6 as #68.7, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 7 as #68.8, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 8 as #68.9, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  

> hide #!68.9 models

> hide #!68.7 models

> hide #!68.6 models

> hide #!68.5 models

> hide #!68.4 models

> hide #!68.3 models

> hide #!68.2 models

> hide #!68.1 models

> color #68.8 #b2b2b2ff models

> color #68.8 #b2b2b276 models

> color #68.8 #b2b2b249 models

> color #68.8 #b2b2b24c models

> select clear

[Repeated 1 time(s)]

> select add #67

3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #67/B

1 atom, 1 residue, 1 model selected  

> show sel atoms

> select clear

[Repeated 2 time(s)]

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV-
> Cl_OF.png width 809 height 738 supersample 3 transparentBackground true

> hide #!67 models

> hide #!68 models

> show #!19 models

> show #!19.3 models

> show #!18 models

> color #19.3 #b2b2b29f models

> close #19

> show #!68 models

> show #!68.1 models

> hide #!68.1 models

> show #!68.7 models

> close #68

> select add #67

3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected  

> show #!67 models

> hide #!18 models

> hide #17.1 models

> show sel cartoons

> show sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

19 atoms, 20 bonds, 1 residue, 1 model selected  

> color sel hot pink

> select clear

> color zone #17 near #67 distance 3.02

> show #!66 models

> select add #66

11 models selected  

> close #66

> show #!35 models

> close #35

> show #!17 models

> show #17.1 models

> color zone #17 near #67 distance 3.02

> volume splitbyzone #17

Opened rOAT1-TVF_OF.mrc 0 as #19.1, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 1 as #19.2, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 3 as #19.4, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 4 as #19.5, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  
Opened rOAT1-TVF_OF.mrc 5 as #19.6, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32  

> hide #!19.2 models

> hide #!19.1 models

> hide #!19.3 models

> hide #!19.6 models

> show #!19.6 models

> hide #!19.6 models

> select add #67

3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select #67:601

19 atoms, 20 bonds, 1 residue, 1 model selected  

> show sel atoms

> color #67 #b2b2b2ff

> color #19.4 #b2b2b2ff models

> color #19.4 #b2b2b280 models

> select #67:601

19 atoms, 20 bonds, 1 residue, 1 model selected  

> color sel lime

> color sel hot pink

> color sel byhetero

> select clear

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF-
> TFV.png width 809 height 738 supersample 3 transparentBackground true

> color #19.4 #b2b2b29b models

> color #19.4 #b2b2b29a models

> color #19.4 #b2b2b280 models

> select clear

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> select clear

> lighting flat

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> lighting flat

[Repeated 2 time(s)]

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> graphics silhouettes false

> lighting flat

> select clear

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF-
> TFV.png width 809 height 738 supersample 3 transparentBackground true

> color #19.4 black models

> color #19.4 #00000008 models

> color #19.4 #0000000a models

> color #19.4 transparent models

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> select clear

> color #19.4 #929292ff models

> color #19.4 #797979ff models

> color #19.4 #79797980 models

> color #19.4 silver models

> color #19.4 #c0c0c080 models

> lighting flat

> lighting shadows true intensity 0.5

> lighting flat

> graphics silhouettes false

> lighting flat

> color #19.4 #929292ff models

> color #19.4 #9292927e models

> color #19.4 darkgrey models

> color #19.4 silver models

> select clear

> volume #19.4 level 0.009812

> surface dust #19.4 size 4.98

> volume #19.4 level 0.008153

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF-
> TFV.png width 809 height 738 supersample 3 transparentBackground true

> volume #19.4 level 0.005723

> surface dust #19.4 size 8

[Repeated 1 time(s)]

> volume #19.4 level 0.007027

> surface dust #19.4 size 8

> volume #19.4 level 0.007797

> surface dust #19.4 size 8

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_OF-
> TFV.png width 809 height 738 supersample 3 transparentBackground true

> hide #!19 models

> hide #!19.4 models

> hide #!19.5 models

> show #!58 models

> hide #!58 models

> show #!58 models

> close #58

> show #!57 models

> hide #!57.1 models

> hide #!57.2 models

> hide #!57.3 models

> show #!57.1 models

> show #!57.2 models

> show #!57.3 models

> hide #!57.2 models

> hide #!57.1 models

> hide #!57.3 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> select #67/A:601@C08

1 atom, 1 residue, 1 model selected  

> select up

19 atoms, 20 bonds, 1 residue, 1 model selected  

> hide #!67 models

> hide #67.1 models

> select add #67

3828 atoms, 3910 bonds, 3 pseudobonds, 504 residues, 2 models selected  

> select subtract #67

Nothing selected  

> select #15:601

31 atoms, 32 bonds, 1 residue, 1 model selected  

> select clear

> color #57.4 #ff69b481 models

> color #57.4 #ff69b480 models

> select #15:601

31 atoms, 32 bonds, 1 residue, 1 model selected  

> show #15 models

> select add #15

3917 atoms, 3998 bonds, 515 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select #15:601

31 atoms, 32 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide #17.1 models

> volume #57.4 level 0.006742

> select #15:601

31 atoms, 32 bonds, 1 residue, 1 model selected  

> color sel hot pink

> color sel byhetero

> select clear

> select H

93 atoms, 8 residues, 7 models selected  

> hide sel & #15 atoms

> color #57.4 #b2b2b280 models

> volume #57.4 level 0.007863

> volume #57.4 level 0.007995

> volume #57.4 level 0.007863

> volume #57.4 level 0.007995

> volume #57.4 level 0.007797

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF-
> TFV.png width 809 height 738 supersample 3 transparentBackground true

> show #!63 models

> hide #!57.4 models

> hide #!57 models

> hide #15 models

> select add #15

3998 atoms, 3998 bonds, 522 residues, 7 models selected  

> select subtract #15

81 atoms, 7 residues, 6 models selected  

> select add #18

3855 atoms, 3876 bonds, 5 pseudobonds, 492 residues, 7 models selected  

> select subtract #18

69 atoms, 6 residues, 5 models selected  

> hide #!63 models

> hide #63.1 models

> open /Volumes/bbc/Lab-
> Jiang/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/inward_j152_2.7A/rOAT1-TFV_IF-
> coot-1_real_space_refined_001_real_space_refined_002.pdb

Chain information for rOAT1-TFV_IF-
coot-1_real_space_refined_001_real_space_refined_002.pdb #35  
---  
Chain | Description  
A | No description available  
  

> show #!57.4 models

> select #35:601

19 atoms, 20 bonds, 1 residue, 1 model selected  

> color sel hot pink

> color sel byhetero

> select clear

> select add #35

3905 atoms, 3986 bonds, 515 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #35:601

19 atoms, 20 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-TFV_IF-
> TFV.png width 809 height 738 supersample 3 transparentBackground true

> hide #35 models

> hide #!57.4 models

> show #!59 models

> hide #!59.3 models

> hide #!59.2 models

> hide #!59.1 models

> show #21 models

> select #21: 601-603

70 atoms, 76 bonds, 2 residues, 1 model selected  

> color sel forest green

> color sel byhetero

> color sel orange

> color sel byhetero

> select add #21

3956 atoms, 4042 bonds, 516 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #21: 601-603

70 atoms, 76 bonds, 2 residues, 1 model selected  

> show sel atoms

> select H

93 atoms, 8 residues, 7 models selected  

> hide sel & #21 atoms

> color #59.4 #b2b2b2ff models

> color #59.4 #b2b2b200 models

> color #59.4 #b2b2b280 models

> surface dust #59.4 size 4.98

> volume #59.4 level 0.01251

> select clear

> save
> /Users/dout2/Documents/Manuscripts/rOAT1_2025/Figures/Color_domain/rOAT1-AAI_IF-
> AAI.png width 809 height 738 supersample 3 transparentBackground true

> save /Users/dout2/Downloads/OAT1_ligand_Colored_domain.cxs includeMaps true

——— End of log from Sun Apr 20 23:23:04 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,5
      Model Number: MPHG3LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 1 day, 16 hours, 18 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
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    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by pett, 6 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by pett, 6 months ago

Resolution: → duplicate
Status: assigned → closed
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