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Opened 4 months ago
Closed 4 months ago
#18077 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x00000003f2807000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003cb203000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034fb9f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034eb93000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034db87000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034cb7b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034bb6f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034ab63000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000349b57000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000348b4b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000347b3f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000346b33000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000345b27000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000344b1b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000343b0f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000342b03000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000341af7000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f656df00 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PIL._imagingmath, chimerax.coulombic._esp (total: 64)
{"app_name":"ChimeraX","timestamp":"2025-06-25 15:27:37.00 +0200","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.5 (24F74)","roots_installed":0,"name":"ChimeraX","incident_id":"73FA1647-91A9-45F0-A0F5-FD7EF413D5FF"}
{
"uptime" : 810000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "Mac16,7",
"coalitionID" : 155860,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-06-25 15:23:09.1682 +0200",
"codeSigningMonitor" : 2,
"incident" : "73FA1647-91A9-45F0-A0F5-FD7EF413D5FF",
"pid" : 4582,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-19 12:49:08.3174 +0200",
"procStartAbsTime" : 14620622444271,
"procExitAbsTime" : 19481905915218,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"C0768033-149E-5E50-AE4E-DBC5AE4AF732","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "EB9E1682-CBEE-85AA-0861-E78724A5DECB",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguage"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "46006F70-646A-48B2-84BF-881DABD3F9BC",
"wakeTime" : 23305,
"sleepWakeUUID" : "9FE1A7C1-76D2-4034-81AC-9DFD7CF7AFD1",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4331929239\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102340000-102344000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":4582},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4331929239\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102340000-102344000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6134938744},{"value":99},{"value":95},{"value":15408},{"value":4878673475},{"value":7339761924150404830},{"value":7339761923442538974},{"value":14757395258967641293},{"value":4294967286},{"value":6134938674},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8444960680},{"value":0},{"value":11},{"value":259},{"value":8427855840,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4353377840,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8389005312,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSFullScreenCreateTileDropTargetController._requestedJoinSpace"},{"value":8389005312,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSFullScreenCreateTileDropTargetController._requestedJoinSpace"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6581250188},"cpsr":{"value":1073741824},"fp":{"value":6134938816},"sp":{"value":6134938784},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6581015432,"matchesCrashFrame":1},"far":{"value":0}},"id":15790289,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":37768,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":164},{"imageOffset":26764,"symbol":"pthread_kill","symbolLocation":296,"imageIndex":165},{"imageOffset":265476,"symbol":"raise","symbolLocation":32,"imageIndex":166},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":1},{"imageOffset":13860,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":167},{"imageOffset":349344,"imageIndex":69},{"imageOffset":349160,"imageIndex":69},{"imageOffset":381384,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":244,"imageIndex":168},{"imageOffset":12003112,"symbol":"-[NSWindow _postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":192,"imageIndex":168},{"imageOffset":2071916,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":432,"imageIndex":168},{"imageOffset":508016,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":108,"imageIndex":168},{"imageOffset":2071472,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":96,"imageIndex":168},{"imageOffset":513468,"symbol":"-[NSWindow _setFrameCommon:display:fromServer:]","symbolLocation":2016,"imageIndex":168},{"imageOffset":11973440,"symbol":"-[NSWindow(NSScreenLayout) _setFrame:fromAdjustmentToScreen:anchorIfNeeded:animate:]","symbolLocation":616,"imageIndex":168},{"imageOffset":3237004,"symbol":"-[NSWindow _adjustWindowToScreen]","symbolLocation":1184,"imageIndex":168},{"imageOffset":3366632,"symbol":"-[NSWindow 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/modelXfold.cxs
> format session
opened ChimeraX session
> hide #!14 models
> show #!14 models
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> show #30 models
> hide #28 models
> show #28 models
> show #!27 models
> close #28-29#27
> open
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster11_1.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster11_2.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster11_3.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster11_4.pdb
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster11_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_19w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
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REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_19.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster11_2.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_38w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_38.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster11_3.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_131w.pdb0"
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REMARK ===============================================================
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REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_131.pdb
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REMARK ===============================================================
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Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster11_4.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_9w.pdb0"
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REMARK ===============================================================
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REMARK HADDOCK run for complex
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REMARK initial structure: complex_9.pdb
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REMARK ===============================================================
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Chain information for cluster11_1.pdb #27
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster11_2.pdb #28
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster11_3.pdb #29
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster11_4.pdb #40
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> view #27 clip false
> hide #28 models
> hide #29 models
> hide #30 models
> hide #40 models
> select clear
> select #27/B:18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> color sel orange
> show #28 models
> show #29 models
> open
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster1_1.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster1_2.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster1_3.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster1_4.pdb
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster1_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_92w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_92.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster1_2.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_49w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
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REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_49.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
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Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster1_3.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_133w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_133.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster1_4.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_82w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_82.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster1_1.pdb #41
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster1_2.pdb #42
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster1_3.pdb #43
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster1_4.pdb #44
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #27-29,40-44 to #3
Computing secondary structure
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 7kp4, chain A (#3) with cluster11_1.pdb, chain A (#27), sequence
alignment score = 927.5
RMSD between 177 pruned atom pairs is 0.795 angstroms; (across all 182 pairs:
0.870)
Matchmaker 7kp4, chain A (#3) with cluster11_2.pdb, chain A (#28), sequence
alignment score = 909.5
RMSD between 180 pruned atom pairs is 1.022 angstroms; (across all 182 pairs:
1.040)
Matchmaker 7kp4, chain A (#3) with cluster11_3.pdb, chain A (#29), sequence
alignment score = 912.5
RMSD between 180 pruned atom pairs is 0.801 angstroms; (across all 182 pairs:
0.835)
Matchmaker 7kp4, chain A (#3) with cluster11_4.pdb, chain A (#40), sequence
alignment score = 914.3
RMSD between 182 pruned atom pairs is 0.824 angstroms; (across all 182 pairs:
0.824)
Matchmaker 7kp4, chain A (#3) with cluster1_1.pdb, chain A (#41), sequence
alignment score = 920.3
RMSD between 181 pruned atom pairs is 0.762 angstroms; (across all 182 pairs:
0.776)
Matchmaker 7kp4, chain A (#3) with cluster1_2.pdb, chain A (#42), sequence
alignment score = 920.3
RMSD between 180 pruned atom pairs is 0.796 angstroms; (across all 182 pairs:
0.831)
Matchmaker 7kp4, chain A (#3) with cluster1_3.pdb, chain A (#43), sequence
alignment score = 928.7
RMSD between 182 pruned atom pairs is 0.686 angstroms; (across all 182 pairs:
0.686)
Matchmaker 7kp4, chain A (#3) with cluster1_4.pdb, chain A (#44), sequence
alignment score = 923.3
RMSD between 178 pruned atom pairs is 0.887 angstroms; (across all 182 pairs:
0.944)
> view clip false
> select #29/B:18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> select add #43/B:16
299 atoms, 304 bonds, 31 residues, 2 models selected
> select up
582 atoms, 594 bonds, 60 residues, 2 models selected
> select add #41/B:21
596 atoms, 608 bonds, 61 residues, 3 models selected
> select up
873 atoms, 891 bonds, 90 residues, 3 models selected
> select add #44/B:21
887 atoms, 905 bonds, 91 residues, 4 models selected
> select up
1164 atoms, 1188 bonds, 120 residues, 4 models selected
> color sel lime
> select clear
> select add #28/B:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> select add #27/B:14
302 atoms, 307 bonds, 31 residues, 2 models selected
> select up
582 atoms, 594 bonds, 60 residues, 2 models selected
> rainbow sel
> select clear
> select add #29/B:17
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> select add #43/B:15
299 atoms, 304 bonds, 31 residues, 2 models selected
> select up
582 atoms, 594 bonds, 60 residues, 2 models selected
> select add #28/B:19
587 atoms, 598 bonds, 61 residues, 3 models selected
> select up
873 atoms, 891 bonds, 90 residues, 3 models selected
> select add #42/B:24
881 atoms, 898 bonds, 91 residues, 4 models selected
> select up
1164 atoms, 1188 bonds, 120 residues, 4 models selected
> select add #27/B:25
1173 atoms, 1196 bonds, 121 residues, 5 models selected
> select up
1455 atoms, 1485 bonds, 150 residues, 5 models selected
> rainbow sel
> select clear
> select add #41/B:30
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> select add #44/B:30
303 atoms, 309 bonds, 31 residues, 2 models selected
> select up
582 atoms, 594 bonds, 60 residues, 2 models selected
> rainbow sel
> select clear
> hide #42 models
> hide #43 models
> hide #44 models
> hide #41 models
> show #41 models
> hide #41 models
> show #41 models
> hide #41 models
> show #41 models
> hide #41 models
> show #40 models
> hide #40 models
> show #41 models
> hide #41 models
> show #41 models
> show #42 models
> show #43 models
> show #44 models
> hide #43 models
> show #43 models
> hide #43 models
> hide #29 models
> hide #28 models
> hide #44 models
> hide #42 models
> show #!6 models
> hide #!6 models
> show #9 models
> hide #9 models
> show #9 models
> show #6.2 models
> hide #6.1 models
> show #6.1 models
> hide #6.2 models
> hide #41 models
> hide #27 models
> show #27 models
> hide #27 models
> show #27 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #11 models
> hide #11 models
> show #12 models
> hide #27 models
> hide #12 models
> close #40
> close #42-44
> close #28-29
> show #41 models
> show #27 models
> hide #!6 models
> open
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster4_1.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster2_1.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster16_1.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster5_1.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster7_1.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster3_1.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster12_1.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster8_2.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster8_1.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster1_1.pdb
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster11_1.pdb
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster4_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_86w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_86.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster2_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_13w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_13.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster16_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_174w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_174.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster5_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_25w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_25.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster7_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_47w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_47.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster3_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_14w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_14.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster12_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_33w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_33.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster8_2.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_1w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_1.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster8_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_3w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_3.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster1_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_92w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_92.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Summary of feedback from opening
/Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/Haddock/507098-Cpe-30_AF3_0_summary/cluster11_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_19w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_19.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster4_1.pdb #28
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster2_1.pdb #29
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster16_1.pdb #40
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster5_1.pdb #42
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster7_1.pdb #43
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster3_1.pdb #44
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster12_1.pdb #45
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster8_2.pdb #46
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster8_1.pdb #47
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster1_1.pdb #48
---
Chain | Description
A | No description available
B | No description available
Chain information for cluster11_1.pdb #49
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> close #27-29
> close #46
> ui tool show Matchmaker
> matchmaker #40-45,47-49 to #3
Computing secondary structure
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 7kp4, chain A (#3) with cluster16_1.pdb, chain A (#40), sequence
alignment score = 918.5
RMSD between 179 pruned atom pairs is 0.788 angstroms; (across all 182 pairs:
0.830)
Matchmaker 7kp4, chain A (#3) with cluster1_1.pdb, chain A (#41), sequence
alignment score = 920.3
RMSD between 181 pruned atom pairs is 0.762 angstroms; (across all 182 pairs:
0.776)
Matchmaker 7kp4, chain A (#3) with cluster5_1.pdb, chain A (#42), sequence
alignment score = 900.5
RMSD between 167 pruned atom pairs is 0.813 angstroms; (across all 182 pairs:
1.088)
Matchmaker 7kp4, chain A (#3) with cluster7_1.pdb, chain A (#43), sequence
alignment score = 917.3
RMSD between 182 pruned atom pairs is 0.810 angstroms; (across all 182 pairs:
0.810)
Matchmaker 7kp4, chain A (#3) with cluster3_1.pdb, chain A (#44), sequence
alignment score = 932.3
RMSD between 181 pruned atom pairs is 0.673 angstroms; (across all 182 pairs:
0.696)
Matchmaker 7kp4, chain A (#3) with cluster12_1.pdb, chain A (#45), sequence
alignment score = 914.3
RMSD between 162 pruned atom pairs is 0.867 angstroms; (across all 182 pairs:
1.170)
Matchmaker 7kp4, chain A (#3) with cluster8_1.pdb, chain A (#47), sequence
alignment score = 909.5
RMSD between 180 pruned atom pairs is 0.747 angstroms; (across all 182 pairs:
0.785)
Matchmaker 7kp4, chain A (#3) with cluster1_1.pdb, chain A (#48), sequence
alignment score = 920.3
RMSD between 181 pruned atom pairs is 0.762 angstroms; (across all 182 pairs:
0.776)
Matchmaker 7kp4, chain A (#3) with cluster11_1.pdb, chain A (#49), sequence
alignment score = 927.5
RMSD between 177 pruned atom pairs is 0.795 angstroms; (across all 182 pairs:
0.870)
> select #41/B:20
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> select add #43/B:16
299 atoms, 304 bonds, 31 residues, 2 models selected
> select up
582 atoms, 594 bonds, 60 residues, 2 models selected
> select add #45/B:18
590 atoms, 601 bonds, 61 residues, 3 models selected
> select up
757 atoms, 774 bonds, 77 residues, 3 models selected
> select up
873 atoms, 891 bonds, 90 residues, 3 models selected
> select add #42/B:18
881 atoms, 898 bonds, 91 residues, 4 models selected
> select up
1164 atoms, 1188 bonds, 120 residues, 4 models selected
> select add #40/B:21
1178 atoms, 1202 bonds, 121 residues, 5 models selected
> select up
1455 atoms, 1485 bonds, 150 residues, 5 models selected
> select add #47/B:6
1467 atoms, 1496 bonds, 151 residues, 6 models selected
> select up
1746 atoms, 1782 bonds, 180 residues, 6 models selected
> select add #44/B:2
1755 atoms, 1790 bonds, 181 residues, 7 models selected
> select up
2037 atoms, 2079 bonds, 210 residues, 7 models selected
> ui tool show "Color Actions"
> color sel red
> color sel light coral
> select clear
> select add #41/A:41
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
67 atoms, 66 bonds, 8 residues, 1 model selected
> select add #43/A:41
75 atoms, 73 bonds, 9 residues, 2 models selected
> select up
158 atoms, 157 bonds, 18 residues, 2 models selected
> select add #45/A:41
166 atoms, 164 bonds, 19 residues, 3 models selected
> select up
225 atoms, 223 bonds, 26 residues, 3 models selected
> select add #40/A:70
234 atoms, 231 bonds, 27 residues, 4 models selected
> select up
296 atoms, 295 bonds, 34 residues, 4 models selected
> select clear
> hide #41 models
> hide #42 models
> hide #43 models
> hide #44 models
> hide #45 models
> hide #47 models
> hide #48 models
> hide #49 models
> show #!7 models
> show #9 models
> hide #6.1 models
> show #6.1 models
> hide #6.1 models
> hide #!6 models
> hide #!7 models
> show #10 models
> hide #10 models
> show #10 models
> hide #9 models
> hide #10 models
> show #10 models
> show #41 models
> hide #41 models
> show #42 models
> hide #40 models
> hide #42 models
> show #40 models
> show #43 models
> hide #43 models
> show #44 models
> hide #44 models
> show #45 models
> hide #45 models
> show #45 models
> hide #45 models
> show #47 models
> hide #47 models
> show #48 models
> hide #48 models
> show #48 models
> hide #48 models
> show #49 models
> hide #49 models
> show #49 models
> hide #49 models
> show #49 models
> hide #49 models
> hide #40 models
> show #40 models
> hide #40 models
> show #49 models
> select add #49/B:13
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> hide #10 models
> ui tool show H-Bonds
> hbonds sel color #e000ec dashes 6 interModel false distSlop 0.8 angleSlop
> 60.0 reveal true retainCurrent true
34 hydrogen bonds found
> hbonds sel color #fcff06 dashes 6 interModel false distSlop 0.8 angleSlop
> 60.0 reveal true retainCurrent true
34 hydrogen bonds found
> hbonds sel color #fcff06 dashes 6 interModel false distSlop 0.8 angleSlop
> 60.0 intraMol false reveal true retainCurrent true
12 hydrogen bonds found
> hbonds sel color #fcff06 dashes 6 restrict cross interModel false distSlop
> 0.8 angleSlop 60.0 intraMol false reveal true retainCurrent true
12 hydrogen bonds found
> hbonds sel color #fcff06 restrict cross interModel false distSlop 0.8
> angleSlop 60.0 intraMol false reveal true
12 hydrogen bonds found
> hide #!49 models
> show #41 models
> select #41/B:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> hbonds sel color #ff36d8 restrict cross interModel false distSlop 0.8
> angleSlop 60.0 intraMol false reveal true
20 hydrogen bonds found
> color sel byhetero
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #6.1 models
> hide #6.1 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!41 models
> hide #!6 models
> show #42 models
> hide #!41 models
> select #42/B:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> hbonds sel color #ff36d8 restrict cross interModel false distSlop 0.8
> angleSlop 60.0 intraMol false reveal true
24 hydrogen bonds found
> color sel byhetero
> hide #!42 models
> select add #42
1900 atoms, 1929 bonds, 24 pseudobonds, 212 residues, 2 models selected
> select subtract #42
Nothing selected
> show #43 models
> select #43/B:24
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> hbonds sel color #00ff0b restrict cross interModel false distSlop 0.8
> angleSlop 60.0 intraMol false reveal true
19 hydrogen bonds found
> color sel byhetero
> hide #!43 models
> show #44 models
> show #!43 models
> show #!41 models
> show #!42 models
> hide #44 models
> hide #!43 models
> hide #!42 models
> hide #!41 models
> show #40 models
> select #40/B:27
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #00ff0b restrict cross interModel false distSlop 0.8
> angleSlop 60.0 intraMol false reveal true
13 hydrogen bonds found
> color sel byhetero
> show #6.1 models
> hide #!6 models
> show #9 models
> hide #9 models
> show #9 models
> hide #!40 models
> show #!40 models
> show #!49 models
> hide #9 models
> hide #!40 models
> select #49/B:10
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
291 atoms, 297 bonds, 30 residues, 1 model selected
> show #!42 models
> hide #!42 models
> show #!41 models
> hide #!41 models
> show #9 models
> select #9/B:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
240 atoms, 246 bonds, 30 residues, 1 model selected
> hbonds sel color #00ff0b restrict cross interModel false distSlop 0.8
> angleSlop 60.0 intraMol false reveal true
2 hydrogen bonds found
> hide #!49 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!49 models
> hide #!9 models
> hide #6.1 models
> show #6.1 models
> select #6/B:227
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
67 atoms, 69 bonds, 7 residues, 2 models selected
> select up
1057 atoms, 1079 bonds, 134 residues, 2 models selected
> hbonds sel color #ff0018 restrict cross interModel false distSlop 0.8
> angleSlop 60.0 intraMol false reveal true
25 hydrogen bonds found
> hide #!49 models
> hide #6.1 models
> select up
2375 atoms, 2421 bonds, 316 residues, 2 models selected
> color (#!6 & sel) byhetero
> select clear
> save
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/Structures/modelXfold_Haddock.cxs
> hide #6.3 models
> hide #!6 models
> show #35 models
> show #36 models
> show #37 models
> show #38 models
> show #39 models
> hide #39 models
> hide #38 models
> hide #37 models
> hide #36 models
> show #!49 models
> ui tool show Matchmaker
[deleted to fit within ticket limits]
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select clear
> open AF-O15551
'AF-O15551' has no suffix
> open alphafold AF-O15551
'alphafold' has no suffix
> open alphafold3 AF-O15551
'alphafold3' has no suffix
> open psb AF-O15551
'psb' has no suffix
> open pdb AF-O15551
'pdb' has no suffix
> open AF-O15551 pdb
'AF-O15551' has no suffix
> open alphafold:AF-O15551
UniProt identifiers must be 6 or 10 characters long, got "AF-O15551"
> open alphafold:O15551
Summary of feedback from opening O15551 fetched from alphafold
---
notes | Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold O15551 from
https://alphafold.ebi.ac.uk/files/AF-O15551-F1-model_v3.cif
Chain information for AlphaFold O15551 #9
---
Chain | Description | UniProt
A | Claudin-3 | CLD3_HUMAN 1-220
Color AlphaFold O15551 by residue attribute pLDDT_score
Associated AlphaFold O15551 chain A to sp|O15551|CLD3_HUMAN with 0 mismatches
> rename #9 "Claudin-3_human AlphaFold O15551"
> open 6AKE
Summary of feedback from opening 6AKE fetched from pdb
---
note | Fetching compressed mmCIF 6ake from http://files.rcsb.org/download/6ake.cif
6ake title:
Crystal structure of mouse claudin-3 in complex with C-terminal fragment of
Clostridium perfringens enterotoxin [more info...]
Chain information for 6ake #10
---
Chain | Description | UniProt
A C | Claudin-3 | CLD3_MOUSE 1-183
B D | Heat-labile enterotoxin B chain | ELTB_CLOPF 203-319
6ake mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open alphafold:O35054
Summary of feedback from opening O35054 fetched from alphafold
---
note | Fetching compressed AlphaFold O35054 from https://alphafold.ebi.ac.uk/files/AF-O35054-F1-model_v3.cif
Chain information for AlphaFold O35054 #11
---
Chain | Description | UniProt
A | Claudin-4 | CLD4_MOUSE 1-210
Color AlphaFold O35054 by residue attribute pLDDT_score
Associated AlphaFold O35054 chain A to sp|O35054|CLD4_MOUSE with 0 mismatches
> open alphafold:Q9Z262
Summary of feedback from opening Q9Z262 fetched from alphafold
---
note | Fetching compressed AlphaFold Q9Z262 from https://alphafold.ebi.ac.uk/files/AF-Q9Z262-F1-model_v3.cif
Chain information for AlphaFold Q9Z262 #12
---
Chain | Description | UniProt
A | Claudin-6 | CLD6_MOUSE 1-219
Color AlphaFold Q9Z262 by residue attribute pLDDT_score
Associated AlphaFold Q9Z262 chain A to sp|Q9Z262|CLD6_MOUSE with 0 mismatches
> open alphafold:Q9Z261
Summary of feedback from opening Q9Z261 fetched from alphafold
---
note | Fetching compressed AlphaFold Q9Z261 from https://alphafold.ebi.ac.uk/files/AF-Q9Z261-F1-model_v3.cif
Chain information for AlphaFold Q9Z261 #13
---
Chain | Description | UniProt
A | Claudin-7 | CLD7_MOUSE 1-211
Color AlphaFold Q9Z261 by residue attribute pLDDT_score
Associated AlphaFold Q9Z261 chain A to sp|Q9Z261|CLD7_MOUSE with 0 mismatches
> rename #10 "Claudin-3 mouse 6ake"
> rename #10 "Claudin-3_mouse 6ake"
> rename #11 "Claudine-4_mous AlphaFold O35054"
> rename #11 "Claudine-4_mouse AlphaFold O35054"
> rename #12 "Claudine-6_mouse AlphaFold Q9Z262"
> rename #13 "Claudine-7_mouse AlphaFold Q9Z261"
> open alphafold:Q9Z260
Summary of feedback from opening Q9Z260 fetched from alphafold
---
note | Fetching compressed AlphaFold Q9Z260 from https://alphafold.ebi.ac.uk/files/AF-Q9Z260-F1-model_v3.cif
Chain information for AlphaFold Q9Z260 #14
---
Chain | Description | UniProt
A | Claudin-8 | CLD8_MOUSE 1-225
Color AlphaFold Q9Z260 by residue attribute pLDDT_score
Associated AlphaFold Q9Z260 chain A to sp|Q9Z260|CLD8_MOUSE with 0 mismatches
> rename #14 "Claudin-8_mouse AlphaFold Q9Z260"
> rename #13 "Claudin-7_mouse AlphaFold Q9Z261"
> rename #12 "Claudin-6_mouse AlphaFold Q9Z262"
> rename #11 "Claudin-4_mouse AlphaFold O35054"
> open alphafold:Q9Z0S3
Summary of feedback from opening Q9Z0S3 fetched from alphafold
---
note | Fetching compressed AlphaFold Q9Z0S3 from https://alphafold.ebi.ac.uk/files/AF-Q9Z0S3-F1-model_v3.cif
Chain information for AlphaFold Q9Z0S3 #15
---
Chain | Description | UniProt
A | Claudin-14 | CLD14_MOUSE 1-239
Color AlphaFold Q9Z0S3 by residue attribute pLDDT_score
Associated AlphaFold Q9Z0S3 chain A to sp|Q9Z0S3|CLD14_MOUSE with 0 mismatches
> rename #15 "Claudin-14_mouse AlphaFold Q9Z0S3"
> open alphafold:O95832
Summary of feedback from opening O95832 fetched from alphafold
---
note | Fetching compressed AlphaFold O95832 from https://alphafold.ebi.ac.uk/files/AF-O95832-F1-model_v3.cif
Chain information for AlphaFold O95832 #16
---
Chain | Description | UniProt
A | Claudin-1 | CLD1_HUMAN 1-211
Color AlphaFold O95832 by residue attribute pLDDT_score
Associated AlphaFold O95832 chain A to sp|O95832|CLD1_HUMAN with 0 mismatches
> rename #16 "Claudin-1_human AlphaFold O95832"
> open alphafold:P57739
Summary of feedback from opening P57739 fetched from alphafold
---
note | Fetching compressed AlphaFold P57739 from https://alphafold.ebi.ac.uk/files/AF-P57739-F1-model_v3.cif
Chain information for AlphaFold P57739 #17
---
Chain | Description | UniProt
A | Claudin-2 | CLD2_HUMAN 1-230
Color AlphaFold P57739 by residue attribute pLDDT_score
Associated AlphaFold P57739 chain A to sp|P57739|CLD2_HUMAN with 0 mismatches
> rename #17 "Claudin-2_human AlphaFold P57739"
> open alphafold:O00501
Summary of feedback from opening O00501 fetched from alphafold
---
note | Fetching compressed AlphaFold O00501 from https://alphafold.ebi.ac.uk/files/AF-O00501-F1-model_v3.cif
Chain information for AlphaFold O00501 #18
---
Chain | Description | UniProt
A | Claudin-5 | CLD5_HUMAN 1-218
Color AlphaFold O00501 by residue attribute pLDDT_score
Associated AlphaFold O00501 chain A to sp|O00501|CLD5_HUMAN with 0 mismatches
> open alphafold:O00501
Chain information for AlphaFold O00501 #19
---
Chain | Description | UniProt
A | Claudin-5 | CLD5_HUMAN 1-218
Color AlphaFold O00501 by residue attribute pLDDT_score
Associated AlphaFold O00501 chain A to sp|O00501|CLD5_HUMAN with 0 mismatches
> close #19
> hide #18 models
> show #18 models
> rename #18 "Claudin-5_human AlphaFold O00501"
> open alphafold:O88551
Summary of feedback from opening O88551 fetched from alphafold
---
note | Fetching compressed AlphaFold O88551 from https://alphafold.ebi.ac.uk/files/AF-O88551-F1-model_v3.cif
Chain information for AlphaFold O88551 #19
---
Chain | Description | UniProt
A | Claudin-1 | CLD1_MOUSE 1-211
Color AlphaFold O88551 by residue attribute pLDDT_score
Associated AlphaFold O88551 chain A to sp|O88551|CLD1_MOUSE with 0 mismatches
> rename #19 "Claudin-1_mouse AlphaFold O88551"
> open alphafold:O88552
Summary of feedback from opening O88552 fetched from alphafold
---
note | Fetching compressed AlphaFold O88552 from https://alphafold.ebi.ac.uk/files/AF-O88552-F1-model_v3.cif
Chain information for AlphaFold O88552 #20
---
Chain | Description | UniProt
A | Claudin-2 | CLD2_MOUSE 1-230
Color AlphaFold O88552 by residue attribute pLDDT_score
Associated AlphaFold O88552 chain A to sp|O88552|CLD2_MOUSE with 0 mismatches
> rename #20 "Claudine-2_mouse AlphaFold O88552"
> rename #20 "Claudin-2_mouse AlphaFold O88552"
> open alphafold:O54942
Summary of feedback from opening O54942 fetched from alphafold
---
note | Fetching compressed AlphaFold O54942 from https://alphafold.ebi.ac.uk/files/AF-O54942-F1-model_v3.cif
Chain information for AlphaFold O54942 #21
---
Chain | Description | UniProt
A | Claudin-5 | CLD5_MOUSE 1-218
Color AlphaFold O54942 by residue attribute pLDDT_score
Associated AlphaFold O54942 chain A to sp|O54942|CLD5_MOUSE with 0 mismatches
> rename #21 "Claudin-5_mouse AlphaFold O54942"
> open alphafold:O95471
Summary of feedback from opening O95471 fetched from alphafold
---
note | Fetching compressed AlphaFold O95471 from https://alphafold.ebi.ac.uk/files/AF-O95471-F1-model_v3.cif
Chain information for AlphaFold O95471 #22
---
Chain | Description | UniProt
A | Claudin-7 | CLD7_HUMAN 1-211
Color AlphaFold O95471 by residue attribute pLDDT_score
Associated AlphaFold O95471 chain A to sp|O95471|CLD7_HUMAN with 0 mismatches
> rename #22 "Clausin-7_mouse AlphaFold O95471"
> hide #9 models
> hide #!10 models
> hide #11-22#!100 target m
> select #17/A:149
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #17/A:149 #20/A:149 #15/A:149 #14/A:150 #13/A:150 #22/A:150 #16/A:150
> #19/A:150 #18/A:149 #21/A:149 #12/A:149 #9/A:148
92 atoms, 80 bonds, 12 residues, 12 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|P57739|CLD2_HUMAN..sp|Q9Z0G9|CLD3_MOUSE [150] RMSD: 40.040
> select #17/A:149 #20/A:149 #15/A:149 #14/A:150 #13/A:150 #22/A:150 #16/A:150
> #19/A:150 #18/A:149 #21/A:149 #12/A:149 #9/A:148
92 atoms, 80 bonds, 12 residues, 12 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|P57739|CLD2_HUMAN..sp|Q9Z0G9|CLD3_MOUSE [150] RMSD: 40.040
> select clear
> select #9/A:148 #11/A:149 #1/A:149 #2/A:149 #3/A:149 #6/A:149 #7/A:149
> #8/A:149 #100.1/A:149
72 atoms, 63 bonds, 9 residues, 9 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|O95484|CLD9_HUMAN..tr|G7P183|G7P183_MACFA [150] RMSD: 57.961
> select clear
> select #15/A:149 #14/A:150 #13/A:150 #22/A:150 #16/A:150 #19/A:150 #18/A:149
> #21/A:149 #12/A:149 #9/A:148 #11/A:149 #1/A:149 #2/A:149 #3/A:149 #6/A:149
> #7/A:149 #8/A:149 #100.1/A:149
144 atoms, 126 bonds, 18 residues, 18 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|Q9Z0S3|CLD14_MOUSE..tr|G7P183|G7P183_MACFA [150] RMSD: 79.708
> select #15/A:149 #14/A:150 #13/A:150 #22/A:150 #16/A:150 #19/A:150 #18/A:149
> #21/A:149 #12/A:149 #9/A:148 #11/A:149 #1/A:149 #2/A:149 #3/A:149 #6/A:149
> #7/A:149 #8/A:149 #100.1/A:149
144 atoms, 126 bonds, 18 residues, 18 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|Q9Z0S3|CLD14_MOUSE..tr|G7P183|G7P183_MACFA [150] RMSD: 79.708
> select #17/A:149
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #17/A:149 #20/A:149 #15/A:149 #14/A:150 #13/A:150 #22/A:150 #16/A:150
> #19/A:150 #18/A:149 #21/A:149 #12/A:149 #9/A:148 #11/A:149
100 atoms, 87 bonds, 13 residues, 13 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|P57739|CLD2_HUMAN..sp|O35054|CLD4_MOUSE [150] RMSD: 39.689
> select #17/A:149
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #17/A:149 #20/A:149 #15/A:149 #14/A:150 #13/A:150 #22/A:150 #16/A:150
> #19/A:150 #18/A:149 #21/A:149 #12/A:149 #9/A:148 #11/A:149 #1/A:149 #2/A:149
> #3/A:149 #6/A:149 #7/A:149 #8/A:149 #100.1/A:149
156 atoms, 136 bonds, 20 residues, 20 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|P57739|CLD2_HUMAN..tr|G7P183|G7P183_MACFA [150] RMSD: 77.954
> select #3/A:31,33,48,76,138,141,142,146,150,151,156,158
110 atoms, 104 bonds, 21 pseudobonds, 12 residues, 3 models selected
> hide #!3 models
> show #!3 models
> show #!7 models
> hide #!3 models
> select #17/A:31,33,48,76,138,141,142,146,150,151,156,158
102 atoms, 97 bonds, 12 residues, 1 model selected
> select #7/A:31,33,48,76,138,141,142,146,150,151,156,158
110 atoms, 104 bonds, 12 residues, 1 model selected
> show sel cartoons
> color sel byhetero
> style sel ball
Changed 110 atom styles
> show sel cartoons
> show sel atoms
> ui tool show H-Bonds
> hbonds sel color #8efa00 dashes 6 restrict cross interModel false distSlop
> 0.8 angleSlop 60.0 reveal true retainCurrent true
33 hydrogen bonds found
> hide #!7 models
> show #!7 models
> hide #7.3 models
> select subtract #7.1
1 model selected
> hide #!7 models
> show #!3 models
> select #17/A:145 #20/A:145 #15/A:145 #14/A:146 #13/A:146 #22/A:146 #16/A:146
> #19/A:146 #18/A:145 #21/A:145 #12/A:145 #9/A:144 #11/A:145 #1/A:145 #2/A:145
> #3/A:145 #6/A:145 #7/A:145 #8/A:145 #100.1/A:145
190 atoms, 170 bonds, 20 residues, 20 models selected
> select #17/A:149 #20/A:149 #15/A:149 #14/A:150 #13/A:150 #22/A:150 #16/A:150
> #19/A:150 #18/A:149 #21/A:149 #12/A:149 #9/A:148 #11/A:149 #1/A:149 #2/A:149
> #3/A:149 #6/A:149 #7/A:149 #8/A:149 #100.1/A:149
156 atoms, 136 bonds, 20 residues, 20 models selected
> ui tool show H-Bonds
> hbonds sel color #8efa00 dashes 6 interModel false distSlop 0.8 angleSlop
> 60.0 reveal true retainCurrent true
108 hydrogen bonds found
> hbonds sel color #8efa00 dashes 6 restrict cross interModel false distSlop
> 0.8 angleSlop 60.0 reveal true retainCurrent true
108 hydrogen bonds found
> select up
2554 atoms, 2606 bonds, 340 residues, 25 models selected
> select down
156 atoms, 136 bonds, 20 residues, 25 models selected
> select clear
> select #3/A:149@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hbonds sel color #8efa00 dashes 6 restrict cross interModel false distSlop
> 0.8 angleSlop 60.0 reveal true retainCurrent true
6 hydrogen bonds found
> show #3.3 models
> hbonds sel color #8efa00 restrict cross interModel false distSlop 0.8
> angleSlop 60.0 reveal true
6 hydrogen bonds found
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #3.3 models
> hide #!3 models
> open 6ov2
Summary of feedback from opening 6ov2 fetched from pdb
---
note | Fetching compressed mmCIF 6ov2 from http://files.rcsb.org/download/6ov2.cif
6ov2 title:
Crystal structure of human claudin-9 in complex with Clostridium perfringens
entertoxin C-terminal domain in closed form [more info...]
Chain information for 6ov2 #23
---
Chain | Description | UniProt
A | Claudin-9 | CLD9_HUMAN 1-217
B | Heat-labile enterotoxin B chain | ELTB_CLOPF 194-319
Non-standard residues in 6ov2 #23
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Associated 6ov2 chain A to sp|O95484|CLD9_HUMAN with 0 mismatches
> view #23 clip false
> open 6ov3
Summary of feedback from opening 6ov3 fetched from pdb
---
note | Fetching compressed mmCIF 6ov3 from http://files.rcsb.org/download/6ov3.cif
6ov3 title:
Crystal structure of human claudin-9 in complex with Clostridium perfringens
entertoxin C-terminal domain in open form [more info...]
Chain information for 6ov3 #24
---
Chain | Description | UniProt
A | Claudin-9 | CLD9_HUMAN 1-217
B | Heat-labile enterotoxin B chain | ELTB_CLOPF 194-319
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Associated 6ov3 chain A to sp|O95484|CLD9_HUMAN with 0 mismatches
> rename #22 "Claudin-7_mouse AlphaFold O95471"
> rename #23 Claudin6ov2
> rename #23 "Claudin-9_human 6ov2 "
> rename #23 "Claudin-9_human closed 6ov2 "
> rename #24 "Claudin-9_human open 6ov4"
> open alphafold:O19005
Summary of feedback from opening O19005 fetched from alphafold
---
note | Fetching compressed AlphaFold O19005 from https://alphafold.ebi.ac.uk/files/AF-O19005-F1-model_v3.cif
Chain information for AlphaFold O19005 #25
---
Chain | Description | UniProt
A | Claudin-4 | CLD4_CHLAE 1-209
Color AlphaFold O19005 by residue attribute pLDDT_score
Associated AlphaFold O19005 chain A to tr|G7P183|G7P183_MACFA with 0
mismatches
> rename #25 "Claudin-4_AlphaFold O19005"
> rename #25 "Claudin-4_Monkey AlphaFold O19005"
> save
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/sequences/claudins.cxs
> ui tool show Matchmaker
> matchmaker #23-25#!9-22 to #3
Computing secondary structure
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 7kp4, chain A (#3) with Claudin-9_human closed 6ov2 , chain A
(#23), sequence alignment score = 769.2
RMSD between 161 pruned atom pairs is 0.857 angstroms; (across all 182 pairs:
1.561)
Matchmaker 7kp4, chain A (#3) with Claudin-9_human open 6ov4, chain A (#24),
sequence alignment score = 766.2
RMSD between 151 pruned atom pairs is 0.929 angstroms; (across all 179 pairs:
1.572)
Matchmaker 7kp4, chain A (#3) with Claudin-4_Monkey AlphaFold O19005, chain A
(#25), sequence alignment score = 971.8
RMSD between 164 pruned atom pairs is 0.669 angstroms; (across all 182 pairs:
1.322)
Matchmaker 7kp4, chain A (#3) with Claudin-3_human AlphaFold O15551, chain A
(#9), sequence alignment score = 770.9
RMSD between 149 pruned atom pairs is 0.768 angstroms; (across all 182 pairs:
2.081)
Matchmaker 7kp4, chain A (#3) with Claudin-3_mouse 6ake, chain A (#10),
sequence alignment score = 691.3
RMSD between 130 pruned atom pairs is 0.971 angstroms; (across all 175 pairs:
2.931)
Matchmaker 7kp4, chain A (#3) with Claudin-4_mouse AlphaFold O35054, chain A
(#11), sequence alignment score = 882.5
RMSD between 165 pruned atom pairs is 0.776 angstroms; (across all 182 pairs:
1.394)
Matchmaker 7kp4, chain A (#3) with Claudin-6_mouse AlphaFold Q9Z262, chain A
(#12), sequence alignment score = 720.6
RMSD between 161 pruned atom pairs is 0.782 angstroms; (across all 182 pairs:
1.549)
Matchmaker 7kp4, chain A (#3) with Claudin-7_mouse AlphaFold Q9Z261, chain A
(#13), sequence alignment score = 604.4
RMSD between 142 pruned atom pairs is 0.798 angstroms; (across all 182 pairs:
1.790)
Matchmaker 7kp4, chain A (#3) with Claudin-8_mouse AlphaFold Q9Z260, chain A
(#14), sequence alignment score = 548.8
RMSD between 150 pruned atom pairs is 0.851 angstroms; (across all 182 pairs:
3.363)
Matchmaker 7kp4, chain A (#3) with Claudin-14_mouse AlphaFold Q9Z0S3, chain A
(#15), sequence alignment score = 549.5
RMSD between 142 pruned atom pairs is 0.751 angstroms; (across all 182 pairs:
1.962)
Matchmaker 7kp4, chain A (#3) with Claudin-1_human AlphaFold O95832, chain A
(#16), sequence alignment score = 591.7
RMSD between 153 pruned atom pairs is 0.814 angstroms; (across all 182 pairs:
1.592)
Matchmaker 7kp4, chain A (#3) with Claudin-2_human AlphaFold P57739, chain A
(#17), sequence alignment score = 508.5
RMSD between 154 pruned atom pairs is 0.861 angstroms; (across all 182 pairs:
1.536)
Matchmaker 7kp4, chain A (#3) with Claudin-5_human AlphaFold O00501, chain A
(#18), sequence alignment score = 614.7
RMSD between 144 pruned atom pairs is 0.835 angstroms; (across all 182 pairs:
2.253)
Matchmaker 7kp4, chain A (#3) with Claudin-1_mouse AlphaFold O88551, chain A
(#19), sequence alignment score = 578.6
RMSD between 155 pruned atom pairs is 0.822 angstroms; (across all 182 pairs:
1.583)
Matchmaker 7kp4, chain A (#3) with Claudin-2_mouse AlphaFold O88552, chain A
(#20), sequence alignment score = 517
RMSD between 153 pruned atom pairs is 0.853 angstroms; (across all 182 pairs:
1.544)
Matchmaker 7kp4, chain A (#3) with Claudin-5_mouse AlphaFold O54942, chain A
(#21), sequence alignment score = 617.4
RMSD between 143 pruned atom pairs is 0.857 angstroms; (across all 182 pairs:
2.305)
Matchmaker 7kp4, chain A (#3) with Claudin-7_mouse AlphaFold O95471, chain A
(#22), sequence alignment score = 594.9
RMSD between 142 pruned atom pairs is 0.830 angstroms; (across all 182 pairs:
1.861)
> view #3 clip false
> hide #!6 models
> show #!3 models
> select subtract #3.1
1 model selected
> hide #23 models
> hide #24 models
> hide #25 models
> show #!11 models
> hide #!11 models
> hide #!3 models
> show #100.1.2 models
> hide #100.1.2 models
> show #!11 models
> color #11 #ff2600ff
> hide #!11 models
> show #!11 models
> select #11/A:31,33,48,76,138,141,142,146,150,151,156,158
110 atoms, 104 bonds, 12 residues, 1 model selected
> show sel atoms
> select clear
> select #11/A:31,33,48,76,138,141,142,146,150,151,156,158
110 atoms, 104 bonds, 12 residues, 1 model selected
> color sel byhetero
> select clear
> select #11/A:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/A:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #100.2 models
> select #11/A:31,33,48,76,138,141,142,146,150,151,156,158
> #12/A:31,33,48,76,138,141,142,146,150,151,156,158
216 atoms, 204 bonds, 24 residues, 2 models selected
> show #!12 models
> hide #!11 models
> show sel & #!12 atoms
> color sel & #!12 byhetero
> color #12 #9437ffff
> hide #100.2 models
> hide #!100 models
> color sel & #!12 byhetero
> select clear
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> select #9/A:31,33,48,76,138,141,142,146,150,151,156,158
> #10/A:31,33,48,76,138,141,142,146,150,151,156,158
> #13/A:31,33,48,76,138,141,142,146,150,151,156,158
> #14/A:31,33,48,76,138,141,142,146,150,151,156,158
> #15/A:31,33,48,76,138,141,142,146,150,151,156,158
465 atoms, 424 bonds, 2 pseudobonds, 60 residues, 7 models selected
> show #!12 atoms
> hide #!12 models
> show #!13 models
> show sel & #!13 cartoons
> show sel & #!13 atoms
> color sel & #!13 byhetero
> show #!14 models
> hide #!13 models
> show sel & #!14 atoms
> color sel & #!14 byhetero
> show #!15 models
> hide #!14 models
> show sel & #!15 atoms
> color sel & #!15 byhetero
> show #!16 models
> hide #!15 models
> show #!16 atoms
> hide #!16 models
> show #!13 models
> select add #13
1934 atoms, 1934 bonds, 7 pseudobonds, 259 residues, 7 models selected
> select subtract #13
377 atoms, 344 bonds, 1 pseudobond, 48 residues, 5 models selected
> select add #14
2029 atoms, 2041 bonds, 5 pseudobonds, 261 residues, 5 models selected
> select subtract #14
284 atoms, 260 bonds, 36 residues, 3 models selected
> select add #15
1970 atoms, 1994 bonds, 4 pseudobonds, 263 residues, 4 models selected
> select subtract #15
177 atoms, 159 bonds, 24 residues, 2 models selected
> select add #9
1721 atoms, 1743 bonds, 4 pseudobonds, 232 residues, 3 models selected
> select subtract #9
89 atoms, 80 bonds, 12 residues, 1 model selected
> select add #10
4306 atoms, 4391 bonds, 3 pseudobonds, 579 residues, 3 models selected
> select subtract #10
Nothing selected
> color #13 #0096ffff
> color #14 #ff9300ff
> color #15 #73fcd6ff
> show #!15 models
> show #!14 models
> show #!12 models
> show #!11 models
> show #!10 models
> select #10/C:131
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
255 atoms, 260 bonds, 33 residues, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/A
1635 atoms, 1668 bonds, 5 pseudobonds, 219 residues, 2 models selected
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> show #!12 models
> hide sel atoms
> select subtract #12
Nothing selected
> select #9/A:31,33,48,76,138,141,142,146,150,151,156,158
> #10/A:31,33,48,76,138,141,142,146,150,151,156,158
> #13/A:31,33,48,76,138,141,142,146,150,151,156,158
> #14/A:31,33,48,76,138,141,142,146,150,151,156,158
> #15/A:31,33,48,76,138,141,142,146,150,151,156,158
465 atoms, 424 bonds, 2 pseudobonds, 60 residues, 7 models selected
> show sel & #!10,13-15 cartoons
> color sel & #!10,13-15 byhetero
> select #10/C
1211 atoms, 1232 bonds, 2 pseudobonds, 168 residues, 2 models selected
> hide sel cartoons
> select #10/D
899 atoms, 920 bonds, 115 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #9/A:31,33,48,76,138,141,142,146,150,151,156,158
> #10/A:31,33,48,76,138,141,142,146,150,151,156,158
> #13/A:31,33,48,76,138,141,142,146,150,151,156,158
> #14/A:31,33,48,76,138,141,142,146,150,151,156,158
> #15/A:31,33,48,76,138,141,142,146,150,151,156,158
> #10/A:31,33,48,76,138,141,142,146,150,151,156,158
> #11/A:31,33,48,76,138,141,142,146,150,151,156,158
> #12/A:31,33,48,76,138,141,142,146,150,151,156,158
> #15/A:31,33,48,76,138,141,142,146,150,151,156,158
681 atoms, 628 bonds, 2 pseudobonds, 84 residues, 9 models selected
> hide #* target a
> show (#!10-15 & sel) target ab
> hide #!15 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> show #!3 models
> select #3/A:31,33,48,76,138,141,142,146,150,151,156,158
110 atoms, 104 bonds, 13 pseudobonds, 12 residues, 2 models selected
> show sel atoms
> select clear
> select #100/A:31,33,48,76,138,141,142,146,150,151,156,158
110 atoms, 104 bonds, 8 pseudobonds, 12 residues, 2 models selected
> hide #!100.1 models
> show #!100 models
> hide #!3 models
> show #!100.1 models
> show sel atoms
> style sel ball
Changed 110 atom styles
> show #100.1.2 models
> hide #!100.1 models
> show #!100.1 models
> select subtract #100.1.2
1 model selected
> select add #100.1.2
1318 atoms, 182 residues, 1 model selected
> transparency (#!100.1 & sel) 40
> transparency (#!100.1 & sel) 70
> select clear
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!100 models
> show #!100 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> select #9/A:31,33,48,76,138,141,142,146,150,151,156,158
88 atoms, 79 bonds, 12 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide #100.1.2 models
> hide #!100 models
> show #!100 models
> hide #!100 models
> hide sel atoms
> color #9 #ffd479ff
> select clear
> show #!3 models
> hide #!3 models
> show #!100 models
> hide #!9 models
> show #!16 models
> show #!19 models
> select /A:149
206 atoms, 189 bonds, 24 residues, 24 models selected
> show sel & #!16,19#!100.1 atoms
> select clear
> select /A:149
206 atoms, 189 bonds, 24 residues, 24 models selected
> hide sel & #!16,19#!100.1 atoms
> select clear
> select #100.1/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #16/A:150
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #100.1/A:156
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #19/A:150
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #16/A:150
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> color sel byhetero
> show #23 models
> select add #23
2346 atoms, 2384 bonds, 316 residues, 3 models selected
> select subtract #23
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #23
2346 atoms, 2384 bonds, 316 residues, 3 models selected
> select subtract #23
16 atoms, 14 bonds, 2 residues, 2 models selected
> hide #!16 models
> show #!18 models
> hide #!19 models
> hide #23 models
> hide #!100 models
> hide #!18 models
> show #!18 models
> show #!100 models
> hide #!100 models
> select #18/A:146
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> style sel ball
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #17/A:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #17/A:146 #20/A:146 #15/A:146 #14/A:147 #13/A:147 #22/A:147 #16/A:147
> #19/A:147 #18/A:146 #21/A:146 #12/A:146 #23/A:146 #24/A:146 #9/A:145
> #11/A:146 #1/A:146 #2/A:146 #3/A:146 #6/A:146 #7/A:146 #8/A:146 #100.1/A:146
> #25/A:146
188 atoms, 165 bonds, 23 residues, 23 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|P57739|CLD2_HUMAN..tr|G7P183|G7P183_MACFA [147] RMSD: 1.373
> show sel & #!18 atoms
> color sel & #!18 byhetero
> hide #!18 models
> show #!100 models
> hide sel & #!100.1 atoms
> select #17/A:149
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #17/A:149 #20/A:149 #15/A:149 #14/A:150 #13/A:150 #22/A:150 #16/A:150
> #19/A:150 #18/A:149 #21/A:149 #12/A:149 #23/A:149 #24/A:149 #9/A:148
> #11/A:149 #1/A:149 #2/A:149 #3/A:149 #6/A:149 #7/A:149 #8/A:149 #100.1/A:149
> #25/A:149
180 atoms, 157 bonds, 23 residues, 23 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|P57739|CLD2_HUMAN..tr|G7P183|G7P183_MACFA [150] RMSD: 0.852
> show sel & #!100.1 atoms
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!100 models
> show sel & #!9 atoms
> color sel & #!9 byhetero
> hide #!9 models
> show #!16 models
> show #!18 models
> show #!17 models
> show sel & #!16-18 atoms
> color sel & #!16-18 byhetero
> show #!100 models
> show #100.2 models
> select add #100.2/B:311
187 atoms, 164 bonds, 24 residues, 29 models selected
> select up
2758 atoms, 2814 bonds, 366 residues, 29 models selected
> select down
187 atoms, 164 bonds, 24 residues, 29 models selected
> select up
2758 atoms, 2814 bonds, 366 residues, 29 models selected
> select down
187 atoms, 164 bonds, 24 residues, 29 models selected
> select add #100.2/B:232
199 atoms, 176 bonds, 25 residues, 29 models selected
> select clear
> select #100.2/B:232
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
69 atoms, 72 bonds, 8 residues, 1 model selected
> select up
1057 atoms, 1079 bonds, 134 residues, 1 model selected
> select add #100.1/A:149@ND2
1058 atoms, 1079 bonds, 135 residues, 2 models selected
> select up
1065 atoms, 1086 bonds, 135 residues, 3 models selected
> select up
1067 atoms, 1087 bonds, 136 residues, 4 models selected
> select add #16/A:150@OD2
1068 atoms, 1087 bonds, 137 residues, 5 models selected
> select up
1081 atoms, 1100 bonds, 137 residues, 5 models selected
> ui tool show H-Bonds
> hbonds sel color #8efa00 restrict cross distSlop 0.8 angleSlop 60.0 reveal
> true
4150 hydrogen bonds found
> hide #100.2 models
> show #100.2 models
> select subtract #100.2
24 atoms, 21 bonds, 3 residues, 4 models selected
> select add #100.2
1081 atoms, 1100 bonds, 137 residues, 5 models selected
> select subtract #100.1.2
1073 atoms, 1093 bonds, 136 residues, 4 models selected
> select add #100.1.2
2391 atoms, 1093 bonds, 318 residues, 4 models selected
> select subtract #100.1.2
1073 atoms, 1093 bonds, 136 residues, 4 models selected
> select add #100
2391 atoms, 2435 bonds, 5 pseudobonds, 318 residues, 6 models selected
> select subtract #100
16 atoms, 14 bonds, 2 residues, 3 models selected
> select add #18
1630 atoms, 1669 bonds, 7 pseudobonds, 219 residues, 3 models selected
> select subtract #18
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #16
1592 atoms, 1628 bonds, 5 pseudobonds, 211 residues, 2 models selected
> select subtract #16
Nothing selected
> hide #16-18#100.2#!100.1 atoms
> hide #16 models
> hide #17 models
> hide #18 models
> hide #100.2 models
> hide #!100.1 models
> show #!100.1 models
> select #1/A:149 #2/A:149 #3/A:149 #6/A:149 #7/A:149 #8/A:149 #100.1/A:149
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #1/A:149-153 #2/A:149-153 #3/A:149-153 #6/A:149-153 #7/A:149-153
> #8/A:149-153 #100.1/A:149-153
245 atoms, 245 bonds, 15 pseudobonds, 35 residues, 8 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region sp|O14493|CLD4_HUMAN
[150-154] RMSD: 0.656
> select clear
> select #3/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:149-155
45 atoms, 45 bonds, 7 residues, 1 model selected
> select #9/A:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:148-154
50 atoms, 51 bonds, 7 residues, 1 model selected
> select #1/A:155-156 #2/A:155-156 #3/A:155-156 #6/A:155-156 #7/A:155-156
> #8/A:155-156 #100.1/A:155-156
91 atoms, 84 bonds, 14 residues, 7 models selected
> select #1/A:149-156 #2/A:149-156 #3/A:149-156 #6/A:149-156 #7/A:149-156
> #8/A:149-156 #100.1/A:149-156
378 atoms, 378 bonds, 15 pseudobonds, 56 residues, 8 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region sp|O14493|CLD4_HUMAN
[150-157] RMSD: 1.033
> show #100.2 models
> show #9 models
> show sel & #!100.1 atoms
> select #9/A:148-154
50 atoms, 51 bonds, 7 residues, 1 model selected
> select #9/A:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:148-155
59 atoms, 60 bonds, 8 residues, 1 model selected
> show sel cartoons
> show sel atoms
> style sel stick
Changed 59 atom styles
> color sel byhetero
> hide #100.2 models
> select clear
> select #1/A:149 #2/A:149 #3/A:149 #6/A:149 #7/A:149 #8/A:149 #100.1/A:149
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #1/A:149-153 #2/A:149-153 #3/A:149-153 #6/A:149-153 #7/A:149-153
> #8/A:149-153 #100.1/A:149-153
245 atoms, 245 bonds, 15 pseudobonds, 35 residues, 8 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region sp|O14493|CLD4_HUMAN
[150-154] RMSD: 0.656
> show #100.2 models
> select clear
> hide #100.2 models
> hide #!100.1 models
> show #!100.1 models
> hide #!100 models
> show #!100 models
> hide #!100.1 models
> show #!100.1 models
> hide #!100.1 models
> hide #!100 models
> hide #9 models
> show #!100 models
> show #!100.1 models
> select #100.1/A:141
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
294 atoms, 300 bonds, 39 residues, 2 models selected
> select up
1318 atoms, 1342 bonds, 182 residues, 2 models selected
> select up
1318 atoms, 1342 bonds, 182 residues, 2 models selected
> select down
1 model selected
> select #100.1/A:141
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
294 atoms, 300 bonds, 39 residues, 2 models selected
> select up
1318 atoms, 1342 bonds, 182 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep pink target s
> color sel deep pink target acs
> color sel magenta target acs
> color sel rebecca purple target acs
> set bgColor white
> color sel medium aquamarine target acs
> color sel teal target acs
> color sel deep pink target acs
> color sel byhetero
> select clear
> select #1/A:149 #2/A:149 #3/A:149 #6/A:149 #7/A:149 #8/A:149 #100.1/A:149
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #1/A:149-153 #2/A:149-153 #3/A:149-153 #6/A:149-153 #7/A:149-153
> #8/A:149-153 #100.1/A:149-153
245 atoms, 245 bonds, 15 pseudobonds, 35 residues, 8 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region sp|O14493|CLD4_HUMAN
[150-154] RMSD: 0.656
> hide #* target a
> show (#!100.1 & sel) target ab
> select clear
> select #9/A:148-154
50 atoms, 51 bonds, 7 residues, 1 model selected
> select #9/A:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:148-153
45 atoms, 46 bonds, 6 residues, 1 model selected
> select #1/A:149-153 #2/A:149-153 #3/A:149-153 #6/A:149-153 #7/A:149-153
> #8/A:149-153 #100.1/A:149-153
245 atoms, 245 bonds, 15 pseudobonds, 35 residues, 8 models selected
> select #9/A:148-153
45 atoms, 46 bonds, 6 residues, 1 model selected
> select #9/A:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:148-152
36 atoms, 37 bonds, 5 residues, 1 model selected
> show #9 models
> show sel atoms
> select clear
> style #9#!100.1 stick
Changed 2950 atom styles
> show #!10 models
> hide #9 models
> select #10/B:302
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
69 atoms, 69 bonds, 9 residues, 1 model selected
> select up
918 atoms, 939 bonds, 117 residues, 1 model selected
> select down
69 atoms, 69 bonds, 9 residues, 1 model selected
> select down
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> split #10
Split Claudin-3_mouse 6ake (#10) into 4 models
Chain information for Claudin-3_mouse 6ake A #10.1
---
Chain | Description
A | No description available
Chain information for Claudin-3_mouse 6ake B #10.2
---
Chain | Description
B | No description available
Chain information for Claudin-3_mouse 6ake C #10.3
---
Chain | Description
C | No description available
Chain information for Claudin-3_mouse 6ake D #10.4
---
Chain | Description
D | No description available
> hide #10.4 models
> hide #!10.3 models
> hide #10.2 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> select clear
> show #!10.1#!100.1 atoms
> hide #!10.1#!100.1 atoms
> hide #!100 models
> hide #!100.1 models
> select #1/A:149-153 #2/A:149-153 #3/A:149-153 #6/A:149-153 #7/A:149-153
> #8/A:149-153 #100.1/A:149-153
245 atoms, 245 bonds, 15 pseudobonds, 35 residues, 8 models selected
> show #!10.1 atoms
> hide #!10.1 atoms
> select clear
> select #1/A:149 #2/A:149 #3/A:149 #6/A:149 #7/A:149 #8/A:149 #100.1/A:149
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #1/A:149-153 #2/A:149-153 #3/A:149-153 #6/A:149-153 #7/A:149-153
> #8/A:149-153 #100.1/A:149-153
245 atoms, 245 bonds, 15 pseudobonds, 35 residues, 8 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region sp|O14493|CLD4_HUMAN
[150-154] RMSD: 0.656
> select #9/A:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:148-152
36 atoms, 37 bonds, 5 residues, 1 model selected
> select clear
> select #1/A:149 #2/A:149 #3/A:149 #6/A:149 #7/A:149 #8/A:149 #100.1/A:149
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #1/A:149-153 #2/A:149-153 #3/A:149-153 #6/A:149-153 #7/A:149-153
> #8/A:149-153 #100.1/A:149-153
245 atoms, 245 bonds, 15 pseudobonds, 35 residues, 8 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region sp|O14493|CLD4_HUMAN
[150-154] RMSD: 0.656
> show #!10.1 atoms
> hide #!10.1 models
> show #100.1.2 models
> hide #100.1.2 models
> select subtract #100.1.2
210 atoms, 210 bonds, 30 residues, 11 models selected
> select #1/A:149 #2/A:149 #3/A:149 #6/A:149 #7/A:149 #8/A:149 #100.1/A:149
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #1/A:149-153 #2/A:149-153 #3/A:149-153 #6/A:149-153 #7/A:149-153
> #8/A:149-153 #100.1/A:149-153
245 atoms, 245 bonds, 15 pseudobonds, 35 residues, 8 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region sp|O14493|CLD4_HUMAN
[150-154] RMSD: 0.656
> show sel & #!100.1 atoms
> select #9/A:148-152
36 atoms, 37 bonds, 5 residues, 1 model selected
> hide #!100 models
> show #9 models
> hide #!10 models
> show sel cartoons
> select clear
> select #9/A:148-152
36 atoms, 37 bonds, 5 residues, 1 model selected
> show #!10 models
> hide #9 models
> select add #9
1632 atoms, 1663 bonds, 220 residues, 1 model selected
> select clear
> hide #!10 models
> show #!10.1 models
> select clear
> hide #!10.1 atoms
> select clear
> show #!10.1 atoms
> hide #!10.1 atoms
> select #9/A:148-152
36 atoms, 37 bonds, 5 residues, 1 model selected
> select clear
> select #10.1/A:148
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
30 atoms, 30 bonds, 4 residues, 1 model selected
> show sel atoms
> select #10.1/A:152
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show #9 models
> show #!100 models
> hide #!10.1 models
> select #25/A:153-154
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #17/A:149-154 #20/A:149-154 #15/A:149-154 #14/A:150-155 #13/A:150-155
> #22/A:150-155 #16/A:150-155 #19/A:150-155 #18/A:149-154 #21/A:149-154
> #12/A:149-154 #23/A:149-154 #24/A:149-154 #9/A:148-153 #11/A:149-154
> #1/A:149-154 #2/A:149-154 #3/A:149-154 #6/A:149-154 #7/A:149-154
> #8/A:149-154 #100.1/A:149-154 #25/A:149-154
984 atoms, 994 bonds, 191 pseudobonds, 138 residues, 24 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|P57739|CLD2_HUMAN..tr|G7P183|G7P183_MACFA [150-155] RMSD: 1.247
> select #1/A:149 #2/A:149 #3/A:149 #6/A:149 #7/A:149 #8/A:149 #100.1/A:149
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #1/A:149-153 #2/A:149-153 #3/A:149-153 #6/A:149-153 #7/A:149-153
> #8/A:149-153 #100.1/A:149-153
245 atoms, 245 bonds, 15 pseudobonds, 35 residues, 8 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region sp|O14493|CLD4_HUMAN
[150-154] RMSD: 0.656
> select #17/A:149
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #17/A:149-154 #20/A:149-154 #15/A:149-154 #14/A:150-155 #13/A:150-155
> #22/A:150-155 #16/A:150-155 #19/A:150-155 #18/A:149-154 #21/A:149-154
> #12/A:149-154 #23/A:149-154 #24/A:149-154 #9/A:148-153 #11/A:149-154
> #1/A:149-154 #2/A:149-154 #3/A:149-154 #6/A:149-154 #7/A:149-154
> #8/A:149-154 #100.1/A:149-154 #25/A:149-154
984 atoms, 994 bonds, 191 pseudobonds, 138 residues, 24 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|P57739|CLD2_HUMAN..tr|G7P183|G7P183_MACFA [150-155] RMSD: 1.247
> show #!6 models
> hide #!6 models
> show #!6 models
> select #6/A:147
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
294 atoms, 300 bonds, 39 residues, 2 models selected
> select up
1318 atoms, 1342 bonds, 182 residues, 2 models selected
> select up
2375 atoms, 2421 bonds, 316 residues, 2 models selected
> select down
1318 atoms, 1342 bonds, 182 residues, 3 models selected
> ui tool show "Color Actions"
> color sel deep pink target acs
> color sel byhetero
> select clear
> select #100.1/A:150@CG
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
37 atoms, 37 bonds, 6 residues, 2 models selected
> select down
7 atoms, 7 bonds, 1 residue, 2 models selected
> save
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/sequences/claudins.cxs
Drag select of 2 residues
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
37 atoms, 37 bonds, 6 residues, 2 models selected
> select #9/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
294 atoms, 300 bonds, 39 residues, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> select add #100.1/A:150@CB
9 atoms, 7 bonds, 2 residues, 2 models selected
> select up
15 atoms, 15 bonds, 2 residues, 2 models selected
> select up
17 atoms, 16 bonds, 3 residues, 2 models selected
> select add #6/A:152
24 atoms, 22 bonds, 4 residues, 3 models selected
> select up
30 atoms, 29 bonds, 4 residues, 4 models selected
> select add #6/A:153
35 atoms, 33 bonds, 5 residues, 4 models selected
> select up
368 atoms, 375 bonds, 51 residues, 4 models selected
> select down
35 atoms, 33 bonds, 5 residues, 4 models selected
> show #100.2 models
> hide #!100.1 models
> hide #!100 models
> hide #100.2 models
> hide #!10 models
> show #!100 models
> hide #!100 models
> show #!100 models
> hide #!6 models
> show #!100.1 models
> show #100.2 models
> hide #9 models
> ui tool show H-Bonds
> hbonds sel color #8efa00 interModel false distSlop 0.8 angleSlop 60.0 reveal
> true
7 hydrogen bonds found
> hbonds sel color #8efa00 restrict cross distSlop 0.8 angleSlop 60.0 reveal
> true
238 hydrogen bonds found
> show #100.1.2 models
> hide #100.1.2 models
> hide #100.2 models
> show #100.2 models
> hide #100.2 models
> select #100.1/A:145@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> hide sel atoms
> show #!3 models
> select add #3/A:154
15 atoms, 13 bonds, 2 residues, 3 models selected
> select up
331 atoms, 337 bonds, 45 residues, 4 models selected
> select subtract #3/A:155
327 atoms, 333 bonds, 44 residues, 4 models selected
> show sel atoms
> hide sel atoms
> hide #!100.1 models
> hide #!100 models
> select add #3/A:149@CA
328 atoms, 333 bonds, 45 residues, 4 models selected
> show sel & #!3 atoms
> style sel & #!3 stick
Changed 34 atom styles
> select up
335 atoms, 341 bonds, 45 residues, 4 models selected
> select up
625 atoms, 638 bonds, 84 residues, 4 models selected
> select up
2636 atoms, 2684 bonds, 364 residues, 4 models selected
> color (#!3 & sel) hot pink
> ui tool show "Color Actions"
> color sel deep pink target acs
> color sel & #!3 byhetero
> select #3/B:307
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
69 atoms, 71 bonds, 9 residues, 2 models selected
> select up
1057 atoms, 1079 bonds, 134 residues, 2 models selected
> color (#!3 & sel) gray
> select clear
> select #3/B:255
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
53 atoms, 53 bonds, 6 residues, 2 models selected
> select up
1057 atoms, 1079 bonds, 134 residues, 2 models selected
> hide sel atoms
> style sel stick
Changed 1057 atom styles
> color sel byhetero
> select clear
> select add #3/A:150@CD
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select add #3/A:151@CG
8 atoms, 7 bonds, 2 residues, 2 models selected
> select up
15 atoms, 15 bonds, 2 residues, 2 models selected
> select up
17 atoms, 16 bonds, 3 residues, 2 models selected
> select up
19 atoms, 17 bonds, 4 residues, 2 models selected
> select up
21 atoms, 18 bonds, 5 residues, 2 models selected
> select add #3/A:149@CG
22 atoms, 18 bonds, 6 residues, 2 models selected
> select up
41 atoms, 41 bonds, 6 residues, 2 models selected
> hbonds sel color #8efa00 restrict cross interModel false distSlop 0.8
> angleSlop 60.0 reveal true
12 hydrogen bonds found
> hbonds sel color #00f410 radius 0.105 dashes 7 restrict cross interModel
> false distSlop 0.8 angleSlop 60.0 reveal true
12 hydrogen bonds found
> hbonds sel color #00f410 radius 0.135 dashes 7 restrict cross interModel
> false distSlop 0.8 angleSlop 60.0 reveal true
12 hydrogen bonds found
> hbonds sel color #00f410 radius 0.135 restrict cross interModel false
> distSlop 0.8 angleSlop 60.0 reveal true
12 hydrogen bonds found
> select #3/A:154@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #3/A:153
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 6 residues, 2 models selected
> select add #3/A:149@CG
38 atoms, 37 bonds, 7 residues, 2 models selected
> select subtract #3/A:154
32 atoms, 30 bonds, 6 residues, 2 models selected
> select subtract #3/A:155
28 atoms, 27 bonds, 5 residues, 2 models selected
> hbonds sel color #00f410 radius 0.135 restrict cross interModel false
> distSlop 0.8 angleSlop 60.0 reveal true
7 hydrogen bonds found
> select add #3/A:149@ND2
29 atoms, 27 bonds, 5 residues, 2 models selected
> hbonds sel color #00f410 radius 0.135 restrict cross interModel false
> distSlop 0.8 angleSlop 60.0 reveal true
9 hydrogen bonds found
> hbonds sel color #00f410 radius 0.135 restrict cross interModel false
> distSlop 0.8 angleSlop 60.0 reveal true
9 hydrogen bonds found
Drag select of 6 atoms, 6 residues, 6 bonds
> select clear
> select add #3/A:149@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select add #3/A:150@CD
9 atoms, 7 bonds, 2 residues, 2 models selected
> select up
15 atoms, 15 bonds, 2 residues, 2 models selected
> select up
17 atoms, 16 bonds, 3 residues, 2 models selected
> select add #3/A:152@CB
18 atoms, 16 bonds, 4 residues, 2 models selected
> select up
30 atoms, 30 bonds, 4 residues, 2 models selected
> select up
32 atoms, 31 bonds, 5 residues, 2 models selected
> select subtract backbone
15 atoms, 10 bonds, 5 residues, 2 models selected
> hbonds sel color #9437ff radius 0.135 restrict cross interModel false
> distSlop 0.8 angleSlop 60.0 reveal true
3 hydrogen bonds found
> select #3/B:284@OD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select add #3/B:256@CB
9 atoms, 7 bonds, 2 residues, 2 models selected
> select up
14 atoms, 12 bonds, 2 residues, 2 models selected
> select add #3/B:313@OG
15 atoms, 12 bonds, 3 residues, 2 models selected
> select up
20 atoms, 17 bonds, 3 residues, 2 models selected
> hide sel atoms
> select clear
> ui tool show "Side View"
> show #20 models
> hide #20 models
> show #9 models
> save
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/sequences/claudins.cxs
> save /Users/adaina/Desktop/image1.png supersample 3
> save /Users/adaina/Desktop/image2.png supersample 3
> save
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/sequences/claudins.cxs
> select #17/A:158 #20/A:158 #15/A:158 #14/A:159 #13/A:159 #22/A:159 #16/A:159
> #19/A:159 #18/A:158 #21/A:158 #12/A:158 #23/A:158 #24/A:158 #9/A:157
> #11/A:158 #1/A:158 #2/A:158 #3/A:158 #6/A:158 #7/A:158 #8/A:158 #100.1/A:158
> #25/A:158
259 atoms, 245 bonds, 23 residues, 23 models selected
> open
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/sequences/MUSCLE/CLDN3human-
> CLDN4human-p1m.fa
Sequence 'sp|O14493|CLD4_HUMAN' differs in length from preceding sequences,
and it is therefore impossible to open these sequences as an alignment. If you
want to open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.
> open
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/sequences/MUSCLE/CLDN3human-
> CLDN4human-p1m.fa
Sequence 'sp|O14493|CLD4_HUMAN' differs in length from preceding sequences,
and it is therefore impossible to open these sequences as an alignment. If you
want to open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.
> open
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/sequences/MUSCLE/CLDN3human-
> CLDN4human-p1m.fa
Sequence 'sp|O14493|CLD4_HUMAN' differs in length from preceding sequences,
and it is therefore impossible to open these sequences as an alignment. If you
want to open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.
> show sel & #9#!3 atoms
> show #!10.1 models
> show sel & #9#!3 atoms
> select #10.1/A:157
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #10.2 models
> hide #10.2 models
> hide #!10.1 models
> select #3/A:31,227
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:227
Nothing selected
> select #3/B:227
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #3/A:31@NE
12 atoms, 10 bonds, 2 residues, 2 models selected
> select up
22 atoms, 20 bonds, 2 residues, 3 models selected
> style sel stick
Changed 22 atom styles
> select clear
> select #3/A:48,76,146
25 atoms, 22 bonds, 3 residues, 1 model selected
> show sel atoms
> select #9/A:47
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #9/A:30
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #9/A:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #9/A:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:48,76,146
25 atoms, 22 bonds, 3 residues, 1 model selected
> select #3/A:48,76,146,31,227
36 atoms, 32 bonds, 4 residues, 1 model selected
> hide #!10 models
> show #!10 models
> hide #!10 models
> select clear
> select #17/A:149-154 #20/A:149-154 #15/A:149-154 #14/A:150-155 #13/A:150-155
> #22/A:150-155 #16/A:150-155 #19/A:150-155 #18/A:149-154 #21/A:149-154
> #12/A:149-154 #23/A:149-154 #24/A:149-154 #9/A:148-153 #11/A:149-154
> #1/A:149-154 #2/A:149-154 #3/A:149-154 #6/A:149-154 #7/A:149-154
> #8/A:149-154 #100.1/A:149-154 #25/A:149-154
984 atoms, 994 bonds, 116 pseudobonds, 138 residues, 25 models selected
> show #18 models
> hide #9 models
> hide #18 models
> show #18 models
> hide #18 models
> show #18 models
> open
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/sequences/claudins.cxs
opened ChimeraX session
Exception in thread Thread-2060 (_run_function):
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 1038, in _bootstrap_inner
self.run()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 975, in run
self._target(*self._args, **self._kwargs)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 300, in _run_function
func(*args, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 174, in _relaunch
super().run()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 463, in run
self.monitor()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 199, in monitor
result = self.chimerax_api.get_status(job_id=self.job_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 954, in get_status
(data) = self.get_status_with_http_info(job_id, **kwargs) # noqa: E501
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 990, in
get_status_with_http_info
raise ValueError("Missing the required parameter `job_id` when calling
`get_status`") # noqa: E501
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Missing the required parameter `job_id` when calling `get_status`
> hide #9 models
> show #9 models
> hide #9 models
> show #17 models
> hide #!3 models
> select #17/A:148
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
295 atoms, 303 bonds, 38 residues, 1 model selected
> select up
1722 atoms, 1759 bonds, 230 residues, 1 model selected
> color sel forest green
> hide #17 models
> select subtract #17
Nothing selected
> show #18 models
> select add #18
1622 atoms, 1662 bonds, 218 residues, 1 model selected
> select subtract #18
Nothing selected
> select add #18
1622 atoms, 1662 bonds, 218 residues, 1 model selected
> ui tool show "Color Actions"
> color sel olive drab target acs
> select clear
> open
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/sequences/claudins.cxs
opened ChimeraX session
Exception in thread Thread-2095 (_run_function):
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 1038, in _bootstrap_inner
self.run()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 975, in run
self._target(*self._args, **self._kwargs)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 300, in _run_function
func(*args, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 174, in _relaunch
super().run()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 463, in run
self.monitor()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 199, in monitor
result = self.chimerax_api.get_status(job_id=self.job_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 954, in get_status
(data) = self.get_status_with_http_info(job_id, **kwargs) # noqa: E501
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 990, in
get_status_with_http_info
raise ValueError("Missing the required parameter `job_id` when calling
`get_status`") # noqa: E501
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Missing the required parameter `job_id` when calling `get_status`
> hide #9 models
> hide #!3 models
> show #18 models
> color forest green target acs
> open
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/sequences/claudins.cxs
opened ChimeraX session
Exception in thread Thread-2117 (_run_function):
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 1038, in _bootstrap_inner
self.run()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py",
line 975, in run
self._target(*self._args, **self._kwargs)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 300, in _run_function
func(*args, **kw)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 174, in _relaunch
super().run()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tasks.py", line 463, in run
self.monitor()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/cxservices_job.py", line 199, in monitor
result = self.chimerax_api.get_status(job_id=self.job_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 954, in get_status
(data) = self.get_status_with_http_info(job_id, **kwargs) # noqa: E501
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/cxservices/api/default_api.py", line 990, in
get_status_with_http_info
raise ValueError("Missing the required parameter `job_id` when calling
`get_status`") # noqa: E501
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Missing the required parameter `job_id` when calling `get_status`
> hide #9 models
> hide #!3 models
> show #18 models
> select add #18
1622 atoms, 1662 bonds, 218 residues, 1 model selected
> color sel forest green target acs
> select clear
> select #18/A:149@CA
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
35 atoms, 36 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> show #5 models
> hide #5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> save /Users/adaina/Desktop/image3.png supersample 3
> save /Users/adaina/Desktop/image4.png supersample 3
> select #18/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #18/A:158
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:158
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #18/A:158, 31,146,48,76
48 atoms, 44 bonds, 5 residues, 1 model selected
> show sel atoms
> select #18/A:48,76
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #22/A:113-114
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #22/A:113-158
347 atoms, 355 bonds, 46 residues, 1 model selected
> select #22/A:150
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:150-154
38 atoms, 39 bonds, 5 residues, 1 model selected
> show #22 models
> hide #22 models
> rename #22 "Claudin-7_human AlphaFold O95471"
> show #22 models
> select add #22
1563 atoms, 1596 bonds, 211 residues, 1 model selected
> select subtract #22
Nothing selected
> hide #18 models
> color #22 #76d6ffff
> color #22 #73fdffff
> color #22 #73fcd6ff
> color #22 #76d6ffff
> color deep sky blue target acs
> undo
> color #22#!3 byhetero
> select #22/A:150
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #22/A:151
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #22/A:152
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #22/A:154
30 atoms, 28 bonds, 4 residues, 1 model selected
> select add #22/A:153
38 atoms, 35 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select ~sel & ##selected
1525 atoms, 1557 bonds, 206 residues, 1 model selected
> hide sel atoms
> select #3/A:158@NE
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> hide sel atoms
> save /Users/adaina/Desktop/image5.png supersample 3
> select clear
> save
> /Users/adaina/Documents/PROJETS/DEBIO/service_MM0033_Claudin4/sequences/claudins.cxs
> select #22/A:159
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #22/A:159,32,147,49,77
40 atoms, 36 bonds, 5 residues, 1 model selected
> show sel atoms
> select #3/A:158,31,146,48,76
47 atoms, 42 bonds, 5 residues, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select #22/A:143
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
286 atoms, 292 bonds, 38 residues, 1 model selected
> select up
1563 atoms, 1596 bonds, 211 residues, 1 model selected
> select up
61313 atoms, 62544 bonds, 238 pseudobonds, 8113 residues, 26 models selected
> select down
1563 atoms, 1596 bonds, 211 residues, 17 models selected
> hide sel atoms
> select clear
> select #22/A:159
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #22/A:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #22/A:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #22/A:148
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #22/A:147
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #22/A:148
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #22/A:76
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #22/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #22/A:76
13 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1/A:76 #2/A:76 #3/A:76 #6/A:76 #7/A:76 #8/A:76 #100.1/A:76
56 atoms, 49 bonds, 7 residues, 7 models selected
> select #17/A:76 #20/A:76 #15/A:76 #14/A:76 #13/A:76 #22/A:76 #16/A:76
> #19/A:76 #18/A:76 #21/A:76 #12/A:76 #23/A:76 #24/A:76 #9/A:75 #11/A:76
> #1/A:76 #2/A:76 #3/A:76 #6/A:76 #7/A:76 #8/A:76 #100.1/A:76
170 atoms, 148 bonds, 22 residues, 22 models selected
muscle-I20250623-145406-0980-39275076-p1m.fa [ID:
muscle-I20250623-145406-0980-39275076-p1m.fa] region
sp|P57739|CLD2_HUMAN..sp|O14493|CLD4_HUMAN [76] RMSD: 1.728
> select #25/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #25/A:149-153
35 atoms, 35 bonds, 5 residues, 1 model selected
> select #17/A:145 #20/A:145 #15/A:145 #14/A:146 #13/A:146 #22/A:146 #16/A:146
> #19/A:146 #18/A:145 #21/A:145 #12/A:145 #23/A:145 #24/A:145 #9/A:144
> #11/A:145 #1/A:145 #2/A:145 #3/A:145 #6/A:145 #7/A:145 #8/A:145 #100.1/A:145
> #25/A:145
217 atoms, 194 bonds, 23 residues, 23 models selected
> select #17/A:158 #20/A:158 #15/A:158 #14/A:159 #13/A:159 #22/A:159 #16/A:159
> #19/A:159 #18/A:158 #21/A:158 #12/A:158 #23/A:158 #24/A:158 #9/A:157
> #11/A:158 #1/A:158 #2/A:158 #3/A:158 #6/A:158 #7/A:158 #8/A:158 #100.1/A:158
> #25/A:158
259 atoms, 245 bonds, 23 residues, 23 models selected
> select #17/A:145 #20/A:145 #15/A:145 #14/A:146 #13/A:146 #22/A:146 #16/A:146
> #19/A:146 #18/A:145 #21/A:145 #12/A:145 #23/A:145 #24/A:145 #9/A:144
> #11/A:145 #1/A:145 #2/A:145 #3/A:145 #6/A:145 #7/A:145 #8/A:145 #100.1/A:145
> #25/A:145
217 atoms, 194 bonds, 23 residues, 23 models selected
> select #16/A:150
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #16/A:150-154
37 atoms, 38 bonds, 5 residues, 1 model selected
> color #19 #8efa00ff
> hide #22 models
> show #19 models
> select #19/A:159
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #19/A:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #19/A:148
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #19/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:146@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select #17/A:145 #20/A:145 #15/A:145 #14/A:146 #13/A:146 #22/A:146 #16/A:146
> #19/A:146 #18/A:145 #21/A:145 #12/A:145 #23/A:145 #24/A:145 #9/A:144
> #11/A:145 #1/A:145 #2/A:145 #3/A:145 #6/A:145 #7/A:145 #8/A:145 #100.1/A:145
> #25/A:145
217 atoms, 194 bonds, 23 residues, 23 models selected
> hide #19 models
> show #16 models
> color #16 #8efa00ff
> color #16 #00f900ff
> color #16 #8efa00ff
> color #16 #73fa79ff
> color #16 #d4fb79ff
> color #16 #73fa79ff
> select #16/A:159
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/A:31
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/A:148
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/A:47
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/A:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/A:76
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,7
Model Number: Z1FQ000AKSM/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 48 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 27 days, 48 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P3223QE:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 3840 x 2160 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.0
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.1
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 5.24.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tenacity: 9.0.0
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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