Opened 5 months ago

Closed 5 months ago

#18077 closed defect (duplicate)

Crash on Mac waking from sleep

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

Description (last modified by Eric Pettersen) 

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" : 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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 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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

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> 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  
  
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REMARK initial structure: complex_19.pdb  
  
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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"  
  
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REMARK ===============================================================  
  
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REMARK initial structure: complex_38.pdb  
  
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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_3.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_131w.pdb0"  
  
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REMARK initial structure: complex_131.pdb  
  
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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 initial structure: complex_9.pdb  
  
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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  
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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

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> 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"  
  
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REMARK initial structure: complex_92.pdb  
  
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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_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 ===============================================================  
  
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_49.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_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 Eric Pettersen, 5 months ago

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

comment:2 by Eric Pettersen, 5 months ago

Resolution: → duplicate
Status: assigned → closed
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