![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Last modified 15 months ago
#16003 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070002d6e0000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070002c6dd000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070002b6da000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070002a6d7000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000296d4000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000286d1000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000276ce000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000266cb000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000256c8000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000246c5000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000236c2000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000226bf000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000216bc000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000206b9000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001f6b6000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001e6b3000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001d6b0000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001c6ad000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001b6aa000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff85683bfc0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 62)
{"app_name":"ChimeraX","timestamp":"2024-09-24 10:47:31.00 +1000","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.5 (23F79)","roots_installed":0,"name":"ChimeraX","incident_id":"7EDB3D2F-8F0E-4D4F-93BD-42F25546889B"}
{
"uptime" : 73000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 9052,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-09-24 10:47:16.2949 +1000",
"codeSigningMonitor" : 0,
"incident" : "7EDB3D2F-8F0E-4D4F-93BD-42F25546889B",
"pid" : 40507,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-23 17:24:08.5000 +1000",
"procStartAbsTime" : 72180791856272,
"procExitAbsTime" : 73720859885521,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"C3BA8B9E-1138-5FA2-8C81-49936FF253EE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "324B8216-C495-C2F1-1769-3322C698A086",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 8,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "A7C2F5A5-A2ED-4422-9809-82B4FC869088",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4524302336\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10dab6000-10daba000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":40507},
"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\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4524302336\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10dab6000-10daba000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.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" : [{"queue":"com.apple.main-thread","instructionState":{"instructionStream":{"bytes":[41,7,197,252,41,71,32,72,131,199,64,72,131,234,64,119,237,197,252,17,4,23,197,252,17,68,23,32,197,248,119,93,195,72,137,52,23,72,131,234,8,115,246,72,131,194,8,116,11,64,136,116,23,255,72,131,234,1,117,245,93,195,144,144,144,144,144,144,144,144,144,144,144,144,144,144,144,144,85,72,137,229,72,137,249,72,137,250,72,131,231,240,102,15,239,192,102,15,116,7,102,15,215,240,72,131,225,15,72,131,200,255,72,211,224,33,198,116,23,15,188,198,72,41,215,72,1,248,93,195,102,46,15,31,132,0,0,0,0,0,102,144,72,131,199,16,102,15,239,192,102,15,116,7,102,15,215,240,133,246,116,236,235,211,101,72,139,12,37,24,0,0,0,65,137,200,49,192,240,76,15,177,7,15,133,241,28,0,0,233,0,0],"offset":96}},"frames":[{"imageOffset":33098,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":158},{"imageOffset":24253,"symbol":"pthread_kill","symbolLocation":262,"imageIndex":159},{"imageOffset":282792,"symbol":"raise","symbolLocation":24,"imageIndex":160},{"imageOffset":2540852,"symbol":"faulthandler_fatal_error","symbolLocation":388,"imageIndex":156},{"imageOffset":16349,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":161},{"imageOffset":0,"imageIndex":162},{"imageOffset":38708055,"imageIndex":96},{"imageOffset":38399649,"imageIndex":96},{"imageOffset":36937448,"imageIndex":96},{"imageOffset":36958840,"imageIndex":96},{"imageOffset":108068521,"imageIndex":96},{"imageOffset":108093982,"imageIndex":96},{"imageOffset":82367923,"imageIndex":96},{"imageOffset":50359862,"imageIndex":96},{"imageOffset":50343563,"imageIndex":96},{"imageOffset":75301,"symbol":"displayConfigFinalizedProc","symbolLocation":253,"imageIndex":163},{"imageOffset":43796,"symbol":"CGSPostLocalNotification","symbolLocation":168,"imageIndex":163},{"imageOffset":42603,"symbol":"(anonymous namespace)::notify_datagram_handler(unsigned int, CGSDatagramType, void*, unsigned long, void*)","symbolLocation":96,"imageIndex":163},{"imageOffset":3677260,"symbol":"CGSDatagramReadStream::dispatchMainQueueDatagrams()","symbolLocation":206,"imageIndex":163},{"imageOffset":3677040,"symbol":"invocation function for block in CGSDatagramReadStream::mainQueueWakeup()","symbolLocation":18,"imageIndex":163},{"imageOffset":6854,"symbol":"_dispatch_call_block_and_release","symbolLocation":12,"imageIndex":164},{"imageOffset":11708,"symbol":"_dispatch_client_callout","symbolLocation":8,"imageIndex":164},{"imageOffset":61919,"symbol":"_dispatch_main_queue_drain","symbolLocation":984,"imageIndex":164},{"imageOffset":60921,"symbol":"_dispatch_main_queue_callback_4CF","symbolLocation":31,"imageIndex":164},{"imageOffset":769606,"symbol":"__CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__","symbolLocation":9,"imageIndex":165},{"imageOffset":503925,"symbol":"__CFRunLoopRun","symbolLocation":2459,"imageIndex":165},{"imageOffset":499986,"symbol":"CFRunLoopRunSpecific","symbolLocation":557,"imageIndex":165},{"imageOffset":190985,"symbol":"RunCurrentEventLoopInMode","symbolLocation":292,"imageIndex":166},{"imageOffset":190486,"symbol":"ReceiveNextEventCommon","symbolLocation":665,"imageIndex":166},{"imageOffset":189793,"symbol":"_BlockUntilNextEventMatchingListInModeWithFilter","symbolLocation":66,"imageIndex":166},{"imageOffset":257121,"symbol":"_DPSNextEvent","symbolLocation":880,"imageIndex":167},{"imageOffset":9776576,"symbol":"-[NSApplication(NSEventRouting) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]","symbolLocation":1273,"imageIndex":167},{"imageOffset":196725,"symbol":"-[NSApplication run]","symbolLocation":603,"imageIndex":167},{"imageOffset":93965,"imageIndex":88},{"imageOffset":583190,"symbol":"QEventLoop::exec(QFlags)","symbolLocation":486,"imageIndex":113},{"imageOffset":545047,"symbol":"QCoreApplication::exec()","symbolLocation":119,"imageIndex":113},{"imageOffset":2261324,"symbol":"meth_QApplication_exec(_object*, _object*)","symbolLocation":92,"imageIndex":106},{"imageOffset":1044954,"symbol":"cfunction_call","symbolLocation":90,"imageIndex":156},{"imageOffset":630769,"symbol":"_PyObject_MakeTpCall","symbolLocation":129,"imageIndex":156},{"imageOffset":1868407,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61255,"imageIndex":156},{"imageOffset":1802218,"symbol":"PyEval_EvalCode","symbolLocation":282,"imageIndex":156},{"imageOffset":1779827,"symbol":"builtin_exec","symbolLocation":483,"imageIndex":156},{"imageOffset":1047348,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS","symbolLocation":68,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":2512477,"symbol":"pymain_run_module","symbolLocation":253,"imageIndex":156},{"imageOffset":2511137,"symbol":"Py_RunMain","symbolLocation":2225,"imageIndex":156},{"imageOffset":2515163,"symbol":"pymain_main","symbolLocation":43,"imageIndex":156},{"imageOffset":2515114,"symbol":"Py_Main","symbolLocation":42,"imageIndex":156},{"imageOffset":15770,"symbol":"main","symbolLocation":122,"imageIndex":157},{"imageOffset":25446,"symbol":"start","symbolLocation":1942,"imageIndex":168}],"id":936089,"triggered":true,"threadState":{"r13":{"value":105553126316033},"rax":{"value":0},"rflags":{"value":582},"cpu":{"value":0},"r14":{"value":140704580091840,"symbolLocation":0,"symbol":"_main_thread"},"rsi":{"value":11},"r8":{"value":2},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":140704580091840,"symbolLocation":0,"symbol":"_main_thread"},"r9":{"value":14757395258967641293},"r15":{"value":22},"rbx":{"value":11},"trap":{"value":133},"err":{"value":33554760},"r11":{"value":582},"rip":{"value":140703450276170,"matchesCrashFrame":1},"rbp":{"value":140584817646096},"rsp":{"value":140584817646056},"r12":{"value":259},"rcx":{"value":140584817646056},"flavor":"x86_THREAD_STATE","rdi":{"value":259}},"name":"CrBrowserMain"},{"id":936580,"name":"ThreadPoolServiceThread","threadState":{"r13":{"value":12297829382473034411},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":140584823365888},"rsi":{"value":0},"r8":{"value":4},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":105553177791680},"r9":{"value":0},"r15":{"value":0},"rbx":{"value":123145576230208},"trap":{"value":133},"err":{"value":33554801},"r11":{"value":582},"rip":{"value":140703450287750},"rbp":{"value":123145576230192},"rsp":{"value":123145576230120},"r12":{"value":140584823366000},"rcx":{"value":123145576230120},"flavor":"x86_THREAD_STATE","rdi":{"value":11}},"frames":[{"imageOffset":44678,"symbol":"kevent64","symbolLocation":10,"imageIndex":158},{"imageOffset":75593716,"imageIndex":96},{"imageOffset":75593183,"imageIndex":96},{"imageOffset":75194449,"imageIndex":96},{"imageOffset":74879192,"imageIndex":96},{"imageOffset":75351720,"imageIndex":96},{"imageOffset":75245773,"imageIndex":96},{"imageOffset":75352126,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936581,"name":"ThreadPoolForegroundWorker","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":269393233707008},"r9":{"value":269393233707008},"r15":{"value":269393233707008},"rbx":{"value":123145584631088},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145584630416},"rsp":{"value":123145584630312},"r12":{"value":33000},"rcx":{"value":123145584630312},"flavor":"x86_THREAD_STATE","rdi":{"value":123145584631088}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75293834,"imageIndex":96},{"imageOffset":75297738,"imageIndex":96},{"imageOffset":75295997,"imageIndex":96},{"imageOffset":75295727,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936582,"name":"ThreadPoolBackgroundWorker","threadState":{"r13":{"value":17179869442},"rax":{"value":0},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":267194210451456},"r9":{"value":267194210451456},"r15":{"value":267194210451456},"rbx":{"value":123145593031984},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145593031312},"rsp":{"value":123145593031208},"r12":{"value":33000},"rcx":{"value":123145593031208},"flavor":"x86_THREAD_STATE","rdi":{"value":123145593031984}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75293834,"imageIndex":96},{"imageOffset":75297738,"imageIndex":96},{"imageOffset":75295853,"imageIndex":96},{"imageOffset":75295764,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936583,"name":"Chrome_IOThread","threadState":{"r13":{"value":12297829382473034411},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":140584882818304},"rsi":{"value":0},"r8":{"value":3},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":105553177776832},"r9":{"value":0},"r15":{"value":0},"rbx":{"value":123145601432864},"trap":{"value":133},"err":{"value":33554801},"r11":{"value":582},"rip":{"value":140703450287750},"rbp":{"value":123145601432848},"rsp":{"value":123145601432776},"r12":{"value":140584882818368},"rcx":{"value":123145601432776},"flavor":"x86_THREAD_STATE","rdi":{"value":12}},"frames":[{"imageOffset":44678,"symbol":"kevent64","symbolLocation":10,"imageIndex":158},{"imageOffset":75593716,"imageIndex":96},{"imageOffset":75593183,"imageIndex":96},{"imageOffset":75194449,"imageIndex":96},{"imageOffset":74879192,"imageIndex":96},{"imageOffset":75351720,"imageIndex":96},{"imageOffset":48358146,"imageIndex":96},{"imageOffset":75352126,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936584,"name":"NetworkConfigWatcher","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":254000070918144},"r9":{"value":254000070918144},"r15":{"value":254000070918144},"rbx":{"value":123145609833536},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145609832864},"rsp":{"value":123145609832760},"r12":{"value":0},"rcx":{"value":123145609832760},"flavor":"x86_THREAD_STATE","rdi":{"value":123145609833536}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75039155,"imageIndex":96},{"imageOffset":74666185,"imageIndex":96},{"imageOffset":75194449,"imageIndex":96},{"imageOffset":74879192,"imageIndex":96},{"imageOffset":75351720,"imageIndex":96},{"imageOffset":75352126,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936588,"name":"Chrome_InProcGpuThread","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":248502512779264},"r9":{"value":248502512779264},"r15":{"value":248502512779264},"rbx":{"value":123145643437136},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145643436464},"rsp":{"value":123145643436360},"r12":{"value":230},"rcx":{"value":123145643436360},"flavor":"x86_THREAD_STATE","rdi":{"value":123145643437136}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":74666082,"imageIndex":96},{"imageOffset":75194449,"imageIndex":96},{"imageOffset":74879192,"imageIndex":96},{"imageOffset":75351720,"imageIndex":96},{"imageOffset":75352126,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936589,"name":"Chrome_ChildIOThread","threadState":{"r13":{"value":12297829382473034411},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":140584889364224},"rsi":{"value":0},"r8":{"value":1},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":105553117557120},"r9":{"value":0},"r15":{"value":0},"rbx":{"value":123145651838240},"trap":{"value":133},"err":{"value":33554801},"r11":{"value":582},"rip":{"value":140703450287750},"rbp":{"value":123145651838224},"rsp":{"value":123145651838152},"r12":{"value":140584889364432},"rcx":{"value":123145651838152},"flavor":"x86_THREAD_STATE","rdi":{"value":21}},"frames":[{"imageOffset":44678,"symbol":"kevent64","symbolLocation":10,"imageIndex":158},{"imageOffset":75593716,"imageIndex":96},{"imageOffset":75593183,"imageIndex":96},{"imageOffset":75194449,"imageIndex":96},{"imageOffset":74879192,"imageIndex":96},{"imageOffset":75351720,"imageIndex":96},{"imageOffset":122838530,"imageIndex":96},{"imageOffset":75352126,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936590,"name":"CompositorTileWorker1","threadState":{"r13":{"value":2203318223616},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145660239872},"rsi":{"value":2203318223616},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":512},"r10":{"value":0},"r9":{"value":161},"r15":{"value":512},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145660239568},"rsp":{"value":123145660239416},"r12":{"value":0},"rcx":{"value":123145660239416},"flavor":"x86_THREAD_STATE","rdi":{"value":140584888659768}},"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":75462980,"imageIndex":96},{"imageOffset":113394117,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936591,"name":"ThreadPoolSingleThreadSharedForeground0","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":237507396501504},"r9":{"value":237507396501504},"r15":{"value":237507396501504},"rbx":{"value":123145668640048},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145668639376},"rsp":{"value":123145668639272},"r12":{"value":0},"rcx":{"value":123145668639272},"flavor":"x86_THREAD_STATE","rdi":{"value":123145668640048}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75293834,"imageIndex":96},{"imageOffset":75296343,"imageIndex":96},{"imageOffset":75296045,"imageIndex":96},{"imageOffset":75295784,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936592,"name":"NetworkConfigWatcher","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":232009838362624},"r9":{"value":232009838362624},"r15":{"value":232009838362624},"rbx":{"value":123145677040704},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145677040032},"rsp":{"value":123145677039928},"r12":{"value":0},"rcx":{"value":123145677039928},"flavor":"x86_THREAD_STATE","rdi":{"value":123145677040704}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75039155,"imageIndex":96},{"imageOffset":74666185,"imageIndex":96},{"imageOffset":75194449,"imageIndex":96},{"imageOffset":74879192,"imageIndex":96},{"imageOffset":75351720,"imageIndex":96},{"imageOffset":75352126,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936593,"name":"VizCompositorThread","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":370548303462400},"r9":{"value":370548303462400},"r15":{"value":370548303462400},"rbx":{"value":123145685441616},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145685440944},"rsp":{"value":123145685440840},"r12":{"value":14},"rcx":{"value":123145685440840},"flavor":"x86_THREAD_STATE","rdi":{"value":123145685441616}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":74666082,"imageIndex":96},{"imageOffset":75194449,"imageIndex":96},{"imageOffset":74879192,"imageIndex":96},{"imageOffset":75351720,"imageIndex":96},{"imageOffset":75352126,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936594,"name":"NetworkService","threadState":{"r13":{"value":12297829382473034411},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":140584969171200},"rsi":{"value":0},"r8":{"value":2},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":105553162054336},"r9":{"value":0},"r15":{"value":0},"rbx":{"value":123145693842784},"trap":{"value":133},"err":{"value":33554801},"r11":{"value":582},"rip":{"value":140703450287750},"rbp":{"value":123145693842768},"rsp":{"value":123145693842696},"r12":{"value":140584969171200},"rcx":{"value":123145693842696},"flavor":"x86_THREAD_STATE","rdi":{"value":22}},"frames":[{"imageOffset":44678,"symbol":"kevent64","symbolLocation":10,"imageIndex":158},{"imageOffset":75593716,"imageIndex":96},{"imageOffset":75593183,"imageIndex":96},{"imageOffset":75194449,"imageIndex":96},{"imageOffset":74879192,"imageIndex":96},{"imageOffset":75351720,"imageIndex":96},{"imageOffset":75352126,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936595,"name":"NetworkConfigWatcher","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":366150256951296},"r9":{"value":366150256951296},"r15":{"value":366150256951296},"rbx":{"value":123145702243392},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145702242720},"rsp":{"value":123145702242616},"r12":{"value":0},"rcx":{"value":123145702242616},"flavor":"x86_THREAD_STATE","rdi":{"value":123145702243392}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75039155,"imageIndex":96},{"imageOffset":74666185,"imageIndex":96},{"imageOffset":75194449,"imageIndex":96},{"imageOffset":74879192,"imageIndex":96},{"imageOffset":75351720,"imageIndex":96},{"imageOffset":75352126,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936597,"name":"ThreadPoolSingleThreadForegroundBlocking1","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":295884591988736},"r9":{"value":295884591988736},"r15":{"value":295884591988736},"rbx":{"value":123145710644528},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145710643856},"rsp":{"value":123145710643752},"r12":{"value":0},"rcx":{"value":123145710643752},"flavor":"x86_THREAD_STATE","rdi":{"value":123145710644528}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75293834,"imageIndex":96},{"imageOffset":75297738,"imageIndex":96},{"imageOffset":75296093,"imageIndex":96},{"imageOffset":75295774,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936624,"name":"NetworkConfigWatcher","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":560763815067648},"r9":{"value":560763815067648},"r15":{"value":560763815067648},"rbx":{"value":123145722264640},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145722263968},"rsp":{"value":123145722263864},"r12":{"value":0},"rcx":{"value":123145722263864},"flavor":"x86_THREAD_STATE","rdi":{"value":123145722264640}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75039155,"imageIndex":96},{"imageOffset":74666185,"imageIndex":96},{"imageOffset":75194449,"imageIndex":96},{"imageOffset":74879192,"imageIndex":96},{"imageOffset":75351720,"imageIndex":96},{"imageOffset":75352126,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936642,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":2199023260160},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145762283520},"rsi":{"value":2199023260160},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":512},"r10":{"value":0},"r9":{"value":160},"r15":{"value":512},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145762282064},"rsp":{"value":123145762281912},"r12":{"value":0},"rcx":{"value":123145762281912},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936643,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":2199023259904},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145779073024},"rsi":{"value":2199023259904},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":512},"r10":{"value":0},"r9":{"value":160},"r15":{"value":512},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145779071568},"rsp":{"value":123145779071416},"r12":{"value":0},"rcx":{"value":123145779071416},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936644,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":768},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145795862528},"rsi":{"value":768},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145795861072},"rsp":{"value":123145795860920},"r12":{"value":0},"rcx":{"value":123145795860920},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936645,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":1024},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145812652032},"rsi":{"value":1024},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145812650576},"rsp":{"value":123145812650424},"r12":{"value":0},"rcx":{"value":123145812650424},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936646,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":1280},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145829441536},"rsi":{"value":1280},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145829440080},"rsp":{"value":123145829439928},"r12":{"value":0},"rcx":{"value":123145829439928},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936647,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":1536},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145846231040},"rsi":{"value":1536},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145846229584},"rsp":{"value":123145846229432},"r12":{"value":0},"rcx":{"value":123145846229432},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936648,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":1792},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145863020544},"rsi":{"value":1792},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145863019088},"rsp":{"value":123145863018936},"r12":{"value":0},"rcx":{"value":123145863018936},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936649,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":2048},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145879810048},"rsi":{"value":2048},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145879808592},"rsp":{"value":123145879808440},"r12":{"value":0},"rcx":{"value":123145879808440},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936650,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":2304},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145896599552},"rsi":{"value":2304},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145896598096},"rsp":{"value":123145896597944},"r12":{"value":0},"rcx":{"value":123145896597944},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936651,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":2560},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145913389056},"rsi":{"value":2560},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145913387600},"rsp":{"value":123145913387448},"r12":{"value":0},"rcx":{"value":123145913387448},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936652,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":2816},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145930178560},"rsi":{"value":2816},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145930177104},"rsp":{"value":123145930176952},"r12":{"value":0},"rcx":{"value":123145930176952},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936653,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":3072},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145946968064},"rsi":{"value":3072},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145946966608},"rsp":{"value":123145946966456},"r12":{"value":0},"rcx":{"value":123145946966456},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936654,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":3328},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145963757568},"rsi":{"value":3328},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145963756112},"rsp":{"value":123145963755960},"r12":{"value":0},"rcx":{"value":123145963755960},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936655,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":3584},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145980547072},"rsi":{"value":3584},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145980545616},"rsp":{"value":123145980545464},"r12":{"value":0},"rcx":{"value":123145980545464},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936656,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":3840},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145997336576},"rsi":{"value":3840},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145997335120},"rsp":{"value":123145997334968},"r12":{"value":0},"rcx":{"value":123145997334968},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936657,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":4096},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123146014126080},"rsi":{"value":4096},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123146014124624},"rsp":{"value":123146014124472},"r12":{"value":0},"rcx":{"value":123146014124472},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035272}}},{"id":936658,"frames":[{"imageOffset":33266,"symbol":"poll","symbolLocation":10,"imageIndex":158},{"imageOffset":22181,"symbol":"select_poll_poll","symbolLocation":149,"imageIndex":142},{"imageOffset":703048,"symbol":"method_vectorcall_FASTCALL","symbolLocation":104,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648031,"symbol":"method_vectorcall","symbolLocation":207,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":0},"rax":{"value":4},"rflags":{"value":519},"cpu":{"value":0},"r14":{"value":140585010908912},"rsi":{"value":1},"r8":{"value":936658},"cr2":{"value":0},"rdx":{"value":4294967295},"r10":{"value":123146030915756},"r9":{"value":18446744069414584320},"r15":{"value":18446744073709551615},"rbx":{"value":123146030914176},"trap":{"value":133},"err":{"value":33554662},"r11":{"value":518},"rip":{"value":140703450276338},"rbp":{"value":123146030914272},"rsp":{"value":123146030914168},"r12":{"value":5354333136},"rcx":{"value":123146030914168},"flavor":"x86_THREAD_STATE","rdi":{"value":5206092544}}},{"id":936659,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":822626,"symbol":"calliter_iternext","symbolLocation":82,"imageIndex":156},{"imageOffset":1861149,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":53997,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":1103806595584},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123146047705088},"rsi":{"value":1103806595584},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":256},"r10":{"value":0},"r9":{"value":160},"r15":{"value":256},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123146047703568},"rsp":{"value":123146047703416},"r12":{"value":0},"rcx":{"value":123146047703416},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035528}}},{"id":936660,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":2433570,"symbol":"PyThread_acquire_lock_timed","symbolLocation":434,"imageIndex":156},{"imageOffset":13491,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":211,"imageIndex":81},{"imageOffset":12660,"symbol":"_queue_SimpleQueue_get","symbolLocation":196,"imageIndex":81},{"imageOffset":1048405,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":101,"imageIndex":156},{"imageOffset":1868159,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":61007,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":1881034,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":73882,"imageIndex":156},{"imageOffset":1892992,"symbol":"_PyEval_Vector","symbolLocation":128,"imageIndex":156},{"imageOffset":648278,"symbol":"method_vectorcall","symbolLocation":454,"imageIndex":156},{"imageOffset":2976374,"symbol":"thread_run","symbolLocation":230,"imageIndex":156},{"imageOffset":2432596,"symbol":"pythread_wrapper","symbolLocation":36,"imageIndex":156},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":1103806595584},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123146064494592},"rsi":{"value":1103806595584},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":256},"r10":{"value":0},"r9":{"value":160},"r15":{"value":256},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123146064493136},"rsp":{"value":123146064492984},"r12":{"value":0},"rcx":{"value":123146064492984},"flavor":"x86_THREAD_STATE","rdi":{"value":105553151035656}}},{"id":936689,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":136},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":164931039172352},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145561927680},"rsi":{"value":164931039172352},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":38400},"r10":{"value":0},"r9":{"value":160},"r15":{"value":38400},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145561927536},"rsp":{"value":123145561927384},"r12":{"value":0},"rcx":{"value":123145561927384},"flavor":"x86_THREAD_STATE","rdi":{"value":4711012816,"symbolLocation":80,"symbol":"thread_status"}}},{"id":936690,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":136},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":164931039172352},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145562464256},"rsi":{"value":164931039172352},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":38400},"r10":{"value":0},"r9":{"value":160},"r15":{"value":38400},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145562464112},"rsp":{"value":123145562463960},"r12":{"value":0},"rcx":{"value":123145562463960},"flavor":"x86_THREAD_STATE","rdi":{"value":4711012944,"symbolLocation":208,"symbol":"thread_status"}}},{"id":936691,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":136},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":4294967552},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145563000832},"rsi":{"value":4294967552},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145563000688},"rsp":{"value":123145563000536},"r12":{"value":0},"rcx":{"value":123145563000536},"flavor":"x86_THREAD_STATE","rdi":{"value":4711013072,"symbolLocation":336,"symbol":"thread_status"}}},{"id":936692,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":136},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":4294967552},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145563537408},"rsi":{"value":4294967552},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145563537264},"rsp":{"value":123145563537112},"r12":{"value":0},"rcx":{"value":123145563537112},"flavor":"x86_THREAD_STATE","rdi":{"value":4711013200,"symbolLocation":464,"symbol":"thread_status"}}},{"id":936693,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":136},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":4294967552},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145564073984},"rsi":{"value":4294967552},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145564073840},"rsp":{"value":123145564073688},"r12":{"value":0},"rcx":{"value":123145564073688},"flavor":"x86_THREAD_STATE","rdi":{"value":4711013328,"symbolLocation":592,"symbol":"thread_status"}}},{"id":936694,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":136},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":4294967552},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145564610560},"rsi":{"value":4294967552},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145564610416},"rsp":{"value":123145564610264},"r12":{"value":0},"rcx":{"value":123145564610264},"flavor":"x86_THREAD_STATE","rdi":{"value":4711013456,"symbolLocation":720,"symbol":"thread_status"}}},{"id":936695,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":3470047,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":136},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":4294967552},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145565147136},"rsi":{"value":4294967552},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":0},"r9":{"value":160},"r15":{"value":0},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145565146992},"rsp":{"value":123145565146840},"r12":{"value":0},"rcx":{"value":123145565146840},"flavor":"x86_THREAD_STATE","rdi":{"value":4711013584,"symbolLocation":848,"symbol":"thread_status"}}},{"id":936712,"name":"com.apple.NSEventThread","threadState":{"r13":{"value":21592279046},"rax":{"value":268451845},"rflags":{"value":518},"cpu":{"value":0},"r14":{"value":2},"rsi":{"value":21592279046},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":8589934592},"r10":{"value":435419489501184},"r9":{"value":435419489501184},"r15":{"value":435419489501184},"rbx":{"value":123145565679712},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":518},"rip":{"value":140703450248142},"rbp":{"value":123145565679552},"rsp":{"value":123145565679448},"r12":{"value":4294967295},"rcx":{"value":123145565679448},"flavor":"x86_THREAD_STATE","rdi":{"value":123145565679712}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":508357,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":143,"imageIndex":165},{"imageOffset":502837,"symbol":"__CFRunLoopRun","symbolLocation":1371,"imageIndex":165},{"imageOffset":499986,"symbol":"CFRunLoopRunSpecific","symbolLocation":557,"imageIndex":165},{"imageOffset":1690556,"symbol":"_NSEventThread","symbolLocation":122,"imageIndex":167},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936721,"name":"MemoryInfra","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":743282745278464},"r9":{"value":743282745278464},"r15":{"value":743282745278464},"rbx":{"value":123146098084928},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123146098084256},"rsp":{"value":123146098084152},"r12":{"value":0},"rcx":{"value":123146098084152},"flavor":"x86_THREAD_STATE","rdi":{"value":123146098084928}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75039155,"imageIndex":96},{"imageOffset":74666185,"imageIndex":96},{"imageOffset":75194449,"imageIndex":96},{"imageOffset":74879192,"imageIndex":96},{"imageOffset":75351720,"imageIndex":96},{"imageOffset":75352126,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936722,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking2","threadState":{"r13":{"value":17179869186},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869186},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":569559908089856},"r9":{"value":569559908089856},"r15":{"value":569559908089856},"rbx":{"value":123146106486064},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123146106485392},"rsp":{"value":123146106485288},"r12":{"value":0},"rcx":{"value":123146106485288},"flavor":"x86_THREAD_STATE","rdi":{"value":123146106486064}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75293834,"imageIndex":96},{"imageOffset":75296343,"imageIndex":96},{"imageOffset":75295901,"imageIndex":96},{"imageOffset":75295804,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":936749,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":16492674424576},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145567293440},"rsi":{"value":16492674424576},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":3840},"r10":{"value":0},"r9":{"value":160},"r15":{"value":3840},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145567293216},"rsp":{"value":123145567293064},"r12":{"value":0},"rcx":{"value":123145567293064},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936750,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":18691697680640},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145567830016},"rsi":{"value":18691697680640},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":4352},"r10":{"value":0},"r9":{"value":160},"r15":{"value":4352},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145567829792},"rsp":{"value":123145567829640},"r12":{"value":0},"rcx":{"value":123145567829640},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936751,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":19791209308672},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145729241088},"rsi":{"value":19791209308672},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":4608},"r10":{"value":0},"r9":{"value":160},"r15":{"value":4608},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145729240864},"rsp":{"value":123145729240712},"r12":{"value":0},"rcx":{"value":123145729240712},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936752,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":20890720936704},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145729777664},"rsi":{"value":20890720936704},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":4864},"r10":{"value":0},"r9":{"value":160},"r15":{"value":4864},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145729777440},"rsp":{"value":123145729777288},"r12":{"value":0},"rcx":{"value":123145729777288},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936753,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":21990232564736},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145730314240},"rsi":{"value":21990232564736},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":5120},"r10":{"value":0},"r9":{"value":160},"r15":{"value":5120},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145730314016},"rsp":{"value":123145730313864},"r12":{"value":0},"rcx":{"value":123145730313864},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936754,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":8796093028352},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145730850816},"rsi":{"value":8796093028352},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":2048},"r10":{"value":0},"r9":{"value":160},"r15":{"value":2048},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145730850592},"rsp":{"value":123145730850440},"r12":{"value":0},"rcx":{"value":123145730850440},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936755,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":24189255820800},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145731387392},"rsi":{"value":24189255820800},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":5632},"r10":{"value":0},"r9":{"value":160},"r15":{"value":5632},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145731387168},"rsp":{"value":123145731387016},"r12":{"value":0},"rcx":{"value":123145731387016},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936756,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":23089744192768},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145731923968},"rsi":{"value":23089744192768},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":5376},"r10":{"value":0},"r9":{"value":160},"r15":{"value":5376},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145731923744},"rsp":{"value":123145731923592},"r12":{"value":0},"rcx":{"value":123145731923592},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936757,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":25288767448832},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145732460544},"rsi":{"value":25288767448832},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":5888},"r10":{"value":0},"r9":{"value":160},"r15":{"value":5888},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145732460320},"rsp":{"value":123145732460168},"r12":{"value":0},"rcx":{"value":123145732460168},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936758,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":9895604656384},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145732997120},"rsi":{"value":9895604656384},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":2304},"r10":{"value":0},"r9":{"value":160},"r15":{"value":2304},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145732996896},"rsp":{"value":123145732996744},"r12":{"value":0},"rcx":{"value":123145732996744},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936759,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":10995116284416},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145733533696},"rsi":{"value":10995116284416},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":2560},"r10":{"value":0},"r9":{"value":160},"r15":{"value":2560},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145733533472},"rsp":{"value":123145733533320},"r12":{"value":0},"rcx":{"value":123145733533320},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936760,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":12094627912448},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145734070272},"rsi":{"value":12094627912448},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":2816},"r10":{"value":0},"r9":{"value":160},"r15":{"value":2816},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145734070048},"rsp":{"value":123145734069896},"r12":{"value":0},"rcx":{"value":123145734069896},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936761,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":13194139540480},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145734606848},"rsi":{"value":13194139540480},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":3072},"r10":{"value":0},"r9":{"value":160},"r15":{"value":3072},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145734606624},"rsp":{"value":123145734606472},"r12":{"value":0},"rcx":{"value":123145734606472},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936762,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":14293651168512},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145735143424},"rsi":{"value":14293651168512},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":3328},"r10":{"value":0},"r9":{"value":160},"r15":{"value":3328},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145735143200},"rsp":{"value":123145735143048},"r12":{"value":0},"rcx":{"value":123145735143048},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936763,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":17592186052608},"rax":{"value":4},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145735680000},"rsi":{"value":17592186052608},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":4096},"r10":{"value":0},"r9":{"value":160},"r15":{"value":4096},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145735679776},"rsp":{"value":123145735679624},"r12":{"value":0},"rcx":{"value":123145735679624},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":936764,"frames":[{"imageOffset":16250,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":158},{"imageOffset":26355,"symbol":"_pthread_cond_wait","symbolLocation":1211,"imageIndex":159},{"imageOffset":48402,"symbol":"std::__1::condition_variable::wait(std::__1::unique_lock&)","symbolLocation":18,"imageIndex":169},{"imageOffset":108261782,"imageIndex":96},{"imageOffset":108267659,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}],"threadState":{"r13":{"value":15393162796544},"rax":{"value":260},"rflags":{"value":583},"cpu":{"value":0},"r14":{"value":123145736216576},"rsi":{"value":15393162796544},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":3584},"r10":{"value":0},"r9":{"value":160},"r15":{"value":3584},"rbx":{"value":22},"trap":{"value":133},"err":{"value":33554737},"r11":{"value":582},"rip":{"value":140703450259322},"rbp":{"value":123145736216352},"rsp":{"value":123145736216200},"r12":{"value":0},"rcx":{"value":123145736216200},"flavor":"x86_THREAD_STATE","rdi":{"value":105553167357408}}},{"id":986197,"frames":[{"imageOffset":6848,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":159}],"threadState":{"r13":{"value":0},"rax":{"value":33554800},"rflags":{"value":512},"cpu":{"value":0},"r14":{"value":0},"rsi":{"value":162203},"r8":{"value":409604},"cr2":{"value":0},"rdx":{"value":123145566232576},"r10":{"value":0},"r9":{"value":18446744073709551615},"r15":{"value":0},"rbx":{"value":123145566756864},"trap":{"value":133},"err":{"value":33554800},"r11":{"value":582},"rip":{"value":140703450491584},"rbp":{"value":0},"rsp":{"value":123145566756864},"r12":{"value":0},"rcx":{"value":0},"flavor":"x86_THREAD_STATE","rdi":{"value":123145566756864}}},{"id":986578,"frames":[{"imageOffset":6848,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":159}],"threadState":{"r13":{"value":0},"rax":{"value":33554800},"rflags":{"value":512},"cpu":{"value":0},"r14":{"value":1},"rsi":{"value":28939},"r8":{"value":409602},"cr2":{"value":0},"rdx":{"value":123145565696000},"r10":{"value":0},"r9":{"value":18446744073709551615},"r15":{"value":123145566219128},"rbx":{"value":123145566220288},"trap":{"value":133},"err":{"value":33554800},"r11":{"value":582},"rip":{"value":140703450491584},"rbp":{"value":0},"rsp":{"value":123145566220288},"r12":{"value":5193734},"rcx":{"value":0},"flavor":"x86_THREAD_STATE","rdi":{"value":123145566220288}}},{"id":986682,"frames":[{"imageOffset":6848,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":159}],"threadState":{"r13":{"value":0},"rax":{"value":33554800},"rflags":{"value":512},"cpu":{"value":0},"r14":{"value":0},"rsi":{"value":156755},"r8":{"value":409602},"cr2":{"value":0},"rdx":{"value":123145609846784},"r10":{"value":0},"r9":{"value":18446744073709551615},"r15":{"value":0},"rbx":{"value":123145610371072},"trap":{"value":133},"err":{"value":33554800},"r11":{"value":582},"rip":{"value":140703450491584},"rbp":{"value":0},"rsp":{"value":123145610371072},"r12":{"value":0},"rcx":{"value":0},"flavor":"x86_THREAD_STATE","rdi":{"value":123145610371072}}},{"id":987016,"name":"ThreadPoolForegroundWorker","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":650013235478528},"r9":{"value":650013235478528},"r15":{"value":650013235478528},"rbx":{"value":123145618771248},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145618770576},"rsp":{"value":123145618770472},"r12":{"value":33000},"rcx":{"value":123145618770472},"flavor":"x86_THREAD_STATE","rdi":{"value":123145618771248}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75293834,"imageIndex":96},{"imageOffset":75296343,"imageIndex":96},{"imageOffset":75295997,"imageIndex":96},{"imageOffset":75295727,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]},{"id":987414,"frames":[{"imageOffset":6848,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":159}],"threadState":{"r13":{"value":0},"rax":{"value":33554800},"rflags":{"value":512},"cpu":{"value":0},"r14":{"value":1},"rsi":{"value":174623},"r8":{"value":5193730},"cr2":{"value":0},"rdx":{"value":123145618784256},"r10":{"value":0},"r9":{"value":1},"r15":{"value":123145619307392},"rbx":{"value":123145619308544},"trap":{"value":133},"err":{"value":33554800},"r11":{"value":582},"rip":{"value":140703450491584},"rbp":{"value":0},"rsp":{"value":123145619307376},"r12":{"value":1966080},"rcx":{"value":123145619307392},"flavor":"x86_THREAD_STATE","rdi":{"value":123145619308544}}},{"id":987430,"name":"ThreadPoolBackgroundWorker","threadState":{"r13":{"value":17179869442},"rax":{"value":268451845},"rflags":{"value":514},"cpu":{"value":0},"r14":{"value":32},"rsi":{"value":17179869442},"r8":{"value":0},"cr2":{"value":0},"rdx":{"value":0},"r10":{"value":787503728558080},"r9":{"value":787503728558080},"r15":{"value":787503728558080},"rbx":{"value":123145627708720},"trap":{"value":133},"err":{"value":16777263},"r11":{"value":514},"rip":{"value":140703450248142},"rbp":{"value":123145627708048},"rsp":{"value":123145627707944},"r12":{"value":33000},"rcx":{"value":123145627707944},"flavor":"x86_THREAD_STATE","rdi":{"value":123145627708720}},"frames":[{"imageOffset":5070,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":158},{"imageOffset":64648,"symbol":"mach_msg2_internal","symbolLocation":84,"imageIndex":158},{"imageOffset":34064,"symbol":"mach_msg_overwrite","symbolLocation":653,"imageIndex":158},{"imageOffset":5821,"symbol":"mach_msg","symbolLocation":19,"imageIndex":158},{"imageOffset":75634614,"imageIndex":96},{"imageOffset":75039302,"imageIndex":96},{"imageOffset":75293834,"imageIndex":96},{"imageOffset":75296343,"imageIndex":96},{"imageOffset":75295853,"imageIndex":96},{"imageOffset":75295764,"imageIndex":96},{"imageOffset":75466040,"imageIndex":96},{"imageOffset":24971,"symbol":"_pthread_start","symbolLocation":99,"imageIndex":159},{"imageOffset":6883,"symbol":"thread_start","symbolLocation":15,"imageIndex":159}]}],
"usedImages" : [
{
"source" : "P",
"arch" : "x86_64",
"base" : 5637345280,
"size" : 81920,
"uuid" : "34acef9d-ca82-3fc2-8719-453f3bf3da79",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/chem_group\/_chem_group.cpython-311-darwin.so",
"name" : "_chem_group.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5622636544,
"size" : 49152,
"uuid" : "5a8c2b45-6fbf-384e-aa16-53365b54f7fb",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atom_search\/ast.cpython-311-darwin.so",
"name" : "ast.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5769842688,
"size" : 147456,
"uuid" : "a66bb1e2-ecf4-3220-9c8e-a465d9305940",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5782953984,
"size" : 4210688,
"uuid" : "08a0cdf4-85d3-328a-98ac-8a7ec48356eb",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5765169152,
"size" : 16384,
"uuid" : "62001a43-deed-3f40-8d2d-57ad475e6c95",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
"name" : "_psutil_posix.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5767708672,
"size" : 32768,
"uuid" : "cc4a7194-2678-3514-acc4-75a7275bf407",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so",
"name" : "_psutil_osx.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5764681728,
"size" : 180224,
"uuid" : "6d0a4aa1-f80b-3e16-baed-3f694111a75d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5771431936,
"size" : 442368,
"uuid" : "9141612b-bf67-390f-8b66-18a585729cab",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5768040448,
"size" : 524288,
"uuid" : "58e1300b-c472-3863-8fc4-4eb27185cbbf",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5760569344,
"size" : 32768,
"uuid" : "3b76dfeb-802d-3ce8-9151-7ec4ff5a682b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5760389120,
"size" : 98304,
"uuid" : "ae16bb51-bedf-3c8a-9b96-5684b608789d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5760692224,
"size" : 49152,
"uuid" : "0e674aef-d74d-34e9-a46b-63ce1a6729b4",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5762453504,
"size" : 49152,
"uuid" : "c84a9a90-56dd-385a-aad3-a15d44bc216b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5765267456,
"size" : 737280,
"uuid" : "85293474-c54e-32bd-967c-f9f9839646ae",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
"name" : "QtOpenGL.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5761159168,
"size" : 131072,
"uuid" : "99497e49-7155-3c86-b62e-dd8a79f1be5d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
"name" : "_cmsgpack.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5760897024,
"size" : 131072,
"uuid" : "272f9886-859c-3c84-8ea4-2bde196ca08b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
"name" : "_serialize.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5759930368,
"size" : 212992,
"uuid" : "9ff84874-4ecd-3fed-ba32-23b23bfaaecc",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
"name" : "_frame.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5760241664,
"size" : 98304,
"uuid" : "3064d9b7-75d7-343e-bf98-036ded114223",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
"name" : "_version.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5707300864,
"size" : 32768,
"uuid" : "20c4af3a-4b84-3cc8-aa82-b08768c1116d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5707403264,
"size" : 65536,
"uuid" : "5cfe15a5-c7e4-36db-be9c-4d4ef3728796",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/numpy_formathandler.cpython-311-darwin.so",
"name" : "numpy_formathandler.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5280911360,
"size" : 16384,
"uuid" : "79f78529-d885-34a6-92be-87f1fda28bed",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_posixshmem.cpython-311-darwin.so",
"name" : "_posixshmem.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5280845824,
"size" : 16384,
"uuid" : "946403b9-d874-3c5d-bc5b-104d68f45c19",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_multiprocessing.cpython-311-darwin.so",
"name" : "_multiprocessing.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5263589376,
"size" : 16384,
"uuid" : "136e83be-523c-3e0a-8ee9-ac44338f577c",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_mac_util.cpython-311-darwin.so",
"name" : "_mac_util.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 5262041088,
"size" : 53248,
"uuid" : "caf1eb21-6511-3736-9b71-deedf5e9226b",
"path" : "\/usr\/lib\/libobjc-trampolines.dylib",
"name" : "libobjc-trampolines.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5262254080,
"size" : 32768,
"uuid" : "eca278d3-d60a-39de-8179-e4e3d7044450",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqmacjp2.dylib",
"name" : "libqmacjp2.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5261832192,
"size" : 32768,
"uuid" : "52133b8a-b7f2-307f-99eb-74e22691cf79",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqtga.dylib",
"name" : "libqtga.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5261733888,
"size" : 32768,
"uuid" : "0372cf7c-a608-3177-b1e1-bd312f0a6434",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqicns.dylib",
"name" : "libqicns.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5261942784,
"size" : 32768,
"uuid" : "cbbb200f-5258-33bb-baf8-e08d98ddc672",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqpdf.dylib",
"name" : "libqpdf.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5280985088,
"size" : 8765440,
"uuid" : "14ff39ad-fca1-3b61-ada4-f5f95bd02945",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtPdf.framework\/Versions\/A\/QtPdf",
"name" : "QtPdf"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5259546624,
"size" : 32768,
"uuid" : "24897911-1bb1-3eb1-99c4-dc57d4440d49",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqsvg.dylib",
"name" : "libqsvg.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5260656640,
"size" : 245760,
"uuid" : "535f7dfd-d62a-33b3-9e52-af14094c4e5e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtSvg.framework\/Versions\/A\/QtSvg",
"name" : "QtSvg"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5262737408,
"size" : 442368,
"uuid" : "7a23c3a8-9cd7-3b95-9f4c-fe861273501d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqtiff.dylib",
"name" : "libqtiff.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5259952128,
"size" : 622592,
"uuid" : "8fa53a40-5029-35c1-b403-de4b5ebc296b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqjpeg.dylib",
"name" : "libqjpeg.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5259448320,
"size" : 32768,
"uuid" : "587053e8-9ed2-37b5-bae3-52598b1c0ed9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqmacheif.dylib",
"name" : "libqmacheif.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5259853824,
"size" : 32768,
"uuid" : "6be87464-6bae-3acd-ba8a-0ad9c42d2192",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqico.dylib",
"name" : "libqico.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5261062144,
"size" : 589824,
"uuid" : "3b812afb-4558-3629-a105-54f0123a8756",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqwebp.dylib",
"name" : "libqwebp.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5259755520,
"size" : 32768,
"uuid" : "6665c7fa-5429-307c-ae72-f02b4663e991",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqwbmp.dylib",
"name" : "libqwbmp.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5259657216,
"size" : 32768,
"uuid" : "04424808-7083-3ca4-9997-8dae04f5e18a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqgif.dylib",
"name" : "libqgif.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5211664384,
"size" : 180224,
"uuid" : "cd62d8e3-6428-319c-b174-d861a467788d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/surface\/_surface.cpython-311-darwin.so",
"name" : "_surface.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5180919808,
"size" : 16384,
"uuid" : "5c82e5f4-7664-3325-95c1-a2286b531838",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb_lib\/_load_libs.cpython-311-darwin.so",
"name" : "_load_libs.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5192048640,
"size" : 32768,
"uuid" : "9c20a913-80f2-3790-82d6-f5f257f40a80",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb_lib\/lib\/libpdbconnect.dylib",
"name" : "libpdbconnect.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5193093120,
"size" : 98304,
"uuid" : "7927d573-a75a-3483-b846-b34afb8cd28d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/vbo.cpython-311-darwin.so",
"name" : "vbo.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5182836736,
"size" : 32768,
"uuid" : "ada3a7a8-1026-3b4a-9d87-6fce8df2fb33",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/latebind.cpython-311-darwin.so",
"name" : "latebind.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5178544128,
"size" : 32768,
"uuid" : "1936789e-b9b0-3e1f-8cfa-fc88f0803ad5",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/formathandler.cpython-311-darwin.so",
"name" : "formathandler.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5192732672,
"size" : 180224,
"uuid" : "d98e7117-18dd-37b7-9c74-472d0c79861a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/wrapper.cpython-311-darwin.so",
"name" : "wrapper.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5191720960,
"size" : 163840,
"uuid" : "84c28449-2886-395e-a902-73f67264df32",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/arraydatatype.cpython-311-darwin.so",
"name" : "arraydatatype.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5175246848,
"size" : 32768,
"uuid" : "2e49f12e-2bd1-36ff-a452-6af1ad840335",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/errorchecker.cpython-311-darwin.so",
"name" : "errorchecker.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5192503296,
"size" : 163840,
"uuid" : "fe32f21a-cd3a-3ad4-9176-dddbd203789a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/matplotlib\/_image.cpython-311-darwin.so",
"name" : "_image.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5192257536,
"size" : 98304,
"uuid" : "b95403ec-ebee-307e-a234-a98fa49425bf",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/kiwisolver\/_cext.cpython-311-darwin.so",
"name" : "_cext.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5193433088,
"size" : 671744,
"uuid" : "9f323cc7-da32-3fe1-b98b-163a8b0bc4f6",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/matplotlib\/ft2font.cpython-311-darwin.so",
"name" : "ft2font.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5182640128,
"size" : 131072,
"uuid" : "72e8fb51-e1eb-3955-ad6f-f9d432bd89fd",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/matplotlib\/_path.cpython-311-darwin.so",
"name" : "_path.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5168975872,
"size" : 16384,
"uuid" : "ab1ede05-8390-3ffd-92d7-7ce53a7c9be2",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/matplotlib\/_c_internal_utils.cpython-311-darwin.so",
"name" : "_c_internal_utils.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5168910336,
"size" : 16384,
"uuid" : "e8200b4e-f282-3cd7-9be9-8f3798584047",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/termios.cpython-311-darwin.so",
"name" : "termios.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5181001728,
"size" : 393216,
"uuid" : "3d435819-60f1-382a-b0ff-03aa1fec22a9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imaging.cpython-311-darwin.so",
"name" : "_imaging.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5179838464,
"size" : 655360,
"uuid" : "de0a2e7d-b9a1-33f1-9bf1-e8db3a502cb9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libtiff.6.dylib",
"name" : "libtiff.6.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5182988288,
"size" : 671744,
"uuid" : "5077f363-3598-3431-bc7b-2cfbf3a714d9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libjpeg.62.4.0.dylib",
"name" : "libjpeg.62.4.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5183741952,
"size" : 557056,
"uuid" : "5375f006-b7eb-3be7-88de-a910b38e7627",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libopenjp2.2.5.2.dylib",
"name" : "libopenjp2.2.5.2.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5178363904,
"size" : 131072,
"uuid" : "84f3a08c-6bf8-33d7-89c0-5e8026f4e202",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libz.1.3.1.dylib",
"name" : "libz.1.3.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5174968320,
"size" : 163840,
"uuid" : "5070a345-658e-31a4-80b9-d06f9abe9d5b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libxcb.1.dylib",
"name" : "libxcb.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5180608512,
"size" : 245760,
"uuid" : "2f03407e-0f9b-3146-b009-33e0f793869a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/liblzma.5.dylib",
"name" : "liblzma.5.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5170831360,
"size" : 16384,
"uuid" : "2b102593-309d-3ad2-98ff-fd87e42302d8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libXau.6.0.0.dylib",
"name" : "libXau.6.0.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5170438144,
"size" : 278528,
"uuid" : "6bf62b8d-952b-3c3e-87b6-67992b1c9e85",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_decimal.cpython-311-darwin.so",
"name" : "_decimal.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5169065984,
"size" : 16384,
"uuid" : "83a52d52-e452-3db7-8c1f-eee3d4bbc071",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_uuid.cpython-311-darwin.so",
"name" : "_uuid.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5168074752,
"size" : 32768,
"uuid" : "b7700fae-a522-3c9e-81c7-8301374c2b6e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_multibytecodec.cpython-311-darwin.so",
"name" : "_multibytecodec.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5178658816,
"size" : 1114112,
"uuid" : "0cfdf335-42fa-36ab-845a-44fda5a4f103",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/unicodedata.cpython-311-darwin.so",
"name" : "unicodedata.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5168648192,
"size" : 147456,
"uuid" : "d1f6d0b1-d05a-3cc7-8c15-0d72176e5bcb",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/charset_normalizer\/md__mypyc.cpython-311-darwin.so",
"name" : "md__mypyc.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5144027136,
"size" : 16384,
"uuid" : "143bfd0a-fbaa-3849-bbaa-9d3b2d44c38f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/charset_normalizer\/md.cpython-311-darwin.so",
"name" : "md.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5175398400,
"size" : 671744,
"uuid" : "99f6a3dc-9f85-3a3d-8ee5-4560b2308969",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/map\/_map.cpython-311-darwin.so",
"name" : "_map.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5167943680,
"size" : 49152,
"uuid" : "f6ffe558-91c7-3148-a81a-e03bb00eac29",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/cytmpl.cpython-311-darwin.so",
"name" : "cytmpl.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5169143808,
"size" : 114688,
"uuid" : "60d71170-122f-3388-8946-9dc82b508714",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/tinyarray.cpython-311-darwin.so",
"name" : "tinyarray.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5167239168,
"size" : 458752,
"uuid" : "cd45a26e-b65b-3ce2-beb8-3b85f74e2cad",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/cymol.cpython-311-darwin.so",
"name" : "cymol.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5168173056,
"size" : 212992,
"uuid" : "06f666f8-e01d-3977-8588-cd8763539de2",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/libmolc.dylib",
"name" : "libmolc.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5143961600,
"size" : 16384,
"uuid" : "d0ba4ed3-33c4-30c0-9fb8-0fcdd129cd4a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/_load_libs.cpython-311-darwin.so",
"name" : "_load_libs.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5170937856,
"size" : 1196032,
"uuid" : "61f0a987-8fa6-31d7-9915-0429ef9f504e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/lib\/libatomstruct.dylib",
"name" : "libatomstruct.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5142667264,
"size" : 32768,
"uuid" : "d58debec-4cde-3edd-9365-e9ebb03fd2b0",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/lib\/libelement.dylib",
"name" : "libelement.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5142781952,
"size" : 16384,
"uuid" : "3edbdaff-bca7-3dde-878a-d25fb44e9018",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic_lib\/lib\/libpyinstance.dylib",
"name" : "libpyinstance.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5143879680,
"size" : 32768,
"uuid" : "9b9ef339-f44c-3452-b5b0-92e4c1cfabb7",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_csv.cpython-311-darwin.so",
"name" : "_csv.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5143814144,
"size" : 16384,
"uuid" : "ed64b7f2-4c49-3dd2-ae71-a987d310a8d5",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/grp.cpython-311-darwin.so",
"name" : "grp.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5143748608,
"size" : 16384,
"uuid" : "82f64d2e-cca2-34b8-bb59-0743603ce84d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_scproxy.cpython-311-darwin.so",
"name" : "_scproxy.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5142294528,
"size" : 98304,
"uuid" : "65c5907a-9e69-3d89-a863-0f7df59fe19b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_ssl.cpython-311-darwin.so",
"name" : "_ssl.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5143142400,
"size" : 393216,
"uuid" : "35eaab10-69c7-3234-bb9c-f3ec617bade8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/libssl.1.1.dylib",
"name" : "libssl.1.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4993998848,
"size" : 16384,
"uuid" : "ab3e7bb1-b4dd-35a0-a44b-f87a59b1adbb",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_queue.cpython-311-darwin.so",
"name" : "_queue.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4978327552,
"size" : 16384,
"uuid" : "1fceb320-1415-384c-914b-89deb7181eee",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_heapq.cpython-311-darwin.so",
"name" : "_heapq.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5142552576,
"size" : 49152,
"uuid" : "19fe4936-cd05-35cf-b67f-f07ddb83c195",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/array.cpython-311-darwin.so",
"name" : "array.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4993867776,
"size" : 65536,
"uuid" : "9b2e2c2e-1abb-329d-aeb2-9921c2085377",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_socket.cpython-311-darwin.so",
"name" : "_socket.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5142863872,
"size" : 180224,
"uuid" : "2eccca6e-b160-375e-979b-d1d174cf5497",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/pyexpat.cpython-311-darwin.so",
"name" : "pyexpat.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4995608576,
"size" : 163840,
"uuid" : "b955d9be-5646-38cb-aba8-4337ae17c16d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/styles\/libqmacstyle.dylib",
"name" : "libqmacstyle.dylib"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 5144125440,
"CFBundleShortVersionString" : "5.5.17",
"CFBundleIdentifier" : "com.apple.AMDRadeonX6000GLDriver",
"size" : 1376256,
"uuid" : "b17bd962-c606-34e5-9a5e-3b043285955d",
"path" : "\/System\/Library\/Extensions\/AMDRadeonX6000GLDriver.bundle\/Contents\/MacOS\/AMDRadeonX6000GLDriver",
"name" : "AMDRadeonX6000GLDriver",
"CFBundleVersion" : "5.0.5"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4994691072,
"size" : 655360,
"uuid" : "a9df58b1-89b1-36c8-9d9e-fe251bf025f2",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4994068480,
"size" : 229376,
"uuid" : "e05fb3ee-5d42-3121-a19c-5ced50cb3132",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWebEngineCore.abi3.so",
"name" : "QtWebEngineCore.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4926984192,
"size" : 32768,
"uuid" : "9d400ff9-e70a-351e-bb34-5259e39c88b8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWebChannel.abi3.so",
"name" : "QtWebChannel.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4926640128,
"size" : 147456,
"uuid" : "34ad5a58-946c-3e72-bdbb-522e51148d3a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtPrintSupport.abi3.so",
"name" : "QtPrintSupport.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4984799232,
"size" : 475136,
"uuid" : "9513715b-6b36-3b31-8470-149dba6c1656",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtNetwork.abi3.so",
"name" : "QtNetwork.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4562116608,
"size" : 65536,
"uuid" : "e61f8860-5bfc-3097-919d-761e57850659",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWebEngineWidgets.abi3.so",
"name" : "QtWebEngineWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4558082048,
"size" : 98304,
"uuid" : "c2859284-9c93-3dd9-a78b-839df778dfea",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineWidgets.framework\/Versions\/A\/QtWebEngineWidgets",
"name" : "QtWebEngineWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4977606656,
"size" : 294912,
"uuid" : "5154fa08-ddcc-3174-a42d-4e333e150ee9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtPrintSupport.framework\/Versions\/A\/QtPrintSupport",
"name" : "QtPrintSupport"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5355663360,
"size" : 183599104,
"uuid" : "af091873-5278-3492-8e76-7c22e65c04ac",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4995944448,
"size" : 4210688,
"uuid" : "1b342485-b5a8-3134-8fbe-a4e607e770f3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtQuick.framework\/Versions\/A\/QtQuick",
"name" : "QtQuick"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4976623616,
"size" : 425984,
"uuid" : "78a08e9f-03a8-3e55-b319-5d7390d883d3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGL.framework\/Versions\/A\/QtOpenGL",
"name" : "QtOpenGL"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4986298368,
"size" : 557056,
"uuid" : "17e7e0a2-1745-3a18-a3d2-87857777737e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtQmlModels.framework\/Versions\/A\/QtQmlModels",
"name" : "QtQmlModels"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4922331136,
"size" : 180224,
"uuid" : "de6e3816-a208-301f-a7fc-0bbbb64c78a8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebChannel.framework\/Versions\/A\/QtWebChannel",
"name" : "QtWebChannel"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4987052032,
"size" : 4292608,
"uuid" : "33075afc-2a8b-3528-b0dd-4a5b769a2f54",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtQml.framework\/Versions\/A\/QtQml",
"name" : "QtQml"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5001695232,
"size" : 1146880,
"uuid" : "b57854a4-c721-36b4-830e-2fe9e929a811",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtNetwork.framework\/Versions\/A\/QtNetwork",
"name" : "QtNetwork"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4992196608,
"size" : 458752,
"uuid" : "f7f96df9-e51a-3764-90a4-730a57198670",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtPositioning.framework\/Versions\/A\/QtPositioning",
"name" : "QtPositioning"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4558311424,
"size" : 81920,
"uuid" : "a2d3acde-e0db-3d21-acc4-ebfa3db5fd5c",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtQuickWidgets.framework\/Versions\/A\/QtQuickWidgets",
"name" : "QtQuickWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4923363328,
"size" : 1523712,
"uuid" : "8cf677f1-f820-300f-bbea-491cfe548a9b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtGui.abi3.so",
"name" : "QtGui.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4915154944,
"size" : 2867200,
"uuid" : "04d3e498-8e36-3f03-9aa5-8a19040cc57f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4978393088,
"size" : 4931584,
"uuid" : "6b647ba7-e77f-36aa-937c-028f9cb4875c",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
"name" : "QtWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4965957632,
"size" : 7274496,
"uuid" : "57e18c1d-e3ae-37c5-ada4-dcc62718794e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4922658816,
"size" : 540672,
"uuid" : "8b52e419-6929-39c7-8f25-239bd787b9b0",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtDBus.framework\/Versions\/A\/QtDBus",
"name" : "QtDBus"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4644118528,
"size" : 98304,
"uuid" : "3a35763b-1c12-3805-b15b-6ffa69bd1f52",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/sip.cpython-311-darwin.so",
"name" : "sip.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4561784832,
"CFBundleShortVersionString" : "3.0",
"CFBundleIdentifier" : "com.apple.security.csparser",
"size" : 94208,
"uuid" : "0c023137-d800-3c4d-942f-c41bb63a4ae9",
"path" : "\/System\/Library\/Frameworks\/Security.framework\/Versions\/A\/PlugIns\/csparser.bundle\/Contents\/MacOS\/csparser",
"name" : "csparser",
"CFBundleVersion" : "61123.121.1"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4640157696,
"size" : 1720320,
"uuid" : "d186fce2-169a-3875-8ca4-f2fcd55371cf",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtCore.abi3.so",
"name" : "QtCore.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4927123456,
"size" : 5373952,
"uuid" : "f4950342-54e3-3755-a88f-e2a6406c1fc3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4554436608,
"size" : 32768,
"uuid" : "b334e8fd-e63d-3cac-89e8-071a263d4818",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_json.cpython-311-darwin.so",
"name" : "_json.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4559441920,
"size" : 147456,
"uuid" : "2c719e3d-a419-3692-a578-2819f3d838f6",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/geometry\/_geometry.cpython-311-darwin.so",
"name" : "_geometry.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4552069120,
"size" : 16384,
"uuid" : "4161acf6-42c3-3364-aca8-8d14917132b0",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_opcode.cpython-311-darwin.so",
"name" : "_opcode.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4558540800,
"size" : 770048,
"uuid" : "15252f8d-5c11-35f9-8f3b-b8c1dd465de8",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_generator.cpython-311-darwin.so",
"name" : "_generator.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4553883648,
"size" : 49152,
"uuid" : "9215cc4e-48d6-384f-aa4e-fa2ce81a8a1f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_sfc64.cpython-311-darwin.so",
"name" : "_sfc64.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4554289152,
"size" : 81920,
"uuid" : "9e7a3d28-fb10-3335-bbe0-1f2a4e6e237a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_pcg64.cpython-311-darwin.so",
"name" : "_pcg64.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4554735616,
"size" : 65536,
"uuid" : "b543ab2e-918d-3187-88cc-ed0733756a55",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_philox.cpython-311-darwin.so",
"name" : "_philox.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4554588160,
"size" : 81920,
"uuid" : "5b3a56f1-c5e3-344a-86ff-810850013d80",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_mt19937.cpython-311-darwin.so",
"name" : "_mt19937.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4553441280,
"size" : 327680,
"uuid" : "05826eca-98c1-3b93-b72a-5c523819d49a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_bounded_integers.cpython-311-darwin.so",
"name" : "_bounded_integers.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4551987200,
"size" : 32768,
"uuid" : "1de3cb49-cee7-3aec-9885-69438bcbb671",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_blake2.cpython-311-darwin.so",
"name" : "_blake2.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4534394880,
"size" : 32768,
"uuid" : "c8a36b29-9fb1-3c9e-bb16-9698b6a379d4",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_hashlib.cpython-311-darwin.so",
"name" : "_hashlib.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4636192768,
"size" : 2260992,
"uuid" : "9077f550-4289-3012-8803-cca73b9d943d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/libcrypto.1.1.dylib",
"name" : "libcrypto.1.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4554010624,
"size" : 196608,
"uuid" : "9de7ed17-62fe-3c59-a8e9-3d3074cb449e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/_common.cpython-311-darwin.so",
"name" : "_common.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4551741440,
"size" : 163840,
"uuid" : "188f02a8-df66-3e0c-8946-153af5eaba44",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/bit_generator.cpython-311-darwin.so",
"name" : "bit_generator.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4554952704,
"size" : 655360,
"uuid" : "f65b5844-4c12-381e-8af8-637620272103",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/random\/mtrand.cpython-311-darwin.so",
"name" : "mtrand.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4544151552,
"size" : 81920,
"uuid" : "2c97d6ef-aec3-361d-bc4d-0dd7137ad6ed",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/fft\/_pocketfft_internal.cpython-311-darwin.so",
"name" : "_pocketfft_internal.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4552163328,
"size" : 163840,
"uuid" : "95ecdafc-7133-362d-9f9c-dd26ff543a5b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/linalg\/_umath_linalg.cpython-311-darwin.so",
"name" : "_umath_linalg.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4534214656,
"size" : 81920,
"uuid" : "cc072b20-11ee-3eb4-b287-8393ef51db95",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_ctypes.cpython-311-darwin.so",
"name" : "_ctypes.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4534521856,
"size" : 81920,
"uuid" : "79cd772e-9106-339a-acb7-ba43552b15a7",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/core\/_multiarray_tests.cpython-311-darwin.so",
"name" : "_multiarray_tests.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4533977088,
"size" : 16384,
"uuid" : "6f069f98-51a6-3478-9053-9d1f2fbebd9b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_contextvars.cpython-311-darwin.so",
"name" : "_contextvars.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4533780480,
"size" : 114688,
"uuid" : "79de93b8-7f0e-3adc-8fde-969984151905",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_pickle.cpython-311-darwin.so",
"name" : "_pickle.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4535996416,
"size" : 4947968,
"uuid" : "fd4b95ff-f84a-34d3-939c-f932f374ddb9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/core\/_multiarray_umath.cpython-311-darwin.so",
"name" : "_multiarray_umath.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4644425728,
"size" : 66404352,
"uuid" : "7048d1fd-b9a9-3f6a-b752-ae8be69f6c3f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4562280448,
"size" : 6565888,
"uuid" : "ae37c55e-f850-3cf7-86e4-bbd86809bc1d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libgfortran.5.dylib",
"name" : "libgfortran.5.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4541698048,
"size" : 319488,
"uuid" : "a1783d23-d187-3d92-ade7-2a80619e7485",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libquadmath.0.dylib",
"name" : "libquadmath.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4534075392,
"size" : 69632,
"uuid" : "6d59656e-a224-3642-80b9-ca07ca06e7c1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libgcc_s.1.1.dylib",
"name" : "libgcc_s.1.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4531539968,
"size" : 16384,
"uuid" : "968f7d44-5fa3-31d9-8b22-92eb2206cc84",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/arrays\/_arrays.cpython-311-darwin.so",
"name" : "_arrays.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4534685696,
"size" : 1130496,
"uuid" : "4442f722-a049-33ee-8cfe-e5e288b44421",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/arrays\/lib\/libarrays.dylib",
"name" : "libarrays.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4531458048,
"size" : 32768,
"uuid" : "ce09d1ac-f6df-3770-9dda-8f52871a152d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/select.cpython-311-darwin.so",
"name" : "select.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4531617792,
"size" : 16384,
"uuid" : "8d17df9f-a171-32fe-848a-1380ca2546d4",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_posixsubprocess.cpython-311-darwin.so",
"name" : "_posixsubprocess.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4529238016,
"size" : 16384,
"uuid" : "1348d940-0f3a-37cb-9a27-37db7b4734d1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/fcntl.cpython-311-darwin.so",
"name" : "fcntl.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4529139712,
"size" : 32768,
"uuid" : "6333bf6e-f980-3714-b65f-a12997bfe10a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_struct.cpython-311-darwin.so",
"name" : "_struct.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4531376128,
"size" : 32768,
"uuid" : "dc4ae342-b3c4-3716-a530-b1568a67f912",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/binascii.cpython-311-darwin.so",
"name" : "binascii.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4531294208,
"size" : 32768,
"uuid" : "4e6494eb-704b-3e1a-9d97-751ef9b2d06a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_sha512.cpython-311-darwin.so",
"name" : "_sha512.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4531228672,
"size" : 16384,
"uuid" : "de8dfc82-ec28-378b-b945-07e7671a35b1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_random.cpython-311-darwin.so",
"name" : "_random.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4531163136,
"size" : 16384,
"uuid" : "cc52d89b-b174-3a9a-94ae-0c556ec7b21b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bisect.cpython-311-darwin.so",
"name" : "_bisect.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4529520640,
"size" : 196608,
"uuid" : "0fa75f51-66bf-3a60-a393-65ceea03012e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_lzma.cpython-311-darwin.so",
"name" : "_lzma.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4529455104,
"size" : 16384,
"uuid" : "4921b552-b90a-39c6-b791-14028366f5a0",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bz2.cpython-311-darwin.so",
"name" : "_bz2.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4529356800,
"size" : 32768,
"uuid" : "6c0e3849-f845-3996-a69e-e956c62499ff",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
"name" : "zlib.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4526821376,
"size" : 16384,
"uuid" : "52112d00-a676-3fba-b4d8-69e98fe5e2c3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_typing.cpython-311-darwin.so",
"name" : "_typing.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4526673920,
"size" : 65536,
"uuid" : "ce1cdda7-c310-3834-8656-4829f8b0fa2a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
"name" : "_datetime.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4526927872,
"size" : 49152,
"uuid" : "c4d4107c-7508-3d61-88f1-4f1a33945090",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
"name" : "math.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4544335872,
"CFBundleShortVersionString" : "3.11.4, (c) 2001-2023 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 4030464,
"uuid" : "514efc82-c424-3863-84a8-e24ffd50343d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.4"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4524302336,
"CFBundleShortVersionString" : "1.8.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "194a3167-3db5-3029-8d22-1d742b826bb9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.8.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703450243072,
"size" : 241656,
"uuid" : "13597eeb-2ea0-3d48-8be1-dfc4872a784b",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703450484736,
"size" : 49144,
"uuid" : "25b2f3eb-07b4-3cb9-9457-2c26210c27c8",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703449092096,
"size" : 557048,
"uuid" : "93fb3816-608b-33af-83d2-209b4bd673ad",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703450685440,
"size" : 45048,
"uuid" : "acde8386-eb3f-36f2-bc5e-069cc59d079c",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703541563392,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4595703,
"uuid" : "c85f48c7-7d13-316b-a28b-cfbd2693b663",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703448788992,
"size" : 290802,
"uuid" : "511b909b-7a60-3295-9981-a508477c7893",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703450906624,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4829181,
"uuid" : "59d4644f-7aa6-3767-80ab-73d7a388a4ff",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "2503.1"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703629578240,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2732020,
"uuid" : "de4aeb8b-676c-3a36-9364-1cdee78a3b41",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703508234240,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21164019,
"uuid" : "33ecd3dc-c895-35e2-a1fd-c1761b155964",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.60.105"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703446765568,
"size" : 592800,
"uuid" : "baa6f02e-dff3-3562-8c99-ea2820c91ad9",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703449649152,
"size" : 503796,
"uuid" : "e443af07-488b-3b1b-83ae-31bd883e6ef1",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
"base" : 140703446069248,
"size" : 25769803776,
"uuid" : "b48cfc6b-b7ed-3343-97fb-f5187dc04df8"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=2.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 152K 19 \nColorSync 252K 31 \nCoreAnimation 464K 59 \nCoreGraphics 16K 3 \nCoreUI image data 5164K 49 \nFoundation 16K 1 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.5G 461 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 264K 66 \nStack 478.5M 67 \nStack Guard 56.0M 1 \nVM_ALLOCATE 280.9M 326 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 44.2M 765 \n__DATA_CONST 61.6M 434 \n__DATA_DIRTY 1691K 221 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 212.6M 160 \n__OBJC_RO 71.8M 1 \n__OBJC_RW 2200K 2 \n__TEXT 1.0G 771 \ndyld private memory 292K 4 \nmapped file 231.3M 61 \nshared memory 3508K 29 \n=========== ======= ======= \nTOTAL 4.1G 3556 \nTOTAL, minus reserved VM space 4.0G 3556 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "9b32d37eed40f7db94dcf0c0e7f64901f98a5d9d",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63508950b3714d3622fc77f7",
"factorPackIds" : {
"SIRI_MEMORY_SYNC_CONFIG" : "6526e111d0c9ce2f459b54a8"
},
"deploymentId" : 240000015
},
{
"rolloutId" : "61675b89201f677a9a4cbd65",
"factorPackIds" : {
"HEALTH_FEATURE_AVAILABILITY" : "65a855f5f087695cfac03d1f"
},
"deploymentId" : 240000142
}
],
"experiments" : [
{
"treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_GPR3_8U8F.cxs"
Opened emd_38015_8X2K.map as #4, grid size 320,320,320, pixel 0.85, shown at
level 0.396, step 2, values float32
Opened emd_38015_8X2K.map copy as #6, grid size 320,320,320, pixel 0.85, shown
at level 0.396, step 1, values float32
Opened emd_37881_8WW2.map as #5, grid size 256,256,256, pixel 1.1, shown at
level 0.526, step 1, values float32
Opened emd_37881_8WW2.map copy as #8, grid size 256,256,256, pixel 1.1, shown
at level 0.526, step 1, values float32
Opened emd_38015_8X2K.map copy as #9, grid size 320,320,320, pixel 0.85, shown
at level 0.396, step 1, values float32
Opened emd_37881_8WW2.map copy as #11, grid size 256,256,256, pixel 1.1, shown
at level 0.526, step 1, values float32
Opened emd_42023_8U8F.map as #10, grid size 256,256,256, pixel 0.86, shown at
level 0.364, step 1, values float32
Opened emd_42023_8U8F.map copy as #13, grid size 256,256,256, pixel 0.86,
shown at level 0.364, step 1, values float32
Log from Mon Sep 23 15:58:13 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4_GPR3_updated_no8U9F.cxs"
Opened emd_38015_8X2K.map as #4, grid size 320,320,320, pixel 0.85, shown at
level 0.396, step 2, values float32
Opened emd_38015_8X2K.map copy as #6, grid size 320,320,320, pixel 0.85, shown
at level 0.396, step 1, values float32
Opened emd_37881_8WW2.map as #5, grid size 256,256,256, pixel 1.1, shown at
level 0.526, step 1, values float32
Opened emd_37881_8WW2.map copy as #8, grid size 256,256,256, pixel 1.1, shown
at level 0.526, step 1, values float32
Opened emd_38015_8X2K.map copy as #9, grid size 320,320,320, pixel 0.85, shown
at level 0.396, step 1, values float32
Opened emd_37881_8WW2.map copy as #11, grid size 256,256,256, pixel 1.1, shown
at level 0.526, step 1, values float32
Opened emd_42023_8U8F.map as #10, grid size 256,256,256, pixel 0.86, shown at
level 0.167, step 1, values float32
Log from Mon Sep 23 15:26:47 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_GPR3_with maps.cxs"
Opened emd_38015_8X2K.map as #4, grid size 320,320,320, pixel 0.85, shown at
level 0.396, step 2, values float32
Opened emd_38015_8X2K.map copy as #6, grid size 320,320,320, pixel 0.85, shown
at level 0.396, step 1, values float32
Opened emd_37881_8WW2.map as #5, grid size 256,256,256, pixel 1.1, shown at
level 0.526, step 1, values float32
Opened emd_37881_8WW2.map copy as #8, grid size 256,256,256, pixel 1.1, shown
at level 0.526, step 1, values float32
Log from Mon Jun 17 15:55:50 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_174_v3.cxs" format session
Opened emd_33479_7XV3.map as #3, grid size 256,256,256, pixel 1.1, shown at
level 1.52, step 1, values float32
Opened emd_33479_7XV3.map copy as #6, grid size 256,256,256, pixel 1.1, shown
at level 1.52, step 1, values float32
Opened emd_35838_8IZB.map as #5, grid size 192,192,192, pixel 1.07, shown at
level 0.31, step 1, values float32
Opened emd_35838_8IZB.map copy as #9, grid size 192,192,192, pixel 1.07, shown
at level 0.31, step 1, values float32
Opened emd_35838_8IZB.map copy as #10, grid size 192,192,192, pixel 1.07,
shown at level 0.31, step 1, values float32
Not registering illegal selector name "1_hydrophobic_cleft"
Not registering illegal selector name "1_head_interact"
Log from Sun Jun 16 23:57:53 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_174_v3.cxs"
Opened emd_33479_7XV3.map as #3, grid size 256,256,256, pixel 1.1, shown at
level 1.52, step 1, values float32
Opened emd_33479_7XV3.map copy as #6, grid size 256,256,256, pixel 1.1, shown
at level 1.52, step 1, values float32
Opened emd_35838_8IZB.map as #5, grid size 192,192,192, pixel 1.07, shown at
level 0.31, step 1, values float32
Opened emd_35838_8IZB.map copy as #9, grid size 192,192,192, pixel 1.07, shown
at level 0.31, step 1, values float32
Opened emd_35838_8IZB.map copy as #10, grid size 192,192,192, pixel 1.07,
shown at level 0.31, step 1, values float32
Not registering illegal selector name "1_hydrophobic_cleft"
Not registering illegal selector name "1_head_interact"
Log from Fri Jun 14 01:29:38 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4A_119_LPC.cxs" format session
Opened emd_33525_7xz5.map as #2, grid size 200,200,200, pixel 1.07, shown at
level 0.0208, step 1, values float32
Opened emd_33525_7xz5.map copy as #4, grid size 200,200,200, pixel 1.07, shown
at level 0.0208, step 1, values float32
Log from Mon Jun 10 00:01:24 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 7/Figure7C.cxs"
Log from Thu May 30 20:40:46 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NSMB/All Figures-
> draft/Figure7/Figure 7D-GPR61-BRIL fused structure v2.cxs"
Log from Thu Apr 4 16:40:01 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
> draft/Figure 7D-GPR61-BRIL fused structure.cxs"
Log from Mon Apr 1 18:14:01 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
> draft/Fig3B_inactive GPR20 with the map.cxs"
Opened emd_34993_8HSC.map as #4, grid size 288,288,288, pixel 0.832, shown at
level 0.13, step 2, values float32
Opened emd_34984_8HS3.map as #5, grid size 256,256,256, pixel 0.832, shown at
level 0.148, step 1, values float32
Opened emd_34983_8HS2.map as #6, grid size 288,288,288, pixel 0.832, shown at
level 0.0931, step 1, values float32
Opened emd_34983_8HS2.map copy as #8, grid size 288,288,288, pixel 0.832,
shown at level 0.0678, step 1, values float32
Log from Wed Feb 28 18:29:12 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-
> Monash/NRE/Figure2_DL/Fig2B_GPR21 and 52.cxs"
Not registering illegal selector name "GPR21_binding sites"
Log from Tue Feb 27 18:06:41 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NRE/Figure2_DL/Aligned
> overall_17_21_52_161.cxs" format session
Log from Wed Feb 14 23:29:37 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/dongju/Desktop/Research projects-Monash/NRE/Figure 2 -
> Autoactivated/20240206_Figure_2.cxs"
Log from Tue Feb 6 18:08:29 2024UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> C:/Users/fbumb/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231026_Figure_2.cxs
Log from Thu Oct 26 20:27:55 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> C:\Users\Midget\OneDrive\MIPS\papers\GPR_mini_review\Figures\20231025_Figure_2.cxs
> format session
Log from Thu Oct 26 16:19:56 2023UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> C:\Users\Midget\OneDrive\MIPS\papers\GPR_mini_review\Figures\20231025_Figure_2.cxs
> format session
Log from Thu Oct 26 00:31:26 2023You can double click a model's Name or ID in
the model panel to edit those fields
Updating list of available bundles failed: [Errno 11001] getaddrinfo failed
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/structures/GPR12_Gs.pdb
GPR12_Gs.pdb title:
Cryo-em structure of A class A orphan GPCR [more info...]
Chain information for GPR12_Gs.pdb #1
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN
B | transducin β chain 1 | GBB1_HUMAN
G | G γ-I | GBG2_HUMAN
N | nanobody 35 |
R | G-protein coupled receptor 12 | GPR12_HUMAN
> open
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/structures/GPR17_7y89.pdb
GPR17_7y89.pdb title:
Structure of the GPR17-gi complex [more info...]
Chain information for GPR17_7y89.pdb #2
---
Chain | Description | UniProt
A | uracil nucleotide/cysteinyl leukotriene receptor | GPR17_HUMAN
B | transducin β chain 1 | GBB1_HUMAN
C | adenylate cyclase-inhibiting G α protein | GNAI1_HUMAN
G | guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit β-1 |
S | guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit γ-2 |
> open
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/structures/GPR21_8hmv.pdb
GPR21_8hmv.pdb title:
Structure of GPR21-GS complex [more info...]
Chain information for GPR21_8hmv.pdb #3
---
Chain | Description | UniProt
A | probable G-protein coupled receptor 21 | GPR21_HUMAN
B | transducin β chain 1 | GBB1_HUMAN
C | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN
G | G γ-I | GBG2_HUMAN
N | nanobody NB35 |
> open
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/structures/GPR52_6li3.pdb
GPR52_6li3.pdb title:
Cryo-em structure of GPR52-minigs-NB35 [more info...]
Chain information for GPR52_6li3.pdb #4
---
Chain | Description | UniProt
A | guanine nucleotide-binding protein G(S) subunit α isoforms short | GNAS2_HUMAN
B | transducin β chain 1 | GBB1_HUMAN
G | G γ-I | GBG2_HUMAN
N | nanobody NB35 |
R | G-protein coupled receptor 52 | GPR52_HUMAN
> ui tool show "Fit to Segments"
> ui tool show "Fit in Map"
QWindowsWindow::setGeometry: Unable to set geometry 3200x1653+0+55 (frame:
3232x1741-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
16, 16 minimum size: 630x661 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1607,
y=1741)))
> select add #1
7903 atoms, 8059 bonds, 4 pseudobonds, 1005 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1
7903 atoms, 8059 bonds, 4 pseudobonds, 1005 residues, 2 models selected
> select subtract #1.1
7903 atoms, 8059 bonds, 1005 residues, 1 model selected
> select add #1
7903 atoms, 8059 bonds, 4 pseudobonds, 1005 residues, 2 models selected
> ui tool show "Model Panel"
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> select add #2
16544 atoms, 16886 bonds, 8 pseudobonds, 2115 residues, 4 models selected
> select add #3
24671 atoms, 25193 bonds, 12 pseudobonds, 3137 residues, 6 models selected
> select subtract #3.1
24671 atoms, 25193 bonds, 8 pseudobonds, 3137 residues, 5 models selected
> select add #4
32960 atoms, 33668 bonds, 10 pseudobonds, 4182 residues, 7 models selected
> select add #3.1
32960 atoms, 33668 bonds, 14 pseudobonds, 4182 residues, 8 models selected
> select subtract #3
24833 atoms, 25361 bonds, 10 pseudobonds, 3160 residues, 6 models selected
> select add #3
32960 atoms, 33668 bonds, 14 pseudobonds, 4182 residues, 8 models selected
> show sel cartoons
> hide sel atoms
> view #3 clip false
> show #!3 target m
> select subtract #4
24671 atoms, 25193 bonds, 12 pseudobonds, 3137 residues, 6 models selected
> select subtract #3
16544 atoms, 16886 bonds, 8 pseudobonds, 2115 residues, 4 models selected
> select subtract #2
7903 atoms, 8059 bonds, 4 pseudobonds, 1005 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1/G#3/G#4/G
1308 atoms, 1326 bonds, 171 residues, 3 models selected
> select add #2/C
2947 atoms, 2990 bonds, 3 pseudobonds, 377 residues, 5 models selected
> select add #1/A#3/C
6710 atoms, 6821 bonds, 9 pseudobonds, 828 residues, 7 models selected
> select add #2/S
8482 atoms, 8639 bonds, 10 pseudobonds, 1061 residues, 7 models selected
> select add #2/G
8894 atoms, 9057 bonds, 10 pseudobonds, 1114 residues, 7 models selected
> select add #4/A
10883 atoms, 11084 bonds, 11 pseudobonds, 1354 residues, 8 models selected
> select add #1/N
11844 atoms, 12065 bonds, 11 pseudobonds, 1480 residues, 8 models selected
> select add #3/N#4/N
13766 atoms, 14031 bonds, 11 pseudobonds, 1732 residues, 8 models selected
> select add #1/B#2/B#3/B#4/B
24097 atoms, 24550 bonds, 11 pseudobonds, 3077 residues, 8 models selected
> delete atoms (#!1-4 & sel)
> delete bonds (#!1-4 & sel)
> ui tool show "Volume Viewer"
QWindowsWindow::setGeometry: Unable to set geometry 3200x1730+0+55 (frame:
3232x1818-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
16, 16 minimum size: 426x692 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1097,
y=1818)))
QWindowsWindow::setGeometry: Unable to set geometry 3200x1835+0+55 (frame:
3232x1923-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
16, 16 minimum size: 426x734 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1097,
y=1923)))
> select add #1
2035 atoms, 2084 bonds, 1 pseudobond, 260 residues, 2 models selected
> select add #3
4272 atoms, 4392 bonds, 2 pseudobonds, 534 residues, 4 models selected
> select add #4
6575 atoms, 6768 bonds, 3 pseudobonds, 818 residues, 6 models selected
> select subtract #4.1
6575 atoms, 6768 bonds, 2 pseudobonds, 818 residues, 5 models selected
> select add #4.1
6575 atoms, 6768 bonds, 3 pseudobonds, 818 residues, 6 models selected
> select add #2
8863 atoms, 9118 bonds, 3 pseudobonds, 1105 residues, 7 models selected
> help help:user
> ui tool show Matchmaker
> matchmaker #!2-4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR17_7y89.pdb, chain A (#2),
sequence alignment score = 311.8
RMSD between 118 pruned atom pairs is 1.154 angstroms; (across all 256 pairs:
5.669)
Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR21_8hmv.pdb, chain A (#3),
sequence alignment score = 398.2
RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 255 pairs:
4.042)
Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 369.8
RMSD between 122 pruned atom pairs is 1.221 angstroms; (across all 258 pairs:
5.085)
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR17_7y89.pdb, chain A (#2),
sequence alignment score = 311.8
RMSD between 118 pruned atom pairs is 1.154 angstroms; (across all 256 pairs:
5.669)
> matchmaker #!3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR21_8hmv.pdb, chain A (#3),
sequence alignment score = 398.2
RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 255 pairs:
4.042)
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 369.8
RMSD between 122 pruned atom pairs is 1.221 angstroms; (across all 258 pairs:
5.085)
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 369.8
RMSD between 122 pruned atom pairs is 1.221 angstroms; (across all 258 pairs:
5.085)
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> view
> set bgColor white
> lighting soft
> ui tool show "Side View"
QWindowsWindow::setGeometry: Unable to set geometry 3200x1910+0+55 (frame:
3232x1998-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
16, 16 minimum size: 426x764 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1097,
y=1998)))
> ui tool show "Side View"
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting full
> lighting soft
> graphics silhouettes true
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> view
> view sel
> ui tool show "Side View"
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> cartoon style protein modeHelix default arrows false xsection round width 1
> thickness 1
> ui tool show "Basic Actions"
QWindowsWindow::setGeometry: Unable to set geometry 3200x1750+0+55 (frame:
3232x1838-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
16, 16 minimum size: 426x700 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1097,
y=1838)))
> undo
> ui tool show "Surface Color"
QWindowsWindow::setGeometry: Unable to set geometry 3200x2108+0+55 (frame:
3232x2196-16-17) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 3200x1644+0+56 (frame: 3232x1732-16-16) margins: 16, 72,
16, 16 minimum size: 426x843 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1097,
y=2196)))
> tile
4 models tiled
> help help:user
> tile columns 4
4 models tiled
> help help:user
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> tile columns 4 spacingFactor 4
4 models tiled
> tile columns 4 spacingFactor 1
4 models tiled
> tile columns 4 spacingFactor 0.7
4 models tiled
> color #1/R #dd53ff target c
[Repeated 1 time(s)]
> color #2/A #34ff3b target c
[Repeated 1 time(s)]
> color #3/A #0000ff target c
[Repeated 1 time(s)]
> color #3/A #5555ff target c
[Repeated 1 time(s)]
> color #4/R #ffaaff target c
[Repeated 1 time(s)]
> color #2/A #00ff7f target c
[Repeated 1 time(s)]
> color #1/R #aa557f target c
[Repeated 1 time(s)]
> color #1/R #aa5500 target c
[Repeated 1 time(s)]
> select subtract #1
6828 atoms, 7034 bonds, 2 pseudobonds, 845 residues, 5 models selected
> select subtract #2
4540 atoms, 4684 bonds, 2 pseudobonds, 558 residues, 4 models selected
> select subtract #2.1
4540 atoms, 4684 bonds, 2 pseudobonds, 558 residues, 4 models selected
> select subtract #3
2303 atoms, 2376 bonds, 1 pseudobond, 284 residues, 2 models selected
> select subtract #4
Nothing selected
> lighting soft
> lighting simple
> color #1/R #bc5e00 target c
[Repeated 1 time(s)]
> color #1/R #c56300 target c
[Repeated 1 time(s)]
> color #3/A #5582ff target c
[Repeated 1 time(s)]
> save
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231025_Figure_2_v1.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
->
'Basic Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for
'tools' -> ->
'Basic Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 225, in take_snapshot
self.add_webview_state(data)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\basic_actions\tool.py", line 260, in add_webview_state
event_loop.exec_()
AttributeError: 'QEventLoop' object has no attribute 'exec_'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
->
'Basic Actions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for
'tools' -> ->
'Basic Actions'
ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while
saving session data for 'tools' -> -> 'Basic Actions'
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231025_Figure_2.cxs
——— End of log from Thu Oct 26 00:31:26 2023 ———
opened ChimeraX session
> select add #1
2035 atoms, 2084 bonds, 1 pseudobond, 260 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R
Alignment identifier is 1/R
> select #1/R:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/R:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/R:188
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/R:188
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #1/R:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/R:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> select #1/R:186
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/R:186
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #1/R:180
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #1/R:193
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:193
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #1/R:192
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/R:192
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #1/R:191
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select
> #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
1625 atoms, 1653 bonds, 210 residues, 1 model selected
> select #1/R:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/R:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select
> #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
1625 atoms, 1653 bonds, 210 residues, 1 model selected
> select #1/R:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select
> #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
1625 atoms, 1653 bonds, 210 residues, 1 model selected
> select #1/R:117
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:117
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select
> #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
1625 atoms, 1653 bonds, 210 residues, 1 model selected
> select #1/R:195
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/R:195
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:204
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:204
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:201
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:201
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:208
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:208
7 atoms, 6 bonds, 1 residue, 1 model selected
> select
> #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
1950 atoms, 1992 bonds, 244 residues, 1 model selected
> select #2/A:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select
> #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
1950 atoms, 1992 bonds, 244 residues, 1 model selected
> select #2/A:132
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:132
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select
> #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
1950 atoms, 1992 bonds, 244 residues, 1 model selected
> select #2/A:213
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:213
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #2/A:214
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:214
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #2/A:223-238
121 atoms, 124 bonds, 16 residues, 1 model selected
> select #2/A:163-238
594 atoms, 611 bonds, 76 residues, 1 model selected
> select
> #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
1950 atoms, 1992 bonds, 244 residues, 1 model selected
> select #2/A:308
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:308
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select
> #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
1950 atoms, 1992 bonds, 244 residues, 1 model selected
> select #2/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select
> #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
1950 atoms, 1992 bonds, 244 residues, 1 model selected
> select #2/A:139
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:139
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select
> #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
1950 atoms, 1992 bonds, 244 residues, 1 model selected
> select #2/A:140
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:140
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select
> #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
1950 atoms, 1992 bonds, 244 residues, 1 model selected
> select #2/A:279
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:279
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:170
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:170
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:176
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:176
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:174
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:174
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:173-174
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #3/A:173
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #3/A:168
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:168
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:168
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:168
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> hide sel atoms
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:178
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:178
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:177
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #3/A:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:180
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:180
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:122
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:122
6 atoms, 5 bonds, 1 residue, 1 model selected
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:102
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:102
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> lighting soft
> save
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231025_Figure_2.cxs
> ui tool show "Show Sequence Viewer"
> sequence chain #4/R
Alignment identifier is 4/R
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> select #4/R:114
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:114
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> select #4/R:193
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:193
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #4/R:69
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:69-129
476 atoms, 489 bonds, 61 residues, 1 model selected
> select #4/R:67-81
126 atoms, 131 bonds, 15 residues, 1 model selected
> select #4/R:67-111
350 atoms, 361 bonds, 45 residues, 1 model selected
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> select #4/R:40
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:40
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #4/R:185
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4/R:185
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select #4/R:186
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/R:186
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> select #4/R:188
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:188
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #4/R:189
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:189
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #4/R:190
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:190
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel cartoons
> style sel stick
Changed 11 atom styles
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> select #4/R:281
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> select #4/R:284
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4/R:284
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> select #4/R:285
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:285
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> select #4/R:300
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:300
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:300
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:300
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> hide sel atoms
> show sel atoms
> style sel ball
Changed 11 atom styles
> hide sel atoms
> ui tool show "Color Actions"
> color sel byhetero
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> color sel byhetero
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> color sel byhetero
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select
> #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
1950 atoms, 1992 bonds, 244 residues, 1 model selected
> color sel byhetero
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R
Alignment identifier is 1/R
> select
> #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
1625 atoms, 1653 bonds, 210 residues, 1 model selected
> color sel byhetero
delivering touch update to same window GraphicsWindow(0x2840860fb50) not
QWidgetWindow(0x28461326800, name="PopupClassWindow")
delivering touch update to same window QWidgetWindow(0x28461326800,
name="PopupClassWindow") not GraphicsWindow(0x2840860fb50)
delivering touch update to same window GraphicsWindow(0x2840860fb50) not
QWidgetWindow(0x28461326800, name="PopupClassWindow")
delivering touch update to same window QWidgetWindow(0x28461326800,
name="PopupClassWindow") not GraphicsWindow(0x2840860fb50)
delivering touch update to same window GraphicsWindow(0x2840860fb50) not
QWidgetWindow(0x28461326800, name="PopupClassWindow")
delivering touch update to same window QWidgetWindow(0x28461326800,
name="PopupClassWindow") not GraphicsWindow(0x2840860fb50)
delivering touch update to same window GraphicsWindow(0x2840860fb50) not
QWidgetWindow(0x28461326800, name="PopupClassWindow")
delivering touch update to same window QWidgetWindow(0x28461326800,
name="PopupClassWindow") not GraphicsWindow(0x2840860fb50)
delivering touch update to same window GraphicsWindow(0x2840860fb50) not
QWidgetWindow(0x28461326800, name="PopupClassWindow")
delivering touch update to same window QWidgetWindow(0x28461326800,
name="PopupClassWindow") not GraphicsWindow(0x2840860fb50)
delivering touch update to same window GraphicsWindow(0x2840860fb50) not
QWidgetWindow(0x28461326800, name="PopupClassWindow")
delivering touch update to same window QWidgetWindow(0x28461326800,
name="PopupClassWindow") not GraphicsWindow(0x2840860fb50)
delivering touch update to same window GraphicsWindow(0x2840860fb50) not
QWidgetWindow(0x28461326800, name="PopupClassWindow")
delivering touch update to same window QWidgetWindow(0x28461326800,
name="PopupClassWindow") not GraphicsWindow(0x2840860fb50)
> ui tool show "Side View"
> tile columns 4 spacingFactor 0.7
4 models tiled
> lighting soft
> view
> ui tool show "Side View"
> tile columns 4 spacingFactor 0.7
4 models tiled
> tile columns 4 spacingFactor 0.7
4 models tiled
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
> lighting full
[Repeated 1 time(s)]
> lighting soft
> save
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231025_Figure_2.cxs
——— End of log from Thu Oct 26 16:19:56 2023 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain #4/R
Alignment identifier is 4/R
> select #4/R:155-156
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #4/R:149-156
64 atoms, 65 bonds, 8 residues, 1 model selected
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> select #4/R:185-186
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #4/R:183-186
33 atoms, 35 bonds, 4 residues, 1 model selected
> select #4/R:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:178-182
42 atoms, 44 bonds, 5 residues, 1 model selected
> select #4/R:181
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/R:181
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/R:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:179
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/R:179
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/R:199
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/R:199
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/R:179-199
171 atoms, 180 bonds, 21 residues, 1 model selected
> color sel light sea green
> select #4/R:246
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:246
6 atoms, 5 bonds, 1 residue, 1 model selected
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> color sel byhetero
> select #4/R:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:71
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> color sel byhetero
> select #4/R:198
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:198
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:199
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/R:179-199
171 atoms, 180 bonds, 21 residues, 1 model selected
> color sel byhetero
> select #4/R:150-151
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #4/R:150-151
17 atoms, 16 bonds, 2 residues, 1 model selected
> view sel
> view
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R
Alignment identifier is 1/R
> select #1/R:175-176
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/R:175-192
140 atoms, 143 bonds, 18 residues, 1 model selected
> select #1/R:193
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:175-193
147 atoms, 151 bonds, 19 residues, 1 model selected
> color sel light sea green
> select
> #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
1625 atoms, 1653 bonds, 210 residues, 1 model selected
> select #1/R:175-193
147 atoms, 151 bonds, 19 residues, 1 model selected
> color sel byhetero
> select
> #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
1625 atoms, 1653 bonds, 210 residues, 1 model selected
> select #1/R:150
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/R:150
6 atoms, 5 bonds, 1 residue, 1 model selected
> select
> #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
1625 atoms, 1653 bonds, 210 residues, 1 model selected
> select #1/R:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
1625 atoms, 1653 bonds, 210 residues, 1 model selected
> select #1/R:194
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel light sea green
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:198
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:198-218
168 atoms, 170 bonds, 21 residues, 1 model selected
> color sel light sea green
> color sel byhetero
> select
> #2/A:55-87,92-121,128-162,165-170,172-197,209-213,219-249,254-291,296-327,332-339
1950 atoms, 1992 bonds, 244 residues, 1 model selected
> select #2/A:252
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:252
11 atoms, 10 bonds, 1 residue, 1 model selected
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:166-167
21 atoms, 22 bonds, 2 residues, 1 model selected
> select #3/A:166-187
191 atoms, 203 bonds, 22 residues, 1 model selected
> color sel light sea green
> color sel byhetero
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:108
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:108
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:166-167
21 atoms, 22 bonds, 2 residues, 1 model selected
> select #3/A:166-186
184 atoms, 196 bonds, 21 residues, 1 model selected
> select #3/A:187
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:166-187
191 atoms, 203 bonds, 22 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select #3/A:249
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:249
11 atoms, 10 bonds, 1 residue, 1 model selected
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:198
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:198-215
148 atoms, 150 bonds, 18 residues, 1 model selected
> select #2/A:218
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:198-218
168 atoms, 170 bonds, 21 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select #2/A:252
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:252
11 atoms, 10 bonds, 1 residue, 1 model selected
QMainWindowLayout::tabPosition called with out-of-bounds value '0'
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R
Alignment identifier is 1/R
> select #1/R:175
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:175-194
155 atoms, 159 bonds, 20 residues, 1 model selected
> select #1/R:175-176
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/R:175-193
147 atoms, 151 bonds, 19 residues, 1 model selected
> select #1/R:175
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:175-194
155 atoms, 159 bonds, 20 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select
> #1/R:45-72,77-103,112-144,153-174,194-206,209-237,247-274,280-302,305-311
1625 atoms, 1653 bonds, 210 residues, 1 model selected
> select #1/R:207
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:207
8 atoms, 7 bonds, 1 residue, 1 model selected
> view
> ui tool show "Show Sequence Viewer"
> sequence chain #4/R
Alignment identifier is 4/R
> select #4/R:179
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/R:179-199
171 atoms, 180 bonds, 21 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select #4/R:245-246
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #4/R:245-246
13 atoms, 13 bonds, 2 residues, 1 model selected
> save
> C:/Users/Midget/OneDrive/MIPS/papers/GPR_mini_review/Figures/20231026_Figure_2.cxs
——— End of log from Thu Oct 26 20:27:55 2023 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> color sel cornflower blue
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel #5582ffff
> color sel byhetero
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select clear
> select #3/A:271
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:271
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:272
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:272
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:275
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:275
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #3/A:276
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:276
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #3/A:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #3/A:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #3/A:65
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:65-277
1635 atoms, 1691 bonds, 1 pseudobond, 198 residues, 2 models selected
> select #3/A:224
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:188-224
310 atoms, 319 bonds, 37 residues, 1 model selected
> select #3/A:271
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:271
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> select #3/A:271
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:271
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel #aaaa7fff target a
> style sel stick
Changed 12 atom styles
> color sel byhetero
> select clear
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel byhetero
> color sel #acac80ff
> color sel #b8b889ff
> color sel #b9b98aff
> color sel #bdbd8dff
> color sel #bfbf8eff
> color sel #c2c291ff
> color sel #c3c391ff
> undo
[Repeated 2 time(s)]
> color sel #5582ffff
> ui tool show "Color Actions"
> color sel #aaaa7fff target a
> color sel #acac80ff target a
> color sel #adad81ff target a
> color sel #c7c794ff target a
> color sel #caca97ff target a
> color sel #cbcb97ff target a
> color sel #cfcf9aff target a
> color sel #d0d09bff target a
> color sel #d1d19cff target a
> color sel #d5d59fff target a
> color sel #d8d8a1ff target a
> color sel #d9d9a2ff target a
> color sel #dadaa2ff target a
> color sel #dcdca4ff target a
> color sel #dddda5ff target a
> color sel #d6d69fff target a
> color sel #c8c895ff target a
> color sel #c7c794ff target a
> color sel #c6c694ff target a
> color sel #c3c391ff target a
> select #3/A:271
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:271
12 atoms, 12 bonds, 1 residue, 1 model selected
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:268
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel byhetero target a
[Repeated 1 time(s)]
> color sel byhetero
> select ~sel
8851 atoms, 9104 bonds, 3 pseudobonds, 1104 residues, 7 models selected
> select clear
> select #3/A:271
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:271
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:105
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:105
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:117
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:117
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #4/R:122
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:122
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #4/R:125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:125
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #4/R:304
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #4/R:304
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #4/R:303
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/R:303
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #4/R:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:307
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> select #4/R:121
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:121
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #4/R:122
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:122
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:110
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:110
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #4/R:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> hide sel atoms
> select #4/R:110
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:110
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/R:199-200
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #4/R:199
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #4/R:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #4/R:111
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:111
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #4/R:192
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #4/R:192
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #4/R:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:176
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:176
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #4/R:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> hide sel atoms
> select #4/R:173
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:173
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #4/R:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:183
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #4/R:190
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:190
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #4/R:300
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:300
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #3/A:287
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:287
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #3/A:291
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:291
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #3/A:290
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:290
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #3/A:187
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:187
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #4/R:289
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/R:289
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #3/A:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #3/A:180
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:180
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #3/A:99
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:99
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> select #3/A:178
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:178
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:105
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:105
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:179
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/R:179
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/R:175
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:175
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:179-180
18 atoms, 19 bonds, 2 residues, 1 model selected
> select #4/R:179-181
22 atoms, 23 bonds, 3 residues, 1 model selected
> select #4/R:190
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:190
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/R:309
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:273-309
315 atoms, 326 bonds, 37 residues, 1 model selected
> select
> #4/R:37-68,74-104,108-145,154-178,191-196,200-244,266-290,295-321,323-337
1983 atoms, 2034 bonds, 244 residues, 1 model selected
> select #4/R:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:187
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/R:187
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 4 atom styles
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 4 atom styles
> color sel byhetero
> select #4/R:188
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:188-189
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #4/R:155-191
309 atoms, 322 bonds, 37 residues, 1 model selected
> select #4/R:43-191
1185 atoms, 1221 bonds, 149 residues, 1 model selected
> select #4/R:43
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/R:43
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> hide sel atoms
> select #4/R:175
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/R:175
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:171
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:171-172
11 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select #3/A:165
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:165
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:161
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:161
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select #3/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> save
> C:/Users/fbumb/OneDrive/MIPS/papers/GPR_mini_review/Figures/20240206_Figure_2.cxs
——— End of log from Tue Feb 6 18:08:29 2024 ———
opened ChimeraX session
> open 8KH4
Summary of feedback from opening 8KH4 fetched from pdb
---
note | Fetching compressed mmCIF 8kh4 from http://files.rcsb.org/download/8kh4.cif
8kh4 title:
Cryo-EM structure of the GPR161-Gs complex [more info...]
Chain information for 8kh4 #5
---
Chain | Description | UniProt
A | G-protein coupled receptor 161 | GP161_HUMAN 2-348
B | Guanine nucleotide-binding protein G(olf) subunit alpha,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAL_HUMAN 5-195, GNAS2_HUMAN 204-394
C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
E | Nanobody 35 |
Non-standard residues in 8kh4 #5
---
CLR — cholesterol
> select #5/A
2076 atoms, 2142 bonds, 1 pseudobond, 267 residues, 2 models selected
> cartoon (#!5 & sel)
> surface hidePatches (#!5 & sel)
> select add #5
7511 atoms, 7684 bonds, 2 pseudobonds, 1002 residues, 2 models selected
> select subtract #5
Nothing selected
> select add #5
7511 atoms, 7684 bonds, 2 pseudobonds, 1002 residues, 2 models selected
> cartoon (#!5 & sel)
> hide (#!5 & sel) target a
> surface hidePatches (#!5 & sel)
> select #5/E
936 atoms, 958 bonds, 127 residues, 1 model selected
> cartoon hide sel
> select #5/D
265 atoms, 267 bonds, 44 residues, 1 model selected
> select #5/C
2425 atoms, 2471 bonds, 336 residues, 1 model selected
> cartoon hide sel
> select #5/D
265 atoms, 267 bonds, 44 residues, 1 model selected
> cartoon hide sel
> select #5/B
1809 atoms, 1846 bonds, 1 pseudobond, 228 residues, 2 models selected
> cartoon hide (#!5 & sel)
> tile columns 2
5 models tiled
> tile columns 1
5 models tiled
> tile rows 1
Expected a models specifier or a keyword
> tile rows 0
Expected a models specifier or a keyword
> tile columns 0
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/tile.py", line 32, in tile
row, col = divmod(i, columns)
^^^^^^^^^^^^^^^^^^
ZeroDivisionError: integer division or modulo by zero
ZeroDivisionError: integer division or modulo by zero
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/tile.py", line 32, in tile
row, col = divmod(i, columns)
^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> tile columns 1
5 models tiled
> tile columns 2
5 models tiled
> tile columns 3
5 models tiled
> tile columns 5
5 models tiled
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR17_7y89.pdb, chain A (#2),
sequence alignment score = 311.8
RMSD between 118 pruned atom pairs is 1.154 angstroms; (across all 256 pairs:
5.669)
> matchmaker #!3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR21_8hmv.pdb, chain A (#3),
sequence alignment score = 398.2
RMSD between 136 pruned atom pairs is 1.140 angstroms; (across all 255 pairs:
4.042)
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR12_Gs.pdb, chain R (#1) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 369.8
RMSD between 122 pruned atom pairs is 1.221 angstroms; (across all 258 pairs:
5.085)
> matchmaker #!5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR12_Gs.pdb, chain R (#1) with 8kh4, chain A (#5), sequence
alignment score = 317.9
RMSD between 99 pruned atom pairs is 1.217 angstroms; (across all 248 pairs:
4.726)
> matchmaker #!5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR12_Gs.pdb, chain R (#1) with 8kh4, chain A (#5), sequence
alignment score = 317.9
RMSD between 99 pruned atom pairs is 1.217 angstroms; (across all 248 pairs:
4.726)
> tile columns 5
5 models tiled
> color #5 #9437ffff
> color #5 #941751ff
> color #5 #945200ff
> color #5 #ff9300ff
> color #5 #e03d2cff
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:121
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:121-129
76 atoms, 77 bonds, 9 residues, 1 model selected
> select #5/A:129
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:121-129
76 atoms, 77 bonds, 9 residues, 1 model selected
> ui mousemode right select
> select clear
> select #5/A:156
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:154-156
24 atoms, 24 bonds, 3 residues, 1 model selected
> select #5/A:27-91,96-131,134-165,185-219,267-297,302-338
1805 atoms, 1852 bonds, 236 residues, 1 model selected
> select #5/A:169-172,177-180
61 atoms, 60 bonds, 8 residues, 1 model selected
> select #5/A:166
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:166-184
157 atoms, 163 bonds, 19 residues, 1 model selected
> color sel cyan
Drag select of 13 residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right rotate
> tile spacingFactor 0.5 columns 5
5 models tiled
> tile spacingFactor 0.4 columns 5
5 models tiled
> tile spacingFactor 0.7 columns 5
5 models tiled
> ui mousemode right translate
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:169-172,177-180
61 atoms, 60 bonds, 8 residues, 1 model selected
> select #5/A:27-91,96-131,134-165,185-219,267-297,302-338
1805 atoms, 1852 bonds, 236 residues, 1 model selected
> select #5/A:169-172,177-180
61 atoms, 60 bonds, 8 residues, 1 model selected
> select sequence 178
Nothing selected
> select sequence C178
Nothing selected
> select sequence C178
Nothing selected
> select sequence C
442 atoms, 375 bonds, 74 residues, 5 models selected
> help help:user/findseq.html
> ui mousemode right select
> select clear
> select #5/A:169-172,177-180
61 atoms, 60 bonds, 8 residues, 1 model selected
> select #5/A:174-175
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #5/A:174-178
48 atoms, 50 bonds, 5 residues, 1 model selected
> select #5/A:181-182
19 atoms, 20 bonds, 2 residues, 1 model selected
> select #5/A:174-182
79 atoms, 83 bonds, 9 residues, 1 model selected
> select #5/A:178
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:178
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 6 atom styles
> color sel byelement
> select clear
[Repeated 1 time(s)]
> save "/Users/dongju/Desktop/Research projects-Monash/NRE/Fig2 with 161.aln"
> color #5 #ff2600ff
Drag select of 19 residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right zoom
> ui mousemode right rotate
> ui mousemode right zoom
> ui mousemode right rotate
> ui mousemode right translate
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> tile spacingFactor 0.8 columns 5
5 models tiled
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right rotate
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right zoom
> ui mousemode right translate
> select #5/A:169-172,177-180
61 atoms, 60 bonds, 8 residues, 1 model selected
> select #5/A:180
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:172-180
73 atoms, 75 bonds, 9 residues, 1 model selected
> select #5/A:166-167
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/A:166-184
157 atoms, 163 bonds, 19 residues, 1 model selected
> color sel cyan
> select #5/A:178
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:178
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> show sel target ab
> color sel byelement
> ui mousemode right select
> select clear
> select #5/A:182-183
24 atoms, 26 bonds, 2 residues, 1 model selected
> select #5/A:183
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:182-183
24 atoms, 26 bonds, 2 residues, 1 model selected
> select #5/A:182-183
24 atoms, 26 bonds, 2 residues, 1 model selected
> select #5/A:182
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 14 atom styles
> color sel byelement
> select clear
[Repeated 1 time(s)]Drag select of 3 residues
> select clear
[Repeated 1 time(s)]
> select #5/A:182
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel light sea green
> color sel cyan
> color sel byhetero
> select clear
> select #5/A:178
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:178
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:182
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/A:182
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/A:178
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:178
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
Drag select of 10 residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right "translate selected models"
> select #5/A:178
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel cyan
> color sel byhetero
> ui mousemode right select
> select clear
> select #5/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 7 atom styles
> select clear
> select #5/A:189@CB
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right translate
> color #5 #de723dff
> color #5 #e07139ff
> color #5 #e56c2fff
> color #5 #ea692dff
> select #5/A:166-167
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/A:166-184
157 atoms, 163 bonds, 19 residues, 1 model selected
> color sel cyan
> select #5/A:178
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 6 atom styles
> color sel byhetero
> select #5/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:189
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel stick
Changed 7 atom styles
> color sel forest green
> color sel lime
> color sel medium blue
> color sel byhetero
> select #5/A:182-183
24 atoms, 26 bonds, 2 residues, 1 model selected
> select #5/A:182-183
24 atoms, 26 bonds, 2 residues, 1 model selected
> select #5/A:182
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/A:182
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel byhetero
> save "/Users/dongju/Desktop/Research projects-Monash/NRE/Figure2_DL/Aligned
> overall_17_21_52_161.cxs"
> ui mousemode right select
> select clear
> select #5/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:177
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:177
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:177
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:177
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:177,179
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 15 atom styles
> color sel byhetero
> select clear
> select #5/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:179
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
[Repeated 4 time(s)]
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right rotate
[Repeated 1 time(s)]
> ui mousemode right select
> select clear
Drag select of 24 residues
> select clear
> ui tool show "Side View"
> volume region all imageMode "full region"
No volumes specified
> view orient
> view
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right "move planes"
> ui mousemode right "rotate slab"
> ui mousemode right "move planes"
> ui mousemode right rotate
> ui mousemode right "move planes"
> view orient
[Repeated 2 time(s)]
> tile spacingFactor 0.8 columns 5
5 models tiled
> ui mousemode right translate
> save "/Users/dongju/Desktop/Research projects-Monash/NRE/Figure2_DL/Aligned
> overall_17_21_52_161.cxs"
——— End of log from Wed Feb 14 23:29:37 2024 ———
opened ChimeraX session
> close #1
> close #2
> close #5
> save "/Users/dongju/Desktop/Research projects-
> Monash/NRE/Figure2_DL/Fig2B_GPR21 and 52.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> sequence chain #4/R
Alignment identifier is 4/R
> transparency #3 90 ribbons
> lighting soft
> graphics silhouettes false
> lighting simple
> transparency #3 0 ribbons
> ui mousemode right select
> select #3/A:180
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:181-182
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/A:181-186
50 atoms, 52 bonds, 6 residues, 1 model selected
> select #3/A:180
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:180-270
654 atoms, 676 bonds, 1 pseudobond, 76 residues, 2 models selected
> select clear
> select
> #3/A:30-55,63-90,97-133,136-165,173-177,188-233,250-278,282-306,308-317
1922 atoms, 1966 bonds, 236 residues, 1 model selected
> select clear
> select #3/A:180
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:180-278
721 atoms, 745 bonds, 1 pseudobond, 84 residues, 2 models selected
> select clear
[Repeated 1 time(s)]
> select #3/A:164@CB
1 atom, 1 residue, 1 model selected
> select #3/A:166
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:166
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/A:164@CB
12 atoms, 11 bonds, 2 residues, 1 model selected
> select add #3/A:167
22 atoms, 21 bonds, 3 residues, 1 model selected
> select add #3/A:168
36 atoms, 36 bonds, 4 residues, 1 model selected
> select add #3/A:169
40 atoms, 39 bonds, 5 residues, 1 model selected
> select add #3/A:170
49 atoms, 47 bonds, 6 residues, 1 model selected
> select add #3/A:171
56 atoms, 54 bonds, 7 residues, 1 model selected
> select add #3/A:172
60 atoms, 57 bonds, 8 residues, 1 model selected
> select add #3/A:173
72 atoms, 69 bonds, 9 residues, 1 model selected
> select add #3/A:174
82 atoms, 79 bonds, 10 residues, 1 model selected
> select add #3/A:175
86 atoms, 82 bonds, 11 residues, 1 model selected
> select add #3/A:176
94 atoms, 89 bonds, 12 residues, 1 model selected
> select add #3/A:177
101 atoms, 95 bonds, 13 residues, 1 model selected
> select add #3/A:178
112 atoms, 106 bonds, 14 residues, 1 model selected
> select add #3/A:179
121 atoms, 114 bonds, 15 residues, 1 model selected
> select add #3/A:180
135 atoms, 129 bonds, 16 residues, 1 model selected
> select add #3/A:181
141 atoms, 134 bonds, 17 residues, 1 model selected
> select add #3/A:183
150 atoms, 142 bonds, 18 residues, 1 model selected
> select add #3/A:184
156 atoms, 147 bonds, 19 residues, 1 model selected
> select add #3/A:185
170 atoms, 162 bonds, 20 residues, 1 model selected
> select add #3/A:186
180 atoms, 172 bonds, 21 residues, 1 model selected
> select add #3/A:187
187 atoms, 178 bonds, 22 residues, 1 model selected
> select add #3/A:99@CB
188 atoms, 178 bonds, 23 residues, 1 model selected
> select add #3/A:102
194 atoms, 184 bonds, 24 residues, 1 model selected
> select add #3/A:105@CB
195 atoms, 184 bonds, 25 residues, 1 model selected
> select add #3/A:105@CZ
196 atoms, 185 bonds, 25 residues, 1 model selected
> select add #3/A:161
207 atoms, 196 bonds, 26 residues, 1 model selected
> select add #3/A:275
216 atoms, 204 bonds, 27 residues, 1 model selected
> select add #3/A:287
227 atoms, 215 bonds, 28 residues, 1 model selected
> select add #3/A:290
234 atoms, 221 bonds, 29 residues, 1 model selected
> select add #3/A:268
246 atoms, 233 bonds, 30 residues, 1 model selected
> select add #3/A:271
258 atoms, 245 bonds, 31 residues, 1 model selected
> select add #3/A:291
272 atoms, 260 bonds, 32 residues, 1 model selected
> select add #3/A:109
279 atoms, 266 bonds, 33 residues, 1 model selected
> select add #3/A:113
288 atoms, 274 bonds, 34 residues, 1 model selected
Drag select of 19 atoms, 21 residues, 16 bonds
Drag select of 2 residues
> select #3/A:173
12 atoms, 12 bonds, 1 residue, 1 model selected
Drag select of 9 atoms, 10 residues, 8 bonds
> select #3/A:166
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:167
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3/A:166
21 atoms, 21 bonds, 2 residues, 1 model selected
> select add #3/A:168
35 atoms, 36 bonds, 3 residues, 1 model selected
> select add #3/A:169
39 atoms, 39 bonds, 4 residues, 1 model selected
> select #3/A:170
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:170-173
32 atoms, 33 bonds, 4 residues, 1 model selected
> select #3/A:166
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:166-179
120 atoms, 127 bonds, 14 residues, 1 model selected
> select #3/A:180
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/A:180-187
71 atoms, 75 bonds, 8 residues, 1 model selected
> select #3/A:180-201
190 atoms, 198 bonds, 22 residues, 1 model selected
> select #3/A:180-201
190 atoms, 198 bonds, 22 residues, 1 model selected
> select #3/A:180-201
190 atoms, 198 bonds, 22 residues, 1 model selected
> select #3/A:201
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:188-201
119 atoms, 122 bonds, 14 residues, 1 model selected
> select #3/A:165-166
22 atoms, 23 bonds, 2 residues, 1 model selected
> select #3/A:166-187
191 atoms, 203 bonds, 22 residues, 1 model selected
> name frozen ECL2 sel
> select clear
> select ECL2
191 atoms, 203 bonds, 22 residues, 1 model selected
> name frozen GPR21_ECL2 sel
> select clear
Drag select of 2 atoms, 5 residues, 1 bonds
> select clear
[Repeated 1 time(s)]
> select #3/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:161
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/A:164
17 atoms, 16 bonds, 2 residues, 1 model selected
> select add #3/A:268
29 atoms, 28 bonds, 3 residues, 1 model selected
> select add #3/A:272
40 atoms, 39 bonds, 4 residues, 1 model selected
> select add #3/A:271
52 atoms, 51 bonds, 5 residues, 1 model selected
> select add #3/A:275
61 atoms, 59 bonds, 6 residues, 1 model selected
> select add #3/A:276
67 atoms, 64 bonds, 7 residues, 1 model selected
> select add #3/A:110
73 atoms, 69 bonds, 8 residues, 1 model selected
Drag select of 1 atoms, 3 residues, 1 bonds
Drag select of 3 residues
> select clear
[Repeated 3 time(s)]
> select #3/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #3/A:276
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #3/A:275
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #3/A:272
32 atoms, 29 bonds, 4 residues, 1 model selected
> select add #3/A:271
44 atoms, 41 bonds, 5 residues, 1 model selected
> select add #3/A:105
55 atoms, 52 bonds, 6 residues, 1 model selected
> select add #3/A:99
61 atoms, 57 bonds, 7 residues, 1 model selected
> select add #3/A:290
68 atoms, 63 bonds, 8 residues, 1 model selected
> select add #3/A:110
74 atoms, 68 bonds, 9 residues, 1 model selected
> select add #3/A:287
85 atoms, 79 bonds, 10 residues, 1 model selected
> select add #3/A:161@CA
86 atoms, 79 bonds, 11 residues, 1 model selected
> select subtract #3/A:161
85 atoms, 79 bonds, 10 residues, 1 model selected
> select add #3/A:161
96 atoms, 90 bonds, 11 residues, 1 model selected
> select add #3/A:109
103 atoms, 96 bonds, 12 residues, 1 model selected
> select add #3/A:291
117 atoms, 111 bonds, 13 residues, 1 model selected
> select add #3/A:268
129 atoms, 123 bonds, 14 residues, 1 model selected
> select add #3/A:113
138 atoms, 131 bonds, 15 residues, 1 model selected
> select add #3/A:102
144 atoms, 136 bonds, 16 residues, 1 model selected
> name frozen "GPR21_binding sites" sel
Not registering illegal selector name "GPR21_binding sites"
> name frozen "GPR21_binding sites" sel
Not registering illegal selector name "GPR21_binding sites"
> name frozen GPR21_BS sel
[Repeated 1 time(s)]
> select GPR21_ECL2
191 atoms, 203 bonds, 22 residues, 1 model selected
> transparency #3 90 ribbons
> select ECL2
191 atoms, 203 bonds, 22 residues, 1 model selected
> transparency #3:select 0 ribbons
> transparency #3:select/ 0 ribbons
Missing or invalid "percent" argument: Expected a number
> transparency #3:select 0 ribbons
[Repeated 1 time(s)]
> select GPR21_BS
144 atoms, 140 bonds, 16 residues, 1 model selected
> transparency #3:select 0 ribbons
> transparency #3:select/R 0 ribbons
> transparency #3:select/ 0 ribbons
Missing or invalid "percent" argument: Expected a number
> transparency #3:select 0 ribbons
> transparency #3:select 70 ribbons
> transparency #3:select 0 ribbons
> transparency #3 0 ribbons
> transparency #3/select 90 ribbons
> transparency #3:select 90 ribbons
[Repeated 1 time(s)]
> select #3/A:37
11 atoms, 11 bonds, 1 residue, 1 model selected
> transparency #3:select 90 ribbons
> select GPR21_BS
144 atoms, 140 bonds, 16 residues, 1 model selected
> transparency select 90 ribbons
Missing or invalid "percent" argument: Expected a number
> transparency #3:GPR21_BS GPR21_ECL2 90 ribbons
Missing or invalid "percent" argument: Expected a number
> transparency #3:GPR21_BS/GPR21_ECL2 90 ribbons
> transparency #3:select/GPR21_BS/GPR21_ECL2 90 ribbons
> transparency select/ 90 ribbons
Missing or invalid "percent" argument: Expected a number
> transparency select/ 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #select/ 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #select 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #3:select 90 ribbons
> transparency #3:select/ 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #3:select> 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #3:select transparency #3: transparency #3:>select 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency transparency select> 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency ~select 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #3:~select 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #3:~select/ 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #3~select 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency ~select 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency ~select/ 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency ~select 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #3~select 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency ~select 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency [~select] 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #3:~select 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency #3:~select/ 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency ~sele 90 ribbon
Missing or invalid "percent" argument: Expected a number
> transparency ~select 90 all
Missing or invalid "percent" argument: Expected a number
> transparency #3:~select 90 all
Missing or invalid "percent" argument: Expected a number
> transparency ~$select 90 ribbons
Missing or invalid "percent" argument: Expected a number
> transparency $select 90 ribbons
Missing or invalid "percent" argument: Expected a number
> transparency ~select$ 90 ribbons
Missing or invalid "percent" argument: Expected a number
> select clear
> select #3/A:216
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3/A:220
20 atoms, 18 bonds, 2 residues, 1 model selected
> color sel red
> select clear
> select GPR21_ECL2
191 atoms, 203 bonds, 22 residues, 1 model selected
> transparency sel 90 All
> transparency sel 0 All
> select #3/A:216
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3/A:220
20 atoms, 18 bonds, 2 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #3/A:216
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3/A:220
20 atoms, 18 bonds, 2 residues, 1 model selected
> color sel #5780ffff
> select clear
> transparency #3 90 ribbons
> select GPR21_BS
144 atoms, 140 bonds, 16 residues, 1 model selected
> transparency sel 0 ribbons
> select GPR21_ECL2
191 atoms, 203 bonds, 22 residues, 1 model selected
> transparency sel 0 ribbons
> select clear
[Repeated 2 time(s)]Drag select of 4 atoms, 8 residues, 3 bonds
> select #4/R:179
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/R:179-180
18 atoms, 19 bonds, 2 residues, 1 model selected
> select #4/R:179-209
248 atoms, 260 bonds, 31 residues, 1 model selected
> select #4/R:179-209
248 atoms, 260 bonds, 31 residues, 1 model selected
> select #4/R:179-209
248 atoms, 260 bonds, 31 residues, 1 model selected
> name frozen GPR52_ECL2 sel
> select clear
> select #4/R:117
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #4/R:176
17 atoms, 16 bonds, 2 residues, 1 model selected
> select add #4/R:173
28 atoms, 27 bonds, 3 residues, 1 model selected
> select add #4/R:122
34 atoms, 32 bonds, 4 residues, 1 model selected
> select add #4/R:125
43 atoms, 40 bonds, 5 residues, 1 model selected
> select add #4/R:121
51 atoms, 47 bonds, 6 residues, 1 model selected
> select add #4/R:284
63 atoms, 59 bonds, 7 residues, 1 model selected
> select add #4/R:281
75 atoms, 71 bonds, 8 residues, 1 model selected
> select add #4/R:305
83 atoms, 79 bonds, 9 residues, 1 model selected
> select subtract #4/R:305
75 atoms, 72 bonds, 8 residues, 1 model selected
> select add #4/R:304
89 atoms, 87 bonds, 9 residues, 1 model selected
> select add #4/R:300
100 atoms, 98 bonds, 10 residues, 1 model selected
> select add #4/R:288
109 atoms, 106 bonds, 11 residues, 1 model selected
> select add #4/R:307
117 atoms, 113 bonds, 12 residues, 1 model selected
> select add #4/R:285
128 atoms, 123 bonds, 13 residues, 1 model selected
Drag select of 7 atoms, 5 residues, 6 bonds
> select add #4/R:111@CA
44 atoms, 6 bonds, 7 residues, 1 model selected
> select add #4/R:176
50 atoms, 11 bonds, 8 residues, 1 model selected
> select add #4/R:173
61 atoms, 22 bonds, 9 residues, 1 model selected
> select add #4/R:125
70 atoms, 30 bonds, 10 residues, 1 model selected
> select add #4/R:122
76 atoms, 35 bonds, 11 residues, 1 model selected
> select add #4/R:282
84 atoms, 42 bonds, 12 residues, 1 model selected
> select subtract #4/R:282
76 atoms, 35 bonds, 11 residues, 1 model selected
> select add #4/R:281
88 atoms, 47 bonds, 12 residues, 1 model selected
> select add #4/R:285
99 atoms, 58 bonds, 13 residues, 1 model selected
> select add #4/R:307@CA
100 atoms, 58 bonds, 14 residues, 1 model selected
> select subtract #4/R:307@CA
99 atoms, 58 bonds, 13 residues, 1 model selected
> select add #4/R:307
107 atoms, 65 bonds, 14 residues, 1 model selected
> select add #4/R:121
115 atoms, 72 bonds, 15 residues, 1 model selected
> select add #4/R:304
129 atoms, 87 bonds, 16 residues, 1 model selected
> select add #4/R:300
140 atoms, 98 bonds, 17 residues, 1 model selected
> select add #4/R:289
146 atoms, 103 bonds, 18 residues, 1 model selected
> select add #4/R:303
153 atoms, 109 bonds, 19 residues, 1 model selected
> select add #4/R:284
165 atoms, 121 bonds, 20 residues, 1 model selected
> name frozen GPR52_BS sel
> transparency #4 90 ribbons
> select GPR52_BS
165 atoms, 161 bonds, 20 residues, 1 model selected
> transparency sel 0 ribbons
> select GPR52_ECL2
248 atoms, 263 bonds, 31 residues, 1 model selected
> transparency sel 0 ribbons
> select clear
Drag select of 5 atoms, 26 residues, 4 bonds
> tile Spaingfactor 2 columns 2
Expected a models specifier or a keyword
> tile Spaingfactor 80 columns 2
Expected a models specifier or a keyword
> tile Spaingfactor 0.8 columns 2
Expected a models specifier or a keyword
> tile spacingFactor 2 columns 2
2 models tiled
> tile spacingFactor 9 columns 2
2 models tiled
> tile spacingFactor 0.5 columns 2
2 models tiled
> tile spacingFactor 0.8 columns 2
2 models tiled
> select clear
[Repeated 1 time(s)]
> tile spacingFactor 0.7 columns 2
2 models tiled
> ui tool show Matchmaker
> matchmaker #!4 to #3
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 GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 1120.2
RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
2.619)
> matchmaker #!4 to #3
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 GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 1120.2
RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
2.619)
Drag select of 7 atoms, 15 residues, 7 bonds
> select clear
> tile spacingFactor 0.7 columns 2
2 models tiled
> tile spacingFactor 0.6 columns 2
2 models tiled
> ui mousemode right zoom
> lighting soft
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting soft
> lighting full
> graphics silhouettes false
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> select GPR21_BS
144 atoms, 140 bonds, 16 residues, 1 model selected
> transparency sel 90 ribbons
> select GPR52_BS
165 atoms, 161 bonds, 20 residues, 1 model selected
> transparency sel 90 ribbons
> ui mousemode right select
> select clear
> select GPR52_ECL2
248 atoms, 263 bonds, 31 residues, 1 model selected
Drag select of 43 atoms, 30 residues, 37 bonds
> select clear
> select GPR52_ECL2
248 atoms, 263 bonds, 31 residues, 1 model selected
> select #4/R:114
6 atoms, 5 bonds, 1 residue, 1 model selected
> select GPR52_ECL2
248 atoms, 263 bonds, 31 residues, 1 model selected
> select add #4/R:114
254 atoms, 266 bonds, 32 residues, 1 model selected
> select subtract #4/R:114
248 atoms, 260 bonds, 31 residues, 1 model selected
> select subtract #4/R:200
242 atoms, 253 bonds, 30 residues, 1 model selected
> select subtract #4/R:201
237 atoms, 248 bonds, 29 residues, 1 model selected
> select subtract #4/R:202
225 atoms, 235 bonds, 28 residues, 1 model selected
> select subtract #4/R:203
214 atoms, 223 bonds, 27 residues, 1 model selected
> select subtract #4/R:204
207 atoms, 216 bonds, 26 residues, 1 model selected
> select subtract #4/R:205
203 atoms, 212 bonds, 25 residues, 1 model selected
> select subtract #4/R:206
192 atoms, 200 bonds, 24 residues, 1 model selected
> select subtract #4/R:208
185 atoms, 192 bonds, 23 residues, 1 model selected
> select subtract #4/R:207
177 atoms, 185 bonds, 22 residues, 1 model selected
> select subtract #4/R:209
171 atoms, 180 bonds, 21 residues, 1 model selected
> name frozen GPR52_ECL2 sel
> select GPR52_ECL2
171 atoms, 180 bonds, 21 residues, 1 model selected
> select clear
> select add #4/R:114
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #4/R:200
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #4/R:201
17 atoms, 14 bonds, 3 residues, 1 model selected
> select add #4/R:202
29 atoms, 26 bonds, 4 residues, 1 model selected
> select add #4/R:203
40 atoms, 37 bonds, 5 residues, 1 model selected
> select add #4/R:204
47 atoms, 43 bonds, 6 residues, 1 model selected
> select add #4/R:205
51 atoms, 46 bonds, 7 residues, 1 model selected
> select add #4/R:206
62 atoms, 57 bonds, 8 residues, 1 model selected
> select add #4/R:207
70 atoms, 64 bonds, 9 residues, 1 model selected
> select add #4/R:208
77 atoms, 70 bonds, 10 residues, 1 model selected
> select add #4/R:209
83 atoms, 75 bonds, 11 residues, 1 model selected
> transparency sel 90 ribbons
> select clear
Drag select of 15 residues
> select clear
> select add #3
2237 atoms, 2308 bonds, 1 pseudobond, 274 residues, 2 models selected
> select add #4
4540 atoms, 4684 bonds, 2 pseudobonds, 558 residues, 4 models selected
> cartoon style (#!3-4 & sel & coil) xsection oval
> cartoon style (#!3-4 & sel) xsection barbell modeHelix default
> cartoon style (#!3-4 & sel) modeHelix tube sides 20
> cartoon style (#!3-4 & sel) xsection rectangle modeHelix default
> cartoon style (#!3-4 & sel) xsection oval modeHelix default
> select clear
> select GPR21_BS
144 atoms, 140 bonds, 16 residues, 1 model selected
> transparency sel 90 All
> select GPR52_BS
165 atoms, 161 bonds, 20 residues, 1 model selected
> transparency sel 90 All
> select clear
[Repeated 1 time(s)]
> tile spacingFactor 0.7 columns 2
2 models tiled
> tile spacingFactor 0.5 columns 2
2 models tiled
> select clear
> ui tool show Matchmaker
> matchmaker #!4 to #3
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 GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 1120.2
RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
2.619)
> matchmaker #!4 to #3
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 GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 1120.2
RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
2.619)
> select #3/A:205
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> tile spacingFactor 0.5 columns 2
2 models tiled
> save "/Users/dongju/Desktop/Research projects-
> Monash/NRE/Figure2_DL/Fig2B_GPR21 and 52.cxs"
——— End of log from Tue Feb 27 18:06:41 2024 ———
opened ChimeraX session
> ui tool show Matchmaker
> matchmaker #!4 to #3
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 GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 1120.2
RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
2.619)
> matchmaker #!4 to #3
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 GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 1120.2
RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
2.619)
> ui tool show "Render by Attribute"
> ui tool show Matchmaker
> matchmaker #!4 to #3
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 GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 1120.2
RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
2.619)
> tile spacingFactor 2 columns 2
2 models tiled
> tile spacingFactor 1 columns 2
2 models tiled
> select GPR52_ECL2
171 atoms, 180 bonds, 21 residues, 1 model selected
> color sel purple
> transparency sel 0 All
> color sel byhetero
> ui mousemode right select
> select add #4/R:112
179 atoms, 187 bonds, 22 residues, 1 model selected
> select subtract #4/R:112
171 atoms, 180 bonds, 21 residues, 1 model selected
> select add #4/R:112
179 atoms, 187 bonds, 22 residues, 1 model selected
> select subtract #4/R:112
171 atoms, 180 bonds, 21 residues, 1 model selected
> select add #4/R:114@SG
172 atoms, 180 bonds, 22 residues, 1 model selected
> select subtract #4/R:114@SG
171 atoms, 180 bonds, 21 residues, 1 model selected
> select add #4/R:113
178 atoms, 186 bonds, 22 residues, 1 model selected
> select subtract #4/R:113
171 atoms, 180 bonds, 21 residues, 1 model selected
> select add #4/R:114@CB
172 atoms, 180 bonds, 22 residues, 1 model selected
> select subtract #4/R:193@SG
171 atoms, 180 bonds, 22 residues, 1 model selected
> select add #4/R:193@SG
172 atoms, 180 bonds, 22 residues, 1 model selected
Drag select of 1 bonds
> select GPR52_ECL2
171 atoms, 180 bonds, 21 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right rotate
[Repeated 2 time(s)]
> ui mousemode right select
> select clear
> select #4/R:114@CB
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> ui mousemode right select
> select #4/R:111@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/R:111@OG
1 atom, 1 residue, 1 model selected
> select #4/R:111@OG
1 atom, 1 residue, 1 model selected
Drag select of 1 residues
> select #4/R:111@OG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> select GPR21_ECL2
191 atoms, 203 bonds, 22 residues, 1 model selected
> color sel medium blue
> color sel byhetero
> ui mousemode right select
> select clear
> ui tool show Matchmaker
> matchmaker #!4 to #3
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 GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 1120.2
RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
2.619)
> matchmaker #!4 to #3
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 GPR21_8hmv.pdb, chain A (#3) with GPR52_6li3.pdb, chain R (#4),
sequence alignment score = 1120.2
RMSD between 224 pruned atom pairs is 1.049 angstroms; (across all 273 pairs:
2.619)
Drag select of 8 residues
> select clear
> ui mousemode right translate
> select GPR52_ECL2
171 atoms, 180 bonds, 21 residues, 1 model selected
> color sel hot pink
> color sel #db8de4ff
> color sel #dc8de4ff
[Repeated 1 time(s)]
> color sel #dd90e5ff
> color sel #dd94e5ff
> color sel #de9ae6ff
> color sel #df9ee6ff
> color sel #e0a1e7ff
> color sel #e1a4e7ff
> color sel #e1a5e8ff
> color sel #e1a6e8ff
> color sel #e1a5e8ff
> color sel #e1a6e7ff
> color sel #e0a6e8ff
> color sel #dfa7e8ff
> color sel #dfa6e8ff
> color sel #dea6e8ff
> color sel #dea4e6ff
> color sel #dc9fe6ff
> color sel #d88de4ff
> color sel #d789e3ff
> color sel #d686e3ff
> color sel #d684e2ff
> color sel #d484e2ff
> color sel #d484e3ff
[Repeated 3 time(s)]
> color sel #d283e3ff
[Repeated 2 time(s)]
> color sel #d384e2ff
[Repeated 1 time(s)]
> color sel #d388e3ff
> color sel #d48ae3ff
> color sel #d58de3ff
[Repeated 2 time(s)]
> color sel #d68ee3ff
> color sel #d791e4ff
> color sel #d896e5ff
> color sel #da98e4ff
> color sel #da98e5ff
> color sel #da99e5ff
> color sel #da9ae5ff
> color sel #db9de6ff
> color sel #dc9fe6ff
> color sel #dda2e6ff
[Repeated 1 time(s)]
> color sel #dea5e7ff
> color sel #dfa9e7ff
> color sel #e0ace8ff
> color sel #e0ade9ff
> color sel #e1aee8ff
> color sel #e0ade9ff
> color sel #e1ade9ff
> color sel #e0abe8ff
> color sel #e1aae8ff
> color sel #e1a9e8ff
[Repeated 3 time(s)]
> color sel #e1a7e8ff
> color sel #e1a8e7ff
> color sel #e0a7e7ff
> color sel #e0a8e7ff
> color sel #dfa7e7ff
[Repeated 3 time(s)]
> color sel #dea6e7ff
> color sel #dea6e8ff
[Repeated 2 time(s)]
> color sel #dda6e8ff
[Repeated 1 time(s)]
> color sel #dca7e8ff
[Repeated 4 time(s)]
> color sel #dca7e7ff
> color sel #dba6e8ff
> color sel #dba6e7ff
> color sel #daa6e8ff
> color sel #daa6e7ff
[Repeated 3 time(s)]
> color sel #daa6e8ff
[Repeated 1 time(s)]
> color sel #d9a7e8ff
> color sel #d8a7e8ff
> color sel #d8a7e7ff
> color sel #d6a7e7ff
[Repeated 1 time(s)]
> color sel #d4a6e7ff
> color sel #d4a7e7ff
> color sel #d4a6e7ff
[Repeated 1 time(s)]
> color sel #d4a7e7ff
> color sel #d3a7e7ff
[Repeated 1 time(s)]
> color sel #d4a9e7ff
> color sel #d6ade8ff
> color sel #d7b2eaff
> color sel #d9b7eaff
> color sel #dbbcebff
> color sel #ddbfecff
> color sel #dec1ecff
[Repeated 1 time(s)]
> color sel #dec2edff
> color sel #dfc3edff
[Repeated 1 time(s)]
> color sel #dec1ecff
> color sel #dbbbebff
> color sel #dab9ebff
> color sel #d8b3eaff
> color sel #d4aae7ff
> color sel #ce99e5ff
> color sel #cc94e4ff
> color sel #cb8fe4ff
> color sel #ca8de3ff
[Repeated 1 time(s)]
> color sel #ca8be3ff
> color sel #c886e3ff
> color sel #c783e2ff
> color sel #c781e2ff
> color sel #c680e1ff
> color sel #c77fe1ff
> color sel #c880e1ff
> color sel #c982e2ff
> color sel #ca85e3ff
> color sel #cb89e3ff
> color sel #cc8be3ff
> color sel #cc8ce3ff
> color sel #cd8ce3ff
[Repeated 2 time(s)]
> color sel #cc8be3ff
> color sel #cc8ae3ff
> color sel #cc89e2ff
> color sel #cb89e2ff
> color sel #cb89e3ff
[Repeated 1 time(s)]
> color sel #c989e3ff
> color sel #c989e2ff
[Repeated 1 time(s)]
> color sel #c889e2ff
> color sel #c88ae2ff
> color sel #c88ae3ff
[Repeated 1 time(s)]
> color sel #c88ae2ff
> color sel #c68ae2ff
> color sel #c689e2ff
> color sel #c489e3ff
> color sel #c387e3ff
> color sel #c085e2ff
> color sel #bf84e2ff
> color sel #bf83e2ff
> color sel #bd82e2ff
> color sel #bc7fe1ff
> color sel #bb7ce1ff
> color sel #ba79e1ff
> color sel #b874e1ff
[Repeated 1 time(s)]
> color sel #b670e1ff
> color sel #b468e0ff
> color sel #b060e1ff
> color sel #ae59e1ff
> color sel #ac56e1ff
> color sel #ab55e1ff
[Repeated 1 time(s)]
> color sel #ac55e1ff
[Repeated 1 time(s)]
> color sel #ad56e1ff
> color sel #ae56e1ff
[Repeated 1 time(s)]
> color sel #af57e1ff
> color sel #b157e1ff
[Repeated 1 time(s)]
> color sel #b359e1ff
> color sel #b35ae1ff
> color sel #b35be1ff
> color sel #b35be0ff
[Repeated 1 time(s)]
> color sel #b35ce0ff
> color sel #b45ce0ff
> color sel #b35ce0ff
[Repeated 1 time(s)]
> color sel #b45ce0ff
> color sel #b55de0ff
> color sel #b660e1ff
> color sel #b766e0ff
> color sel #ba6ce0ff
> color sel #bb70e1ff
> color sel #bb72e1ff
[Repeated 1 time(s)]
> color sel #bc72e1ff
> color sel #bc73e1ff
> color sel #bb73e1ff
> color sel #bc74e0ff
> color sel #ba75e1ff
> color sel #ba75e0ff
> color sel #b976e0ff
> color sel #ba78e1ff
> color sel #ba79e1ff
> color sel #b979e1ff
> color sel #ba7ae1ff
> color sel #b97ae1ff
> color sel #b87ae1ff
> color sel #b77ae1ff
> color sel #b87be1ff
> color sel #bb82e2ff
> color sel #be88e3ff
> color sel #c18fe4ff
> color sel #c699e5ff
> color sel #c79ae4ff
[Repeated 1 time(s)]
> color sel #c899e5ff
[Repeated 1 time(s)]
> color sel #c998e5ff
> color sel #ca99e4ff
> color sel #cb98e4ff
[Repeated 2 time(s)]
> color sel #cb99e4ff
[Repeated 1 time(s)]
> color sel #cb98e5ff
[Repeated 1 time(s)]
> color sel #cb97e5ff
> color sel #cc96e4ff
> color sel #cc95e4ff
[Repeated 1 time(s)]
> color sel #cc94e4ff
> color sel #cc93e4ff
> color sel #cc94e4ff
> color sel #cc93e4ff
> color sel #cd94e4ff
[Repeated 1 time(s)]
> color sel #cc93e4ff
[Repeated 1 time(s)]
> color sel #cc92e4ff
> color sel #cc91e3ff
> color sel #cd91e4ff
> color sel #cd90e4ff
> color sel #cd8fe4ff
> color sel #cd8ee3ff
[Repeated 1 time(s)]
> color sel #cc8be3ff
> color sel #c885e3ff
> color sel #c680e1ff
> color sel #c47ae1ff
> color sel #c377e1ff
> color sel #c376e1ff
[Repeated 2 time(s)]
> color sel #c577e1ff
> color sel #c678e1ff
[Repeated 1 time(s)]
> color sel #c778e2ff
> color sel #c678e1ff
> color sel #c478e1ff
> color sel #c379e1ff
> color sel #c278e1ff
> color sel #c178e1ff
> color sel #be79e1ff
> color sel #be79e2ff
[Repeated 2 time(s)]
> color sel #be7ae1ff
> color sel #bc7be1ff
> color sel #bc7ce1ff
> color sel #bc7ee1ff
[Repeated 3 time(s)]
> color sel #bc7fe1ff
> color sel #bc80e2ff
> color sel #ba80e2ff
[Repeated 2 time(s)]
> color sel #bc80e2ff
> color sel #bd80e2ff
[Repeated 1 time(s)]
> color sel #be81e3ff
> color sel #be81e2ff
> color sel #bf82e3ff
[Repeated 3 time(s)]
> color sel #c182e2ff
[Repeated 2 time(s)]
> color sel #c283e2ff
> color sel #c284e2ff
> color sel #c385e2ff
[Repeated 2 time(s)]
> color sel #c386e2ff
> color sel #c488e3ff
> color sel #c58be2ff
> color sel #c78ee4ff
> color sel #c892e4ff
> color sel #c893e4ff
[Repeated 1 time(s)]
> color sel #c993e4ff
[Repeated 1 time(s)]
> color sel #c994e4ff
> color sel #c996e4ff
> color sel #ca97e5ff
> color sel #cb98e4ff
> color sel #cc9ce5ff
> color sel #cd9ee6ff
[Repeated 1 time(s)]
> color sel #ce9fe6ff
> color sel byhetero
> ui mousemode right select
> select clear
> select GPR21_ECL2
191 atoms, 203 bonds, 22 residues, 1 model selected
> color sel #8393e2ff
> color sel #8b99e3ff
> color sel #929fe4ff
> color sel #99a2e4ff
> color sel #9ca5e5ff
> color sel #9da6e5ff
[Repeated 3 time(s)]
> color sel #9ca8e5ff
[Repeated 5 time(s)]
> color sel #9aa6e5ff
> color sel #97a5e4ff
> color sel #93a2e4ff
> color sel #8e9ee3ff
> color sel #8598e2ff
> color sel #8395e3ff
> color sel #8294e2ff
[Repeated 1 time(s)]
> color sel #8194e2ff
> color sel #8093e2ff
> color sel #7e91e1ff
> color sel #798ee1ff
> color sel #758be1ff
> color sel #6d84e1ff
> color sel #6b83e1ff
> color sel #6983e1ff
> color sel #6982e0ff
> color sel #6882e0ff
[Repeated 1 time(s)]
> color sel #607be0ff
> color sel #5975e0ff
> color sel #5473e1ff
> color sel #5172e1ff
> color sel #4f70e1ff
> color sel #4e70e2ff
[Repeated 1 time(s)]
> color sel #4e6fe2ff
> color sel #4c6ee1ff
> color sel #486be1ff
> color sel #4266e2ff
> color sel #3d62e3ff
> color sel #385fe4ff
> color sel #355de4ff
> color sel #345ce5ff
> color sel #325ce5ff
> color sel #2f59e6ff
> color sel #2e59e6ff
> color sel #2e58e6ff
> color sel #2d58e6ff
> color sel #2d59e6ff
[Repeated 1 time(s)]
> color sel #2e5ae7ff
> color sel #2e5be7ff
> color sel #3061e7ff
> color sel #3161e7ff
> color sel #3163e7ff
> color sel #3164e7ff
> color sel #3266e7ff
> color sel #346ae7ff
> color sel #356fe7ff
> color sel #3670e7ff
> color sel #3773e8ff
> color sel #3874e8ff
> color sel #3774e8ff
> color sel #3874e8ff
[Repeated 1 time(s)]
> color sel #3875e8ff
> color sel #3976e8ff
> color sel #3a7ae8ff
> color sel #3b7be8ff
> color sel #3c7ee8ff
[Repeated 1 time(s)]
> color sel #3d80e8ff
> color sel #3e82e8ff
> color sel #3f84e8ff
[Repeated 1 time(s)]
> color sel #3f85e8ff
[Repeated 1 time(s)]
> color sel #3f84e9ff
> color sel #3d83e9ff
> color sel #3a81ebff
[Repeated 1 time(s)]
> color sel #397feaff
> color sel #3a81eaff
> color sel #3981ecff
> color sel #377eecff
> color sel #367deeff
[Repeated 1 time(s)]
> color sel #347aeeff
> color sel #357ceeff
> color sel #337aefff
> color sel #357defff
> color sel #357ef0ff
> color sel #347cf0ff
> color sel #357df0ff
> color sel #347df0ff
> color sel #347cf0ff
> color sel #347df0ff
[Repeated 1 time(s)]
> color sel #347df1ff
[Repeated 1 time(s)]
> color sel #347df2ff
> color sel #357ef1ff
> color sel #347ef1ff
[Repeated 1 time(s)]
> color sel #347ef2ff
> color sel #3681f2ff
[Repeated 1 time(s)]
> color sel #3682f3ff
> color sel #3581f3ff
> color sel #3580f3ff
[Repeated 1 time(s)]
> color sel #3581f4ff
> color sel #3581f3ff
[Repeated 1 time(s)]
> color sel #3580f5ff
[Repeated 3 time(s)]
> color sel #3581f4ff
> color sel #3581f6ff
> color sel #3581f5ff
[Repeated 1 time(s)]
> color sel #3581f6ff
> color sel #3481f7ff
> color sel #3480f7ff
> color sel #327cf6ff
> color sel #327df6ff
> color sel #327cf6ff
> color sel #2f76f5ff
> color sel #2e75f5ff
> color sel #2d74f5ff
[Repeated 1 time(s)]
> color sel #2e74f4ff
> color sel #2e75f4ff
[Repeated 1 time(s)]
> color sel #2e75f3ff
> color sel #2f76f3ff
[Repeated 1 time(s)]
> color sel #3076f2ff
> color sel #3077f1ff
> color sel #3077f0ff
> color sel #3076efff
> color sel #3075eaff
> color sel #3073e0ff
> color sel #3070d8ff
> color sel #306ecfff
> color sel #306bc9ff
> color sel #2f69c6ff
[Repeated 1 time(s)]
> color sel byhetero
> select clear
> save "/Users/dongju/Desktop/Research projects-
> Monash/NRE/Figure2_DL/Fig2B_GPR21 and 52_focus1.png" width 2000 height 1502
> supersample 3
> save "/Users/dongju/Desktop/Research projects-
> Monash/NRE/Figure2_DL/Fig2B_GPR21 and 52_superimposed.cxs"
> close session
> open 8HS3
8hs3 title:
Gi bound orphan GPR20 in ligand-free state [more info...]
Chain information for 8hs3 #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 1-340
C | Ggama |
R | Soluble cytochrome b562,G-protein coupled receptor 20 | C562_ECOLX -106--1, GPR20_HUMAN 1-358
S | scFv16 |
> open 8HS2
Summary of feedback from opening 8HS2 fetched from pdb
---
note | Fetching compressed mmCIF 8hs2 from http://files.rcsb.org/download/8hs2.cif
8hs2 title:
Orphan GPR20 in complex with Fab046 [more info...]
Chain information for 8hs2 #2
---
Chain | Description | UniProt
B | heavy chain of Fab046 |
C | Light chain of Fab046 |
R | Soluble cytochrome b562,G-protein coupled receptor 20 | C562_ECOLX -98--1, GPR20_HUMAN 1-316
> open 8HSC
Summary of feedback from opening 8HSC fetched from pdb
---
note | Fetching compressed mmCIF 8hsc from http://files.rcsb.org/download/8hsc.cif
8hsc title:
Gi bound Orphan GPR20 complex with Fab046 in ligand-free state [more info...]
Chain information for 8hsc #3
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 1-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
E | light chain of Fab046 |
F | heavy chain of Fab046 |
R | Soluble cytochrome b562,G-protein coupled receptor 20 | C562_ECOLX -98--1, GPR20_HUMAN 1-358
S | scFv16 |
> hide atoms
> show cartoons
> hide atoms
> show cartoons
> hide atoms
> show cartoons
> rename #1 GPR20_Gi
> rename #2 GPR20_Gi_Fab046
> rename #3 GPR20_Gi_Fab046_ligand
> ui tool show Matchmaker
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR20_Gi, chain R (#1) with GPR20_Gi_Fab046, chain R (#2), sequence
alignment score = 1937.2
RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
2.786)
Matchmaker GPR20_Gi, chain R (#1) with GPR20_Gi_Fab046_ligand, chain R (#3),
sequence alignment score = 2126.4
RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
1.114)
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR20_Gi, chain R (#1) with GPR20_Gi_Fab046, chain R (#2), sequence
alignment score = 1937.2
RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
2.786)
Matchmaker GPR20_Gi, chain R (#1) with GPR20_Gi_Fab046_ligand, chain R (#3),
sequence alignment score = 2126.4
RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
1.114)
> select clear
[Repeated 2 time(s)]
> ui mousemode right translate
> select #2/B#3/F
2542 atoms, 2605 bonds, 1 pseudobond, 340 residues, 3 models selected
> hide sel cartoons
> select #2/B#3/F
2542 atoms, 2605 bonds, 1 pseudobond, 340 residues, 3 models selected
> hide sel cartoons
> select #3/E
747 atoms, 764 bonds, 105 residues, 1 model selected
> hide sel cartoons
> select #2/C
1623 atoms, 1658 bonds, 211 residues, 1 model selected
> hide sel cartoons
> select #1/C
438 atoms, 444 bonds, 57 residues, 1 model selected
> hide sel cartoons
> select #3/C
438 atoms, 444 bonds, 57 residues, 1 model selected
> hide sel cartoons
> select #1/B#3/B
5180 atoms, 5274 bonds, 676 residues, 2 models selected
> hide sel cartoons
> select #1/A#3/A
3421 atoms, 3479 bonds, 4 pseudobonds, 436 residues, 4 models selected
> hide sel cartoons
> select #1/S#3/S
3520 atoms, 3612 bonds, 2 pseudobonds, 464 residues, 4 models selected
> hide sel cartoons
> color #1 #de9a85ff
> color #2 #6debf4ff
> color #2 #5daee5ff
> color #3 #9ce5a7ff
> color #3 #afe9ccff
> color #3 #a4e7b8ff
> rename #2 8HS2_GPR20_Fab046_inactive
> rename #1 8HS3_GPR20_Gi
> rename #3 8HSC_GPR20_Gi_Fab046
> open /Users/dongju/Downloads/8hsc.cif
8hsc.cif title:
Gi bound Orphan GPR20 complex with Fab046 in ligand-free state [more info...]
Chain information for 8hsc.cif #4
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 1-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
E | light chain of Fab046 |
F | heavy chain of Fab046 |
R | Soluble cytochrome b562,G-protein coupled receptor 20 | C562_ECOLX -98--1, GPR20_HUMAN 1-358
S | scFv16 |
> close #4
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R #3/R
Alignment identifier is 1
> sequence chain #2/R
Alignment identifier is 2/R
> ui mousemode right select
> select #2/R:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/R:31-32
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/R:31-51
172 atoms, 178 bonds, 21 residues, 1 model selected
> select #2/R:51
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/R:50-51
11 atoms, 11 bonds, 2 residues, 1 model selected
> select #2/R:48
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/R:33-48
134 atoms, 138 bonds, 16 residues, 1 model selected
> open /Users/dongju/Downloads/emd_34993_8HSC.map
Opened emd_34993_8HSC.map as #4, grid size 288,288,288, pixel 0.832, shown at
level 0.0663, step 2, values float32
> open /Users/dongju/Downloads/emd_34984_8HS3.map
Opened emd_34984_8HS3.map as #5, grid size 256,256,256, pixel 0.832, shown at
level 0.0743, step 1, values float32
> open /Users/dongju/Downloads/emd_34983_8HS2.map
Opened emd_34983_8HS2.map as #6, grid size 288,288,288, pixel 0.832, shown at
level 0.0516, step 2, values float32
> volume #4 step 1
> volume #4 level 0.1209
> volume #4 level 0.1482
> volume #5 level 0.2588
> ui tool show Matchmaker
> ui tool show "Volume Viewer"
> volume #6 level 0.07988
> volume #6 step 1
> hide #!1 models
> hide #!2 models
> hide #!5 models
> hide #!6 models
> ui tool show Matchmaker
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.66094,-0.49694,0.56232,175.69,-0.53308,0.83831,0.11426,53.27,-0.52819,-0.22424,-0.81898,328.71
> view matrix models
> #2,-0.66094,-0.49694,0.56232,187.93,-0.53308,0.83831,0.11426,49.694,-0.52819,-0.22424,-0.81898,321.04
> ui mousemode right select
> select #3/R:72
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.93357,0.34606,0.093248,-43.297,0.33762,-0.93645,0.095263,167.2,0.12029,-0.057452,-0.99108,194.25
> view matrix models
> #3,-0.51119,0.84884,0.13475,77.887,0.81415,0.42801,0.39238,-82.802,0.27539,0.31028,-0.90988,123.36
> view matrix models
> #3,-0.88503,0.45316,0.10663,174.49,0.42766,0.70091,0.57081,-83.556,0.18393,0.55079,-0.81413,97.227
> view matrix models
> #3,-0.88503,0.45316,0.10663,170.85,0.42766,0.70091,0.57081,-81.442,0.18393,0.55079,-0.81413,95.902
> view matrix models
> #3,-0.80184,0.58234,0.13393,142.41,0.55335,0.63904,0.53426,-86.516,0.22553,0.5025,-0.83464,98.322
> view matrix models
> #3,-0.67352,0.69432,0.25358,100.83,0.69464,0.47726,0.53824,-86.06,0.25269,0.53866,-0.80374,87.501
> view matrix models
> #3,-0.67352,0.69432,0.25358,99.559,0.69464,0.47726,0.53824,-84.317,0.25269,0.53866,-0.80374,86.836
> view matrix models
> #3,-0.67352,0.69432,0.25358,103.6,0.69464,0.47726,0.53824,-78.659,0.25269,0.53866,-0.80374,87.642
> view matrix models
> #3,-0.67352,0.69432,0.25358,101.9,0.69464,0.47726,0.53824,-81.537,0.25269,0.53866,-0.80374,87.881
> view matrix models
> #3,-0.77048,0.63329,-0.072754,154.6,0.61462,0.7683,0.17876,-68.663,0.16911,0.093017,-0.9812,168.54
> view matrix models
> #3,-0.82945,0.55796,-0.026453,166.17,0.54449,0.81819,0.18466,-66.146,0.12467,0.13876,-0.98245,169
> view matrix models
> #3,-0.7649,0.62275,-0.16465,163.96,0.57843,0.77652,0.24987,-72.652,0.28346,0.095892,-0.95418,150.42
> view matrix models
> #3,-0.57526,0.80453,-0.14766,116.89,0.78725,0.59357,0.16707,-69.492,0.22206,-0.020139,-0.97482,173.87
> view matrix models
> #3,-0.52785,0.84917,-0.016692,92.307,0.79491,0.50085,0.34243,-77.518,0.29914,0.16748,-0.93939,138.57
> view matrix models
> #3,-0.52785,0.84917,-0.016692,93.135,0.79491,0.50085,0.34243,-77.648,0.29914,0.16748,-0.93939,138.03
> view matrix models
> #3,0.093474,0.99512,-0.031604,-1.4959,0.97954,-0.086236,0.18183,-16.375,0.17821,-0.047953,-0.98282,182.96
> view matrix models
> #3,0.093474,0.99512,-0.031604,2.2278,0.97954,-0.086236,0.18183,-13.581,0.17821,-0.047953,-0.98282,182.85
> view matrix models
> #3,0.093474,0.99512,-0.031604,-1.127,0.97954,-0.086236,0.18183,-11.923,0.17821,-0.047953,-0.98282,186.13
> view matrix models
> #3,0.093474,0.99512,-0.031604,0.47057,0.97954,-0.086236,0.18183,-11.34,0.17821,-0.047953,-0.98282,185.1
> view matrix models
> #3,-0.66744,0.74453,-0.014128,124.82,0.71103,0.64281,0.28501,-72.629,0.22128,0.18018,-0.95842,150.54
> view matrix models
> #3,-0.80751,0.58888,-0.033914,162.82,0.5487,0.77103,0.32318,-70.785,0.21646,0.24236,-0.94573,142.61
> view matrix models
> #3,-0.80751,0.58888,-0.033914,162.81,0.5487,0.77103,0.32318,-74.395,0.21646,0.24236,-0.94573,141.53
> view matrix models
> #3,-0.80751,0.58888,-0.033914,162.85,0.5487,0.77103,0.32318,-75.3,0.21646,0.24236,-0.94573,142.26
> view matrix models
> #3,-0.80751,0.58888,-0.033914,162.54,0.5487,0.77103,0.32318,-76.609,0.21646,0.24236,-0.94573,142.33
> view matrix models
> #3,-0.80751,0.58888,-0.033914,162.1,0.5487,0.77103,0.32318,-74.881,0.21646,0.24236,-0.94573,139.97
> view matrix models
> #3,-0.80751,0.58888,-0.033914,162.34,0.5487,0.77103,0.32318,-75.253,0.21646,0.24236,-0.94573,140.88
> view matrix models
> #3,0.83163,0.46396,-0.30519,-4.2444,0.41363,-0.88419,-0.21704,189.9,-0.37054,0.054263,-0.92723,235.69
> view matrix models
> #3,0.83163,0.46396,-0.30519,-3.0296,0.41363,-0.88419,-0.21704,193.24,-0.37054,0.054263,-0.92723,236.66
> view matrix models
> #3,0.86824,0.41245,-0.27576,-4.6855,0.41429,-0.90851,-0.054441,179.43,-0.27299,-0.066978,-0.95968,241.67
> view matrix models
> #3,0.89953,0.21953,-0.3777,24.199,0.22188,-0.97434,-0.037874,209.92,-0.37633,-0.049738,-0.92515,249.31
> view matrix models
> #3,0.89953,0.21953,-0.3777,23.944,0.22188,-0.97434,-0.037874,209.58,-0.37633,-0.049738,-0.92515,248.86
> fitmap #3 inMap #4
Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
10180 atoms
average map value = 0.0274, steps = 2000
shifted from previous position = 3.33
rotated from previous position = 5.74 degrees
atoms outside contour = 9387, contour level = 0.14824
Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
coordinates:
Matrix rotation and translation
0.91461808 0.14723549 -0.37655739 30.60679389
0.12928020 -0.98894154 -0.07267228 223.46689144
-0.38309319 0.01778597 -0.92353845 242.16145145
Axis 0.97841004 0.07069214 -0.19420714
Axis point 0.00000000 107.76880125 126.76037093
Rotation angle (degrees) 177.35043408
Shift along axis -1.28613697
> volume #4 level 0.1452
> view matrix models
> #3,0.91462,0.14724,-0.37656,32.421,0.12928,-0.98894,-0.072672,223.3,-0.38309,0.017786,-0.92354,241.83
> view matrix models
> #3,0.91462,0.14724,-0.37656,32.18,0.12928,-0.98894,-0.072672,226.13,-0.38309,0.017786,-0.92354,243.77
> view matrix models
> #3,0.91462,0.14724,-0.37656,32.165,0.12928,-0.98894,-0.072672,226.84,-0.38309,0.017786,-0.92354,244.46
> view matrix models
> #3,0.90511,0.026312,-0.42436,52.339,-0.0035374,-0.99758,-0.0694,244.43,-0.42516,0.064316,-0.90283,242.29
> view matrix models
> #3,0.90252,0.18234,-0.39015,30.999,0.15711,-0.98291,-0.095931,224.96,-0.40097,0.025284,-0.91574,245.07
> view matrix models
> #3,0.88972,0.12733,-0.4384,43.954,0.20136,-0.97131,0.12653,195.32,-0.40971,-0.20085,-0.88983,269.9
> view matrix models
> #3,0.88972,0.12733,-0.4384,40.716,0.20136,-0.97131,0.12653,194.54,-0.40971,-0.20085,-0.88983,269.4
> view matrix models
> #3,0.88972,0.12733,-0.4384,46.55,0.20136,-0.97131,0.12653,190.73,-0.40971,-0.20085,-0.88983,266.09
> view matrix models
> #3,0.32337,-0.74179,-0.58752,235.18,-0.78565,-0.55653,0.27023,253.47,-0.52743,0.3742,-0.76276,201.11
> view matrix models
> #3,0.010257,-0.81438,-0.58024,282.74,-0.92007,-0.23495,0.31349,228.73,-0.39163,0.53064,-0.7517,164.66
> view matrix models
> #3,-0.39048,-0.77953,-0.48976,320.5,-0.88506,0.17147,0.43274,164.75,-0.25335,0.60244,-0.75689,139.21
> view matrix models
> #3,-0.39048,-0.77953,-0.48976,316.86,-0.88506,0.17147,0.43274,167.11,-0.25335,0.60244,-0.75689,139.26
> view matrix models
> #3,-0.39048,-0.77953,-0.48976,318.95,-0.88506,0.17147,0.43274,165.76,-0.25335,0.60244,-0.75689,140.57
> view matrix models
> #3,-0.39048,-0.77953,-0.48976,323.43,-0.88506,0.17147,0.43274,129.86,-0.25335,0.60244,-0.75689,136.61
> view matrix models
> #3,-0.39048,-0.77953,-0.48976,323.18,-0.88506,0.17147,0.43274,132.09,-0.25335,0.60244,-0.75689,136.97
> view matrix models
> #3,-0.39048,-0.77953,-0.48976,323.92,-0.88506,0.17147,0.43274,125.72,-0.25335,0.60244,-0.75689,136.07
> view matrix models
> #3,-0.18508,-0.80947,-0.55722,308.12,-0.93879,-0.02201,0.34378,164.18,-0.29055,0.58674,-0.75585,142.53
> view matrix models
> #3,0.77449,-0.24089,-0.58493,122.45,-0.37681,-0.91839,-0.12071,244.39,-0.50811,0.31389,-0.80205,206.75
> view matrix models
> #3,0.77934,-0.3091,-0.54505,125.72,-0.43088,-0.89592,-0.10802,247.36,-0.45493,0.31904,-0.83142,202.37
> view matrix models
> #3,0.77934,-0.3091,-0.54505,125.74,-0.43088,-0.89592,-0.10802,246.8,-0.45493,0.31904,-0.83142,202.13
> volume #4 level 0.1179
> volume #4 step 2
> volume #4 level 0.112
> view matrix models
> #3,0.77934,-0.3091,-0.54505,125.33,-0.43088,-0.89592,-0.10802,246.76,-0.45493,0.31904,-0.83142,200.81
> view matrix models
> #3,0.082947,-0.78047,-0.61966,276.57,-0.94992,-0.24991,0.18761,207.46,-0.30128,0.57307,-0.76212,144.58
> view matrix models
> #3,-0.4667,-0.70065,-0.53971,329.13,-0.8764,0.28438,0.38866,115.34,-0.11883,0.65439,-0.74676,110.3
> view matrix models
> #3,0.58693,-0.61049,-0.5318,183.62,-0.70194,-0.71102,0.041526,244.5,-0.40348,0.34892,-0.84585,192.25
> view matrix models
> #3,-0.22678,-0.77554,-0.58916,312.34,-0.94693,0.034069,0.31964,160.53,-0.22783,0.63037,-0.74211,126.5
> view matrix models
> #3,-0.22678,-0.77554,-0.58916,312.47,-0.94693,0.034069,0.31964,159.06,-0.22783,0.63037,-0.74211,125.76
> view matrix models
> #3,-0.22678,-0.77554,-0.58916,306.62,-0.94693,0.034069,0.31964,194.89,-0.22783,0.63037,-0.74211,134.82
> view matrix models
> #3,-0.20904,-0.79913,-0.56364,304.52,-0.94623,0.019792,0.32288,196.14,-0.24687,0.60083,-0.7603,142.55
> view matrix models
> #3,-0.40537,-0.74265,-0.53305,319.82,-0.89876,0.21723,0.38083,161.18,-0.16703,0.63347,-0.75553,128.08
> view matrix models
> #3,-0.21668,-0.8158,-0.53621,304.64,-0.94315,0.033144,0.3307,193.39,-0.25201,0.57738,-0.77661,147.59
> view matrix models
> #3,-0.04307,-0.80758,-0.58819,286.86,-0.95413,-0.14134,0.26393,221.93,-0.29628,0.57257,-0.76445,152.55
> view matrix models
> #3,-0.13131,-0.78665,-0.60327,297.2,-0.84368,-0.23086,0.48467,195.82,-0.52054,0.57261,-0.63337,167.77
> view matrix models
> #3,-0.13131,-0.78665,-0.60327,296.82,-0.84368,-0.23086,0.48467,199.02,-0.52054,0.57261,-0.63337,169.11
> view matrix models
> #3,-0.27126,-0.77367,-0.57259,310.01,-0.83724,-0.10381,0.53689,178.07,-0.47482,0.62503,-0.61959,155.77
> view matrix models
> #3,-0.27126,-0.77367,-0.57259,310.24,-0.83724,-0.10381,0.53689,176.06,-0.47482,0.62503,-0.61959,154.92
> view matrix models
> #3,-0.14382,-0.80407,-0.57688,297.99,-0.83585,-0.21337,0.50578,191.82,-0.52978,0.55493,-0.6414,172.31
> view matrix models
> #3,-0.29277,-0.76871,-0.56866,312,-0.84265,-0.073663,0.5334,173.59,-0.45192,0.63534,-0.62619,151.47
> view matrix models
> #3,-0.23586,-0.78322,-0.57527,307.12,-0.84616,-0.1256,0.51792,181.67,-0.47789,0.60893,-0.63311,158.56
> view matrix models
> #3,-0.21033,-0.76212,-0.61232,305.18,-0.8526,-0.16347,0.49633,189.1,-0.47837,0.62645,-0.6154,154.78
> view matrix models
> #3,-0.26491,-0.74784,-0.60873,310.1,-0.75848,-0.22821,0.61044,173.04,-0.59543,0.62342,-0.50676,158.98
> view matrix models
> #3,-0.29475,-0.74763,-0.59512,312.49,-0.75583,-0.19865,0.6239,167.89,-0.58467,0.63371,-0.50653,156.38
> view matrix models
> #3,-0.45299,-0.7036,-0.5475,322.66,-0.73873,-0.047553,0.67232,143.16,-0.49908,0.70901,-0.49823,135.86
> view matrix models
> #3,-0.41221,-0.79577,-0.44366,317.64,-0.72441,-0.0090641,0.68931,135.12,-0.55255,0.60553,-0.57273,162.32
> view matrix models
> #3,-0.45091,-0.78185,-0.43056,319.61,-0.73886,0.056334,0.6715,131.16,-0.50076,0.62091,-0.60308,157.02
> view matrix models
> #3,-0.43427,-0.81195,-0.39007,316.88,-0.76085,0.098815,0.64136,132.07,-0.48221,0.57531,-0.66068,165.84
> view matrix models
> #3,-0.45261,-0.83042,-0.32488,314.73,-0.70845,0.11363,0.69655,118.05,-0.54152,0.54542,-0.63974,174.74
> view matrix models
> #3,-0.32649,-0.87591,-0.35521,307.06,-0.77098,0.029381,0.63619,141.98,-0.54681,0.48157,-0.6849,187.46
> volume #4 level 0.1297
> view matrix models
> #3,-0.61561,-0.73719,-0.27852,319.9,-0.66216,0.29225,0.69002,92,-0.42728,0.60921,-0.66805,155.64
> view matrix models
> #3,-0.61561,-0.73719,-0.27852,320.13,-0.66216,0.29225,0.69002,91.878,-0.42728,0.60921,-0.66805,155.52
> view matrix models
> #3,-0.61561,-0.73719,-0.27852,320.08,-0.66216,0.29225,0.69002,91.943,-0.42728,0.60921,-0.66805,155.44
> view matrix models
> #3,-0.6096,-0.72746,-0.31495,321.89,-0.69807,0.30439,0.64811,99.371,-0.3756,0.61494,-0.69337,150.77
> fitmap #3 inMap #4
Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
10180 atoms
average map value = 0.0221, steps = 104
shifted from previous position = 2.25
rotated from previous position = 3.51 degrees
atoms outside contour = 9538, contour level = 0.12972
Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
coordinates:
Matrix rotation and translation
-0.62301685 -0.69907813 -0.35091276 323.82273294
-0.68755815 0.27551529 0.67182967 98.03304027
-0.37297960 0.65983413 -0.65230754 141.85275258
Axis -0.43411156 0.79858647 0.41690143
Axis point 189.17599306 0.00000000 43.94258769
Rotation angle (degrees) 179.20836547
Shift along axis -3.14871614
> view matrix models
> #3,-0.50698,-0.76943,-0.38852,321.07,-0.75712,0.18207,0.62739,122.31,-0.41199,0.61223,-0.67486,154.67
> view matrix models
> #3,-0.44059,-0.77377,-0.45516,319.91,-0.77446,0.071218,0.6286,137.32,-0.45398,0.62945,-0.63063,153.5
> view matrix models
> #3,-0.43453,-0.81371,-0.38608,316.74,-0.72342,0.059974,0.6878,126.04,-0.53652,0.57816,-0.61472,168.45
> fitmap #3 inMap #4
Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
10180 atoms
average map value = 0.023, steps = 96
shifted from previous position = 2.09
rotated from previous position = 1.11 degrees
atoms outside contour = 9505, contour level = 0.12972
Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
coordinates:
Matrix rotation and translation
-0.44845125 -0.81009030 -0.37768396 315.90059723
-0.71094998 0.06720042 0.70002444 120.88839438
-0.54170249 0.58244124 -0.60606979 166.07985794
Axis -0.52294492 0.72946357 0.44092121
Axis point 207.76601541 0.00000000 34.37096576
Rotation angle (degrees) 173.54492804
Shift along axis -3.78680211
> view matrix models
> #3,-0.44845,-0.81009,-0.37768,317.11,-0.71095,0.0672,0.70002,122.03,-0.5417,0.58244,-0.60607,166.15
> view matrix models
> #3,-0.67213,-0.70147,-0.23705,318.61,-0.62506,0.36592,0.68949,77.347,-0.39691,0.61159,-0.68441,152.29
> fitmap #3 inMap #4
Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
10180 atoms
average map value = 0.02221, steps = 116
shifted from previous position = 4.71
rotated from previous position = 3.45 degrees
atoms outside contour = 9519, contour level = 0.12972
Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
coordinates:
Matrix rotation and translation
-0.68110775 -0.69314286 -0.23589237 317.39915571
-0.59453884 0.33553836 0.73071032 75.24072237
-0.42733570 0.63793964 -0.64063813 150.39958608
Axis -0.39564854 0.81646779 0.42052656
Axis point 182.36124367 0.00000000 44.40256038
Rotation angle (degrees) 173.26723037
Shift along axis -0.89986505
> ui mousemode right select
> select #4
2 models selected
> transparency sel 50
> volume sel style surface
> volume sel style mesh
> volume sel style surface
> volume sel style image
> volume sel style surface
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,2.0559,0,1,0,1.5028,0,0,1,1.3583
> view matrix models #4,1,0,0,1.2063,0,1,0,1.1243,0,0,1,1.5043
> view matrix models
> #4,0.99528,0.092143,0.030326,-13.044,-0.09264,0.99558,0.015378,10.758,-0.028775,-0.018115,0.99942,7.1682
> view matrix models
> #4,0.9954,-0.095297,-0.00972,14.534,0.095052,0.9952,-0.023185,-6.7552,0.011883,0.022155,0.99968,-2.5645
> view matrix models
> #4,0.99962,-0.026307,0.0080892,3.5248,0.026384,0.99961,-0.0096414,-0.80377,-0.0078324,0.0098512,0.99992,1.2291
> view matrix models
> #4,0.99943,-0.014015,-0.030553,6.5485,0.013272,0.99961,-0.024392,2.4556,0.030883,0.023973,0.99924,-4.9672
> view matrix models
> #4,0.99801,0.061414,-0.014131,-4.4232,-0.06141,0.99811,0.00069911,8.4896,0.014147,0.00017007,0.9999,-0.16726
> view matrix models
> #4,0.99089,-0.057526,-0.12175,23.505,0.052269,0.99758,-0.045941,0.63473,0.1241,0.039159,0.9915,-16.875
> ui mousemode right select
> select #3/R:165
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.68111,-0.69314,-0.23589,318.13,-0.59454,0.33554,0.73071,75.013,-0.42734,0.63794,-0.64064,150.08
> view matrix models
> #3,-0.30352,-0.91347,-0.27102,299.3,-0.71182,0.028301,0.70179,128.71,-0.6334,0.40592,-0.65881,205.22
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.39102,-0.87862,-0.27411,306.7,-0.71384,0.10152,0.69291,121.34,-0.58097,0.46661,-0.66689,192.29
> view matrix models
> #3,-0.39102,-0.87862,-0.27411,308.87,-0.71384,0.10152,0.69291,120.65,-0.58097,0.46661,-0.66689,191.34
> view matrix models
> #3,-0.39102,-0.87862,-0.27411,308.84,-0.71384,0.10152,0.69291,120.75,-0.58097,0.46661,-0.66689,191.24
> view matrix models
> #3,-0.087412,-0.95333,-0.28899,280.39,-0.7309,-0.13574,0.66885,153.03,-0.67686,0.26969,-0.68493,228.24
> view matrix models
> #3,-0.11851,-0.95337,-0.27755,283.19,-0.74734,-0.098397,0.65711,151.97,-0.65378,0.2853,-0.70084,225.1
> view matrix models
> #3,0.036028,-0.94281,-0.33138,267.76,-0.67988,-0.26616,0.68332,160.26,-0.73244,0.20068,-0.65058,239.87
> view matrix models
> #3,-0.1925,-0.92137,-0.33766,295.01,-0.80409,-0.049135,0.59248,160.04,-0.56248,0.38556,-0.7314,204.9
> view matrix models
> #3,0.4473,-0.83501,-0.32044,201.69,-0.80506,-0.53198,0.26244,250.05,-0.38961,0.14058,-0.91019,229.64
> view matrix models
> #3,0.4473,-0.83501,-0.32044,195.3,-0.80506,-0.53198,0.26244,240.47,-0.38961,0.14058,-0.91019,233.16
> view matrix models
> #3,0.4473,-0.83501,-0.32044,188.25,-0.80506,-0.53198,0.26244,230.93,-0.38961,0.14058,-0.91019,235.44
> view matrix models
> #3,0.4473,-0.83501,-0.32044,230.96,-0.80506,-0.53198,0.26244,289.01,-0.38961,0.14058,-0.91019,240.37
> view matrix models
> #3,0.4473,-0.83501,-0.32044,223.38,-0.80506,-0.53198,0.26244,247.86,-0.38961,0.14058,-0.91019,226.42
> view matrix models
> #3,0.4473,-0.83501,-0.32044,223.64,-0.80506,-0.53198,0.26244,249.3,-0.38961,0.14058,-0.91019,226.89
> view matrix models
> #3,-0.24783,-0.89783,-0.36398,323.94,-0.86959,0.040535,0.4921,167.4,-0.42707,0.43847,-0.79079,184.78
> view matrix models
> #3,-0.24783,-0.89783,-0.36398,324.62,-0.86959,0.040535,0.4921,170.77,-0.42707,0.43847,-0.79079,187
> view matrix models
> #3,-0.40052,-0.83909,-0.36812,337.64,-0.82293,0.15273,0.54723,146.13,-0.40295,0.52211,-0.75169,170.2
> view matrix models
> #3,-0.66378,-0.71028,-0.23431,342.53,-0.67755,0.43838,0.59055,89.907,-0.31674,0.55075,-0.77224,157.97
> view matrix models
> #3,-0.66378,-0.71028,-0.23431,325.95,-0.67755,0.43838,0.59055,82.907,-0.31674,0.55075,-0.77224,156.03
> view matrix models
> #3,-0.69074,-0.68633,-0.22769,325.92,-0.66086,0.47135,0.58403,77.601,-0.29352,0.55388,-0.77914,153.41
> view matrix models
> #3,-0.69074,-0.68633,-0.22769,320.83,-0.66086,0.47135,0.58403,79.577,-0.29352,0.55388,-0.77914,157.1
> view matrix models
> #3,-0.69074,-0.68633,-0.22769,320.18,-0.66086,0.47135,0.58403,79.727,-0.29352,0.55388,-0.77914,158.04
> view matrix models
> #3,-0.5367,-0.81372,-0.22319,314.96,-0.66133,0.2414,0.71019,93.745,-0.52401,0.52876,-0.6677,178.97
> fitmap #3 inMap #4
Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
10180 atoms
average map value = 0.02623, steps = 168
shifted from previous position = 7.8
rotated from previous position = 5.59 degrees
atoms outside contour = 9480, contour level = 0.12972
Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
coordinates:
Matrix rotation and translation
-0.59306195 -0.73885769 -0.31994817 318.13604787
-0.65777968 0.21544711 0.72173985 93.72466182
-0.46433113 0.63849185 -0.61377906 156.06749494
Axis -0.44916764 0.77902358 0.43745935
Axis point 190.76006571 0.00000000 42.25841955
Rotation angle (degrees) 174.68281772
Shift along axis -1.60951241
> view matrix models
> #3,-0.53041,-0.80704,-0.25953,314.83,-0.63319,0.17359,0.75428,94.005,-0.56368,0.56441,-0.60308,178.09
> view matrix models
> #3,-0.53041,-0.80704,-0.25953,317.35,-0.63319,0.17359,0.75428,94.585,-0.56368,0.56441,-0.60308,178.61
> view matrix models
> #3,-0.53041,-0.80704,-0.25953,316.87,-0.63319,0.17359,0.75428,94.921,-0.56368,0.56441,-0.60308,178.46
> view matrix models
> #3,-0.7039,-0.70885,-0.045309,305.71,-0.45936,0.40564,0.79022,42.071,-0.54177,0.57705,-0.61114,175.02
> view matrix models
> #3,-0.71122,-0.66849,-0.21747,319.47,-0.54681,0.33167,0.76877,64.017,-0.44178,0.66567,-0.60142,150.96
> view matrix models
> #3,-0.71122,-0.66849,-0.21747,318.59,-0.54681,0.33167,0.76877,64.359,-0.44178,0.66567,-0.60142,147.55
> view matrix models
> #3,-0.64685,-0.68909,-0.32671,323.92,-0.65073,0.27534,0.70763,90.387,-0.39767,0.67033,-0.62651,143.94
> view matrix models
> #3,-0.64685,-0.68909,-0.32671,322.75,-0.65073,0.27534,0.70763,92.037,-0.39767,0.67033,-0.62651,143.52
> view matrix models
> #3,-0.64685,-0.68909,-0.32671,323.43,-0.65073,0.27534,0.70763,93.307,-0.39767,0.67033,-0.62651,144.23
> view matrix models
> #3,-0.64685,-0.68909,-0.32671,322.99,-0.65073,0.27534,0.70763,92.41,-0.39767,0.67033,-0.62651,143.82
> view matrix models
> #3,-0.8561,-0.51391,-0.054693,301.52,-0.40635,0.60395,0.68566,25.217,-0.31934,0.60922,-0.72586,151.08
> view matrix models
> #3,-0.89985,0.2759,0.33787,175.05,0.41006,0.79917,0.43951,-76.458,-0.14876,0.53404,-0.83227,148.95
> view matrix models
> #3,-0.89985,0.2759,0.33787,173.89,0.41006,0.79917,0.43951,-75.983,-0.14876,0.53404,-0.83227,149.22
> fitmap #3 inMap #4
Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
10180 atoms
average map value = 0.02646, steps = 268
shifted from previous position = 2.93
rotated from previous position = 9.59 degrees
atoms outside contour = 9392, contour level = 0.12972
Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
coordinates:
Matrix rotation and translation
-0.84257923 0.50989234 0.17340714 152.86231643
0.53790691 0.78072321 0.31800536 -75.48199611
0.02676552 0.36122161 -0.93209578 157.19052038
Axis 0.27805618 0.94350176 0.18024756
Axis point 90.79673476 0.00000000 82.65077544
Rotation angle (degrees) 175.54297318
Shift along axis -0.37987697
> hide #!4 models
> hide #!3 models
> show #!1 models
> show #!5 models
> volume #5 step 2
> volume #5 level 0.1551
> view matrix models
> #3,-0.86911,0.41636,0.26702,157.96,0.49133,0.78889,0.36912,-75.685,-0.056959,0.452,-0.8902,147.3
> view matrix models
> #3,-0.86911,0.41636,0.26702,156.59,0.49133,0.78889,0.36912,-76.483,-0.056959,0.452,-0.8902,140.11
> fitmap #1 inMap #5
Fit molecule 8HS3_GPR20_Gi (#1) to map emd_34984_8HS3.map (#5) using 8258
atoms
average map value = 0.269, steps = 44
shifted from previous position = 0.00996
rotated from previous position = 0.0165 degrees
atoms outside contour = 3526, contour level = 0.15506
Position of 8HS3_GPR20_Gi (#1) relative to emd_34984_8HS3.map (#5)
coordinates:
Matrix rotation and translation
0.99999996 -0.00026805 -0.00008915 0.03509652
0.00026805 0.99999996 -0.00005430 -0.03064672
0.00008916 0.00005428 0.99999999 -0.00869959
Axis 0.18873347 -0.30992483 0.93184027
Axis point 105.08226922 125.27152504 0.00000000
Rotation angle (degrees) 0.01648161
Shift along axis 0.00801544
> view matrix models
> #3,-0.86911,0.41636,0.26702,154.9,0.49133,0.78889,0.36912,-77.884,-0.056959,0.452,-0.8902,134.62
> ui mousemode right translate
> volume #!5 style mesh
> volume #5 color #0029f4
> volume #5 color #0119f0
> volume #5 level 0.1066
> transparency #5.1 50
> volume #!5 style surface
> volume #5 style mesh
> volume #5 level 0.09625
> volume #5 step 4
> volume #5 step 1
> volume #5 level 0.1123
> volume #!5 style surface
> ui mousemode right select
> select #5
2 models selected
> select clear
> select #1/R:48
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #5
2 models selected
> select clear
> vop gaussian #5 sdev 2.5
Opened emd_34984_8HS3.map gaussian as #7, grid size 256,256,256, pixel 0.832,
shown at step 1, values float32
> volume #5 level 0.1324
> volume #!5,7 style surface
> volume #!5,7 style mesh
> surface dust #5 size 8.32
> surface dust #7 size 8.32
> transparency #5 80 All
> close #7
> transparency #5 50 All
> transparency #5 00 All
> transparency #5 0 All
> ui mousemode right translate
> ui mousemode right select
> select #1/R:32
2 atoms, 1 bond, 1 residue, 1 model selected
> select #1/R:32 #3/R:32
9 atoms, 7 bonds, 2 residues, 2 models selected
> select #1/R:32-47 #3/R:32-47
203 atoms, 207 bonds, 32 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[165-180] RMSD: 48.751
> color (#!1 & sel) red
> select clear
> select #1/R:48 #3/R:48
11 atoms, 9 bonds, 2 residues, 2 models selected
> select #1/R:48-50 #3/R:48-50
35 atoms, 35 bonds, 6 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[181-183] RMSD: 52.299
> color (#!1 & sel) red
> select clear
> show #!2 models
> hide #!1 models
> hide #!5 models
> show #!6 models
> select #2/C
1623 atoms, 1658 bonds, 211 residues, 1 model selected
> show sel cartoons
> select #2/B
1617 atoms, 1658 bonds, 1 pseudobond, 218 residues, 2 models selected
> show sel cartoons
> select add #2
5456 atoms, 5592 bonds, 1 pseudobond, 716 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
5456 atoms, 5592 bonds, 1 pseudobond, 716 residues, 2 models selected
> select clear
> select add #2
5456 atoms, 5592 bonds, 1 pseudobond, 716 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.66094,-0.49694,0.56232,186.68,-0.53308,0.83831,0.11426,60.01,-0.52819,-0.22424,-0.81898,281.82
> view matrix models
> #2,-0.66094,-0.49694,0.56232,188.67,-0.53308,0.83831,0.11426,63.838,-0.52819,-0.22424,-0.81898,283.67
> view matrix models
> #2,-0.66094,-0.49694,0.56232,187.08,-0.53308,0.83831,0.11426,60.411,-0.52819,-0.22424,-0.81898,281.41
> view matrix models
> #2,0.58142,0.79399,0.17756,-75.97,0.80952,-0.54272,-0.22392,103,-0.081428,0.27393,-0.9583,182.82
> view matrix models
> #2,0.99888,0.017769,0.043786,-18.095,0.011651,-0.99061,0.13621,214.8,0.045795,-0.13555,-0.98971,220.37
> view matrix models
> #2,0.99888,0.017769,0.043786,-11.26,0.011651,-0.99061,0.13621,224.28,0.045795,-0.13555,-0.98971,218.73
> view matrix models
> #2,0.93929,-0.1923,0.28416,-2.7799,-0.21633,-0.97475,0.055431,257.09,0.26633,-0.11354,-0.95717,187.01
> view matrix models
> #2,0.9123,-0.21473,0.3487,-3.31,-0.24816,-0.96723,0.053642,260.1,0.32576,-0.13547,-0.9357,180.56
> view matrix models
> #2,0.9123,-0.21473,0.3487,0.33037,-0.24816,-0.96723,0.053642,261.34,0.32576,-0.13547,-0.9357,171.44
> view matrix models
> #2,0.96001,-0.08967,0.2652,-12.058,-0.11979,-0.98778,0.099654,244.21,0.25303,-0.12744,-0.95903,181.31
> view matrix models
> #2,0.67114,0.53376,-0.51446,23.927,0.68612,-0.71002,0.15843,110.46,-0.28071,-0.45932,-0.84275,272.34
> view matrix models
> #2,0.33857,0.69362,-0.63582,55.666,0.8656,-0.49454,-0.078568,86.942,-0.36893,-0.52376,-0.76783,283.02
> view matrix models
> #2,0.92958,-0.13757,0.34198,-10.327,-0.13747,-0.9902,-0.024653,258.89,0.34202,-0.024093,-0.93939,156.48
> view matrix models
> #2,0.90289,-0.2973,0.31049,15.171,-0.23737,-0.94699,-0.21649,284.4,0.35839,0.12177,-0.9256,135.62
> view matrix models
> #2,0.88079,-0.47224,0.034439,66.199,-0.47216,-0.88144,-0.011027,283.66,0.035564,-0.0065484,-0.99935,196.23
> view matrix models
> #2,0.88079,-0.47224,0.034439,65.702,-0.47216,-0.88144,-0.011027,282.33,0.035564,-0.0065484,-0.99935,194.5
> view matrix models
> #2,-0.232,-0.93471,0.26924,228.58,-0.86137,0.068819,-0.5033,262.2,0.45191,-0.34868,-0.82109,169.27
> volume #6 level 0.1472
> view matrix models
> #2,-0.232,-0.93471,0.26924,230.61,-0.86137,0.068819,-0.5033,264.67,0.45191,-0.34868,-0.82109,170.66
> view matrix models
> #2,-0.61583,0.78224,-0.094081,104.69,-0.73807,-0.531,0.41628,231.38,0.27567,0.3258,0.90436,-60.945
> view matrix models
> #2,-0.28546,0.89244,-0.34937,77.985,-0.9426,-0.19553,0.2707,229.35,0.17327,0.40659,0.89703,-57.953
> view matrix models
> #2,0.81389,0.5784,-0.055017,-42.181,-0.53846,0.71531,-0.44542,143.18,-0.21828,0.39214,0.89363,-9.9877
> view matrix models
> #2,0.88366,0.448,-0.13582,-26.635,-0.45407,0.74967,-0.48147,132.72,-0.11388,0.48713,0.86587,-30.918
> view matrix models
> #2,0.70269,0.59329,-0.39273,2.5241,-0.71069,0.55904,-0.42707,180.38,-0.033821,0.57921,0.81448,-46.305
> view matrix models
> #2,0.037685,0.96779,-0.24893,21.08,-0.98724,-0.0025044,-0.15919,253.92,-0.15469,0.25175,0.95535,-6.6367
> view matrix models
> #2,0.90926,-0.40815,0.081629,51.992,0.41603,0.89724,-0.14793,-20.088,-0.012863,0.16847,0.98562,-16.222
> view matrix models
> #2,0.96404,-0.26272,-0.04011,40.111,0.25384,0.95494,-0.15382,-7.4497,0.078716,0.13811,0.98728,-23.461
> view matrix models
> #2,0.98153,-0.17266,-0.082332,31.391,0.1637,0.98086,-0.10541,-4.8074,0.098956,0.089983,0.99102,-20.403
> view matrix models
> #2,0.99543,-0.092709,-0.022941,14.242,0.094586,0.99023,0.10251,-18.439,0.013213,-0.10421,0.99447,12.706
> view matrix models
> #2,0.96165,-0.26987,-0.048961,42.129,0.26131,0.95571,-0.13538,-10.247,0.083326,0.11739,0.98958,-21.732
> view matrix models
> #2,0.94523,-0.32565,0.022176,43.726,0.32352,0.92572,-0.19591,-7.9242,0.04327,0.19236,0.98037,-25.159
> view matrix models
> #2,0.9504,-0.30707,0.049457,38.177,0.31086,0.93262,-0.18324,-8.5281,0.010143,0.18953,0.98182,-21.079
> view matrix models
> #2,0.95795,-0.28453,0.037064,35.805,0.28619,0.93816,-0.19483,-5.1547,0.020663,0.19725,0.98014,-23.076
> view matrix models
> #2,0.95795,-0.28453,0.037064,32.871,0.28619,0.93816,-0.19483,-6.5318,0.020663,0.19725,0.98014,-23.265
> view matrix models
> #2,0.95795,-0.28453,0.037064,32.497,0.28619,0.93816,-0.19483,-5.0674,0.020663,0.19725,0.98014,-24.068
> view matrix models
> #2,0.95754,-0.2075,-0.20015,46.769,0.16855,0.96616,-0.19526,5.3874,0.23389,0.15324,0.96011,-41.77
> view matrix models
> #2,0.95754,-0.2075,-0.20015,46.378,0.16855,0.96616,-0.19526,6.915,0.23389,0.15324,0.96011,-42.527
> view matrix models
> #2,0.95754,-0.2075,-0.20015,50.043,0.16855,0.96616,-0.19526,3.4407,0.23389,0.15324,0.96011,-41.412
> view matrix models
> #2,0.98738,-0.15064,-0.048823,24.698,0.14773,0.98729,-0.058587,-10.209,0.057028,0.050636,0.99709,-11.983
> view matrix models
> #2,0.96931,-0.24388,0.030943,30.148,0.24571,0.96513,-0.090284,-15.881,-0.0078458,0.095117,0.99544,-9.5766
> view matrix models
> #2,0.9797,-0.1996,0.018946,24.783,0.20029,0.97012,-0.13694,-6.5359,0.0089525,0.13795,0.9904,-16.209
> fitmap #2 inMap #6
Fit molecule 8HS2_GPR20_Fab046_inactive (#2) to map emd_34983_8HS2.map (#6)
using 5456 atoms
average map value = 0.1675, steps = 132
shifted from previous position = 1.28
rotated from previous position = 14.1 degrees
atoms outside contour = 2742, contour level = 0.14718
Position of 8HS2_GPR20_Fab046_inactive (#2) relative to emd_34983_8HS2.map
(#6) coordinates:
Matrix rotation and translation
0.99999996 0.00029288 0.00005649 -0.04427819
-0.00029287 0.99999995 -0.00015927 0.04795484
-0.00005654 0.00015925 0.99999999 -0.02100094
Axis 0.47100843 0.16715054 -0.86614765
Axis point 160.65915521 159.81308670 0.00000000
Rotation angle (degrees) 0.01937345
Shift along axis 0.00535019
> transparency #6.1 50
> volume #!6 style mesh
> volume #6 color #c64ee2
> view matrix models
> #2,1,0.00029288,5.6495e-05,-0.02648,-0.00029287,1,-0.00015927,0.051205,-5.6542e-05,0.00015925,1,-0.016536
> view matrix models
> #2,1,0.00029288,5.6495e-05,-0.032278,-0.00029287,1,-0.00015927,0.036181,-5.6542e-05,0.00015925,1,0.01956
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> hide #!2 models
> show #!1 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> select #1/C
438 atoms, 444 bonds, 57 residues, 1 model selected
> show #!3 cartoons
> select #1/C
438 atoms, 444 bonds, 57 residues, 1 model selected
> hide #!3 cartoons
> select #3/C
438 atoms, 444 bonds, 57 residues, 1 model selected
> show sel cartoons
> select #3/B
2590 atoms, 2637 bonds, 338 residues, 1 model selected
> show sel cartoons
> select #3/A
1712 atoms, 1741 bonds, 2 pseudobonds, 218 residues, 2 models selected
> show sel cartoons
> select #3/R
2008 atoms, 2057 bonds, 1 pseudobond, 273 residues, 2 models selected
> show sel cartoons
> select #3/S
1760 atoms, 1806 bonds, 1 pseudobond, 232 residues, 2 models selected
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.86911,0.41636,0.26702,155.98,0.49133,0.78889,0.36912,-80.605,-0.056959,0.452,-0.8902,152.29
> view matrix models
> #3,-0.66756,0.22149,0.71085,99.352,0.38154,0.92161,0.071149,-45.825,-0.63937,0.31871,-0.69974,212.86
> view matrix models
> #3,0.54806,0.83275,0.078515,-38.227,-0.8235,0.52075,0.22511,125.94,0.14657,-0.18803,0.97116,-31.727
> view matrix models
> #3,0.64327,0.71665,0.26948,-58.656,-0.75863,0.64412,0.097917,121.17,-0.1034,-0.26742,0.95802,7.736
> view matrix models
> #3,0.64327,0.71665,0.26948,-54.188,-0.75863,0.64412,0.097917,120.75,-0.1034,-0.26742,0.95802,37.301
> view matrix models
> #3,0.89172,-0.010251,0.45248,-16.627,-0.13029,0.95161,0.27833,-14.608,-0.43344,-0.30715,0.84723,95.327
> view matrix models
> #3,0.82502,0.49556,0.27159,-48.362,-0.5611,0.77551,0.28941,56.534,-0.067198,-0.39116,0.91787,53.591
> view matrix models
> #3,0.96478,0.11914,0.23454,-13.248,-0.21008,0.88555,0.41433,-14.52,-0.15833,-0.44901,0.87939,76.455
> view matrix models
> #3,0.81556,0.10096,0.5698,-36.594,-0.22318,0.96336,0.14875,11.541,-0.53391,-0.24848,0.80821,104.88
> view matrix models
> #3,0.60976,0.79249,0.012723,-26.618,-0.73923,0.56284,0.3698,93.574,0.2859,-0.23489,0.92903,-8.8083
> view matrix models
> #3,0.84238,-0.53604,0.055253,105.66,0.52292,0.8379,0.15647,-61.633,-0.13017,-0.10291,0.98614,16.383
> view matrix models
> #3,0.84238,-0.53604,0.055253,93.688,0.52292,0.8379,0.15647,-73.491,-0.13017,-0.10291,0.98614,34.825
> view matrix models
> #3,0.91319,-0.38121,-0.14409,91.777,0.38033,0.9242,-0.034755,-42.825,0.14641,-0.023062,0.98895,-8.0004
> view matrix models
> #3,0.91319,-0.38121,-0.14409,81.07,0.38033,0.9242,-0.034755,-27.667,0.14641,-0.023062,0.98895,-12.814
> view matrix models
> #3,0.98085,-0.12237,-0.15153,41.896,0.12265,0.99242,-0.0074978,-9.3413,0.1513,-0.011231,0.98842,-14.791
> view matrix models
> #3,0.98005,-0.13189,-0.14868,42.807,0.13018,0.99126,-0.021211,-8.3175,0.15018,0.0014318,0.98866,-16.263
> view matrix models
> #3,0.98005,-0.13189,-0.14868,36.695,0.13018,0.99126,-0.021211,-11.96,0.15018,0.0014318,0.98866,-17.284
> view matrix models
> #3,0.97548,-0.19276,-0.10619,39.328,0.19111,0.98123,-0.025622,-17.313,0.10914,0.0046991,0.99402,-13.551
> view matrix models
> #3,0.97548,-0.19276,-0.10619,38.988,0.19111,0.98123,-0.025622,-15.234,0.10914,0.0046991,0.99402,-13.389
> fitmap #3 inMap #4
Fit molecule 8HSC_GPR20_Gi_Fab046 (#3) to map emd_34993_8HSC.map (#4) using
10180 atoms
average map value = 0.2065, steps = 128
shifted from previous position = 2.41
rotated from previous position = 8.13 degrees
atoms outside contour = 4469, contour level = 0.12972
Position of 8HSC_GPR20_Gi_Fab046 (#3) relative to emd_34993_8HSC.map (#4)
coordinates:
Matrix rotation and translation
0.99999999 0.00003315 -0.00001114 0.00119912
-0.00003315 0.99999999 0.00008964 -0.01294704
0.00001114 -0.00008964 0.99999999 0.01100475
Axis -0.93162165 -0.11577308 -0.34449629
Axis point 0.00000000 109.66127837 148.84780670
Rotation angle (degrees) 0.00551275
Shift along axis -0.00340930
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right select
> select clear
> show #!1 models
> show #!2 models
> show #!5 models
> show #!6 models
> ui tool show Matchmaker
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
R (#2), sequence alignment score = 1937.2
RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
2.786)
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
(#3), sequence alignment score = 2126.4
RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
1.114)
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
R (#2), sequence alignment score = 1937.2
RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
2.786)
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
(#3), sequence alignment score = 2126.4
RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
1.114)
> select clear
[Repeated 2 time(s)]
> ui mousemode right translate
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!6 models
> ui mousemode right select
> select #1/R:32
2 atoms, 1 bond, 1 residue, 1 model selected
> select #1/R:32-33 #3/R:32-33
19 atoms, 18 bonds, 4 residues, 2 models selected
> select #1/R:32-54 #3/R:32-54
286 atoms, 294 bonds, 46 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[165-187] RMSD: 1.016
> select #1/R:32-56 #3/R:32-56
308 atoms, 316 bonds, 50 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[165-187] + 1 other block RMSD: 1.000
> color (#!1 & sel) #de9a85ff
> select clear
[Repeated 3 time(s)]
> ui mousemode right translate
> show #!2 models
> show #!6 models
> hide #!5 models
> hide #!1 models
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-7.5788,0,1,0,-21.126,0,0,1,10.346
> view matrix models #6,1,0,0,-6.7037,0,1,0,-18.716,0,0,1,9.1326
> view matrix models #6,1,0,0,-4.7324,0,1,0,-13.395,0,0,1,6.3349
> view matrix models
> #6,-0.46718,0.86174,0.19788,46.733,0.83372,0.35484,0.42308,-79.394,0.29437,0.36263,-0.88422,122.6
> view matrix models
> #6,-0.46718,0.86174,0.19788,33.776,0.83372,0.35484,0.42308,-88.419,0.29437,0.36263,-0.88422,157.01
> view matrix models
> #6,-0.92366,0.26069,0.28089,150.28,0.35867,0.84619,0.3941,-87.267,-0.13495,0.46476,-0.87509,194.82
> view matrix models
> #6,-0.91473,0.33219,0.23003,146.01,0.40057,0.82022,0.40839,-90.628,-0.053009,0.46571,-0.88335,185.86
> view matrix models
> #6,-0.093186,0.99094,-0.096728,4.5688,0.68576,0.13431,0.71532,-74.932,0.72184,0.00032588,-0.69207,129.45
> view matrix models
> #6,-0.093186,0.99094,-0.096728,2.9774,0.68576,0.13431,0.71532,-69.177,0.72184,0.00032588,-0.69207,135.21
> view matrix models
> #6,-0.57974,0.80882,0.098567,61.982,0.69174,0.42463,0.58412,-90.682,0.43059,0.40682,-0.80566,133.35
> view matrix models
> #6,-0.53845,0.81858,0.19998,45.503,0.71628,0.31962,0.62031,-84.905,0.44385,0.47725,-0.75844,118.59
> view matrix models
> #6,-0.53845,0.81858,0.19998,45.239,0.71628,0.31962,0.62031,-93.444,0.44385,0.47725,-0.75844,116.99
> view matrix models
> #6,-0.53845,0.81858,0.19998,41.776,0.71628,0.31962,0.62031,-94.277,0.44385,0.47725,-0.75844,113.51
> view matrix models
> #6,-0.63642,0.77126,0.011,78.417,0.51175,0.41152,0.75417,-94.706,0.57713,0.4856,-0.65659,86.262
> view matrix models
> #6,-0.63642,0.77126,0.011,83.544,0.51175,0.41152,0.75417,-92.652,0.57713,0.4856,-0.65659,90.441
> view matrix models
> #6,-0.61271,0.79005,-0.020348,81.744,0.49944,0.40703,0.76478,-91.758,0.61249,0.45842,-0.64397,88.168
> view matrix models
> #6,-0.61271,0.79005,-0.020348,81.505,0.49944,0.40703,0.76478,-97.794,0.61249,0.45842,-0.64397,82.105
> view matrix models
> #6,-0.61271,0.79005,-0.020348,81.581,0.49944,0.40703,0.76478,-96.533,0.61249,0.45842,-0.64397,83.763
> view matrix models
> #6,-0.61271,0.79005,-0.020348,81.439,0.49944,0.40703,0.76478,-97.445,0.61249,0.45842,-0.64397,82.956
> view matrix models
> #6,-0.76991,-0.21513,0.6008,154.88,-0.068878,0.96398,0.25691,-43.708,-0.63442,0.15642,-0.75699,277.86
> view matrix models
> #6,-0.90769,-0.086655,0.4106,175.58,0.095072,0.91054,0.40233,-71.769,-0.40874,0.40423,-0.81825,228.17
> view matrix models
> #6,-0.90769,-0.086655,0.4106,179.77,0.095072,0.91054,0.40233,-68.884,-0.40874,0.40423,-0.81825,233.72
> view matrix models
> #6,-0.862,0.26626,0.43135,130.53,0.42367,0.84564,0.32466,-92.112,-0.27832,0.46261,-0.84174,213.8
> view matrix models
> #6,-0.862,0.26626,0.43135,129.93,0.42367,0.84564,0.32466,-93.494,-0.27832,0.46261,-0.84174,216.86
> view matrix models
> #6,-0.862,0.26626,0.43135,125.46,0.42367,0.84564,0.32466,-95.767,-0.27832,0.46261,-0.84174,212.15
> view matrix models
> #6,-0.9278,0.28405,0.24186,150.65,0.33474,0.92007,0.2035,-81.565,-0.16473,0.26977,-0.94873,232.5
> view matrix models
> #6,-0.9278,0.28405,0.24186,157.88,0.33474,0.92007,0.2035,-78.095,-0.16473,0.26977,-0.94873,240.3
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.9278,0.28405,0.24186,150.7,0.33474,0.92007,0.2035,-71.058,-0.16473,0.26977,-0.94873,238.81
> view matrix models
> #6,-0.81634,0.56079,0.13821,115.48,0.57751,0.78886,0.21018,-84.976,0.0088387,0.2514,-0.96784,222.41
> view matrix models
> #6,-0.81634,0.56079,0.13821,118.12,0.57751,0.78886,0.21018,-88.409,0.0088387,0.2514,-0.96784,222.87
> view matrix models
> #6,-0.72877,0.68433,0.024424,104.87,0.66878,0.70364,0.24005,-92.216,0.14709,0.19127,-0.97045,213.88
> view matrix models
> #6,-0.90019,-0.046344,0.43302,169.43,0.063082,0.96996,0.23495,-51.468,-0.4309,0.23882,-0.87023,266.36
> view matrix models
> #6,-0.60307,-0.60859,0.51568,192.19,-0.56167,0.78301,0.26724,41.245,-0.56642,-0.12848,-0.81404,320.02
> view matrix models
> #6,-0.60307,-0.60859,0.51568,192.34,-0.56167,0.78301,0.26724,41.792,-0.56642,-0.12848,-0.81404,319.91
> view matrix models
> #6,-0.60307,-0.60859,0.51568,187.97,-0.56167,0.78301,0.26724,41.027,-0.56642,-0.12848,-0.81404,318.56
> view matrix models
> #6,-0.58764,-0.56507,0.57911,174.47,-0.52116,0.81183,0.2633,33.233,-0.61892,-0.14708,-0.77156,322.6
> view matrix models
> #6,-0.585,-0.56083,0.58587,172.96,-0.51905,0.81395,0.2609,32.978,-0.62319,-0.15147,-0.76726,323.18
> view matrix models
> #6,-0.585,-0.56083,0.58587,173.17,-0.51905,0.81395,0.2609,34.93,-0.62319,-0.15147,-0.76726,323.99
> view matrix models
> #6,-0.62592,-0.52364,0.57795,174.44,-0.48265,0.84219,0.24033,29.403,-0.61259,-0.12852,-0.77988,321.33
> view matrix models
> #6,-0.69111,-0.45479,0.56172,175.69,-0.42947,0.88352,0.18694,23.722,-0.58131,-0.11205,-0.80593,318.36
> view matrix models
> #6,-0.65976,-0.48623,0.57297,174.54,-0.42481,0.87026,0.24935,18.312,-0.61988,-0.078893,-0.78072,316.41
> view matrix models
> #6,-0.77557,-0.36253,0.51678,179.41,-0.37089,0.92414,0.091687,21.793,-0.51081,-0.12056,-0.8512,315.68
> fitmap #2 inMap #6
Fit molecule 8HS2_GPR20_Fab046_inactive (#2) to map emd_34983_8HS2.map (#6)
using 5456 atoms
average map value = 0.1675, steps = 100
shifted from previous position = 5.08
rotated from previous position = 11.4 degrees
atoms outside contour = 2741, contour level = 0.14718
Position of 8HS2_GPR20_Fab046_inactive (#2) relative to emd_34983_8HS2.map
(#6) coordinates:
Matrix rotation and translation
0.99999997 0.00023517 -0.00007495 -0.02467320
-0.00023517 0.99999997 0.00004464 0.02238681
0.00007496 -0.00004462 1.00000000 -0.01444419
Axis -0.17792930 -0.29884110 -0.93756875
Axis point 109.46996506 96.42443602 0.00000000
Rotation angle (degrees) 0.01437141
Shift along axis 0.01124241
> ui tool show "Fit in Map"
> fitmap #2 inMap #6
Fit molecule 8HS2_GPR20_Fab046_inactive (#2) to map emd_34983_8HS2.map (#6)
using 5456 atoms
average map value = 0.1675, steps = 44
shifted from previous position = 0.0144
rotated from previous position = 0.0126 degrees
atoms outside contour = 2742, contour level = 0.14718
Position of 8HS2_GPR20_Fab046_inactive (#2) relative to emd_34983_8HS2.map
(#6) coordinates:
Matrix rotation and translation
0.99999998 0.00016427 0.00012151 -0.03276013
-0.00016428 0.99999998 0.00011396 0.00467381
-0.00012149 -0.00011398 0.99999999 0.03076738
Axis -0.48712062 0.51931506 -0.70215766
Axis point 38.59729398 208.97661225 0.00000000
Rotation angle (degrees) 0.01340494
Shift along axis -0.00321824
> ui mousemode right select
> select clear
> show #!1 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
R (#2), sequence alignment score = 1937.2
RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
2.786)
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
(#3), sequence alignment score = 2126.4
RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
1.114)
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
R (#2), sequence alignment score = 1937.2
RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
2.786)
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
(#3), sequence alignment score = 2126.4
RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
1.114)
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> undo
[Repeated 3 time(s)]
> select clear
> hide #!1 models
> hide #!5 models
> fitmap #2 inMap #6
Fit molecule 8HS2_GPR20_Fab046_inactive (#2) to map emd_34983_8HS2.map (#6)
using 5456 atoms
average map value = 0.1675, steps = 100
shifted from previous position = 5.08
rotated from previous position = 11.4 degrees
atoms outside contour = 2741, contour level = 0.14718
Position of 8HS2_GPR20_Fab046_inactive (#2) relative to emd_34983_8HS2.map
(#6) coordinates:
Matrix rotation and translation
0.99999997 0.00023517 -0.00007495 -0.02467320
-0.00023517 0.99999997 0.00004464 0.02238681
0.00007496 -0.00004462 1.00000000 -0.01444419
Axis -0.17792930 -0.29884110 -0.93756875
Axis point 109.46996368 96.42443805 0.00000000
Rotation angle (degrees) 0.01437141
Shift along axis 0.01124241
Drag select of 7 residues, 6 emd_34983_8HS2.map
> select clear
> ui mousemode right translate
> volume #5 level 0.1484
> volume #6 level 0.1934
> volume #6 level 0.1195
> hide #!6 models
> show #!1 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
R (#2), sequence alignment score = 1937.2
RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
2.786)
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
(#3), sequence alignment score = 2126.4
RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
1.114)
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HS2_GPR20_Fab046_inactive, chain
R (#2), sequence alignment score = 1937.2
RMSD between 209 pruned atom pairs is 1.012 angstroms; (across all 278 pairs:
2.786)
Matchmaker 8HS3_GPR20_Gi, chain R (#1) with 8HSC_GPR20_Gi_Fab046, chain R
(#3), sequence alignment score = 2126.4
RMSD between 261 pruned atom pairs is 0.809 angstroms; (across all 271 pairs:
1.114)
> select #1/R:32-56 #3/R:32-56
308 atoms, 316 bonds, 50 residues, 2 models selected
> select #1/R:38 #3/R:38
22 atoms, 22 bonds, 2 residues, 2 models selected
> select #1/R:38 #3/R:38
22 atoms, 22 bonds, 2 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[171] RMSD: 0.428
> ui mousemode right select
> select add #2/R:38
33 atoms, 33 bonds, 3 residues, 3 models selected
> select subtract #1/R:38
22 atoms, 22 bonds, 2 residues, 2 models selected
> select add #1/R:38
33 atoms, 33 bonds, 3 residues, 3 models selected
> select subtract #3/R:38
22 atoms, 22 bonds, 2 residues, 2 models selected
> style sel stick
Changed 22 atom styles
> show sel atoms
> select add #3/R:38
33 atoms, 33 bonds, 3 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 33 atom styles
> name frozen F84 sel
> color sel byhetero
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> select #1/R:130-131 #3/R:130-131
46 atoms, 48 bonds, 4 residues, 2 models selected
> select #1/R:130 #3/R:130
24 atoms, 24 bonds, 2 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[263] RMSD: 0.875
> ui mousemode right select
> select add #2/R:131
35 atoms, 35 bonds, 3 residues, 3 models selected
> select subtract #1/R:130
23 atoms, 23 bonds, 2 residues, 2 models selected
> select add #1/R:130
35 atoms, 35 bonds, 3 residues, 3 models selected
> select subtract #3/R:130
23 atoms, 23 bonds, 2 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 23 atom styles
> select add #3/R:131
34 atoms, 34 bonds, 3 residues, 3 models selected
> select subtract #3/R:131
23 atoms, 23 bonds, 2 residues, 2 models selected
> select add #3/R:130
35 atoms, 35 bonds, 3 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 35 atom styles
> name frozen Y130 sel
> color sel byhetero
> select subtract #2/R:131
24 atoms, 24 bonds, 2 residues, 2 models selected
> select add #2/R:131
35 atoms, 35 bonds, 3 residues, 3 models selected
> select subtract #2/R:131
24 atoms, 24 bonds, 2 residues, 2 models selected
> select add #2/R:130
36 atoms, 36 bonds, 3 residues, 3 models selected
> show sel atoms
> name frozen Y130 sel
> color sel byhetero
> select clear
> select #2/R:131
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select Y130
36 atoms, 36 bonds, 3 residues, 3 models selected
> select clear
> select #1/R:134 #3/R:134
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/R:134 #3/R:134
16 atoms, 14 bonds, 2 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[267] RMSD: 1.838
> select add #2/R:134
24 atoms, 21 bonds, 3 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> name frozen M134 sel
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> select #1/R:257-258 #3/R:257-258
42 atoms, 44 bonds, 4 residues, 2 models selected
> select #1/R:257-258 #3/R:257-258
42 atoms, 44 bonds, 4 residues, 2 models selected
> select #1/R:257-258 #3/R:257-258
42 atoms, 44 bonds, 4 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[390-391] RMSD: 0.722
> select #1/R:257-258 #3/R:257-258
42 atoms, 44 bonds, 4 residues, 2 models selected
> select #1/R:257-258 #3/R:257-258
42 atoms, 44 bonds, 4 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[390-391] RMSD: 0.722
> select #1/R:257 #3/R:257
22 atoms, 22 bonds, 2 residues, 2 models selected
> select #1/R:257 #3/R:257
22 atoms, 22 bonds, 2 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[390] RMSD: 0.473
> select subtract #1/R:257
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1/R:257
22 atoms, 22 bonds, 2 residues, 2 models selected
> select add #2/R:258
32 atoms, 32 bonds, 3 residues, 3 models selected
> select subtract #2/R:258
22 atoms, 22 bonds, 2 residues, 2 models selected
> select add #2/R:257
33 atoms, 33 bonds, 3 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 33 atom styles
> color sel byhetero
> name frozen F257 sel
> select clear
> select #2/B
1617 atoms, 1658 bonds, 1 pseudobond, 218 residues, 2 models selected
> hide sel cartoons
> select #2/C
1623 atoms, 1658 bonds, 211 residues, 1 model selected
> hide sel cartoons
> select #3/C
438 atoms, 444 bonds, 57 residues, 1 model selected
> hide sel cartoons
> select #3/B
2590 atoms, 2637 bonds, 338 residues, 1 model selected
> hide sel cartoons
> select #3/A
1712 atoms, 1741 bonds, 2 pseudobonds, 218 residues, 2 models selected
> hide sel cartoons
> select #3/S
1760 atoms, 1806 bonds, 1 pseudobond, 232 residues, 2 models selected
> hide sel cartoons
> select #2/R:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/R:32
2 atoms, 1 bond, 1 residue, 1 model selected
> select #1/R:32-33 #3/R:32-33
19 atoms, 18 bonds, 4 residues, 2 models selected
> select #1/R:32-52 #3/R:32-52
256 atoms, 262 bonds, 42 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[165-185] RMSD: 1.047
> select #1/R:32 #3/R:32
9 atoms, 7 bonds, 2 residues, 2 models selected
> select #1/R:32-49 #3/R:32-49
228 atoms, 233 bonds, 36 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[165-182] RMSD: 1.077
> select subtract #1/R:38@CG
227 atoms, 230 bonds, 36 residues, 2 models selected
> select subtract #3/R:38
216 atoms, 217 bonds, 35 residues, 2 models selected
> select subtract #1/R:38@CZ
215 atoms, 215 bonds, 35 residues, 2 models selected
> select subtract #1/R:38@CE1
214 atoms, 214 bonds, 35 residues, 2 models selected
> select subtract #1/R:38@CD1
213 atoms, 214 bonds, 35 residues, 2 models selected
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select subtract #1/R:38@CD2
212 atoms, 212 bonds, 35 residues, 2 models selected
> select subtract #1/R:38@CE2
211 atoms, 212 bonds, 35 residues, 2 models selected
> select subtract #1/R:38@CB
210 atoms, 212 bonds, 35 residues, 2 models selected
> select clear
> select sequence VPLFHLFARLDEELHGFT
Nothing selected
> select sequence VPLFHLFARLDEELHGFT
Nothing selected
> select sequence VPLFHLFARLDEELHGFT
Nothing selected
> select sequence VPLFHLFARLDEELHGFT
Nothing selected
> select sequence VPLFHLFARLDEELHGFT
Nothing selected
> select #1/R:32 #3/R:32
9 atoms, 7 bonds, 2 residues, 2 models selected
> select #1/R:32-49 #3/R:32-49
228 atoms, 233 bonds, 36 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[165-182] RMSD: 1.077
> select clear
> select #1/R:32 #3/R:32
9 atoms, 7 bonds, 2 residues, 2 models selected
> select #1/R:32-49 #3/R:32-49
228 atoms, 233 bonds, 36 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[165-182] RMSD: 1.077
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R #3/R
Alignment identifier is 1
> select #1/R:32 #3/R:32
9 atoms, 7 bonds, 2 residues, 2 models selected
> select #1/R:32-49 #3/R:32-49
228 atoms, 233 bonds, 36 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[165-182] RMSD: 1.077
> select clear
> transparency #1 #2 #3 70 ribbons
> select #1/R:32 #3/R:32
9 atoms, 7 bonds, 2 residues, 2 models selected
> select #1/R:32-49 #3/R:32-49
228 atoms, 233 bonds, 36 residues, 2 models selected
Soluble Cytochrome b562,G-protein Coupled Receptor 20 [ID: 1] region 2 chains
[165-182] RMSD: 1.077
> transparency sel 0 ribbons
> ui tool show "Show Sequence Viewer"
> sequence chain #2/R
Alignment identifier is 2/R
> select #2/R:32
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/R:32-49
152 atoms, 157 bonds, 18 residues, 1 model selected
> transparency sel 0 ribbons
> select clear
> select F257
33 atoms, 33 bonds, 3 residues, 3 models selected
> transparency sel 0 ribbons
> select F84
33 atoms, 33 bonds, 3 residues, 3 models selected
> transparency sel 0 ribbons
> select M134
24 atoms, 21 bonds, 3 residues, 3 models selected
> transparency sel 0 ribbons
> select Y130
36 atoms, 36 bonds, 3 residues, 3 models selected
> transparency sel 0 ribbons
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui mousemode right translate
> save "/Users/dongju/Desktop/Research projects-
> Monash/NRE/Figure2_DL/Fig3A_overlay with N-cap.cxs"
> save "/Users/dongju/Desktop/Research projects-
> Monash/NRE/Figure2_DL/Fig3A_overlay with N-cap.png" width 3000 height 2253
> supersample 3
> ui mousemode right select
> select #2/R:278
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2/R:277
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #1/R:278
19 atoms, 16 bonds, 3 residues, 2 models selected
> select add #1/R:280
29 atoms, 26 bonds, 4 residues, 2 models selected
> select add #1/R:279
41 atoms, 38 bonds, 5 residues, 2 models selected
> select add #1/R:282
46 atoms, 42 bonds, 6 residues, 2 models selected
> select add #2/R:282
51 atoms, 46 bonds, 7 residues, 2 models selected
> select add #1/R:281
56 atoms, 50 bonds, 8 residues, 2 models selected
> select add #2/R:281
63 atoms, 56 bonds, 9 residues, 2 models selected
> select add #1/R:257
74 atoms, 67 bonds, 10 residues, 2 models selected
> select add #1/R:255
81 atoms, 73 bonds, 11 residues, 2 models selected
> select add #1/R:256
88 atoms, 80 bonds, 12 residues, 2 models selected
> select add #2/R:256
95 atoms, 87 bonds, 13 residues, 2 models selected
> transparency sel 80 ribbons
> select #2/R:257
11 atoms, 11 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #1/R:256
7 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #2/R:256
7 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #2/R:278
7 atoms, 6 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #1/R:278
5 atoms, 4 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #1/R:279
12 atoms, 12 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #2/R:280
10 atoms, 10 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #2/R:281
7 atoms, 6 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #1/R:281
5 atoms, 4 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #2/R:282
5 atoms, 4 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #2/R:281
7 atoms, 6 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #3/R:283
7 atoms, 6 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #1/R:284
7 atoms, 6 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #1/R:283
7 atoms, 6 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #2/R:256
7 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #1/R:256
7 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #1/R:255
7 atoms, 6 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #2/R:255
7 atoms, 6 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #1/R:257
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/R:257
11 atoms, 11 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #2/R:284
7 atoms, 6 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #2/R:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #1/R:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #3/R:284
7 atoms, 6 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> select #3/R:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 80 ribbons
> save "/Users/dongju/Desktop/Research projects-
> Monash/NRE/Figure2_DL/Fig3A_overlay focus on sites.png" width 2000 height
> 1502 supersample 3 transparentBackground true
> hide #!1 models
> hide #!3 models
> show #!6 models
> fitmap #2 inMap #6
Fit molecule 8HS2_GPR20_Fab046_inactive (#2) to map emd_34983_8HS2.map (#6)
using 5456 atoms
average map value = 0.1675, steps = 100
shifted from previous position = 5.08
rotated from previous position = 11.4 degrees
atoms outside contour = 2107, contour level = 0.11947
Position of 8HS2_GPR20_Fab046_inactive (#2) relative to emd_34983_8HS2.map
(#6) coordinates:
Matrix rotation and translation
0.99999997 0.00023103 -0.00007011 -0.02470953
-0.00023103 0.99999997 0.00004231 0.02222854
0.00007012 -0.00004230 1.00000000 -0.01412533
Axis -0.17258750 -0.28605508 -0.94254233
Axis point 110.09560083 98.58536558 0.00000000
Rotation angle (degrees) 0.01404400
Shift along axis 0.01121969
> volume #!6 showOutlineBox true
> transparency #6.1 50
> volume #!6 style surface
> transparency #6.1 0
> transparency #6.1 50
> ui tool show "Volume Viewer"
> volume #6 level 0.09308
Drag select of 4 residues, 6 emd_34983_8HS2.map
> select clear
> ui mousemode right translate
> transparency #2 0 ribbons
> ui mousemode right select
> select #6
2 models selected
> select #6
2 models selected
> select #6
2 models selected
> select #6
2 models selected
> select #6
2 models selected
> select #6
2 models selected
> ui mousemode right "map eraser"
> ui mousemode right translate
> ui mousemode right zone
> ui mousemode right select
> select clear
> ui mousemode right zone
> surface dust #6 size 8.32
> color zone #6 near #2 distance 4.99
> transparency #6.1 0
> transparency #6.1 50
> color zone #6 near #2 distance 4.99
> volume #!6 style mesh
> volume #!6 style surface
> transparency #6.1 0
> transparency #6.1 50
> ui tool show "Show Volume Menu"
> ui tool show "Map Eraser"
> volume erase #6 center 124.57,110.05,133.7 radius 6.5895
Opened emd_34983_8HS2.map copy as #8, grid size 288,288,288, pixel 0.832,
shown at step 1, values float32
> volume erase #8 center 120.56,104.96,144.21 radius 6.5894
> volume erase #8 center 117.1,104.97,149.62 radius 6.5894
> volume erase #8 center 120.05,95.441,152.15 radius 6.5894
> volume erase #8 center 109.24,96.945,141.85 radius 8.3866 outside true
> volume erase #8 center 118.04,103.24,141.03 radius 8.3866
> volume erase #8 center 111.63,95.96,140.03 radius 7.3083 outside true
> ui mousemode right translate
> ui mousemode right "map eraser"
> volume erase #8 center 115.66,94.691,144.82 radius 3.2348
> volume erase #8 center 113.16,95.458,147.38 radius 3.2348
> volume erase #8 center 112.7,100.2,146.3 radius 3.2348
> volume erase #8 center 110.12,98.585,145.4 radius 3.2348
> volume erase #8 center 105.8,98.357,144.04 radius 3.2348
> volume erase #8 center 105.85,99.35,141.39 radius 3.2348
> volume erase #8 center 114.67,98.698,141.82 radius 3.2348
> volume erase #8 center 113.72,98.218,138.99 radius 3.2348
> volume erase #8 center 116.45,94.204,139.61 radius 3.2348
> ui mousemode right translate
> ui mousemode right "map eraser"
> volume erase #8 center 108.61,87.652,142 radius 3.2348
> volume erase #8 center 102.85,92.868,142.98 radius 3.2348
> volume erase #8 center 103.11,93.869,142.87 radius 3.2348
> volume erase #8 center 102.9,94.021,139.02 radius 3.2348
> ui mousemode right translate
> ui mousemode right "map eraser"
> volume erase #8 center 103.68,93.71,140.23 radius 3.2348
> undo
[Repeated 2 time(s)]
> volume erase #8 center 106.2,89.507,139.97 radius 3.2348
> volume erase #8 center 109.44,100.3,138.17 radius 3.2348
> volume erase #8 center 107.5,101.57,137.78 radius 3.2348
> ui mousemode right translate
> ui mousemode right "map eraser"
> volume erase #8 center 108.5,101.66,141.97 radius 3.2348
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right translate
> select add #8
4 models selected
> volume sel & #!8 style mesh
> volume sel & #!8 style surface
> volume sel & #!8 style image
> volume sel & #!8 style mesh
> volume #8 color #c64ee2
> volume #8 color #c64ee200
> volume #8 color #d736f5
> volume #8 step 2
> volume #8 step 1
> ui mousemode right select
> select clear
> transparency #2 70 ribbons
> volume #8 level 0.06783
> ui mousemode right "map eraser"
> volume erase #8 center 112.61,89.834,142.12 radius 1.8827
> ui mousemode right select
> ui mousemode right translate
> ui mousemode right "map eraser"
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> select add #2
5456 atoms, 5592 bonds, 1 pseudobond, 716 residues, 2 models selected
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> save "/Users/dongju/Desktop/Research projects-
> Monash/NRE/Figure2_DL/Fig3B_inactive GPR20 with the map.cxs"
——— End of log from Wed Feb 28 18:29:12 2024 ———
opened ChimeraX session
> volume #!8 showOutlineBox false
> hide #!8 models
> save "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
> draft/Figure 7C-GPR20 inactive-no G protein.cxs"
> select add #2
5456 atoms, 5592 bonds, 1 pseudobond, 716 residues, 2 models selected
> show sel cartoons
> ui mousemode right select
> select clear
> select #2/C
1623 atoms, 1658 bonds, 211 residues, 1 model selected
> color sel #d3b5eaff
> color sel #d4b6eaff
> color sel #d7b9eaff
> color sel #d8baebff
> color sel #dbbdebff
> color sel #dcbdebff
> color sel #ddc0ecff
[Repeated 1 time(s)]
> color sel #dcc1ecff
> color sel #dcc1edff
> color sel #dcc3edff
> color sel #ddc3edff
[Repeated 1 time(s)]
> color sel #dcc3edff
[Repeated 1 time(s)]
> color sel #dcc4edff
> color sel #ddc6edff
> color sel #dcc8eeff
[Repeated 1 time(s)]
> color sel #dbc8eeff
[Repeated 2 time(s)]
> color sel #dac8eeff
[Repeated 2 time(s)]
> color sel #d9c8eeff
> color sel #d9caefff
[Repeated 1 time(s)]
> color sel #d8caefff
> color sel #d7caefff
> color sel #d7cbefff
> color sel #d7caefff
> color sel #d5caefff
[Repeated 1 time(s)]
> color sel #d4c9eeff
> color sel #d3c8edff
> color sel #d2c8edff
> color sel #d1c7edff
> color sel #d0c6edff
[Repeated 1 time(s)]
> color sel #cfc4ecff
> color sel #c9beebff
> color sel #c7baebff
> color sel #c3b5e9ff
> color sel #c1b2e9ff
> color sel #c0b1e9ff
> color sel #bfafe8ff
> color sel #b5a2e6ff
> color sel #b09ce5ff
> color sel #ae9be5ff
> color sel #ab98e4ff
> color sel #a696e4ff
> color sel #a496e4ff
> color sel #a093e4ff
> color sel #9e93e4ff
> color sel #9d93e4ff
> color sel #9e93e3ff
[Repeated 2 time(s)]
> color sel #9d93e3ff
[Repeated 1 time(s)]
> color sel #9e94e4ff
> color sel #aaa1e5ff
> color sel #bab3e9ff
> color sel #c3bdebff
> color sel #c4beebff
> color sel #c4beecff
> color sel #c4bfecff
> color sel #c6c1ecff
> color sel #cbc7edff
> color sel #d1ccefff
> color sel #d1cdefff
[Repeated 1 time(s)]
> color sel #d2cef0ff
> color sel #d3d0f0ff
> color sel #d6d4f0ff
> color sel #dedcf2ff
> color sel #e4e2f5ff
> color sel #e5e4f6ff
> color sel #ecebf7ff
[Repeated 3 time(s)]
> color sel #ebe8f6ff
> color sel #e6e3f5ff
> color sel #ded6f1ff
> color sel #d8cdefff
> color sel #c5afe8ff
> color sel #bca2e6ff
> color sel #b292e4ff
> color sel #af8de3ff
> color sel #af8ce3ff
> color sel #af8de3ff
> color sel #b18de3ff
> color sel #b58ee3ff
> color sel #bf8de3ff
> color sel #c68ee4ff
> color sel #d391e4ff
> color sel #d993e4ff
> color sel #dc94e5ff
> color sel #dd95e4ff
> color sel #dd95e3ff
> color sel #dd94e3ff
> color sel #dd95e1ff
> color sel #de98dfff
> color sel #df9de0ff
> color sel #e1a7e2ff
> color sel #e5b6e5ff
> color sel #e8bee7ff
> color sel #e9c3e7ff
> color sel #e9c4e8ff
> color sel #eac5e9ff
> color sel #eed4ecff
> color sel #efd8edff
> color sel #f0d9eeff
> color sel #f0daeeff
> color sel #f0daedff
[Repeated 2 time(s)]
> color sel #efd8ecff
> color sel #eac6e4ff
> color sel #e8c1e3ff
> color sel #e8c0e3ff
[Repeated 1 time(s)]
> color sel #e7bde2ff
> color sel #e6b9e0ff
> color sel #e5b7e0ff
> color sel #e5b2deff
> color sel #e3aedcff
> color sel #e3addcff
[Repeated 5 time(s)]
> color sel #e3addaff
[Repeated 2 time(s)]
> color sel #e3add9ff
[Repeated 1 time(s)]
> color sel #e3aedaff
> color sel #e4b0daff
> color sel #e5b3dbff
> color sel #e5b3dcff
> color sel #e5b4dbff
> color sel #e6b8ddff
> color sel #e8c1dfff
> color sel #e8c2e0ff
[Repeated 1 time(s)]
> color sel #e9c2e0ff
> color sel #e8c2e0ff
> color sel #e8c2dfff
> color sel #e9c3e0ff
[Repeated 2 time(s)]
> select #2/B
1617 atoms, 1658 bonds, 1 pseudobond, 218 residues, 2 models selected
> color (#!2 & sel) #3e6122ff
> color (#!2 & sel) #3e6323ff
> color (#!2 & sel) #406924ff
> color (#!2 & sel) #406c25ff
> color (#!2 & sel) #416f26ff
> color (#!2 & sel) #437126ff
> color (#!2 & sel) #447327ff
> color (#!2 & sel) #467a2aff
> color (#!2 & sel) #477c2aff
[Repeated 2 time(s)]
> color (#!2 & sel) #487b2aff
> color (#!2 & sel) #497b2aff
> color (#!2 & sel) #4b7829ff
> color (#!2 & sel) #4b7528ff
> color (#!2 & sel) #4c7428ff
> color (#!2 & sel) #4c7327ff
> color (#!2 & sel) #4c7227ff
[Repeated 1 time(s)]
> color (#!2 & sel) #4d6f27ff
> color (#!2 & sel) #4f6d26ff
> color (#!2 & sel) #516d26ff
> color (#!2 & sel) #536d26ff
> color (#!2 & sel) #556e27ff
> color (#!2 & sel) #566d26ff
> color (#!2 & sel) #5a6d27ff
> color (#!2 & sel) #5b6c27ff
> color (#!2 & sel) #5e6d27ff
[Repeated 1 time(s)]
> color (#!2 & sel) #5f6d27ff
> color (#!2 & sel) #616f27ff
> color (#!2 & sel) #626f28ff
> color (#!2 & sel) #68762aff
> color (#!2 & sel) #74832eff
> color (#!2 & sel) #7d8b31ff
> color (#!2 & sel) #808f32ff
> color (#!2 & sel) #899835ff
> color (#!2 & sel) #8e9e36ff
> color (#!2 & sel) #93a438ff
> color (#!2 & sel) #97a93aff
> color (#!2 & sel) #99ac3aff
> color (#!2 & sel) #9ab13cff
> color (#!2 & sel) #9db63dff
> color (#!2 & sel) #a0ba3eff
> color (#!2 & sel) #a1bc3fff
> color (#!2 & sel) #a7c542ff
> color (#!2 & sel) #a7c842ff
> color (#!2 & sel) #a8ca43ff
> color (#!2 & sel) #a8cb43ff
[Repeated 1 time(s)]
> color (#!2 & sel) #a6ca43ff
> color (#!2 & sel) #a5c942ff
> color (#!2 & sel) #a1c842ff
> color (#!2 & sel) #9ec541ff
> color (#!2 & sel) #96be3fff
> color (#!2 & sel) #92b83dff
> color (#!2 & sel) #8baf3bff
> color (#!2 & sel) #86ab39ff
> color (#!2 & sel) #83a738ff
> color (#!2 & sel) #79a036ff
> color (#!2 & sel) #729934ff
> color (#!2 & sel) #709733ff
> color (#!2 & sel) #6e9633ff
> color (#!2 & sel) #6d9532ff
> color (#!2 & sel) #6b9332ff
> color (#!2 & sel) #699231ff
> color (#!2 & sel) #659131ff
> color (#!2 & sel) #618d30ff
> color (#!2 & sel) #5f8c30ff
[Repeated 1 time(s)]
> color (#!2 & sel) #5f8d30ff
> color (#!2 & sel) #5e8d30ff
> color (#!2 & sel) #5d8f30ff
> color (#!2 & sel) #5c9231ff
> color (#!2 & sel) #5c9331ff
> color (#!2 & sel) #5d9732ff
> color (#!2 & sel) #5c9732ff
> color (#!2 & sel) #5d9833ff
> color (#!2 & sel) #5d9c34ff
> color (#!2 & sel) #5fa035ff
> color (#!2 & sel) #61a336ff
> color (#!2 & sel) #62a737ff
> color (#!2 & sel) #62a837ff
> color (#!2 & sel) #62a937ff
> color (#!2 & sel) #62aa38ff
> color (#!2 & sel) #63ac38ff
> color (#!2 & sel) #63af39ff
> color (#!2 & sel) #66b53aff
> color (#!2 & sel) #68bb3cff
> color (#!2 & sel) #6ac03eff
> color (#!2 & sel) #6bc13eff
> color (#!2 & sel) #6cc23eff
> color (#!2 & sel) #6ac43eff
> color (#!2 & sel) #6cc840ff
> color (#!2 & sel) #6ecc41ff
> color (#!2 & sel) #6fd042ff
> color (#!2 & sel) #70d242ff
[Repeated 1 time(s)]
> color (#!2 & sel) #6fd242ff
[Repeated 1 time(s)]
> color (#!2 & sel) #6cd041ff
> color (#!2 & sel) #67c840ff
> color (#!2 & sel) #64c33eff
> color (#!2 & sel) #5eb73bff
> color (#!2 & sel) #5db53aff
[Repeated 2 time(s)]
> color (#!2 & sel) #5ab139ff
> color (#!2 & sel) #58af39ff
> color (#!2 & sel) #55ab37ff
> color (#!2 & sel) #50a536ff
> color (#!2 & sel) #4da235ff
> color (#!2 & sel) #489832ff
> color (#!2 & sel) #459030ff
> color (#!2 & sel) #42892eff
> color (#!2 & sel) #3d7e2bff
> color (#!2 & sel) #3c7c2aff
> color (#!2 & sel) #3a7929ff
> color (#!2 & sel) #397628ff
> color (#!2 & sel) #387528ff
> color (#!2 & sel) #397528ff
> color (#!2 & sel) #377227ff
> color (#!2 & sel) #377127ff
[Repeated 1 time(s)]
> color (#!2 & sel) #367026ff
> color (#!2 & sel) #356c25ff
> color (#!2 & sel) #377127ff
> color (#!2 & sel) #3c7c2bff
> color (#!2 & sel) #3e822eff
> color (#!2 & sel) #3f822eff
> color (#!2 & sel) #3f842eff
> color (#!2 & sel) #438c30ff
> color (#!2 & sel) #469333ff
[Repeated 2 time(s)]
> color (#!2 & sel) #479534ff
> color (#!2 & sel) #4a9b35ff
> color (#!2 & sel) #4c9f37ff
> color (#!2 & sel) #4ea338ff
> color (#!2 & sel) #50a839ff
> color (#!2 & sel) #52ad3bff
> color (#!2 & sel) #57b83eff
> color (#!2 & sel) #57b93eff
> color (#!2 & sel) #58b93eff
> color (#!2 & sel) #5bc140ff
> color (#!2 & sel) #60cb43ff
> color (#!2 & sel) #61ce44ff
> color (#!2 & sel) #62d044ff
> color (#!2 & sel) #63d345ff
> color (#!2 & sel) #64d446ff
> color (#!2 & sel) #64d546ff
[Repeated 1 time(s)]
> color (#!2 & sel) #65d646ff
> color (#!2 & sel) #65d746ff
> color (#!2 & sel) #66d847ff
> color (#!2 & sel) #66d945ff
> color (#!2 & sel) #67db45ff
> color (#!2 & sel) #69df46ff
> color (#!2 & sel) #69e046ff
> color (#!2 & sel) #6ae146ff
> color (#!2 & sel) #6ae346ff
> color (#!2 & sel) #6ce447ff
[Repeated 3 time(s)]
> color (#!2 & sel) #6de447ff
> color (#!2 & sel) #6ee547ff
> color (#!2 & sel) #6ee447ff
> color (#!2 & sel) #6fe347ff
> color (#!2 & sel) #71e246ff
> color (#!2 & sel) #71e146ff
> color (#!2 & sel) #73e146ff
[Repeated 1 time(s)]
> color (#!2 & sel) #73e046ff
[Repeated 1 time(s)]
> color (#!2 & sel) #73df45ff
> color (#!2 & sel) #74de45ff
> color (#!2 & sel) #75df46ff
> color (#!2 & sel) #74dd45ff
> color (#!2 & sel) #74db45ff
> color (#!2 & sel) #74da44ff
> color (#!2 & sel) #74d844ff
> color (#!2 & sel) #74d543ff
> color (#!2 & sel) #73d342ff
> color (#!2 & sel) #73d242ff
> color (#!2 & sel) #72d042ff
> color (#!2 & sel) #6ecd41ff
> color (#!2 & sel) #6dcb40ff
> color (#!2 & sel) #69c83fff
> color (#!2 & sel) #68c63fff
> color (#!2 & sel) #67c53eff
> color (#!2 & sel) #66c33eff
> color (#!2 & sel) #64c33eff
> color (#!2 & sel) #61c03dff
> color (#!2 & sel) #5fbf3dff
> color (#!2 & sel) #5fbe3dff
> color (#!2 & sel) #5dbd3cff
> color (#!2 & sel) #5cbd3cff
[Repeated 1 time(s)]
> color (#!2 & sel) #5cbc3cff
[Repeated 3 time(s)]
> color (#!2 & sel) #5bbb3cff
[Repeated 1 time(s)]
> color (#!2 & sel) #5abb3cff
[Repeated 2 time(s)]
> color (#!2 & sel) #59bb3cff
[Repeated 8 time(s)]
> color (#!2 & sel) #58bb3cff
> color (#!2 & sel) #59bb3cff
> color (#!2 & sel) #58bb3cff
> color (#!2 & sel) #59bb3dff
[Repeated 1 time(s)]
> color (#!2 & sel) #59bc3eff
[Repeated 6 time(s)]
> color (#!2 & sel) #59bd3fff
[Repeated 2 time(s)]
> color (#!2 & sel) #59bd40ff
[Repeated 1 time(s)]
> color (#!2 & sel) #5abe40ff
[Repeated 1 time(s)]
> color (#!2 & sel) #5bc041ff
> color (#!2 & sel) #5cc342ff
[Repeated 1 time(s)]
> color (#!2 & sel) #5dc444ff
> color (#!2 & sel) #5ec745ff
> color (#!2 & sel) #5fc945ff
> color (#!2 & sel) #5fca46ff
> color (#!2 & sel) #60cb46ff
> color (#!2 & sel) #5dc645ff
> color (#!2 & sel) #5bbf42ff
> color (#!2 & sel) #59bc42ff
[Repeated 3 time(s)]
> color (#!2 & sel) #58bb41ff
> color (#!2 & sel) #56b540ff
> color (#!2 & sel) #55b440ff
> color (#!2 & sel) #55b33fff
[Repeated 2 time(s)]
> color (#!2 & sel) #53af3eff
> color (#!2 & sel) #52ae3eff
> color (#!2 & sel) #53ae40ff
> color (#!2 & sel) #52ae40ff
> color (#!2 & sel) #53ae41ff
> color (#!2 & sel) #54b143ff
> color (#!2 & sel) #54b245ff
[Repeated 1 time(s)]
> color (#!2 & sel) #55b345ff
> color (#!2 & sel) #56b646ff
> color (#!2 & sel) #58b949ff
> color (#!2 & sel) #59bc4bff
> color (#!2 & sel) #59bd4cff
> color (#!2 & sel) #5abf4cff
> color (#!2 & sel) #5bc14dff
> color (#!2 & sel) #5dc44fff
> color (#!2 & sel) #5ec852ff
> color (#!2 & sel) #5fc953ff
[Repeated 2 time(s)]
> color (#!2 & sel) #5fca53ff
[Repeated 2 time(s)]
> color (#!2 & sel) #5fc953ff
> color (#!2 & sel) #5bc151ff
> color (#!2 & sel) #5abf50ff
> color (#!2 & sel) #59bd4fff
[Repeated 1 time(s)]
> color (#!2 & sel) #58bb4fff
> color (#!2 & sel) #57b74bff
> color (#!2 & sel) #54b246ff
> color (#!2 & sel) #54b245ff
> color (#!2 & sel) #53b041ff
> color (#!2 & sel) #53af41ff
[Repeated 2 time(s)]
> color (#!2 & sel) #53af40ff
> color (#!2 & sel) #51ab3aff
> color (#!2 & sel) #4fa636ff
> color (#!2 & sel) #4e9f34ff
> color (#!2 & sel) #4b9932ff
> color (#!2 & sel) #3f7929ff
[Repeated 1 time(s)]
> color (#!2 & sel) #3e7829ff
> color (#!2 & sel) #3d7628ff
> color (#!2 & sel) #396e25ff
> color (#!2 & sel) #315e21ff
> color (#!2 & sel) #2f5a1fff
> color (#!2 & sel) #2b531dff
> color (#!2 & sel) #294d1bff
> color (#!2 & sel) #27491aff
> color (#!2 & sel) #28481aff
> color (#!2 & sel) #284719ff
> color (#!2 & sel) #294619ff
> color (#!2 & sel) #2a4619ff
[Repeated 1 time(s)]
> color (#!2 & sel) #2b4519ff
> color (#!2 & sel) #2c4519ff
> color (#!2 & sel) #2e471aff
> color (#!2 & sel) #30491aff
> color (#!2 & sel) #334b1bff
> color (#!2 & sel) #37511dff
> color (#!2 & sel) #3c561fff
> color (#!2 & sel) #3e5920ff
> color (#!2 & sel) #445f22ff
> color (#!2 & sel) #466122ff
> color (#!2 & sel) #476223ff
> color (#!2 & sel) #4b6825ff
> color (#!2 & sel) #517027ff
> color (#!2 & sel) #547629ff
> color (#!2 & sel) #557a2aff
> color (#!2 & sel) #577c2bff
> color (#!2 & sel) #577e2bff
> color (#!2 & sel) #5a812cff
> color (#!2 & sel) #5c852dff
> color (#!2 & sel) #5e882eff
> color (#!2 & sel) #5f8b2fff
> color (#!2 & sel) #639231ff
[Repeated 1 time(s)]
> color (#!2 & sel) #639331ff
[Repeated 1 time(s)]
> color (#!2 & sel) #659733ff
> color (#!2 & sel) #669933ff
> color (#!2 & sel) #679b34ff
[Repeated 2 time(s)]
> color (#!2 & sel) #679933ff
> color (#!2 & sel) #6b9933ff
> color (#!2 & sel) #6b9a33ff
> color (#!2 & sel) #6c9933ff
> color (#!2 & sel) #6f9934ff
> color (#!2 & sel) #709934ff
> color (#!2 & sel) #729934ff
> color (#!2 & sel) #739934ff
> color (#!2 & sel) #739834ff
> color (#!2 & sel) #729834ff
> color (#!2 & sel) #749834ff
> color (#!2 & sel) #759834ff
> color (#!2 & sel) #779834ff
> color (#!2 & sel) #789834ff
[Repeated 1 time(s)]
> color (#!2 & sel) #7a9834ff
[Repeated 1 time(s)]
> color (#!2 & sel) #7b9734ff
[Repeated 2 time(s)]
> color (#!2 & sel) #7c9734ff
> color (#!2 & sel) #7c9834ff
[Repeated 1 time(s)]
> color (#!2 & sel) #7f9834ff
[Repeated 1 time(s)]
> color (#!2 & sel) #809734ff
> color (#!2 & sel) #829534ff
> color (#!2 & sel) #839634ff
> color (#!2 & sel) #829533ff
[Repeated 1 time(s)]
> color (#!2 & sel) #829534ff
> color (#!2 & sel) #839534ff
> color (#!2 & sel) #829533ff
> color (#!2 & sel) #839534ff
[Repeated 4 time(s)]
> color (#!2 & sel) #839634ff
[Repeated 1 time(s)]
> color (#!2 & sel) #839734ff
> color (#!2 & sel) #819533ff
> color (#!2 & sel) #798b30ff
> color (#!2 & sel) #778930ff
> color (#!2 & sel) #74882fff
> color (#!2 & sel) #71862fff
> color (#!2 & sel) #6e852eff
> color (#!2 & sel) #6d852eff
> color (#!2 & sel) #69842eff
> color (#!2 & sel) #68842eff
> color (#!2 & sel) #68832dff
> color (#!2 & sel) #66832dff
[Repeated 1 time(s)]
> color (#!2 & sel) #65832dff
> color (#!2 & sel) #63832dff
> color (#!2 & sel) #60822cff
[Repeated 2 time(s)]
> color (#!2 & sel) #5e822cff
> color (#!2 & sel) #5c822cff
[Repeated 2 time(s)]
> color (#!2 & sel) #5b822cff
> color (#!2 & sel) #5a822cff
> color (#!2 & sel) #5a832dff
> color (#!2 & sel) #5c882eff
> color (#!2 & sel) #5b8b2fff
> color (#!2 & sel) #5c8d30ff
> color (#!2 & sel) #5e9131ff
> color (#!2 & sel) #609532ff
[Repeated 2 time(s)]
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> transparency all 0 ribbons
> lighting soft
> save "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
> draft/Figure 7C-GPR20 inactive-no G protein.cxs"
> save "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
> draft/Figure 7C-GPR20 inactive structure with tags.png" width 1751 height
> 1200 supersample 3
> close session
> open 8tb7
8tb7 title:
Cryo-EM Structure of GPR61- [more info...]
Chain information for 8tb7 #1
---
Chain | Description | UniProt
H | Fab24 BAK5 heavy chain |
L | Fab24 BAK5 light chain |
N | Fab hinge-binding nanobody |
R | G-protein coupled receptor 61,Soluble cytochrome b562 | GPR61_HUMAN 11-242 365-532, C562_ECOLX 248-352
Non-standard residues in 8tb7 #1
---
ZOB —
6-{[(3,5-difluoropyridin-4-yl)methyl]amino}-N-(4-ethoxy-6-methylpyrimidin-2-yl)-2-methoxy-N-(2-methoxyethyl)pyridine-3-sulfonamide
> rename #1 GPR61_BRIL_8tb7
> hide atoms
> select /R
5276 atoms, 5329 bonds, 4 pseudobonds, 330 residues, 2 models selected
> color (#!1 & sel) byhetero
> color (#!1 & sel) #131db3ff
> color (#!1 & sel) #101dbfff
> color (#!1 & sel) #0b1ccfff
> color (#!1 & sel) #061cd8ff
> color (#!1 & sel) #001aeeff
> color (#!1 & sel) #001bf1ff
> color (#!1 & sel) #001bf3ff
> color (#!1 & sel) #001bf5ff
> color (#!1 & sel) #001df1ff
> color (#!1 & sel) #001ef0ff
[Repeated 1 time(s)]
> color (#!1 & sel) #001feeff
> color (#!1 & sel) #0923eaff
> color (#!1 & sel) #0b26ebff
> color (#!1 & sel) #2150ebff
> color (#!1 & sel) #4ca7edff
> color (#!1 & sel) #61d3f1ff
> color (#!1 & sel) #70f1eeff
> color (#!1 & sel) #71f1e5ff
[Repeated 1 time(s)]
> color (#!1 & sel) #70efe6ff
> color (#!1 & sel) #70e9ebff
> color (#!1 & sel) #6cdceaff
> color (#!1 & sel) #5bade5ff
> color (#!1 & sel) #5391e3ff
> color (#!1 & sel) #528ee3ff
> color (#!1 & sel) #5391e3ff
> color (#!1 & sel) #65b3e4ff
> color (#!1 & sel) #72cae5ff
> color (#!1 & sel) #76cce4ff
> color (#!1 & sel) #84d1e5ff
> color (#!1 & sel) #8ad4e5ff
[Repeated 1 time(s)]
> color (#!1 & sel) #8ad5e5ff
> color (#!1 & sel) #8cd8e5ff
> color (#!1 & sel) #8edae5ff
> color (#!1 & sel) #8cd3e4ff
> color (#!1 & sel) #8194e2ff
> color (#!1 & sel) #7d7fe1ff
> color (#!1 & sel) #817fe1ff
> color (#!1 & sel) #857fe2ff
> color (#!1 & sel) #8d7ae1ff
> color (#!1 & sel) #ab77e0ff
> color (#!1 & sel) #c26ae1ff
> color (#!1 & sel) #c368e0ff
[Repeated 1 time(s)]
> color (#!1 & sel) #c86de1ff
> color (#!1 & sel) #cd74e1ff
> color (#!1 & sel) #d078e1ff
> color (#!1 & sel) #d27ee2ff
> color (#!1 & sel) #d486e3ff
> color (#!1 & sel) #d488e3ff
> color (#!1 & sel) #d58ae3ff
> color (#!1 & sel) #d893e4ff
> color (#!1 & sel) #d995e5ff
[Repeated 1 time(s)]
> color (#!1 & sel) #dc9ae5ff
> color (#!1 & sel) #e1a1e7ff
[Repeated 1 time(s)]
> color (#!1 & sel) #e1a2e6ff
> color (#!1 & sel) #e0a2e5ff
> color (#!1 & sel) #df9ee2ff
> color (#!1 & sel) #d978d8ff
> color (#!1 & sel) #da47d4ff
> color (#!1 & sel) #e439d5ff
> color (#!1 & sel) #e738d7ff
> color (#!1 & sel) #e937c8ff
> color (#!1 & sel) #dd36bcff
> color (#!1 & sel) #d935b7ff
> color (#!1 & sel) #d734b5ff
> color (#!1 & sel) #cb33b4ff
> color (#!1 & sel) #b830b3ff
> color (#!1 & sel) #af30b6ff
> color (#!1 & sel) #ae2fb6ff
[Repeated 1 time(s)]
> color (#!1 & sel) #a82eb4ff
> color (#!1 & sel) #a42db3ff
> color (#!1 & sel) #a42eb3ff
[Repeated 1 time(s)]
> color (#!1 & sel) #b531ceff
> color (#!1 & sel) #bd32dbff
[Repeated 1 time(s)]
> color (#!1 & sel) #c233ddff
> color (#!1 & sel) #c533deff
> color (#!1 & sel) #c934dfff
> color (#!1 & sel) #d136ddff
> color (#!1 & sel) #ce35d0ff
> color (#!1 & sel) #c933c2ff
> color (#!1 & sel) #c633baff
> color (#!1 & sel) #c132b3ff
> color (#!1 & sel) #b12f9bff
> color (#!1 & sel) #a72d93ff
> color (#!1 & sel) #a52d91ff
> color (#!1 & sel) #a52c90ff
> color (#!1 & sel) #9a2a8aff
> color (#!1 & sel) #902886ff
> color (#!1 & sel) #85267cff
> color (#!1 & sel) #7c2473ff
> color (#!1 & sel) #7b2472ff
> color (#!1 & sel) #7c2470ff
> color (#!1 & sel) #7f2468ff
> color (#!1 & sel) #812465ff
> color (#!1 & sel) #822464ff
> color (#!1 & sel) #8e287eff
> color (#!1 & sel) #922983ff
[Repeated 1 time(s)]
> color (#!1 & sel) #9c2ba1ff
> color (#!1 & sel) #a02ca9ff
> color (#!1 & sel) #a32dadff
> color (#!1 & sel) #aa2fb5ff
[Repeated 1 time(s)]
> color (#!1 & sel) #b230bbff
> color (#!1 & sel) #b630b0ff
> color (#!1 & sel) #b630acff
> color (#!1 & sel) #b630aaff
> color (#!1 & sel) #b630a9ff
> color (#!1 & sel) #b730a3ff
> color (#!1 & sel) #b730a0ff
> color (#!1 & sel) #b9309cff
> color (#!1 & sel) #ba2f98ff
> color (#!1 & sel) #bb3097ff
> color (#!1 & sel) #bb308fff
> color (#!1 & sel) #be3086ff
> color (#!1 & sel) #bf3086ff
> color (#!1 & sel) #bf3084ff
> color (#!1 & sel) #be3086ff
> color (#!1 & sel) #b02e83ff
> color (#!1 & sel) #aa2c83ff
> color (#!1 & sel) #a02b80ff
> color (#!1 & sel) #9c2a7fff
> color (#!1 & sel) #9b2a7eff
> color (#!1 & sel) #932979ff
> color (#!1 & sel) #8a2774ff
> color (#!1 & sel) #892673ff
> color (#!1 & sel) #882672ff
> color (#!1 & sel) #832572ff
> color (#!1 & sel) #832571ff
> color (#!1 & sel) #8a2774ff
> color (#!1 & sel) #92287aff
> color (#!1 & sel) #95297bff
> color (#!1 & sel) #98297dff
> color (#!1 & sel) #9c2a80ff
> color (#!1 & sel) #9e2a81ff
> color (#!1 & sel) #9f2b82ff
> color (#!1 & sel) #ae2e8fff
> color (#!1 & sel) #b62f94ff
[Repeated 2 time(s)]
> color (#!1 & sel) #ae2e95ff
> color (#!1 & sel) #a32c93ff
> color (#!1 & sel) #a12c91ff
> color (#!1 & sel) #9f2b90ff
> color (#!1 & sel) #9e2b93ff
> color (#!1 & sel) #9e2b94ff
> color (#!1 & sel) #962a95ff
> color (#!1 & sel) #962a96ff
> color (#!1 & sel) #972b96ff
> color (#!1 & sel) #9b2b9bff
> color (#!1 & sel) #9e2c9eff
> color (#!1 & sel) #a22da7ff
> color (#!1 & sel) #a42eadff
> color (#!1 & sel) #a62eb0ff
> color (#!1 & sel) #a72eb2ff
> color (#!1 & sel) #a82eb3ff
> color (#!1 & sel) #ac2fb7ff
> color (#!1 & sel) #b030bbff
> color (#!1 & sel) #b030bcff
> color (#!1 & sel) #b330bfff
> color (#!1 & sel) #ba32c5ff
> color (#!1 & sel) #be32c9ff
> color (#!1 & sel) #c133ccff
> color (#!1 & sel) #c233cdff
> color (#!1 & sel) #c233ceff
> color (#!1 & sel) #bc32d2ff
> color (#!1 & sel) #b731d4ff
> color (#!1 & sel) #b631d4ff
> color (#!1 & sel) #b12fd4ff
> color (#!1 & sel) #b02fd5ff
> color (#!1 & sel) #ac2fd6ff
> color (#!1 & sel) #ac2ed7ff
> color (#!1 & sel) #ac2fd9ff
> color (#!1 & sel) #ad2fd9ff
> color (#!1 & sel) #ae2fdbff
> color (#!1 & sel) #b22fdfff
> color (#!1 & sel) #b330e1ff
> color (#!1 & sel) #b630e3ff
> color (#!1 & sel) #c232eaff
> color (#!1 & sel) #c733ebff
> color (#!1 & sel) #ca34ecff
> color (#!1 & sel) #cf35edff
> color (#!1 & sel) #d035edff
> color (#!1 & sel) #d336eeff
> color (#!1 & sel) #db37f0ff
> color (#!1 & sel) #e038f1ff
> color (#!1 & sel) #e639f2ff
> color (#!1 & sel) #e739efff
> color (#!1 & sel) #e839ebff
> color (#!1 & sel) #e839e9ff
[Repeated 1 time(s)]
> color (#!1 & sel) #e938e2ff
> color (#!1 & sel) #e837cdff
> color (#!1 & sel) #c63191ff
> color (#!1 & sel) #b82e86ff
> color (#!1 & sel) #b72f8fff
> color (#!1 & sel) #b42f96ff
> color (#!1 & sel) #ae2e96ff
> color (#!1 & sel) #a52d94ff
> color (#!1 & sel) #a12c97ff
> color (#!1 & sel) #a02c96ff
> color (#!1 & sel) #9f2c95ff
> color (#!1 & sel) #9e2b96ff
> color (#!1 & sel) #9e2b99ff
> color (#!1 & sel) #9d2b98ff
> color (#!1 & sel) #9c2b98ff
[Repeated 1 time(s)]
> color (#!1 & sel) #9c2b94ff
> color (#!1 & sel) #9d2b87ff
> color (#!1 & sel) #9e2a81ff
> color (#!1 & sel) #9e2a80ff
> color (#!1 & sel) #a02b7cff
> color (#!1 & sel) #a12b7cff
> color (#!1 & sel) #a22b79ff
> color (#!1 & sel) #a32b72ff
> color (#!1 & sel) #a22b6eff
> color (#!1 & sel) #a22a69ff
> color (#!1 & sel) #a12a62ff
> color (#!1 & sel) #a02a5cff
> color (#!1 & sel) #9f2a5cff
> color (#!1 & sel) #9f2a5bff
> color (#!1 & sel) #93286bff
> color (#!1 & sel) #902772ff
> color (#!1 & sel) #902873ff
> color (#!1 & sel) #8f2874ff
> color (#!1 & sel) #8c2774ff
[Repeated 3 time(s)]
> color (#!1 & sel) #8d2771ff
[Repeated 1 time(s)]
> color (#!1 & sel) #8e276eff
> color (#!1 & sel) #8f2769ff
> color (#!1 & sel) #8f286aff
> color (#!1 & sel) #96296fff
> color (#!1 & sel) #9d2a76ff
> color (#!1 & sel) #9e2a77ff
> color (#!1 & sel) #9e2a76ff
> color (#!1 & sel) #9e2a74ff
[Repeated 1 time(s)]
> color (#!1 & sel) #9e2a75ff
> color (#!1 & sel) #a22b79ff
> select /L
3197 atoms, 3234 bonds, 212 residues, 1 model selected
> color sel #d3f0edff
[Repeated 1 time(s)]
> color sel #d5f1edff
> color sel #d7f2ecff
> color sel #d9f2ebff
> color sel #daf2ebff
> color sel #daf3ebff
> color sel #dbf3ecff
> color sel #dcf3eeff
> color sel #dff3eeff
> color sel #e1f5f0ff
> color sel #e4f6f2ff
> color sel #e5f6f2ff
[Repeated 2 time(s)]
> color sel #e5f5f2ff
> color sel #e6f6f3ff
> color sel #e7f7f4ff
> color sel #e8f7f4ff
[Repeated 2 time(s)]
> color sel #e7f6f3ff
> color sel #e6f6f2ff
> color sel #e5f6f2ff
> color sel #e4f6f2ff
> color sel #e3f5f1ff
> color sel #e2f5f0ff
> color sel #e0f4efff
> color sel #dff3eeff
> color sel #dbf3ecff
> color sel #daf3ebff
> color sel #d9f2ebff
> color sel #d8f2eaff
> color sel #d7f2e8ff
> color sel #d6f2e8ff
[Repeated 1 time(s)]
> color sel #d5f2e8ff
> color sel #d2f0e7ff
> color sel #d1f0e5ff
> color sel #ccefe3ff
> color sel #cbeee2ff
> color sel #caeee2ff
[Repeated 2 time(s)]
> color sel #c9eee3ff
> color sel #c9eee2ff
> color sel #c7eee0ff
> color sel #c5eddfff
> color sel #c4eddfff
> color sel #c3eddfff
> color sel #c3eddeff
> color sel #c2eddcff
> color sel #c1ecd9ff
> color sel #beecd7ff
> color sel #bcecd6ff
> color sel #b8ebd3ff
> color sel #b8ebd2ff
> color sel #b6ead2ff
> color sel #b5e9d2ff
> color sel #b1e9d0ff
> color sel #afe8cfff
> color sel #aee8ceff
> color sel #ace8ceff
> color sel #abe8cfff
> color sel #aae8d0ff
> color sel #a9e7d1ff
[Repeated 1 time(s)]
> color sel #a8e7d1ff
> color sel #a7e7d0ff
> color sel #a5e7cfff
> color sel #a3e7ceff
> color sel #9fe6ccff
> color sel #99e5c9ff
> color sel #98e5c8ff
[Repeated 2 time(s)]
> color sel #99e5cbff
> color sel #9ae5ceff
> color sel #9be5d3ff
> color sel #9ce6d9ff
> color sel #9ce6daff
> color sel #9ce6dbff
[Repeated 1 time(s)]
> color sel #9ce6dcff
[Repeated 1 time(s)]
> color sel #9ce6ddff
> color sel #9ce6deff
> color sel #9de6dfff
> color sel #9de6e1ff
> color sel #9ee6e2ff
> color sel #9fe6e4ff
> color sel #9fe6e5ff
> color sel #9fe6e6ff
> color sel #9fe6e7ff
[Repeated 1 time(s)]
> color sel #a0e6e8ff
> color sel #a0e2e8ff
> color sel #a1e2e8ff
> color sel #a1e0e8ff
> color sel #a1dbe7ff
> color sel #a1d8e7ff
> color sel #a1d7e7ff
> color sel #a1d5e7ff
> color sel #a1d2e7ff
> color sel #a1d1e7ff
[Repeated 1 time(s)]
> color sel #a1d0e7ff
> color sel #a1cce6ff
[Repeated 1 time(s)]
> color sel #a1cbe6ff
> color sel #a2cbe6ff
> color sel #a3cae7ff
> color sel #a3c8e7ff
> color sel #a5c7e8ff
> color sel #a9c6e8ff
> color sel #aac7e9ff
> color sel #acc7e8ff
> color sel #adc7e9ff
[Repeated 1 time(s)]
> color sel #afc8e9ff
> color sel #afc7e9ff
> color sel #b0c7e9ff
> color sel #b2c6e9ff
> color sel #b4c7eaff
> color sel #b6c8eaff
> color sel #b7c8eaff
> color sel #b8c8eaff
> color sel #b9c9eaff
[Repeated 1 time(s)]
> color sel #bacaebff
[Repeated 1 time(s)]
> color sel #bacaecff
> color sel #bbc9ebff
> color sel #bccaebff
> color sel #becaebff
> color sel #bfcbebff
> color sel #c1cbecff
[Repeated 2 time(s)]
> color sel #c2ccecff
> color sel #c1ccecff
[Repeated 1 time(s)]
> color sel #b8c0eaff
> color sel #b7beeaff
> color sel #b5bee9ff
> color sel #b3bceaff
> color sel #b1bae9ff
> color sel #afb8e8ff
> color sel #adb8e8ff
[Repeated 1 time(s)]
> color sel #acb7e8ff
> color sel #abb6e8ff
> color sel #abb5e8ff
> color sel #a9b4e8ff
> color sel #a7b2e7ff
[Repeated 2 time(s)]
> color sel #a6b1e7ff
> color sel #a5b0e7ff
> color sel #a4b0e7ff
> select /H
3275 atoms, 3324 bonds, 1 pseudobond, 222 residues, 2 models selected
> color (#!1 & sel) #efddccff
[Repeated 1 time(s)]
> color (#!1 & sel) #eedcccff
> color (#!1 & sel) #eedbcaff
> color (#!1 & sel) #eedbc9ff
> color (#!1 & sel) #ecd6c3ff
> color (#!1 & sel) #ebd3bfff
> color (#!1 & sel) #ebd3beff
> color (#!1 & sel) #ecdac3ff
> color (#!1 & sel) #eeddc6ff
> color (#!1 & sel) #eedec8ff
> color (#!1 & sel) #eedfc8ff
> color (#!1 & sel) #efe0caff
> color (#!1 & sel) #efe1cdff
> color (#!1 & sel) #f0e3ceff
> color (#!1 & sel) #efe3cdff
> color (#!1 & sel) #eeddc8ff
> color (#!1 & sel) #ead0baff
> color (#!1 & sel) #e8c9b2ff
> color (#!1 & sel) #e6c3abff
> color (#!1 & sel) #e3b89fff
> color (#!1 & sel) #e1ae94ff
> color (#!1 & sel) #dfa58aff
> color (#!1 & sel) #de9f84ff
> color (#!1 & sel) #de9d82ff
> color (#!1 & sel) #de9e82ff
[Repeated 2 time(s)]
> color (#!1 & sel) #de9c82ff
[Repeated 1 time(s)]
> color (#!1 & sel) #de9d83ff
> color (#!1 & sel) #de9c83ff
[Repeated 2 time(s)]
> color (#!1 & sel) #de9d85ff
> color (#!1 & sel) #de9e8aff
> color (#!1 & sel) #dfa390ff
> color (#!1 & sel) #e0a895ff
> color (#!1 & sel) #e1aa99ff
> color (#!1 & sel) #e2ad9cff
> color (#!1 & sel) #e2ad9dff
> color (#!1 & sel) #e2ae9dff
[Repeated 1 time(s)]
> color (#!1 & sel) #e2af9dff
> color (#!1 & sel) #e2ae9cff
> color (#!1 & sel) #e0aa93ff
> color (#!1 & sel) #dea184ff
> color (#!1 & sel) #dea082ff
[Repeated 1 time(s)]
> color (#!1 & sel) #dea081ff
> color (#!1 & sel) #de9f81ff
> color (#!1 & sel) #dd9c7dff
> color (#!1 & sel) #dd9b7bff
[Repeated 2 time(s)]
> color (#!1 & sel) #dc9878ff
> color (#!1 & sel) #dc9473ff
> color (#!1 & sel) #dc936eff
> color (#!1 & sel) #dc946eff
> color (#!1 & sel) #dc946dff
[Repeated 1 time(s)]
> color (#!1 & sel) #dc956dff
[Repeated 1 time(s)]
> color (#!1 & sel) #dc966eff
> color (#!1 & sel) #dd996eff
> color (#!1 & sel) #dd9c6eff
> color (#!1 & sel) #dd9f6fff
> color (#!1 & sel) #dea16fff
> color (#!1 & sel) #dea26fff
> color (#!1 & sel) #dea570ff
> color (#!1 & sel) #dfa972ff
> color (#!1 & sel) #dfad77ff
> color (#!1 & sel) #e0b37cff
> color (#!1 & sel) #e1b47eff
> color (#!1 & sel) #e0b47eff
[Repeated 1 time(s)]
> color (#!1 & sel) #e1b782ff
> color (#!1 & sel) #e2bc87ff
> color (#!1 & sel) #e2bd8aff
> color (#!1 & sel) #e3bf8dff
> color (#!1 & sel) #e3c08fff
> color (#!1 & sel) #e4c293ff
[Repeated 2 time(s)]
> color (#!1 & sel) #e2bc87ff
> color (#!1 & sel) #e0b67dff
> color (#!1 & sel) #e0b073ff
> color (#!1 & sel) #dfac6cff
> color (#!1 & sel) #dfa564ff
> color (#!1 & sel) #de9a5dff
> color (#!1 & sel) #dd9058ff
> color (#!1 & sel) #dd8952ff
> color (#!1 & sel) #dc804eff
> color (#!1 & sel) #dc7b4aff
> color (#!1 & sel) #dc7847ff
> color (#!1 & sel) #dc7746ff
> color (#!1 & sel) #dc7345ff
> color (#!1 & sel) #dc7244ff
> color (#!1 & sel) #dc7142ff
> color (#!1 & sel) #dd7041ff
> color (#!1 & sel) #dd6e3fff
> color (#!1 & sel) #dd6f3fff
> color (#!1 & sel) #dd6e3fff
> color (#!1 & sel) #dd7040ff
> color (#!1 & sel) #dd7442ff
> color (#!1 & sel) #dd7742ff
> color (#!1 & sel) #dd7843ff
[Repeated 2 time(s)]
> color (#!1 & sel) #dd7943ff
> color (#!1 & sel) #dd7944ff
> color (#!1 & sel) #dd7e45ff
> color (#!1 & sel) #de8347ff
> color (#!1 & sel) #de8648ff
> color (#!1 & sel) #df8a48ff
[Repeated 1 time(s)]
> color (#!1 & sel) #df8c48ff
> color (#!1 & sel) #df954bff
> color (#!1 & sel) #e09d4dff
> color (#!1 & sel) #e0a14eff
> color (#!1 & sel) #e1a44fff
[Repeated 2 time(s)]
> color (#!1 & sel) #e1a650ff
[Repeated 1 time(s)]
> color (#!1 & sel) #e09d4dff
> color (#!1 & sel) #df8e48ff
> color (#!1 & sel) #de7a40ff
> color (#!1 & sel) #de6f3cff
> color (#!1 & sel) #de6c3cff
> color (#!1 & sel) #dd673aff
> color (#!1 & sel) #de6038ff
> color (#!1 & sel) #dd5b38ff
> color (#!1 & sel) #dd5937ff
[Repeated 1 time(s)]
> color (#!1 & sel) #dd5a38ff
> color (#!1 & sel) #dc603dff
> color (#!1 & sel) #db6745ff
> color (#!1 & sel) #db6846ff
[Repeated 1 time(s)]
> color (#!1 & sel) #db6747ff
> color (#!1 & sel) #d95f49ff
> color (#!1 & sel) #d95e4bff
> color (#!1 & sel) #d95c4cff
> color (#!1 & sel) #d95b4cff
[Repeated 1 time(s)]
> color (#!1 & sel) #d95a4eff
> color (#!1 & sel) #d95b4eff
[Repeated 1 time(s)]
> color (#!1 & sel) #d86157ff
> color (#!1 & sel) #d9655bff
> color (#!1 & sel) #d9665bff
> color (#!1 & sel) #d9675dff
> color (#!1 & sel) #d9685dff
> color (#!1 & sel) #d8685eff
> color (#!1 & sel) #d86b62ff
> color (#!1 & sel) #d96d64ff
> color (#!1 & sel) #d97369ff
> color (#!1 & sel) #d97870ff
> color (#!1 & sel) #da7e76ff
[Repeated 1 time(s)]
> color (#!1 & sel) #da8077ff
> color (#!1 & sel) #db8179ff
> color (#!1 & sel) #db857dff
> color (#!1 & sel) #dc8980ff
> color (#!1 & sel) #dc8a81ff
[Repeated 4 time(s)]
> select /N
1746 atoms, 1764 bonds, 1 pseudobond, 117 residues, 2 models selected
> color (#!1 & sel) #66af39ff
> color (#!1 & sel) #60a235ff
> color (#!1 & sel) #5a9732ff
> color (#!1 & sel) #548a2eff
> color (#!1 & sel) #50832cff
> color (#!1 & sel) #4d7f2bff
> color (#!1 & sel) #4c7e2bff
> color (#!1 & sel) #4b7d2aff
> color (#!1 & sel) #4b7c2aff
> color (#!1 & sel) #4b7b2aff
[Repeated 1 time(s)]
> color (#!1 & sel) #4f7d2bff
> color (#!1 & sel) #517f2bff
> color (#!1 & sel) #51802bff
> color (#!1 & sel) #52822cff
> color (#!1 & sel) #5f9632ff
> color (#!1 & sel) #65a035ff
> color (#!1 & sel) #67a236ff
> color (#!1 & sel) #68a336ff
> color (#!1 & sel) #69a737ff
> color (#!1 & sel) #69a937ff
> color (#!1 & sel) #6aae39ff
> color (#!1 & sel) #6bb23aff
> color (#!1 & sel) #6bb83bff
> color (#!1 & sel) #6cbc3dff
> color (#!1 & sel) #6dbd3dff
[Repeated 1 time(s)]
> color (#!1 & sel) #6bbc3dff
> color (#!1 & sel) #64b83bff
> color (#!1 & sel) #61b63bff
> color (#!1 & sel) #5db53aff
[Repeated 1 time(s)]
> color (#!1 & sel) #5cb73bff
> color (#!1 & sel) #5fbd3cff
> color (#!1 & sel) #63c73fff
> color (#!1 & sel) #64ca40ff
> color (#!1 & sel) #64ce41ff
> color (#!1 & sel) #64d242ff
> color (#!1 & sel) #64d443ff
[Repeated 1 time(s)]
> color (#!1 & sel) #64d544ff
> color (#!1 & sel) #64d545ff
> color (#!1 & sel) #63d346ff
> color (#!1 & sel) #61ce46ff
> color (#!1 & sel) #5abf42ff
> color (#!1 & sel) #59bc42ff
> color (#!1 & sel) #57b841ff
> color (#!1 & sel) #55b440ff
> color (#!1 & sel) #52ad3eff
> color (#!1 & sel) #4a9c38ff
> color (#!1 & sel) #459135ff
> color (#!1 & sel) #428a33ff
[Repeated 1 time(s)]
> color (#!1 & sel) #428933ff
> color (#!1 & sel) #418837ff
[Repeated 2 time(s)]
> color (#!1 & sel) #418938ff
> color (#!1 & sel) #489740ff
> color (#!1 & sel) #4fa74cff
> color (#!1 & sel) #50a84fff
> color (#!1 & sel) #50a950ff
> color (#!1 & sel) #4fa74eff
> color (#!1 & sel) #499a49ff
> color (#!1 & sel) #449046ff
> color (#!1 & sel) #448f46ff
> color (#!1 & sel) #479444ff
> color (#!1 & sel) #489842ff
> color (#!1 & sel) #489742ff
> color (#!1 & sel) #469441ff
> color (#!1 & sel) #469341ff
> color (#!1 & sel) #469241ff
> color (#!1 & sel) #459140ff
> color (#!1 & sel) #45903fff
> color (#!1 & sel) #448e3fff
> color (#!1 & sel) #428b3eff
[Repeated 1 time(s)]
> color (#!1 & sel) #428a3eff
> color (#!1 & sel) #428a3dff
> color (#!1 & sel) #41873cff
[Repeated 2 time(s)]
> ui mousemode right select
> select clear
> ui mousemode right translate
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Alignment identifier is 1/R
> lighting soft
> save "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
> draft/Figure 7D-GPR61-BRIL fused structure.cxs"
——— End of log from Mon Apr 1 18:14:01 2024 ———
opened ChimeraX session
Could not find virtual screen for QCocoaScreen(0x600001b2b9c0, "DELL P2422H",
QRect(-1920,0 1920x1080), dpr=1, displayId=4128833, ) with displayId 4128833
> open 8TB0
8tb0 title:
Cryo-EM Structure of GPR61-G protein complex stabilized by scFv16 [more
info...]
Chain information for 8tb0 #2
---
Chain | Description | UniProt
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 1-340
F | Single-chain Fv16 |
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
R | GPR61 fused to dominant negative G alpha S/I N18 chimera | GPR61_HUMAN 2-1446, GNAS2_HUMAN 1481-1849
> ui tool show Matchmaker
> matchmaker #!1 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
alignment score = 1623.9
RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
1.770)
> matchmaker #!1 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
alignment score = 1623.9
RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
1.770)
> select #2/G
385 atoms, 391 bonds, 50 residues, 1 model selected
> color sel #e9e19aff
> color sel #e9e19eff
> color sel #eae2a1ff
> color sel #eae2a3ff
> color sel #ede7b6ff
> color sel #ede9b9ff
> color sel #eeeabdff
> color sel #f1edc9ff
[Repeated 4 time(s)]
> color sel #f1ecc8ff
> color sel #f0ebc8ff
> color sel #f0e8c8ff
> color sel #f0e7ccff
> color sel #f0e6cdff
> color sel #f0e6ccff
> color sel #f0e5cdff
> color sel #f0e5ccff
> color sel #f0e5cdff
[Repeated 3 time(s)]
> color sel #f0e8cdff
[Repeated 1 time(s)]
> select #2/B
2539 atoms, 2587 bonds, 333 residues, 1 model selected
> color sel #c5caecff
[Repeated 2 time(s)]
> color sel #c8cbeeff
> color sel #c9cdeeff
> color sel #cacdeeff
> color sel #caceeeff
[Repeated 1 time(s)]
> color sel #cbcfefff
> color sel #cccfeeff
> color sel #cdcfeeff
> color sel #b8b9ebff
> color sel #b7b8ebff
> color sel #b7b7eaff
> color sel #b6b7eaff
> color sel #b6b6eaff
> color sel #b5b5eaff
> color sel #b6b6eaff
> color sel #b7b6eaff
> color sel #b8b6e9ff
> color sel #bbb6e9ff
> color sel #bcb6e9ff
> color sel #bdb7eaff
> color sel #c5beecff
[Repeated 2 time(s)]
> color sel #c4beebff
> color sel #c5beecff
> color sel #c6bfecff
> color sel #c7bfecff
> color sel #cac2ebff
> color sel #d0caeeff
> color sel #d1caefff
> color sel #d5cdeeff
> color sel #dfd7f1ff
> color sel #e1d8f1ff
> color sel #e2d8f1ff
> color sel #e1d6f1ff
> color sel #dfd3f1ff
> color sel #dbcbeeff
> color sel #d0bcebff
> color sel #cebaebff
> color sel #cdb7eaff
> color sel #c9b3e9ff
> color sel #c9b2e9ff
> color sel #c7afe8ff
> color sel #c5ade8ff
> color sel #c4ace8ff
> color sel #c5ace8ff
> color sel #bda1e6ff
> color sel #bc9ee6ff
[Repeated 1 time(s)]
> color sel #bb9de5ff
> color sel #b99ce5ff
> color sel #b899e4ff
> color sel #b798e5ff
[Repeated 2 time(s)]
> color sel #c299e4ff
> color sel #c29ae4ff
[Repeated 1 time(s)]
> color sel #c299e4ff
> color sel #c29ae4ff
> color sel #c39ae4ff
> color sel #c49ce6ff
> color sel #c49de5ff
> color sel #c49ee5ff
> color sel #c59fe6ff
> color sel #c6a0e6ff
> color sel #ceade8ff
> color sel #d2b6eaff
> color sel #d8beebff
> color sel #dcc4edff
> color sel #ddc6edff
> color sel #ddc7edff
> color sel #e7cdefff
> color sel #e8cdefff
> color sel #e9ceefff
> color sel #ebcbedff
> color sel #ecccecff
> color sel #ecccebff
> color sel #eccce7ff
> color sel #eccde7ff
[Repeated 2 time(s)]
> color sel #eccee6ff
[Repeated 1 time(s)]
> color sel #edcfe6ff
> color sel #edd1e8ff
> color sel #eed3e8ff
> color sel #efd6e8ff
> color sel #efd7e9ff
> color sel #f0d9e9ff
> color sel #f1dbeaff
> color sel #f1dcebff
> color sel #f2deecff
> color sel #f2dfecff
> color sel #f3dfecff
> color sel #f3e2eeff
> color sel #f5e6f0ff
> color sel #f8f0f6ff
> color sel #fbf7faff
> color sel #fcf8fbff
> color sel #fcf8faff
[Repeated 1 time(s)]
> color sel #fbf7faff
[Repeated 1 time(s)]
> color sel #f8eff7ff
> color sel #f7ecf6ff
> color sel #f5e9f5ff
> color sel #f5e8f5ff
> color sel #f5e5f4ff
> color sel #f3e3f4ff
> color sel #f0daf1ff
> color sel #efd6f1ff
> color sel #edd2efff
> color sel #eccdefff
> color sel #e6bdebff
[Repeated 1 time(s)]
> color sel #e6bcebff
> color sel #e5bbebff
> color sel #e3b7eaff
[Repeated 1 time(s)]
> color sel #e2b6e9ff
[Repeated 1 time(s)]
> color sel #e3b7eaff
[Repeated 1 time(s)]
> color sel #e3bdebff
> color sel #e3c1ecff
[Repeated 3 time(s)]
> color sel #e4c1ecff
> color sel #e4c2ecff
[Repeated 2 time(s)]
> color sel #e3c3edff
> color sel #e4c3edff
[Repeated 1 time(s)]
> color sel #e4c5edff
> color sel #e3c7eeff
> color sel #e4caefff
> color sel #e5cdefff
> color sel #e6cfefff
> color sel #e5cfefff
[Repeated 3 time(s)]
> color sel #e5d0efff
[Repeated 3 time(s)]
> color sel #e4d2f1ff
> color sel #e4d3f1ff
[Repeated 1 time(s)]
> color sel #e4d4f1ff
[Repeated 1 time(s)]
> select #2/F
1780 atoms, 1826 bonds, 1 pseudobond, 233 residues, 2 models selected
> color (#!2 & sel) #d6edbeff
> color (#!2 & sel) #d8edbfff
> color (#!2 & sel) #dceec4ff
> color (#!2 & sel) #dfeec6ff
> color (#!2 & sel) #e4f0ceff
> color (#!2 & sel) #e5f1d0ff
> color (#!2 & sel) #e7f3d7ff
> color (#!2 & sel) #e9f3dcff
> color (#!2 & sel) #e8f3dbff
> color (#!2 & sel) #e8f3d9ff
> color (#!2 & sel) #e8f3d7ff
> color (#!2 & sel) #e8f3d6ff
[Repeated 1 time(s)]
> color (#!2 & sel) #e8f2d3ff
> color (#!2 & sel) #e6f1ceff
> color (#!2 & sel) #e5f1cdff
> color (#!2 & sel) #e7efc5ff
> color (#!2 & sel) #e9efc3ff
> color (#!2 & sel) #e5efc4ff
> color (#!2 & sel) #e1efc4ff
> color (#!2 & sel) #deeec5ff
> color (#!2 & sel) #dbefc7ff
> color (#!2 & sel) #dbefc8ff
> color (#!2 & sel) #daefc8ff
> color (#!2 & sel) #daf0c9ff
> color (#!2 & sel) #daf0caff
> color (#!2 & sel) #dbf0ccff
> color (#!2 & sel) #dbf0cdff
> color (#!2 & sel) #daf0cdff
[Repeated 1 time(s)]
> color (#!2 & sel) #d9f0cdff
> color (#!2 & sel) #d8f0cdff
[Repeated 3 time(s)]
> color (#!2 & sel) #d7f0cdff
> color (#!2 & sel) #d6f0cdff
> color (#!2 & sel) #d6f0ccff
> color (#!2 & sel) #cdeec6ff
> color (#!2 & sel) #cbeec4ff
> color (#!2 & sel) #caeec3ff
> color (#!2 & sel) #c4edbeff
[Repeated 1 time(s)]
> color (#!2 & sel) #c4edbdff
> color (#!2 & sel) #c3ecbcff
> color (#!2 & sel) #c2ecbaff
> color (#!2 & sel) #c2ecbbff
> color (#!2 & sel) #c2edbcff
[Repeated 1 time(s)]
> color (#!2 & sel) #c3edbdff
> color (#!2 & sel) #c8eec4ff
> color (#!2 & sel) #c9eec5ff
> color (#!2 & sel) #c9eec6ff
> color (#!2 & sel) #cbeec9ff
> color (#!2 & sel) #cdefccff
> color (#!2 & sel) #ceefccff
[Repeated 1 time(s)]
> color (#!2 & sel) #cbeecaff
> color (#!2 & sel) #c8eec8ff
> color (#!2 & sel) #c6edc4ff
> color (#!2 & sel) #c3edc3ff
> color (#!2 & sel) #c2edc2ff
[Repeated 1 time(s)]
> color (#!2 & sel) #b6eab6ff
> color (#!2 & sel) #ace8acff
> color (#!2 & sel) #ace8abff
> color (#!2 & sel) #abe8aaff
> color (#!2 & sel) #a9e7a7ff
[Repeated 2 time(s)]
> select #2/G
385 atoms, 391 bonds, 50 residues, 1 model selected
> hide sel cartoons
> select #2/B
2539 atoms, 2587 bonds, 333 residues, 1 model selected
> hide sel cartoons
> select #2/F
1780 atoms, 1826 bonds, 1 pseudobond, 233 residues, 2 models selected
> hide sel cartoons
> select #2/R
3756 atoms, 3841 bonds, 7 pseudobonds, 474 residues, 2 models selected
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> open 3SN6
Summary of feedback from opening 3SN6 fetched from pdb
---
note | Fetching compressed mmCIF 3sn6 from http://files.rcsb.org/download/3sn6.cif
3sn6 title:
Crystal structure of the beta2 adrenergic receptor-Gs protein complex [more
info...]
Chain information for 3sn6 #3
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_BOVIN 1-394
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_RAT 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_BOVIN 1-68
N | Camelid antibody VHH fragment |
R | Endolysin,Beta-2 adrenergic receptor | ENLYS_BPT4 1002-1161, ADRB2_HUMAN 29-365
Non-standard residues in 3sn6 #3
---
P0G —
8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one
> select add #3
10274 atoms, 10478 bonds, 6 pseudobonds, 1319 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #!1,3 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
alignment score = 1623.9
RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
1.770)
Matchmaker 8tb0, chain R (#2) with 3sn6, chain A (#3), sequence alignment
score = 1487.5
RMSD between 167 pruned atom pairs is 1.125 angstroms; (across all 219 pairs:
1.940)
> matchmaker #!1,3 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
alignment score = 1623.9
RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
1.770)
Matchmaker 8tb0, chain R (#2) with 3sn6, chain A (#3), sequence alignment
score = 1487.5
RMSD between 167 pruned atom pairs is 1.125 angstroms; (across all 219 pairs:
1.940)
> select #3/N
970 atoms, 992 bonds, 128 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/N
1746 atoms, 1764 bonds, 1 pseudobond, 117 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/H
3275 atoms, 3324 bonds, 1 pseudobond, 222 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #2/G#3/G
823 atoms, 835 bonds, 108 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select #2/B#3/B
5131 atoms, 5226 bonds, 673 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select #3/A
2814 atoms, 2870 bonds, 3 pseudobonds, 349 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #2/F
1780 atoms, 1826 bonds, 1 pseudobond, 233 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #1/L
3197 atoms, 3234 bonds, 212 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show Matchmaker
> matchmaker #!2-3 to #1/R pairing bs
Parameters
---
Chain pairing | bs
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 GPR61_BRIL_8tb7, chain R (#1) with 8tb0, chain R (#2), sequence
alignment score = 1623.9
RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
1.770)
Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 3sn6, chain R (#3), sequence
alignment score = 339.4
RMSD between 134 pruned atom pairs is 1.200 angstroms; (across all 230 pairs:
5.318)
> matchmaker #!2-3 to #1/R pairing bs
Parameters
---
Chain pairing | bs
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 GPR61_BRIL_8tb7, chain R (#1) with 8tb0, chain R (#2), sequence
alignment score = 1623.9
RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
1.770)
Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 3sn6, chain R (#3), sequence
alignment score = 339.4
RMSD between 134 pruned atom pairs is 1.200 angstroms; (across all 230 pairs:
5.318)
> select #3/R
3460 atoms, 3533 bonds, 3 pseudobonds, 444 residues, 2 models selected
> color (#!3 & sel) #e8652cff
> color (#!3 & sel) #eb652cff
> color (#!3 & sel) #ed652cff
> color (#!3 & sel) #ec642bff
> color (#!3 & sel) #ec622bff
> color (#!3 & sel) #ea5a2aff
> color (#!3 & sel) #e95629ff
> color (#!3 & sel) #e94e28ff
> color (#!3 & sel) #e84326ff
> color (#!3 & sel) #e73e25ff
[Repeated 2 time(s)]
> color (#!3 & sel) #e63d25ff
> color (#!3 & sel) #e63c25ff
[Repeated 2 time(s)]
> color (#!3 & sel) #e73a25ff
> color (#!3 & sel) #e93925ff
> color (#!3 & sel) #e93924ff
> color (#!3 & sel) #eb3c25ff
> color (#!3 & sel) #eb3d25ff
> color (#!3 & sel) #eb3f25ff
> color (#!3 & sel) #eb4025ff
> color (#!3 & sel) #eb4125ff
> color (#!3 & sel) #eb4927ff
> color (#!3 & sel) #ec5f2aff
> color (#!3 & sel) #ed6e2dff
> color (#!3 & sel) #f08a34ff
> color (#!3 & sel) #f19b38ff
> color (#!3 & sel) #efb23fff
> color (#!3 & sel) #ebad3fff
> color (#!3 & sel) #e4953dff
> color (#!3 & sel) #e08440ff
> color (#!3 & sel) #de7e40ff
[Repeated 1 time(s)]
> color (#!3 & sel) #de7e41ff
> color (#!3 & sel) #de7741ff
> color (#!3 & sel) #dd7643ff
> color (#!3 & sel) #dd7445ff
> color (#!3 & sel) #dc7445ff
> color (#!3 & sel) #dc7547ff
> color (#!3 & sel) #db7c56ff
> color (#!3 & sel) #db815fff
> color (#!3 & sel) #dc9578ff
> color (#!3 & sel) #dd997fff
> color (#!3 & sel) #dd9a7eff
> color (#!3 & sel) #dc9373ff
> color (#!3 & sel) #dc7c48ff
> color (#!3 & sel) #e47d36ff
> color (#!3 & sel) #e78736ff
> color (#!3 & sel) #fcec4fff
> color (#!3 & sel) #fdf451ff
> color (#!3 & sel) #fdfb54ff
> color (#!3 & sel) #eefb53ff
> color (#!3 & sel) #e4f652ff
[Repeated 1 time(s)]
> color (#!3 & sel) #e5f552ff
> color (#!3 & sel) #e3f052ff
> color (#!3 & sel) #e0ed56ff
> color (#!3 & sel) #d6ea5bff
> color (#!3 & sel) #d4ea5aff
> color (#!3 & sel) #d1e959ff
> color (#!3 & sel) #c8eb54ff
> color (#!3 & sel) #b9ed50ff
> color (#!3 & sel) #91f34dff
> color (#!3 & sel) #75f74cff
> color (#!3 & sel) #74f756ff
> color (#!3 & sel) #73f560ff
> color (#!3 & sel) #72f465ff
> color (#!3 & sel) #72f269ff
> color (#!3 & sel) #71f06cff
> color (#!3 & sel) #71f06dff
> color (#!3 & sel) #71ee6fff
[Repeated 1 time(s)]
> color (#!3 & sel) #71ee7dff
> color (#!3 & sel) #71ee95ff
> color (#!3 & sel) #72f28aff
> color (#!3 & sel) #75f963ff
> color (#!3 & sel) #6de84cff
> color (#!3 & sel) #68de48ff
> color (#!3 & sel) #66d946ff
> color (#!3 & sel) #61cd41ff
> color (#!3 & sel) #5abf3dff
> color (#!3 & sel) #5abf3cff
> color (#!3 & sel) #5abe3eff
> color (#!3 & sel) #5abe46ff
> color (#!3 & sel) #5dc664ff
> color (#!3 & sel) #62d195ff
> color (#!3 & sel) #67dec8ff
> color (#!3 & sel) #5ccaefff
> color (#!3 & sel) #4baaeeff
> color (#!3 & sel) #347eeeff
> color (#!3 & sel) #001df3ff
> color (#!3 & sel) #0018f4ff
[Repeated 5 time(s)]
> color (#!3 & sel) #0019f5ff
> color (#!3 & sel) #0019f3ff
> color (#!3 & sel) #001af3ff
> color (#!3 & sel) #001af1ff
> color (#!3 & sel) #001af2ff
> color (#!3 & sel) #011bf0ff
> color (#!3 & sel) #0e1deeff
> color (#!3 & sel) #1a20eaff
> color (#!3 & sel) #2427e8ff
> color (#!3 & sel) #2929e6ff
> color (#!3 & sel) #2522eaff
> color (#!3 & sel) #261bf1ff
> color (#!3 & sel) #351bf4ff
> color (#!3 & sel) #3e1cf3ff
> color (#!3 & sel) #461cf3ff
> color (#!3 & sel) #8226e8ff
> color (#!3 & sel) #9d2be8ff
> color (#!3 & sel) #a82de8ff
> color (#!3 & sel) #bf31f1ff
> color (#!3 & sel) #c131f5ff
> color (#!3 & sel) #c131f6ff
> color (#!3 & sel) #c231f6ff
> color (#!3 & sel) #c532f6ff
> color (#!3 & sel) #c732f5ff
> color (#!3 & sel) #c234edff
> color (#!3 & sel) #c335eeff
> color (#!3 & sel) #c437ebff
> color (#!3 & sel) #c73ee6ff
[Repeated 1 time(s)]
> color (#!3 & sel) #c33ee7ff
> color (#!3 & sel) #bb39e8ff
> color (#!3 & sel) #a22febff
> color (#!3 & sel) #8226f2ff
> color (#!3 & sel) #541ff1ff
> color (#!3 & sel) #4b1fe2ff
> color (#!3 & sel) #121db9ff
> color (#!3 & sel) #4b9d5bff
> color (#!3 & sel) #4c9f3fff
> color (#!3 & sel) #4c9f36ff
> color (#!3 & sel) #56a235ff
> color (#!3 & sel) #63a235ff
> color (#!3 & sel) #a1a339ff
> color (#!3 & sel) #ad5728ff
> color (#!3 & sel) #b73e25ff
> color (#!3 & sel) #c43324ff
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #ea332440
> color (#!3 & sel) #ea3424ff
> color (#!3 & sel) #eb3824ff
> color (#!3 & sel) #eb4826ff
> color (#!3 & sel) #ec5028ff
> color (#!3 & sel) #ec5228ff
[Repeated 1 time(s)]
> color (#!3 & sel) #ec5128ff
[Repeated 2 time(s)]
> color (#!3 & sel) #ec5028ff
[Repeated 1 time(s)]
> color (#!3 & sel) #ec4f28ff
> color (#!3 & sel) #e94b27ff
> color (#!3 & sel) #e74b28ff
[Repeated 1 time(s)]
> color (#!3 & sel) #e54b29ff
> color (#!3 & sel) #e34c2aff
> color (#!3 & sel) #e04b2dff
> color (#!3 & sel) #df4d30ff
> color (#!3 & sel) #de4a31ff
> color (#!3 & sel) #de4b33ff
> color (#!3 & sel) #db483aff
> color (#!3 & sel) #da483cff
> color (#!3 & sel) #da4a40ff
> color (#!3 & sel) #d94c44ff
> color (#!3 & sel) #d9534ded
> color (#!3 & sel) #d8554f36
> color (#!3 & sel) #ffffffff
> color (#!3 & sel) #d86d696d
> color (#!3 & sel) #d97673fe
> color (#!3 & sel) #da7b79c2
> color (#!3 & sel) #da7c799a
> color (#!3 & sel) #da7c79a4
> color (#!3 & sel) #da7b79ff
> color (#!3 & sel) #d97771ff
> color (#!3 & sel) #d96f67ff
> color (#!3 & sel) #d86a61ff
> color (#!3 & sel) #da5241ff
> color (#!3 & sel) #db4c39ff
> color (#!3 & sel) #dc4a38ff
> color (#!3 & sel) #dc4a37ff
> color (#!3 & sel) #dc4937ff
> color (#!3 & sel) #dd4734ff
> color (#!3 & sel) #dd4531ff
[Repeated 1 time(s)]
> color (#!3 & sel) #de4330ff
> color (#!3 & sel) #df422fff
> color (#!3 & sel) #df422eff
[Repeated 2 time(s)]
> color (#!3 & sel) #df422fff
> color (#!3 & sel) #de4430ff
> color (#!3 & sel) #dd4632ff
> color (#!3 & sel) #dd4835ff
> color (#!3 & sel) #dc4a37ff
> color (#!3 & sel) #db4c3aff
> color (#!3 & sel) #db4d3bff
> color (#!3 & sel) #db4e3bff
> color (#!3 & sel) #da5644ff
> color (#!3 & sel) #da5a47ff
> color (#!3 & sel) #d95f4aff
> color (#!3 & sel) #da644eff
> color (#!3 & sel) #d9664fff
> color (#!3 & sel) #da6950ff
> color (#!3 & sel) #da6a4fff
> color (#!3 & sel) #db784dff
> color (#!3 & sel) #dc7a4aff
> color (#!3 & sel) #dc7c4aff
> color (#!3 & sel) #de884aff
> color (#!3 & sel) #df954bff
> color (#!3 & sel) #e0994bff
[Repeated 1 time(s)]
> color (#!3 & sel) #e09e4cff
> color (#!3 & sel) #e1a04cff
[Repeated 2 time(s)]
> color (#!3 & sel) #e19f4cff
> color (#!3 & sel) #e19c4bff
> color (#!3 & sel) #e19343ff
> color (#!3 & sel) #e18e40ff
> color (#!3 & sel) #e28b3dff
> color (#!3 & sel) #e3863aff
> color (#!3 & sel) #e38539ff
> color (#!3 & sel) #e48538ff
> color (#!3 & sel) #e48537ff
> color (#!3 & sel) #e58337ff
> color (#!3 & sel) #e58336ff
> color (#!3 & sel) #e58236ff
> color (#!3 & sel) #e78134ff
[Repeated 1 time(s)]
> color (#!3 & sel) #e88134ff
> color (#!3 & sel) #ec7f32ff
[Repeated 3 time(s)]
> color (#!3 & sel) #ed7f31ff
[Repeated 1 time(s)]
> color (#!3 & sel) #ed7e31ff
> color (#!3 & sel) #ef7f31ff
> color (#!3 & sel) #ef8432ff
> color (#!3 & sel) #ee8432ff
[Repeated 3 time(s)]
> color (#!3 & sel) #ed8532ff
> color (#!3 & sel) #ed8432ff
[Repeated 1 time(s)]
> color (#!3 & sel) #ed8533ff
> color (#!3 & sel) #ee8a34ff
> color (#!3 & sel) #ee8b34ff
[Repeated 1 time(s)]
> color (#!3 & sel) #ef8e35ff
> color (#!3 & sel) #ef9135ff
> color (#!3 & sel) #f09637ff
> color (#!3 & sel) #f09a38ff
> color (#!3 & sel) #f2a13aff
> color (#!3 & sel) #f3a93cff
[Repeated 1 time(s)]
> color (#!3 & sel) #f3af3eff
> color (#!3 & sel) #f6c644ff
> color (#!3 & sel) #f7c945ff
> color (#!3 & sel) #fbe94eff
> color (#!3 & sel) #faec4fff
> color (#!3 & sel) #f8ec4fff
> color (#!3 & sel) #f8eb4fff
> color (#!3 & sel) #f8ea4fff
> color (#!3 & sel) #f8e94fff
[Repeated 1 time(s)]
> color (#!3 & sel) #f8e44dff
> color (#!3 & sel) #f6d248ff
> color (#!3 & sel) #f5d047ff
[Repeated 1 time(s)]
> color (#!3 & sel) #f6d047ff
> color (#!3 & sel) #f5ca45ff
> color (#!3 & sel) #f4bd41ff
> color (#!3 & sel) #f4b840ff
[Repeated 3 time(s)]
> color (#!3 & sel) #f4b53fff
> color (#!3 & sel) #f4b23eff
[Repeated 2 time(s)]
> color (#!3 & sel) #f3af3eff
> color (#!3 & sel) #f3ae3dff
[Repeated 1 time(s)]
> color (#!3 & sel) #f2ae3dff
> color (#!3 & sel) #f2a93cff
> color (#!3 & sel) #efa83cff
> color (#!3 & sel) #eea73cff
> color (#!3 & sel) #eda83cff
> color (#!3 & sel) #eda73cff
> color (#!3 & sel) #eda63bff
> color (#!3 & sel) #eca63bff
> color (#!3 & sel) #eca53bff
[Repeated 1 time(s)]
> color (#!3 & sel) #eba63bff
[Repeated 1 time(s)]
> color (#!3 & sel) #eba93cff
[Repeated 1 time(s)]
> color (#!3 & sel) #eaac3dff
> color (#!3 & sel) #e7ab3cff
> color (#!3 & sel) #e7ab3dff
> color (#!3 & sel) #e5aa3cff
> color (#!3 & sel) #e1a73cff
> color (#!3 & sel) #d1a13aff
> color (#!3 & sel) #c89c38ff
> color (#!3 & sel) #c49b38ff
> color (#!3 & sel) #c19938ff
> color (#!3 & sel) #af8c34ff
> color (#!3 & sel) #ac8a33ff
> color (#!3 & sel) #aa8933ff
> color (#!3 & sel) #a98832ff
> color (#!3 & sel) #a78632ff
[Repeated 1 time(s)]
> color (#!3 & sel) #a68131ff
> color (#!3 & sel) #a6782fff
> color (#!3 & sel) #a66c2cff
> color (#!3 & sel) #ab5a29ff
[Repeated 2 time(s)]
> color (#!3 & sel) #ac5929ff
> color (#!3 & sel) #af5a29ff
> color (#!3 & sel) #ba602bff
> color (#!3 & sel) #cd682cff
> color (#!3 & sel) #cf672cff
> color (#!3 & sel) #d4692dff
> color (#!3 & sel) #e06a2dff
> color (#!3 & sel) #e26b2dff
> color (#!3 & sel) #e5692dff
> color (#!3 & sel) #e7682cff
[Repeated 1 time(s)]
> color (#!3 & sel) #e8662cff
> color (#!3 & sel) #e8642cff
> color (#!3 & sel) #e9642cff
> color (#!3 & sel) #ea642cff
> color (#!3 & sel) #ea632bff
[Repeated 1 time(s)]
> color (#!3 & sel) #eb642bff
> color (#!3 & sel) #eb622bff
> color (#!3 & sel) #ec612bff
> color (#!3 & sel) #eb5e2aff
> color (#!3 & sel) #ec5a29ff
[Repeated 1 time(s)]
> color (#!3 & sel) #ec5829ff
> color (#!3 & sel) #ec5529ff
> color (#!3 & sel) #ec5528ff
> color (#!3 & sel) #eb5228ff
> color (#!3 & sel) #eb5128ff
> color (#!3 & sel) #eb5228ff
> color (#!3 & sel) #ea5128ff
> color (#!3 & sel) #ea5229ff
> color (#!3 & sel) #ea5329ff
> color (#!3 & sel) #e7542aff
> color (#!3 & sel) #e5572bff
> color (#!3 & sel) #e4592cff
> color (#!3 & sel) #e25a2fff
> color (#!3 & sel) #e05c31ff
> color (#!3 & sel) #df5e34ff
> color (#!3 & sel) #dd5f3aff
> color (#!3 & sel) #dc603cff
> color (#!3 & sel) #db6442ff
> color (#!3 & sel) #db6444ff
> color (#!3 & sel) #da6448ff
> color (#!3 & sel) #da664bff
> color (#!3 & sel) #da684eff
> color (#!3 & sel) #d96a51ff
> color (#!3 & sel) #d96c53ff
> color (#!3 & sel) #d9715eff
> color (#!3 & sel) #d97260ff
> color (#!3 & sel) #d97362ff
> color (#!3 & sel) #d97264ff
[Repeated 1 time(s)]
> color (#!3 & sel) #d97164ff
> color (#!3 & sel) #d97266ff
> color (#!3 & sel) #d97066ff
> color (#!3 & sel) #d97266ff
> color (#!3 & sel) #d97267ff
> color (#!3 & sel) #d97367ff
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> open 2RH1
2rh1 title:
High resolution crystal structure of human B2-adrenergic G protein-coupled
receptor. [more info...]
Chain information for 2rh1 #4
---
Chain | Description | UniProt
A | beta-2-adrenergic receptor/T4-lysozyme chimera | ADRB2_HUMAN 1-230 263-365, LYS_BPT4 1002-1161
Non-standard residues in 2rh1 #4
---
12P — dodecaethylene glycol (polyethylene glycol PEG400)
ACM — acetamide
BU1 — 1,4-butanediol
CAU — (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
((S)-Carazolol)
CLR — cholesterol
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)
PLM — palmitic acid
SO4 — sulfate ion
> select add #4
3804 atoms, 3842 bonds, 507 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #4#!1,3 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 8tb0, chain R (#2) with 2rh1, chain A (#4), sequence alignment
score = 320.5
RMSD between 104 pruned atom pairs is 1.311 angstroms; (across all 244 pairs:
3.824)
Matchmaker 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
alignment score = 1623.9
RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
1.770)
Matchmaker 8tb0, chain R (#2) with 3sn6, chain R (#3), sequence alignment
score = 428
RMSD between 144 pruned atom pairs is 1.295 angstroms; (across all 245 pairs:
2.972)
> matchmaker #4#!1,3 to #2/R pairing bs
Parameters
---
Chain pairing | bs
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 8tb0, chain R (#2) with 2rh1, chain A (#4), sequence alignment
score = 320.5
RMSD between 104 pruned atom pairs is 1.311 angstroms; (across all 244 pairs:
3.824)
Matchmaker 8tb0, chain R (#2) with GPR61_BRIL_8tb7, chain R (#1), sequence
alignment score = 1623.9
RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
1.770)
Matchmaker 8tb0, chain R (#2) with 3sn6, chain R (#3), sequence alignment
score = 428
RMSD between 144 pruned atom pairs is 1.295 angstroms; (across all 245 pairs:
2.972)
> select clear
> open 2RH1
2rh1 title:
High resolution crystal structure of human B2-adrenergic G protein-coupled
receptor. [more info...]
Chain information for 2rh1 #5
---
Chain | Description | UniProt
A | beta-2-adrenergic receptor/T4-lysozyme chimera | ADRB2_HUMAN 1-230 263-365, LYS_BPT4 1002-1161
Non-standard residues in 2rh1 #5
---
12P — dodecaethylene glycol (polyethylene glycol PEG400)
ACM — acetamide
BU1 — 1,4-butanediol
CAU — (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
((S)-Carazolol)
CLR — cholesterol
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)
PLM — palmitic acid
SO4 — sulfate ion
> close #5
> open 2RH1
2rh1 title:
High resolution crystal structure of human B2-adrenergic G protein-coupled
receptor. [more info...]
Chain information for 2rh1 #5
---
Chain | Description | UniProt
A | beta-2-adrenergic receptor/T4-lysozyme chimera | ADRB2_HUMAN 1-230 263-365, LYS_BPT4 1002-1161
Non-standard residues in 2rh1 #5
---
12P — dodecaethylene glycol (polyethylene glycol PEG400)
ACM — acetamide
BU1 — 1,4-butanediol
CAU — (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
((S)-Carazolol)
CLR — cholesterol
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)
PLM — palmitic acid
SO4 — sulfate ion
> close #5
Drag select of 21 residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 3433 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> ui mousemode right select
> select #4/A:1161
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
Drag select of 34 residues
> delete atoms sel
> delete bonds sel
> undo
Undo failed, probably because structures have been modified.
Drag select of 21 residues
> delete atoms sel
> delete bonds sel
Drag select of 5 residues
Drag select of 39 residues
> delete atoms sel
> delete bonds sel
Drag select of 63 residues, 4 pseudobonds
> delete atoms (#!2,4 & sel)
> delete bonds (#!2,4 & sel)
> hide #!1 models
Drag select of 162 residues, 10 pseudobonds
> delete atoms (#!2,4 & sel)
> delete bonds (#!2,4 & sel)
Drag select of 3 residues
> delete atoms sel
> delete bonds sel
Drag select of 1 pseudobonds
No visible atoms or bonds selected
Drag select of 21 residues, 1 pseudobonds
> delete atoms (#!2,4 & sel)
> delete bonds (#!2,4 & sel)
> select clear
> select #4/A:1102
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4/A:1101
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #4/A:1146
21 atoms, 18 bonds, 1 pseudobond, 3 residues, 2 models selected
> select add #4/A:1149
28 atoms, 24 bonds, 1 pseudobond, 4 residues, 2 models selected
> select add #4/A:1147
37 atoms, 32 bonds, 2 pseudobonds, 5 residues, 3 models selected
> select add #4/A:1145
48 atoms, 42 bonds, 2 pseudobonds, 6 residues, 3 models selected
> select add #4/A:1144
56 atoms, 49 bonds, 2 pseudobonds, 7 residues, 3 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select clear
[Repeated 1 time(s)]Drag select of 3 residues, 1 pseudobonds
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select clear
[Repeated 1 time(s)]Drag select of 2 pseudobonds
> hide #!2-4 cartoons
> undo
Drag select of 11 residues
> select clear
> select #4/A:1010
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4/A:1009
16 atoms, 14 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #2/R:1809
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #2/R:1810
9 atoms, 7 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui mousemode right translate
> ui mousemode right select
Drag select of 158 residues, 1 pseudobonds
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
Drag select of 1 pseudobonds
No visible atoms or bonds selected
> hide #!2-4 cartoons
> show #!2-4 cartoons
> select clear
[Repeated 1 time(s)]Drag select of 6 residues
> select clear
> ui mousemode right translate
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> save "/Users/dongju/Desktop/Research projects-Monash/NRE/All Figures-
> draft/Figure 7D-GPR61-BRIL fused structure v2.cxs"
——— End of log from Thu Apr 4 16:40:01 2024 ———
opened ChimeraX session
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #!3 models
> ui tool show "Side View"
> select ligand
302 atoms, 307 bonds, 19 residues, 3 models selected
> select #1 ligand
Expected a keyword
> select #1:ligand
Nothing selected
> select #2:ligand
Nothing selected
> select #3:ligand
Nothing selected
> select #4:ligand
Nothing selected
> select liand
Expected an objects specifier or a keyword
> select ligand
302 atoms, 307 bonds, 19 residues, 3 models selected
> show sel & #!1 atoms
> color (#!1 & sel) dark gray
> color (#!1 & sel) dim gray
> color (#!1 & sel) byhetero
> select clear
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!2 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R
Alignment identifier is 1/R
> select #1/R:286
12 atoms, 11 bonds, 1 residue, 1 model selected
> select
> #1/R:54-78,85-108,125-160,164-188,216-266,269-288,302-326,331-349,365-392,403-424
4407 atoms, 4449 bonds, 275 residues, 1 model selected
> select clear
> select #1/R:354
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/R:354
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/R:225-354
2086 atoms, 2101 bonds, 130 residues, 1 model selected
> select clear
> hide #!1 models
> show #!1 models
> select ligand
302 atoms, 307 bonds, 19 residues, 3 models selected
> color (#!1 & sel) yellow
> color (#!1 & sel) #eae15aff
> color (#!1 & sel) #e9db5cff
> color (#!1 & sel) #e7d960ff
> color (#!1 & sel) #e6d865ff
> color (#!1 & sel) #e7d868ff
> color (#!1 & sel) #e7d86bff
> color (#!1 & sel) #e6d672ff
> color (#!1 & sel) #e5d47eff
> color (#!1 & sel) #e5d580ff
> color (#!1 & sel) #e6d788ff
> color (#!1 & sel) #e8dc92ff
> color (#!1 & sel) #e8dc94ff
> color (#!1 & sel) #e8dc96ff
> color (#!1 & sel) #e8dd99ff
> color (#!1 & sel) #e9dc9dff
> color (#!1 & sel) #e9dc9eff
> color (#!1 & sel) #e9dfa3ff
> color (#!1 & sel) #eae0a3ff
> color (#!1 & sel) #eae0a4ff
> color (#!1 & sel) #eae1a3ff
> color (#!1 & sel) #e9e0a2ff
> color (#!1 & sel) #eae1a2ff
> color (#!1 & sel) #e9e0a2ff
> color (#!1 & sel) #e9dfa2ff
> color (#!1 & sel) #e9dca3ff
> color (#!1 & sel) #e9daa5ff
> color (#!1 & sel) #e9d9a5ff
> color (#!1 & sel) #e8d6a2ff
> color (#!1 & sel) #e6d399ff
> color (#!1 & sel) #e5cc87ff
> color (#!1 & sel) #e4cb81ff
> color (#!1 & sel) #e3c97eff
> color (#!1 & sel) #e3c87bff
> color (#!1 & sel) #e3c875ff
> color (#!1 & sel) #e3c873ff
> color (#!1 & sel) #e3c76aff
[Repeated 1 time(s)]
> color (#!1 & sel) #e4c669ff
> color (#!1 & sel) #e4c769ff
> color (#!1 & sel) #e4c868ff
> color (#!1 & sel) #e4ca68ff
> color (#!1 & sel) #e4c968ff
> color (#!1 & sel) #e4ca66ff
> color (#!1 & sel) #e4ca64ff
> color (#!1 & sel) #e4c962ff
> color (#!1 & sel) #e4ca63ff
> color (#!1 & sel) #e5cc63ff
> color (#!1 & sel) #e5cd63ff
> color (#!1 & sel) #e5ce63ff
> color (#!1 & sel) #e5d066ff
> color (#!1 & sel) #e6d46aff
[Repeated 1 time(s)]
> color (#!1 & sel) #e6d46bff
> color (#!1 & sel) #e5d66eff
> color (#!1 & sel) #e5d66fff
> color (#!1 & sel) #e5d670ff
> color (#!1 & sel) #e6d571ff
> color (#!1 & sel) #e6d673ff
> color (#!1 & sel) #e6d877ff
> color (#!1 & sel) #e6d879ff
> color (#!1 & sel) #e6dc7dff
> color (#!1 & sel) #e7db7fff
> color (#!1 & sel) #e6dc80ff
[Repeated 1 time(s)]
> color (#!1 & sel) #e6dd80ff
[Repeated 1 time(s)]
> color (#!1 & sel) #e7dd80ff
> color (#!1 & sel) #e7dd7fff
> color (#!1 & sel) #e7dd7eff
> color (#!1 & sel) #e6dd7dff
> color (#!1 & sel) #e6dc7cff
> color (#!1 & sel) #e6da76ff
> color (#!1 & sel) #e6d973ff
> color (#!1 & sel) #e6d972ff
> color (#!1 & sel) #e6d772ff
> color (#!1 & sel) #e6d771ff
> color (#!1 & sel) #e5d770ff
> color (#!1 & sel) #e5d76fff
> color (#!1 & sel) #e5d76eff
> color (#!1 & sel) #e6d56cff
> color (#!1 & sel) #e6d46bff
> color (#!1 & sel) #e6d56bff
> color (#!1 & sel) #e6d56aff
[Repeated 2 time(s)]
> color (#!1 & sel) #e6d469ff
> color (#!1 & sel) #e6d467ff
> color (#!1 & sel) #e6d466ff
> color (#!1 & sel) #e6d366ff
> color (#!1 & sel) #e6d365ff
> color (#!1 & sel) #e6d364ff
> color (#!1 & sel) #e6d463ff
> color (#!1 & sel) #e7d460ff
[Repeated 2 time(s)]
> color (#!1 & sel) #e7d45fff
[Repeated 2 time(s)]
> color (#!1 & sel) byhetero
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 7/Figure7C.cxs"
> open 8KGK
8kgk title:
Cryo-EM structure of the GPR61-Gs complex [more info...]
Chain information for 8kgk #5
---
Chain | Description | UniProt
A | G-protein coupled receptor 61 | GPR61_HUMAN 1-365
B | Guanine nucleotide-binding protein G(olf) subunit alpha,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAL_HUMAN 5-195, GNAS2_HUMAN 204-384
C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
E | Nanobody 35 |
> ui tool show Matchmaker
> matchmaker #!2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 8tb0, chain R (#2), sequence
alignment score = 1623.9
RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
1.770)
Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 3sn6, chain R (#3), sequence
alignment score = 339.4
RMSD between 134 pruned atom pairs is 1.200 angstroms; (across all 230 pairs:
5.318)
Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 2rh1, chain A (#4), sequence
alignment score = 372.2
RMSD between 106 pruned atom pairs is 1.222 angstroms; (across all 221 pairs:
4.766)
Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 8kgk, chain A (#5), sequence
alignment score = 1320.5
RMSD between 188 pruned atom pairs is 0.925 angstroms; (across all 219 pairs:
1.672)
> matchmaker #!2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 8tb0, chain R (#2), sequence
alignment score = 1623.9
RMSD between 186 pruned atom pairs is 0.977 angstroms; (across all 217 pairs:
1.770)
Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 3sn6, chain R (#3), sequence
alignment score = 339.4
RMSD between 134 pruned atom pairs is 1.200 angstroms; (across all 230 pairs:
5.318)
Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 2rh1, chain A (#4), sequence
alignment score = 372.2
RMSD between 106 pruned atom pairs is 1.222 angstroms; (across all 221 pairs:
4.766)
Matchmaker GPR61_BRIL_8tb7, chain R (#1) with 8kgk, chain A (#5), sequence
alignment score = 1320.5
RMSD between 188 pruned atom pairs is 0.925 angstroms; (across all 219 pairs:
1.672)
> show #!1-2,5 atoms
> undo
> show #!1-2,5 cartoons
> select add #5
7470 atoms, 7626 bonds, 4 pseudobonds, 1006 residues, 2 models selected
> hide sel atoms
> show sel atoms
> style sel stick
Changed 7470 atom styles
> hide sel atoms
> select clear
> select #5/D
353 atoms, 359 bonds, 56 residues, 1 model selected
> hide sel cartoons
> select #5/E
928 atoms, 949 bonds, 126 residues, 1 model selected
> hide sel cartoons
> select #5/D
353 atoms, 359 bonds, 56 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/C
2497 atoms, 2544 bonds, 339 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/E
928 atoms, 949 bonds, 126 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #5/B
1804 atoms, 1841 bonds, 1 pseudobond, 229 residues, 2 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select clear
> color #5 #e4c398ff
> color #5 #eae7a0ff
> color #5 #e2b09cff
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 7/Figure7D.cxs"
——— End of log from Thu May 30 20:40:46 2024 ———
opened ChimeraX session
> transparency 80 ribbons
> select
> #1/R:54-78,85-108,125-160,164-188,216-266,269-288,302-326,331-349,365-392,403-424
4407 atoms, 4449 bonds, 275 residues, 1 model selected
> select #1/R:137
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/R:137
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/R:346
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/R:346
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/R:149
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/R:149
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> select #1/R:426
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/R:426
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #1/R:146
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/R:146
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
Drag select of 2 residues
> select clear
> color #1-2,5 byhetero
> select clear
> select #1/R:146
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #1/R:426
28 atoms, 26 bonds, 2 residues, 1 model selected
> select add #1/R:149
52 atoms, 49 bonds, 3 residues, 1 model selected
> ribbon sel suppressBackboneDisplay true
> ribbon sel suppressBackboneDisplay false
> true
Unknown command: true
> select H
2677 atoms, 329 residues, 1 model selected
> hide sel atoms
> select clear
> select #1/R:149@NH2
1 atom, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
> false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 GPR61_BRIL_8tb7
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
> false intraRes false select true reveal true log true
Atom specifier selects no atoms
> select #1/R:426
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
> false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 GPR61_BRIL_8tb7
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GPR61_BRIL_8tb7 #1/R ASN 426 ND2 GPR61_BRIL_8tb7 #1/R ZOB 601 O16 GPR61_BRIL_8tb7 #1/R ASN 426 HD21 3.516 2.918
GPR61_BRIL_8tb7 #1/R ASN 426 ND2 GPR61_BRIL_8tb7 #1/R ZOB 601 O17 GPR61_BRIL_8tb7 #1/R ASN 426 HD21 2.909 2.040
2 hydrogen bonds found
> hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
> false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 GPR61_BRIL_8tb7
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
GPR61_BRIL_8tb7 #1/R ASN 426 ND2 GPR61_BRIL_8tb7 #1/R ZOB 601 O16 GPR61_BRIL_8tb7 #1/R ASN 426 HD21 3.516 2.918
GPR61_BRIL_8tb7 #1/R ASN 426 ND2 GPR61_BRIL_8tb7 #1/R ZOB 601 O17 GPR61_BRIL_8tb7 #1/R ASN 426 HD21 2.909 2.040
GPR61_BRIL_8tb7 #1/R HOH 701 O GPR61_BRIL_8tb7 #1/R ZOB 601 O17 no hydrogen 2.261 N/A
3 hydrogen bonds found
> select clear
> ui tool show "Side View"
> transparency 100 ribbons
> transparency 80 ribbons
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 7/Figure7C_antagonist binding.png" width
> 2000 height 1521 supersample 3 transparentBackground true
> hide #!1 models
> show #!1 models
> select
> #1/R:54-78,85-108,125-160,164-188,216-266,269-288,302-326,331-349,365-392,403-424
4407 atoms, 4449 bonds, 275 residues, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #2/R
Alignment identifier is 2/R
> select #1/R:146
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/R:146
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/R:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/R:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> #1/R:54-78,85-108,125-160,164-188,216-266,269-288,302-326,331-349,365-392,403-424
4407 atoms, 4449 bonds, 275 residues, 1 model selected
> select #1/R:149
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/R:149
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/R:426
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/R:426
14 atoms, 13 bonds, 1 residue, 1 model selected
> select
> #2/R:46-68,70-101,114-145,148-180,202-237,284-313,321-342,345-353,1728-1846
1788 atoms, 1826 bonds, 1 pseudobond, 226 residues, 2 models selected
> close session
> open 7xz5
7xz5 title:
GPR119-Gs-LPC complex [more info...]
Chain information for 7xz5 #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
N | Nanobody35 |
R | Soluble cytochrome b562,Glucose-dependent insulinotropic receptor | C562_ECOLX -121--17, GP119_HUMAN 1-335
Non-standard residues in 7xz5 #1
---
LSC —
(4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium
4-oxide
> style stick
Changed 16508 atom styles
> hide atoms
> show cartoons
> select /A/B/G/N
11812 atoms, 11923 bonds, 2 pseudobonds, 760 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> color #1 #e43426ff
> color #1 #db4739ff
> color #1 #e83624ff
> color #1 #db3624ff
> color #1 #c73725ff
> color #1 #e53424ff
> color #1 #bb3124ff
> color #1 #b23023ff
> color #1 #c23324ff
> color #1 #b23023ff
> color #1 #b23323ff
> color #1 #a82c23ff
> color #1 #b93123ff
> color #1 #c91a07ff
> color #1 #b11707ff
> color #1 #bb1807ff
> color #1 #af1707ff
> color #1 #ac1606ff
> color #1 #a91606ff
> color #1 #be1807ff
> color #1 #be1000ff
> color #1 #be0e00ff
> color #1 #ab0d00ff
> color #1 #a90d00ff
> open /Users/dongju/Downloads/emd_33525_7xz5.map
Opened emd_33525_7xz5.map as #2, grid size 200,200,200, pixel 1.07, shown at
level 0.0158, step 1, values float32
> volume #2 level 0.02079
> fitmap #1 inMap #2
Fit molecule 7xz5 (#1) to map emd_33525_7xz5.map (#2) using 4696 atoms
average map value = 0.02279, steps = 40
shifted from previous position = 0.0482
rotated from previous position = 0.208 degrees
atoms outside contour = 2544, contour level = 0.020794
Position of 7xz5 (#1) relative to emd_33525_7xz5.map (#2) coordinates:
Matrix rotation and translation
0.99999353 0.00337605 -0.00124113 -0.23274448
-0.00337657 0.99999421 -0.00041941 0.38358314
0.00123971 0.00042360 0.99999914 -0.16257974
Axis 0.11638676 -0.34250927 -0.93227760
Axis point 112.78332959 68.91815420 0.00000000
Rotation angle (degrees) 0.20750123
Shift along axis -0.00689971
> color #2 #829abfff models
> color #2 #95bfe5ff models
> volume style image
[Repeated 1 time(s)]
> volume style surface
> transparency 50
> surface dust #2 size 10.7
> select ligand
87 atoms, 86 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 87 atom styles
> color sel #8db9e4ff
> color sel #8ab5e4ff
> color sel #88b4e3ff
> color sel #84b1e3ff
> color sel #7dade2ff
> color sel #7cace2ff
> color sel #7aabe2ff
> color sel #78a9e2ff
> color sel #78aae2ff
[Repeated 1 time(s)]
> color sel #78a9e2ff
[Repeated 1 time(s)]
> color sel #78a6e2ff
> color sel #77a6e2ff
[Repeated 1 time(s)]
> color sel #77a4e2ff
> color sel #77a3e2ff
> color sel #76a0e2ff
> color sel #779fe2ff
> color sel #769be1ff
> color sel #7699e1ff
> color sel #7798e1ff
> color sel #7695e1ff
> color sel #7997e2ff
> color sel #7996e1ff
[Repeated 1 time(s)]
> color sel #7993e1ff
[Repeated 1 time(s)]
> color sel #7891e1ff
> color sel #7791e1ff
> color sel #748de1ff
> color sel #6d88e1ff
> color sel #6a86e1ff
> color sel #6884e1ff
> color sel #6783e0ff
> color sel #6782e0ff
> color sel #6682e0ff
> color sel #6581e0ff
> color sel #6481e0ff
[Repeated 1 time(s)]
> color sel #617fe0ff
> color sel #5e7de0ff
> color sel #5a7ae0ff
> color sel #5777e1ff
> color sel #5475e1ff
> color sel #4e71e2ff
> color sel #4b6fe2ff
> color sel #4a6de1ff
> color sel #486ce2ff
> color sel #476be1ff
> color sel #456ae2ff
> color sel #4368e2ff
> color sel #4066e3ff
> color sel #3f65e3ff
> color sel #3e64e3ff
> color sel #3d63e3ff
> color sel #3b62e3ff
> color sel #3a62e3ff
[Repeated 1 time(s)]
> color sel #3961e4ff
> color sel #3860e4ff
> color sel #375fe4ff
> color sel #355ce4ff
> color sel #345be5ff
> color sel #335be5ff
> color sel #325ae5ff
> color sel #315ae5ff
> color sel #3159e5ff
> color sel #305ae5ff
> color sel #2f5ae6ff
> color sel #2e59e6ff
> color sel #2d5ae7ff
[Repeated 1 time(s)]
> color sel #2c59e7ff
> color sel #2b58e7ff
> color sel #2b58e8ff
> color sel #2957e7ff
> color sel #2857e8ff
> color sel #2856e8ff
> color sel #2756e9ff
> color sel #2655e8ff
> color sel #2654e9ff
> color sel #2554e9ff
[Repeated 1 time(s)]
> color sel #2554eaff
> color sel #2554e9ff
> color sel #2759eaff
> color sel #285beaff
> color sel #2c63eaff
> color sel #2c64eaff
> color sel #2d66eaff
[Repeated 1 time(s)]
> color sel #2f69ebff
[Repeated 1 time(s)]
> color sel #2f6aebff
> color sel #3372ebff
> color sel #3373ebff
> color sel #3474ebff
> color sel #3576ebff
> color sel #387cebff
> color sel byhetero
> select ~sel & ##selected
4609 atoms, 4664 bonds, 1 pseudobond, 292 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> select clear
> select ligand
87 atoms, 86 bonds, 1 residue, 1 model selected
> select H
2402 atoms, 293 residues, 1 model selected
> hide sel atoms
> select clear
> hide cartoons
> ui mousemode right "map eraser"
> volume erase #2 center 98.213,117.33,82.726 radius 15.569 outside true
Opened emd_33525_7xz5.map copy as #4, grid size 200,200,200, pixel 1.07, shown
at step 1, values float32
> volume erase #4 center 99.634,96.291,77.937 radius 15.529
> volume erase #4 center 81.449,107.72,86.478 radius 15.529
> volume erase #4 center 86.376,106.33,90.936 radius 15.529
> volume erase #4 center 110.95,133.83,84.039 radius 15.529
> volume erase #4 center 101.08,108.57,100.43 radius 15.529
> volume erase #4 center 111.29,112.72,96.933 radius 15.529
> volume erase #4 center 116.67,108.27,82.34 radius 15.529
> volume erase #4 center 115.72,109.16,85.984 radius 15.529
> undo
[Repeated 9 time(s)]
> hide #!1 models
> show #!1 models
> hide sel cartoons
> hide #!4 models
> show #!4 models
> close #4
> show #!2 models
> volume erase #2 center 98.575,122.65,81.082 radius 14.458 outside true
Opened emd_33525_7xz5.map copy as #4, grid size 200,200,200, pixel 1.07, shown
at step 1, values float32
> close #4
> show #!2 models
> volume erase #2 center 99.341,121.03,81.417 radius 17.993 outside true
Opened emd_33525_7xz5.map copy as #4, grid size 200,200,200, pixel 1.07, shown
at step 1, values float32
> volume erase #4 center 110.79,124.48,90.565 radius 8.1396
> volume erase #4 center 110.84,122.75,82.866 radius 8.1396
> volume erase #4 center 109.8,120.88,75.103 radius 8.1396
> volume erase #4 center 110.45,116.63,74.645 radius 8.1396
> volume erase #4 center 98.611,132.52,71.034 radius 8.1396
> volume erase #4 center 101.33,130.98,76.631 radius 8.1396
> volume erase #4 center 101.74,127.44,71.519 radius 8.1396
> volume erase #4 center 87.562,133.37,74.695 radius 8.1396
> hide #!1 models
> show #!1 models
> show sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Alignment identifier is 1/R
> select /R:157
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /R:157
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 20 atom styles
> select /R:265
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select /R:241
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /R:241
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> select /R:82
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /R:82
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> select /R:85
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /R:85
16 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select /R:82,85
33 atoms, 31 bonds, 2 residues, 1 model selected
> select /R:82,85,157
53 atoms, 51 bonds, 3 residues, 1 model selected
> select /R:82,85,157,241
73 atoms, 71 bonds, 4 residues, 1 model selected
> select /R:82,85,157,241,265
97 atoms, 96 bonds, 5 residues, 1 model selected
> show sel atoms
> name frozen stacking_pocket sel
> ui mousemode right select
> select clear
> select /R:241
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /R:241
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /R:93,241
36 atoms, 35 bonds, 2 residues, 1 model selected
> select /R:82,93,241
53 atoms, 51 bonds, 3 residues, 1 model selected
> select /R:82,93,157,241
73 atoms, 71 bonds, 4 residues, 1 model selected
> select /R:82,93,157-158,241
93 atoms, 92 bonds, 5 residues, 1 model selected
> select /R:82,93,157-158,161,241
113 atoms, 112 bonds, 6 residues, 1 model selected
> select /R:82,93,157-158,161,165,241
133 atoms, 132 bonds, 7 residues, 1 model selected
> select /R:82,93,157-158,161,165,169,241
152 atoms, 150 bonds, 8 residues, 1 model selected
> select /R:82,93,157-158,161,165,169,174,241
172 atoms, 170 bonds, 9 residues, 1 model selected
> select /R:82,93,157-158,161,165,169,174,238,241
196 atoms, 195 bonds, 10 residues, 1 model selected
> show sel atoms
> name frozen hydrophobic_cavity sel
> select clear
> select /R:156
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /R:156
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /R:65,156
28 atoms, 26 bonds, 2 residues, 1 model selected
> select /R:65,156,262
52 atoms, 49 bonds, 3 residues, 1 model selected
> select /R:65,156,261-262
67 atoms, 64 bonds, 4 residues, 1 model selected
> show sel atoms
> name frozen head_H_bond sel
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dongju/Desktop/movie1.mp4
Movie saved to /Users/dongju/Desktop/movie1.mp4
> show sel atoms
> select clear
> select /R:261
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /R:261-262
39 atoms, 38 bonds, 2 residues, 1 model selected
> select clear
> hide cartoons
> show cartoons
> select H
2402 atoms, 293 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
Drag select of eraser sphere, 36 of 1000 triangles, 4 emd_33525_7xz5.map copy
> select clear
> ui mousemode right "map eraser"
> volume erase #4 center 99.191,131.76,90.892 radius 8.1396
> volume erase #4 center 94.667,131.6,96.584 radius 8.1396
> volume erase #4 center 87.721,132.18,90.667 radius 8.1396
> volume erase #4 center 105.84,126.62,94.736 radius 8.1396
> volume erase #4 center 102.4,128.73,80.393 radius 8.1396
> volume erase #4 center 111.48,120.97,87.878 radius 8.1396
> volume erase #4 center 115.93,111.85,82.092 radius 8.1396
> volume erase #4 center 108.43,107.99,82.775 radius 8.1396
> volume erase #4 center 107.73,105.23,74.587 radius 8.1396
> volume erase #4 center 103.7,108.91,94.52 radius 8.1396
> volume erase #4 center 104.47,110.59,96.834 radius 8.1396
> volume erase #4 center 98.862,114.5,101.46 radius 8.1396
> volume erase #4 center 102.29,112.11,98.729 radius 8.1396
> volume erase #4 center 106.98,108.74,92.776 radius 8.1396
> volume erase #4 center 106.52,109.07,93.154 radius 8.1396
> volume erase #4 center 110.68,111.23,90.78 radius 8.1396
> volume erase #4 center 109.85,112.4,90.895 radius 8.1396
> volume erase #4 center 99.406,103.96,74.532 radius 8.1396
> volume erase #4 center 100.92,103.19,85.616 radius 8.1396
> volume erase #4 center 84.855,122.16,78.913 radius 8.1396
> volume erase #4 center 89.051,127.71,86.6 radius 8.1396
> volume erase #4 center 102.67,123.01,69.123 radius 8.1396
> volume erase #4 center 101.56,117.63,61.877 radius 8.1396
> volume erase #4 center 88.061,108.98,67.752 radius 8.1396
> volume erase #4 center 83.589,109.07,77.579 radius 8.1396
> volume erase #4 center 85.901,111.98,86.928 radius 8.1396
> volume erase #4 center 88.734,108.51,81.138 radius 8.1396
> volume erase #4 center 93.055,109.37,87.843 radius 8.1396
> volume erase #4 center 92.726,112.25,90.113 radius 8.1396
> volume erase #4 center 90.389,114.04,94.248 radius 8.1396
> volume erase #4 center 97.076,112.95,95.797 radius 8.1396
> volume erase #4 center 99.29,112.81,94.683 radius 8.1396
> volume erase #4 center 92.138,113.44,97.971 radius 8.1396
> volume erase #4 center 81.483,121.4,91.171 radius 8.1396
> volume erase #4 center 83.924,123.87,93.478 radius 8.1396
> volume erase #4 center 96.101,123.11,103.59 radius 8.1396
> volume erase #4 center 102.62,117.7,98.5 radius 8.1396
> volume erase #4 center 88.295,135.88,81.964 radius 8.1396
> volume erase #4 center 100.86,140.07,77.596 radius 8.1396
> volume erase #4 center 109.6,135.56,78.637 radius 8.1396
> volume erase #4 center 112.37,133.91,79.144 radius 8.1396
> volume erase #4 center 91.34,129.9,67.561 radius 8.1396
> volume erase #4 center 80.069,119.6,71.426 radius 8.1396
> volume erase #4 center 106.29,107.99,68.884 radius 8.1396
> volume erase #4 center 100.02,106.7,84.175 radius 8.1396
> volume erase #4 center 106.83,115.8,82.832 radius 3.3201
> volume erase #4 center 105.28,116.49,85.129 radius 3.3201
> volume erase #4 center 101.52,119.15,74.378 radius 3.3201
> volume erase #4 center 92.6,113.6,79.794 radius 3.3201
> volume erase #4 center 93.305,125.06,77.822 radius 3.3201
> volume erase #4 center 93.427,111.51,73.545 radius 3.3201
> volume erase #4 center 90.272,115.88,72.197 radius 3.3201
> volume erase #4 center 90.042,119.19,72.194 radius 3.3201
> show cartoons
> hide cartoons
> ui mousemode right "map eraser"
> volume erase #4 center 99.848,120.7,81.785 radius 1.7633
> show cartoons
> ui tool show "Side View"
> select head_H_bond
67 atoms, 64 bonds, 4 residues, 1 model selected
> color sel #20113eff
> color sel #22123fff
> color sel #261342ff
[Repeated 1 time(s)]
> color sel #261240ff
> color sel #251240ff
> color sel #25123fff
[Repeated 1 time(s)]
> color sel #24123eff
[Repeated 1 time(s)]
> color sel #23123dff
> color sel #221139ff
> color sel #1e0f33ff
> color sel #1d0e30ff
> color sel #1d0e2fff
[Repeated 1 time(s)]
> color sel #1c0e2fff
> color sel #1c0d2fff
> color sel #1c0e2fff
> color sel #1b0e2dff
> color sel #1a0d2bff
> color sel #1a0d2aff
> color sel #180d28ff
> color sel #160b24ff
> color sel #150a23ff
> color sel #140a20ff
> color sel #130a20ff
> color sel #12091cff
[Repeated 1 time(s)]
> color sel #11091cff
> color sel #10081bff
> color sel #0c081aff
> color sel #0b091cff
[Repeated 2 time(s)]
> color sel #0b0a1dff
> color sel #0b0a1cff
> color sel #0b0a1dff
[Repeated 1 time(s)]
> color sel #0b091dff
> color sel #0c091dff
[Repeated 1 time(s)]
> color sel #0c091eff
> color sel #0c091fff
[Repeated 1 time(s)]
> color sel #0c0a20ff
> color sel #0d0a21ff
> color sel #0e0b24ff
> color sel #110c29ff
> color sel #140d2dff
> color sel #160e30ff
> color sel #170f31ff
> color sel #180e32ff
[Repeated 1 time(s)]
> color sel #190f33ff
[Repeated 1 time(s)]
> color sel #1a1038ff
> color sel #1a1039ff
> color sel #1a113eff
> color sel #151241ff
> color sel #151242ff
> color sel #141243ff
> color sel #141242ff
> color sel #141243ff
[Repeated 2 time(s)]
> color sel #141242ff
> color sel #141141ff
> color sel #13113eff
> color sel #11113dff
> color sel #11113cff
> color sel #10113cff
[Repeated 1 time(s)]
> color sel #12113cff
> color sel #15113bff
> color sel #1b1139ff
> color sel #1d1138ff
> color sel #1e1037ff
> color sel #1f1037ff
> color sel #200f33ff
> color sel #200e2fff
> color sel #1f0e2dff
> color sel #1e0d29ff
[Repeated 1 time(s)]
> color sel #1d0d28ff
[Repeated 1 time(s)]
> color sel #1d0d26ff
> color sel #1b0c23ff
> color sel #190b20ff
> color sel #180a1eff
> color sel #17091dff
> color sel #16081aff
> color sel #160819ff
[Repeated 2 time(s)]
> color sel #150819ff
> color sel #150818ff
> color sel #140917ff
> color sel #130916ff
[Repeated 2 time(s)]
> color sel #130816ff
[Repeated 1 time(s)]
> color sel #a9a9a9ff
> color sel #929292ff
> color sel #5e5e5eff
> color sel byhetero
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> select hydrophobic_cavity
196 atoms, 195 bonds, 10 residues, 1 model selected
> color sel dim gray
> color sel byhetero
> select clear
> select stacking_pocket
97 atoms, 96 bonds, 5 residues, 1 model selected
> color sel dim gray
> color sel byhetero
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4A_119_LPC.cxs"
——— End of log from Mon Jun 10 00:01:24 2024 ———
opened ChimeraX session
> close session
> open 7Xv3
Summary of feedback from opening 7Xv3 fetched from pdb
---
notes | Fetching compressed mmCIF 7xv3 from http://files.rcsb.org/download/7xv3.cif
Fetching CCD WJS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/WJS/WJS.cif
7xv3 title:
Cryo-EM structure of LPS-bound GPR174 in complex with Gs protein [more
info...]
Chain information for 7xv3 #1
---
Chain | Description | UniProt
A | Engineered G protein subunit S (mini-Gs) |
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
N | Nb35 |
R | Probable G-protein coupled receptor 174 | GP174_HUMAN 1-333
Non-standard residues in 7xv3 #1
---
WJS — (2~{S})-2-$l^{4}-azanyl-3-[[(2~{R})-3-octadecanoyloxy-2-oxidanyl-
propoxy]-oxidanyl-oxidanylidene-$l^{6}-phosphanyl]oxy-propanoic acid
> hide atoms
> show atoms
> style stick
Changed 8347 atom styles
> hide atoms
> show cartoons
> open 8IZB
Summary of feedback from opening 8IZB fetched from pdb
---
note | Fetching compressed mmCIF 8izb from http://files.rcsb.org/download/8izb.cif
8izb title:
Lysophosphatidylserine receptor GPR174-Gs complex [more info...]
Chain information for 8izb #2
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 1-66 205-394
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
N | Nanobody35 |
R | Probable G-protein coupled receptor 174 | GP174_HUMAN 1-309
Non-standard residues in 8izb #2
---
CLR — cholesterol
SER — serine
UBL — [(2R)-2-oxidanyl-3-phosphonooxy-propyl] (Z)-octadec-9-enoate
> style stick
Changed 16669 atom styles
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7xv3, chain B (#1) with 8izb, chain B (#2), sequence alignment
score = 1748.9
RMSD between 338 pruned atom pairs is 0.870 angstroms; (across all 338 pairs:
0.870)
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7xv3, chain B (#1) with 8izb, chain B (#2), sequence alignment
score = 1748.9
RMSD between 338 pruned atom pairs is 0.870 angstroms; (across all 338 pairs:
0.870)
> select #1/R#2/R
4742 atoms, 4879 bonds, 1 pseudobond, 579 residues, 3 models selected
> select ~sel
11927 atoms, 12154 bonds, 2 pseudobonds, 1517 residues, 4 models selected
> delete atoms (#!1-2 & sel)
> delete bonds (#!1-2 & sel)
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7xv3, chain R (#1) with 8izb, chain R (#2), sequence alignment
score = 1530.3
RMSD between 275 pruned atom pairs is 0.891 angstroms; (across all 282 pairs:
0.952)
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7xv3, chain R (#1) with 8izb, chain R (#2), sequence alignment
score = 1530.3
RMSD between 275 pruned atom pairs is 0.891 angstroms; (across all 282 pairs:
0.952)
> color #1 #00f900ff
> color #1 #73fa79ff
> color #1 #8efa00ff
> color #1 #008f00ff
> color #1 #4f8f00ff
> color #1 #71cd02ff
> color #1 #5fac01ff
> color #1 #62b102ff
> color #1 #66b902ff
> color #2 #ff9300ff
> color #2 #ffd479ff
> color #2 #fffc79ff
> color #2 #ff8a76ff
> color #2 #ff5b30ff
> color #2 #ff6542ff
> color #2 #ff694dff
> color #2 #ff7e65ff
> color #2 #ff7d61ff
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_174.cxs"
> hide #!2 models
> show #!2 models
> rename #1 GPR174_7XV3
> rename #2 GPR174_8IZB
> open /Users/dongju/Downloads/emd_33479_7XV3.map
Opened emd_33479_7XV3.map as #3, grid size 256,256,256, pixel 1.1, shown at
level 0.36, step 1, values float32
> volume #3 level 1.405
> volume #3 level 1.24
> hide #!2 models
> fitmap #1 inMap #3
Fit molecule GPR174_7XV3 (#1) to map emd_33479_7XV3.map (#3) using 2405 atoms
average map value = 1.557, steps = 40
shifted from previous position = 0.0106
rotated from previous position = 0.0257 degrees
atoms outside contour = 1086, contour level = 1.2401
Position of GPR174_7XV3 (#1) relative to emd_33479_7XV3.map (#3) coordinates:
Matrix rotation and translation
0.99999993 -0.00006648 0.00036702 -0.03179555
0.00006657 0.99999997 -0.00024767 0.02815569
-0.00036701 0.00024769 0.99999990 0.02266206
Axis 0.55317913 0.81970479 0.14858300
Axis point 58.13526746 0.00000000 99.99218581
Rotation angle (degrees) 0.02565375
Shift along axis 0.00885791
> select clear
> ui tool show "Segment Map"
Segmenting emd_33479_7XV3.map, density threshold 1.240100
Showing 45 region surfaces
1639 watershed regions, grouped to 45 regions
Showing emd_33479_7XV3.seg - 45 regions, 45 surfaces
> volume #3 level 1.625
> volume #3 level 1.515
> select #4.5
1 model selected
> select #4.9
1 model selected
> select #4.33
1 model selected
> select #4.25
1 model selected
> select #4.42
1 model selected
> select #4.32
1 model selected
> select #4.40
1 model selected
> select #4.24
1 model selected
> volume style mesh
> select ligand
126 atoms, 130 bonds, 5 residues, 2 models selected
> show sel & #!1 atoms
> select clear
> ui tool show "Segment Map"
> select clear
Showing 45 region surfaces
> select #4.40
1 model selected
> select clear
> select #4.40
1 model selected
> select add #4.32
2 models selected
> select ligand
126 atoms, 130 bonds, 5 residues, 2 models selected
> color (#!1 & sel) red
> select #4.9
1 model selected
> select #4.22
1 model selected
> select #4.42
1 model selected
> select #4.25
1 model selected
> select #4.24
1 model selected
> select #4.6
1 model selected
> select #4.44
1 model selected
> select #4.43
1 model selected
> select #4.28
1 model selected
> select #4.33
1 model selected
> select #4.5
1 model selected
> select clear
> select #4.36
1 model selected
> select add #4.5
2 models selected
> select #4.36
1 model selected
> select add #4.5
2 models selected
> select #4.36
1 model selected
> select add #4.21
2 models selected
> select add #4.5
3 models selected
> select clear
> select #4.21
1 model selected
> select #4.5
1 model selected
> select clear
> select #4.36
1 model selected
> select clear
Drag select of 2352, 2347, 2356, 2297, 2294, 2350, 2341, 2361, 2355, 2296,
2354, 2357, 2306, 2351, 2358, 2346, 2280, 2330, 2315, 2312, 2335, 2349, 2292,
2304, 2118, 2079, 2089, 2348, 2150, 1146, 65 residues, 3 emd_33479_7XV3.map
> select clear
Drag select of 2352, 2347, 2356, 2297, 14670 of 14696 triangles, 2294, 12950
of 13052 triangles, 2350, 12861 of 12876 triangles, 2341, 2361, 2355, 11674 of
11720 triangles, 2296, 2354, 2357, 2306, 9815 of 9928 triangles, 2351, 2358,
2346, 2280, 2330, 2315, 5332 of 5700 triangles, 2312, 2335, 2349, 2292, 4192
of 4588 triangles, 2304, 2118, 2079, 2089, 2348, 2150, 1146, 1 residues, 3
emd_33479_7XV3.map
> select add #1/R:202
17 atoms, 7 bonds, 2 residues, 33 models selected
> select subtract #1/R:202
9 atoms, 1 residue, 31 models selected
> select #4.5
1 model selected
> select add #4.36
2 models selected
> hide #!3 models
> select clear
> select #4.5
1 model selected
> select clear
Drag select of 2353, 2333, 35 atoms, 196 residues, 34 bonds
> select clear
Drag select of 2353, 2333, 35 atoms, 197 residues, 34 bonds
> select #1/R:40
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4.5
1 model selected
> select add #4.36
2 models selected
Segmenting emd_33479_7XV3.map, density threshold 1.515058
Showing 41 region surfaces
1431 watershed regions, grouped to 41 regions
Showing emd_33479_7XV3.seg - 41 regions, 41 surfaces
> undo
[Repeated 1 time(s)]
> show #!3 models
> ui mousemode right "map eraser"
> volume erase #3 center 140.58,139.71,106.28 radius 11.852 outside true
Opened emd_33479_7XV3.map copy as #6, grid size 256,256,256, pixel 1.1, shown
at step 1, values float32
> volume erase #6 center 137.3,152.38,97.859 radius 11.827
> volume erase #6 center 135.39,152.17,108.13 radius 11.827
> volume erase #6 center 144.73,147.59,113.46 radius 11.827
> volume erase #6 center 146.32,146.11,101.19 radius 5.4912
> volume erase #6 center 152.41,143.39,102.84 radius 5.4912
> volume erase #6 center 138.24,142.17,93.12 radius 5.4912
> volume erase #6 center 136.41,143.11,98.222 radius 5.4912
> volume erase #6 center 137.82,144.4,102.77 radius 5.4912
> volume erase #6 center 131.31,145.4,113.23 radius 5.4912
> volume erase #6 center 132.17,144.82,109.47 radius 5.4912
> volume erase #6 center 131.37,144.07,111.4 radius 5.4912
> volume erase #6 center 132.5,144.22,106.45 radius 5.4912
> volume erase #6 center 130.12,143.49,107.79 radius 5.4912
> volume erase #6 center 129.52,142.42,108.59 radius 5.4912
> volume erase #6 center 129.08,142.98,101.33 radius 5.4912
> volume erase #6 center 145.74,131.78,111.69 radius 5.4912
> volume erase #6 center 150.8,133.41,107.81 radius 5.4912
> volume erase #6 center 151.98,137.02,108.6 radius 5.4912
> volume erase #6 center 143.1,131.49,103.53 radius 5.4912
> undo
[Repeated 1 time(s)]
> show #!3 models
> hide #!3 models
> volume erase #6 center 142.48,134.18,95.914 radius 2.112
> volume erase #6 center 143.41,137.35,104.66 radius 2.112
> volume erase #6 center 142.13,136.54,106.85 radius 2.112
> volume erase #6 center 138.06,135.9,104.81 radius 2.112
> volume erase #6 center 136.16,130.41,103.82 radius 3.3792
> volume erase #6 center 137,131.27,108.9 radius 3.3792
> volume erase #6 center 136.49,131.45,109.31 radius 3.3792
> volume erase #6 center 135.44,130.37,109.42 radius 3.3792
> volume erase #6 center 138.2,132.73,114.96 radius 3.3792
> volume erase #6 center 140.56,135.89,116.43 radius 3.3792
> volume erase #6 center 138.76,138,109.25 radius 3.3792
> volume erase #6 center 139.05,137.66,112.31 radius 3.3792
> volume erase #6 center 142.67,137.36,109.71 radius 3.3792
> volume erase #6 center 141.81,136.15,110.68 radius 3.3792
> ui mousemode right select
> color #4 #bfbb4dff
> color #4 #bfb75cff
> color #6 #8769bfff models
> select clear
> show #!2 models
> hide #!4 models
> hide #!6 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> select ligand
126 atoms, 130 bonds, 5 residues, 2 models selected
> show sel & #!2 atoms
> color (#!2 & sel) cyan
> color (#!2 & sel) byelement
> color (#!2 & sel) cyan
> color (#!2 & sel) byhetero
> select clear
> select ligand
126 atoms, 130 bonds, 5 residues, 2 models selected
> select clear
Drag select of 28 atoms, 14 residues, 31 bonds
> select subtract #2/R:107
124 atoms, 31 bonds, 14 residues, 1 model selected
> select subtract #2/R:108
113 atoms, 31 bonds, 13 residues, 1 model selected
> select subtract #2/R:104
108 atoms, 31 bonds, 12 residues, 1 model selected
> select subtract #2/R:105
102 atoms, 31 bonds, 11 residues, 1 model selected
Drag select of 4 residues
> select subtract #2/R:285
111 atoms, 31 bonds, 12 residues, 1 model selected
> select add #2/R:64
116 atoms, 35 bonds, 13 residues, 1 model selected
> select subtract #2/R:65
108 atoms, 35 bonds, 12 residues, 1 model selected
> select subtract #2/R:286
102 atoms, 35 bonds, 11 residues, 1 model selected
> select subtract #2/R:64
97 atoms, 31 bonds, 10 residues, 1 model selected
> select subtract #2/R:63
89 atoms, 31 bonds, 9 residues, 1 model selected
> select subtract #2/R:61
81 atoms, 31 bonds, 8 residues, 1 model selected
> select subtract #2/R:60
73 atoms, 31 bonds, 7 residues, 1 model selected
> select subtract #2/R:59
65 atoms, 31 bonds, 6 residues, 1 model selected
> select subtract #2/R:56
57 atoms, 31 bonds, 5 residues, 1 model selected
> select subtract #2/R:54
52 atoms, 31 bonds, 4 residues, 1 model selected
> hide sel atoms
> select clear
Drag select of 28 atoms, 43 residues, 31 bonds
> hide sel atoms
> select clear
> open /Users/dongju/Downloads/emd_35838_8IZB.map
Opened emd_35838_8IZB.map as #5, grid size 192,192,192, pixel 1.07, shown at
level 0.109, step 1, values float32
> fitmap #2 inMap #5
Fit molecule GPR174_8IZB (#2) to map emd_35838_8IZB.map (#5) using 2337 atoms
average map value = 0.03112, steps = 212
shifted from previous position = 22.3
rotated from previous position = 24.7 degrees
atoms outside contour = 2133, contour level = 0.10906
Position of GPR174_8IZB (#2) relative to emd_35838_8IZB.map (#5) coordinates:
Matrix rotation and translation
-0.75709552 0.55152368 0.35018282 113.97146734
-0.50474698 -0.83411747 0.22243769 251.71856442
0.41477326 -0.00834714 0.90988651 -4.43581388
Axis -0.21307481 -0.05963389 -0.97521430
Axis point 95.12709807 109.92648099 0.00000000
Rotation angle (degrees) 147.21022229
Shift along axis -34.96953558
> volume #5 level 0.31
> ui tool show "Fit in Map"
> fitmap #2 inMap #5
Fit molecule GPR174_8IZB (#2) to map emd_35838_8IZB.map (#5) using 2337 atoms
average map value = 0.03115, steps = 48
shifted from previous position = 0.025
rotated from previous position = 0.0816 degrees
atoms outside contour = 2259, contour level = 0.30999
Position of GPR174_8IZB (#2) relative to emd_35838_8IZB.map (#5) coordinates:
Matrix rotation and translation
-0.75634424 0.55270285 0.34994707 113.77452372
-0.50587272 -0.83333500 0.22281287 251.71833289
0.41477245 -0.00850545 0.90988542 -4.40405517
Axis -0.21309999 -0.05971981 -0.97520354
Axis point 95.12333021 109.91381983 0.00000000
Rotation angle (degrees) 147.12923511
Shift along axis -34.98307141
> ui mousemode right "translate selected models"
> select add #2
2337 atoms, 2408 bonds, 1 pseudobond, 287 residues, 2 models selected
> view matrix models
> #2,-0.75634,0.5527,0.34995,100.77,-0.50587,-0.83333,0.22281,216.63,0.41477,-0.0085054,0.90989,-31.932
> fitmap #2 inMap #5
Fit molecule GPR174_8IZB (#2) to map emd_35838_8IZB.map (#5) using 2337 atoms
average map value = 0.08239, steps = 112
shifted from previous position = 2.02
rotated from previous position = 15.7 degrees
atoms outside contour = 2038, contour level = 0.30999
Position of GPR174_8IZB (#2) relative to emd_35838_8IZB.map (#5) coordinates:
Matrix rotation and translation
-0.62364597 0.74902223 0.22367702 77.87927936
-0.66907043 -0.65943588 0.34276680 205.54528669
0.40424060 0.06410946 0.91240315 -40.48325695
Axis -0.19132671 -0.12397533 -0.97366535
Axis point 88.49903660 88.11034294 0.00000000
Rotation angle (degrees) 133.26230076
Shift along axis -0.96578672
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.70332,0.62636,0.33617,89.044,-0.54828,-0.77897,0.30429,208.47,0.45246,0.029698,0.89129,-40.182
> view matrix models
> #2,-0.38844,0.53793,0.74816,33.249,-0.82947,-0.55777,-0.029626,241.38,0.40136,-0.63209,0.66285,49.269
> view matrix models
> #2,-0.65242,0.24877,0.71586,91.091,-0.63219,-0.69958,-0.33305,260.16,0.41795,-0.66985,0.61369,55.325
> view matrix models
> #2,-0.5867,0.50734,0.63118,65.537,-0.7995,-0.48686,-0.35181,257.2,0.12881,-0.71103,0.69126,82.133
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.5867,0.50734,0.63118,60.551,-0.7995,-0.48686,-0.35181,261.38,0.12881,-0.71103,0.69126,84.231
> fitmap #2 inMap #5
Fit molecule GPR174_8IZB (#2) to map emd_35838_8IZB.map (#5) using 2337 atoms
average map value = 0.1085, steps = 92
shifted from previous position = 0.937
rotated from previous position = 10 degrees
atoms outside contour = 1891, contour level = 0.30999
Position of GPR174_8IZB (#2) relative to emd_35838_8IZB.map (#5) coordinates:
Matrix rotation and translation
-0.62096528 0.36269632 0.69487660 72.83627793
-0.76631836 -0.46729282 -0.44090089 263.50441797
0.16479771 -0.80628084 0.56811347 99.96027181
Axis -0.28113136 0.40785433 -0.86868867
Axis point 76.22679670 139.73009413 0.00000000
Rotation angle (degrees) 139.47057346
Shift along axis 0.16050012
> view matrix models
> #2,-0.62097,0.3627,0.69488,72.832,-0.76632,-0.46729,-0.4409,263.51,0.1648,-0.80628,0.56811,99.969
> view matrix models
> #2,-0.62097,0.3627,0.69488,72.278,-0.76632,-0.46729,-0.4409,263.09,0.1648,-0.80628,0.56811,99.426
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.88734,-0.45949,0.038594,56.044,0.37767,0.77224,0.51089,-51.449,-0.26456,-0.43876,0.85878,82.396
> view matrix models
> #2,0.68908,-0.72467,-0.004158,105.76,0.64997,0.61549,0.44576,-57.838,-0.32047,-0.30987,0.89514,72.218
> view matrix models
> #2,0.55824,-0.82784,-0.05519,133.24,0.7659,0.48861,0.41792,-54.551,-0.319,-0.27557,0.90681,67.714
> view matrix models
> #2,0.32974,-0.92787,-0.17416,175.64,0.90726,0.26044,0.33022,-38.902,-0.26104,-0.26689,0.9277,59.37
> view matrix models
> #2,0.45763,-0.88555,-0.079857,151.04,0.84987,0.46205,-0.25344,-6.3646,0.26133,0.048115,0.96405,-27.233
> view matrix models
> #2,0.49381,-0.86137,0.11913,129.02,0.8695,0.49087,-0.054935,-27.152,-0.011156,0.13071,0.99136,-10.394
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.49381,-0.86137,0.11913,130.24,0.8695,0.49087,-0.054935,-27.912,-0.011156,0.13071,0.99136,-12.122
> fitmap #2 inMap #5
Fit molecule GPR174_8IZB (#2) to map emd_35838_8IZB.map (#5) using 2337 atoms
average map value = 0.09425, steps = 80
shifted from previous position = 2.89
rotated from previous position = 5.57 degrees
atoms outside contour = 1973, contour level = 0.30999
Position of GPR174_8IZB (#2) relative to emd_35838_8IZB.map (#5) coordinates:
Matrix rotation and translation
0.52515536 -0.85051680 0.02886199 134.01497851
0.84977602 0.52227137 -0.07150763 -24.99386004
0.04574465 0.06207884 0.99702239 -11.46111867
Axis 0.07832154 -0.00989827 0.99687901
Axis point 89.84006467 107.47382746 0.00000000
Rotation angle (degrees) 58.51841098
Shift along axis -0.68169319
> view matrix models
> #2,0.52516,-0.85052,0.028862,134.03,0.84978,0.52227,-0.071508,-24.982,0.045745,0.062079,0.99702,-11.446
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> open 8IZB
8izb title:
Lysophosphatidylserine receptor GPR174-Gs complex [more info...]
Chain information for 8izb #7
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 1-66 205-394
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
N | Nanobody35 |
R | Probable G-protein coupled receptor 174 | GP174_HUMAN 1-309
Non-standard residues in 8izb #7
---
CLR — cholesterol
SER — serine
UBL — [(2R)-2-oxidanyl-3-phosphonooxy-propyl] (Z)-octadec-9-enoate
> show #!2,7 atoms
> hide #!2,7 atoms
> show #!2,7 cartoons
> hide #!2 models
> fitmap #7 inMap #5
Fit molecule 8izb (#7) to map emd_35838_8IZB.map (#5) using 8322 atoms
average map value = 0.528, steps = 48
shifted from previous position = 0.00983
rotated from previous position = 0.0346 degrees
atoms outside contour = 2668, contour level = 0.30999
Position of 8izb (#7) relative to emd_35838_8IZB.map (#5) coordinates:
Matrix rotation and translation
0.99999990 -0.00043812 -0.00007167 0.05733242
0.00043815 0.99999982 0.00040866 -0.10116588
0.00007149 -0.00040870 0.99999991 0.03879010
Axis -0.67728235 -0.11862354 0.72609715
Axis point 230.58619138 132.87307402 0.00000000
Rotation angle (degrees) 0.03457291
Shift along axis 0.00133580
> fitmap #7 inMap #5
Fit molecule 8izb (#7) to map emd_35838_8IZB.map (#5) using 8322 atoms
average map value = 0.528, steps = 40
shifted from previous position = 0.0136
rotated from previous position = 0.0126 degrees
atoms outside contour = 2663, contour level = 0.30999
Position of 8izb (#7) relative to emd_35838_8IZB.map (#5) coordinates:
Matrix rotation and translation
0.99999989 -0.00041193 -0.00021360 0.07185299
0.00041198 0.99999989 0.00024297 -0.07255698
0.00021350 -0.00024306 0.99999995 -0.00480124
Axis -0.46394690 -0.40768761 0.78647574
Axis point 183.61588251 165.89958263 0.00000000
Rotation angle (degrees) 0.03001154
Shift along axis -0.00753145
> select ligand
217 atoms, 226 bonds, 9 residues, 3 models selected
> show sel & #!7 atoms
> style sel & #!7 stick
Changed 91 atom styles
> color (#!7 & sel) cyan
> color (#!7 & sel) byhetero
> ui mousemode right select
> select clear
> color #7 #e97925ff
> select clear
> ui mousemode right "map eraser"
> hide #!5 models
> select ligand
217 atoms, 226 bonds, 9 residues, 3 models selected
> color (#!7 & sel) cyan
> color (#!7 & sel) byhetero
> ui mousemode right select
> select clear
Drag select of 28 atoms, 15 residues, 31 bonds
> hide sel atoms
Drag select of 28 atoms, 36 residues, 31 bonds
> hide sel atoms
> select clear
> ui mousemode right "map eraser"
> show #!5 models
> volume erase #5 center 106.66,103.8,71.644 radius 14.586 outside true
Opened emd_35838_8IZB.map copy as #9, grid size 192,192,192, pixel 1.07, shown
at step 1, values float32
> volume #!9 style mesh
> volume erase #9 center 111.41,89.902,65.361 radius 14.586
> volume erase #9 center 107.94,121.91,67.65 radius 14.586
> volume erase #9 center 111.71,121.18,80.776 radius 14.586
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!7 models
> show #!7 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 2 residues, 1 model selected
> select clear
> select #7/R:501@CAL
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 27 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 2 residues, 1 model selected
> ui tool show "Surface Zone"
> surface zone #5 nearAtoms sel distance 6.42
> show #!5 models
> surface zone #5 nearAtoms sel distance 6.39
> surface zone #5 nearAtoms sel distance 2.37
> volume #!5 style mesh
> select clear
> hide #!5 models
> select #7/R:501@CAL
1 atom, 1 residue, 1 model selected
> select clear
> hide #!7 cartoons
> show #!5 models
> show #!7 cartoons
> surface dust #5 size 10.7
[Repeated 1 time(s)]
> show #!9 models
> hide #!9 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ligand
217 atoms, 226 bonds, 9 residues, 3 models selected
> surface zone #5 nearAtoms sel distance 2.37
> show #!5 models
> surface zone #5 nearAtoms sel distance 2.19
> surface zone #5 nearAtoms sel distance 1.98
> surface zone #5 nearAtoms sel distance 1.92
> surface zone #5 nearAtoms sel distance 2.84
> volume erase #5 center 97.122,114.32,87.432 radius 15.824
Opened emd_35838_8IZB.map copy as #10, grid size 192,192,192, pixel 1.07,
shown at step 1, values float32
> hide #8 models
> hide #!7 models
> show #!7 models
> hide #!10 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> surface zone #5 nearAtoms sel distance 2.88
> surface zone #5 nearAtoms sel distance 3.51
> surface zone #10 nearAtoms sel distance 6.42
> surface zone #10 nearAtoms sel distance 7.4
> surface zone #10 nearAtoms sel distance 2.98
> surface zone #10 nearAtoms sel distance 2.84
> surface zone #10 nearAtoms sel distance 1.07
> surface zone #10 nearAtoms sel distance 1.14
> surface zone #10 nearAtoms sel distance 1.46
> hide #!9 models
> hide #!10 models
> show #!9 models
> ui mousemode right "map eraser"
> show #8 models
> volume erase #9 center 114.38,92.324,58.232 radius 15.819
> volume erase #9 center 111.49,87.981,63.612 radius 15.819
[Repeated 2 time(s)]
> volume erase #9 center 107.71,88.792,66.568 radius 15.819
Drag select of eraser sphere, 12 of 1000 triangles, 1 residues
> volume erase #9 center 105.1,88.752,87.326 radius 15.819
> select clear
[Repeated 1 time(s)]Drag select of eraser sphere, 22 of 1000 triangles
> volume erase #9 center 91.499,94.95,81.957 radius 15.819
> volume erase #9 center 85.413,90.487,70.998 radius 15.819
> volume erase #9 center 86.636,92.277,71.444 radius 15.819
Drag select of 3 residues
> volume erase #9 center 98.241,122.4,57.74 radius 15.819
> volume erase #9 center 102.19,111.25,73.203 radius 5.855
> volume erase #9 center 97.847,107.45,77.377 radius 5.855
> volume erase #9 center 99.791,104.95,73.32 radius 4.2115
> volume erase #9 center 99.143,106.95,70.195 radius 1.5408
> volume erase #9 center 100.36,103.84,59.868 radius 1.5408
> volume erase #9 center 99.493,104.67,62.092 radius 1.5408
> volume erase #9 center 98.056,103.55,61.843 radius 1.5408
> volume erase #9 center 101.99,103.77,60.872 radius 1.5408
> volume erase #9 center 114.36,107.58,72.154 radius 1.5408
> volume erase #9 center 114.63,103.19,73.152 radius 2.6707
> volume erase #9 center 114.95,102.6,75.728 radius 2.6707
> volume erase #9 center 111.11,100.72,76.519 radius 2.6707
> volume erase #9 center 111.56,100.18,79.429 radius 2.6707
> volume erase #9 center 112.28,99.226,83.652 radius 2.6707
> volume erase #9 center 113.98,100.1,82.377 radius 2.6707
> volume erase #9 center 108.54,103.62,85.176 radius 2.6707
> volume erase #9 center 110.25,103.01,85.589 radius 2.6707
> volume erase #9 center 109.53,104.43,84.971 radius 2.6707
> volume erase #9 center 110.73,103.84,85.163 radius 2.6707
> volume erase #9 center 111.12,105.18,86.48 radius 2.6707
> volume erase #9 center 108.43,104.79,87.72 radius 2.6707
> volume erase #9 center 107.37,105.83,85.436 radius 2.6707
> volume erase #9 center 100.71,107.72,83.237 radius 2.6707
> volume erase #9 center 104.99,107.2,81.964 radius 2.6707
> volume erase #9 center 96.298,109.91,77.518 radius 2.6707
> volume erase #9 center 98.754,113.88,76.858 radius 2.6707
> volume erase #9 center 103.49,107.6,70.05 radius 2.6707
> volume erase #9 center 105.05,107.56,75.06 radius 2.6707
> volume erase #9 center 105.08,107.46,78.505 radius 2.6707
> volume erase #9 center 104.93,106.09,79.592 radius 2.6707
> volume erase #9 center 104.63,102.97,82.066 radius 2.6707
> volume erase #9 center 104.29,106.6,79.002 radius 2.6707
> volume erase #9 center 104.49,106.53,79.109 radius 3.1843
> volume erase #9 center 105.6,106.44,76.099 radius 3.1843
> volume erase #9 center 105.35,106.52,74.933 radius 3.1843
> volume erase #9 center 104.88,103.13,76.405 radius 3.1843
> volume erase #9 center 104.98,103.66,75.024 radius 3.1843
> ui mousemode right select
> select clear
> transparency 80 ribbons
> graphics silhouettes width 1.3 depthJump 0.1
> select clear
> color #9 #5884ffff models
> color #9 #2f4688ff models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_8izb.png" width 2000
> height 1253 supersample 3 transparentBackground true
> show #!1 models
> show #!6 models
> hide #!7 models
> show #!1 cartoons
> hide #!9 models
Drag select of 4 residues
> select clear
> select lignad
Expected an objects specifier or a keyword
> select ligand
217 atoms, 226 bonds, 9 residues, 3 models selected
> color (#!1 & sel) byhetero
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_7xv3.png" width 2000
> height 1253 supersample 3 transparentBackground true
[Repeated 5 time(s)]
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R
Alignment identifier is 1/R
> select #1/R:103-104
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #1/R:103-104
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #1/R:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/R:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/R:103,151
20 atoms, 19 bonds, 2 residues, 1 model selected
> select #1/R:103,151-152
31 atoms, 31 bonds, 3 residues, 1 model selected
> select #1/R:103,151-152,155
39 atoms, 38 bonds, 4 residues, 1 model selected
> select #1/R:103,151-152,155,185-186
55 atoms, 53 bonds, 6 residues, 1 model selected
> select #1/R:103,151-152,155,185-186
55 atoms, 53 bonds, 6 residues, 1 model selected
> select #1/R:103,151-152,155,185-186
55 atoms, 53 bonds, 6 residues, 1 model selected
> select #1/R:103,151-152,155,185-187
62 atoms, 60 bonds, 7 residues, 1 model selected
> select #1/R:103,151-152,155,185-187
62 atoms, 60 bonds, 7 residues, 1 model selected
> select #1/R:103,151-152,155,185-187
62 atoms, 60 bonds, 7 residues, 1 model selected
> select clear
> select #1/R:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/R:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/R:103,155-156
31 atoms, 30 bonds, 3 residues, 1 model selected
> select #1/R:103,151-152,155-156
50 atoms, 49 bonds, 5 residues, 1 model selected
> select #1/R:103,151-152,155-156,185
58 atoms, 56 bonds, 6 residues, 1 model selected
> select #1/R:103,151-152,155-156,185,250
69 atoms, 67 bonds, 7 residues, 1 model selected
> select #1/R:103,151-152,155-156,185,250,254
80 atoms, 78 bonds, 8 residues, 1 model selected
> name frozen 1_hydrophobic_cleft sel
Not registering illegal selector name "1_hydrophobic_cleft"
> show sel atoms
> style sel stick
Changed 80 atom styles
> color sel byhetero
> select clear
> select #1/R:18
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/R:18
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/R:18,75
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/R:18,75,79
34 atoms, 32 bonds, 3 residues, 1 model selected
> select #1/R:18,75,79,98
43 atoms, 40 bonds, 4 residues, 1 model selected
> select #1/R:18,75,79,98-99
55 atoms, 53 bonds, 5 residues, 1 model selected
> select #1/R:18,75,79,98-99,156
66 atoms, 63 bonds, 6 residues, 1 model selected
> select #1/R:18,75,79,98-99,156,246
78 atoms, 75 bonds, 7 residues, 1 model selected
> select #1/R:18,75,79,98-99,156,246,257
87 atoms, 83 bonds, 8 residues, 1 model selected
> name frozen 1_head_interact sel
Not registering illegal selector name "1_head_interact"
> show sel atoms
> style sel stick
Changed 87 atom styles
> color sel byhetero
> select clear
> select #1/R:18,75,79,98-99,156,246,257-258
93 atoms, 89 bonds, 9 residues, 1 model selected
> select #1/R:18,75,79,98-99,156,246,257-258
93 atoms, 89 bonds, 9 residues, 1 model selected
> select #1/R:18,75,79,98-99,156,246,257-258
93 atoms, 89 bonds, 9 residues, 1 model selected
> select #1/R:18,75,79,98-99,156,246,256-259
108 atoms, 104 bonds, 11 residues, 1 model selected
> select #1/R:18,75,79,98-99,156,246,256-259
108 atoms, 104 bonds, 11 residues, 1 model selected
> select #1/R:18
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/R:18
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/R:18,75
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/R:18,75,79
34 atoms, 32 bonds, 3 residues, 1 model selected
> select #1/R:18,75,79,98
43 atoms, 40 bonds, 4 residues, 1 model selected
> select #1/R:18,75,79,98-99
55 atoms, 53 bonds, 5 residues, 1 model selected
> select #1/R:18,75,79,98-99,156
66 atoms, 63 bonds, 6 residues, 1 model selected
> select #1/R:18,75,79,98-99,156,246
78 atoms, 75 bonds, 7 residues, 1 model selected
> select #1/R:18,75,79,98-99,156,246,257
87 atoms, 83 bonds, 8 residues, 1 model selected
> name frozen head_interact_1 sel
> hide sel atoms
> select clear
> select #1/R:154
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/R:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/R:151
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #1/R:185
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #1/R:152
35 atoms, 32 bonds, 4 residues, 1 model selected
> select add #1/R:254
46 atoms, 43 bonds, 5 residues, 1 model selected
> select add #1/R:250
57 atoms, 54 bonds, 6 residues, 1 model selected
> select add #1/R:103
69 atoms, 66 bonds, 7 residues, 1 model selected
> name frozen tail_interact_1 sel
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_7xv3_tail.png" width
> 2000 height 1253 supersample 3 transparentBackground true
> select head_interact_1
87 atoms, 83 bonds, 8 residues, 1 model selected
> hide sel atoms
> select tail_interact_1
69 atoms, 67 bonds, 7 residues, 1 model selected
> hide sel atoms
> select head_interact_1
87 atoms, 83 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_7xv3_head.png" width
> 2000 height 1253 supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> hide #!6 models
> show #!9 models
> hide #!2 models
> show #!10 models
> hide #!10 models
> show #!5 models
> hide #!5 models
> show #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #7/R
Alignment identifier is 7/R
> select #7/R:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/R:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/R:103,151
20 atoms, 19 bonds, 2 residues, 1 model selected
> select #7/R:103,151-153
38 atoms, 39 bonds, 4 residues, 1 model selected
> select #7/R:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/R:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/R:152
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #7/R:151-152
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #7/R:103,151-152
31 atoms, 31 bonds, 3 residues, 1 model selected
> select #7/R:103,151-152,185
39 atoms, 38 bonds, 4 residues, 1 model selected
> select #7/R:103,151-152,185,250
50 atoms, 49 bonds, 5 residues, 1 model selected
> select #7/R:103,151-152,185,250,254
61 atoms, 60 bonds, 6 residues, 1 model selected
> select #7/R:103,151-152,155,185,250,254
69 atoms, 67 bonds, 7 residues, 1 model selected
> name frozen tail_interact_2 sel
> show sel atoms
> style sel stick
Changed 69 atom styles
> color sel byhetero
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_8izb_tail.png" width
> 2000 height 1253 supersample 3 transparentBackground true
> select tail_interact_2
69 atoms, 67 bonds, 7 residues, 1 model selected
> hide sel atoms
> select clear
> select #7/R:18
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #7/R:18
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #7/R:18,75
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #7/R:18,75,79
34 atoms, 32 bonds, 3 residues, 1 model selected
> select #7/R:18,75,79,98
43 atoms, 40 bonds, 4 residues, 1 model selected
> select #7/R:18,75,79,98-99
55 atoms, 53 bonds, 5 residues, 1 model selected
> select #7/R:18,75,79,98-99,156
66 atoms, 63 bonds, 6 residues, 1 model selected
> select #7/R:18,75,79,98-99,156,246
78 atoms, 75 bonds, 7 residues, 1 model selected
> select #7/R:18,75,79,98-99,156,246,257
87 atoms, 83 bonds, 8 residues, 1 model selected
> name frozen head_interact_2 sel
> show sel atoms
> style sel stick
Changed 87 atom styles
> color sel byhetero
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_8izb_head.png" width
> 2000 height 1253 supersample 3 transparentBackground true
> select clear
> select #7/R:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #7/R:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 12 atom styles
> ui tool show H-Bonds
> hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
> false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
7 8izb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
> false intraRes false select true reveal true log true
Atom specifier selects no atoms
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_8izb_head.png" width
> 2000 height 1253 supersample 3 transparentBackground true
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_174_v2.cxs"
> hide #!9 models
> show #!9 models
> ui mousemode right "map eraser"
> volume erase #9 center 103.31,102.34,56.196 radius 2.9422
> ui mousemode right select
> hide #!9 models
> show #!9 models
> save /Users/dongju/Desktop/image1.png supersample 3
> hide #!9 models
> show #!9 models
> select tail_interact_2
69 atoms, 67 bonds, 7 residues, 1 model selected
> show sel atoms
> select tail_interact_2
69 atoms, 67 bonds, 7 residues, 1 model selected
> select head_interact_2
87 atoms, 83 bonds, 8 residues, 1 model selected
> hide sel atoms
> select clear
> select head_interact_2
87 atoms, 83 bonds, 8 residues, 1 model selected
> show sel atoms
> show #!1 models
> hide #!7 models
> hide #!9 models
> select tail_interact_1
69 atoms, 67 bonds, 7 residues, 1 model selected
> show sel atoms
> select clear
> show #!2 models
> show #!10 models
> hide #!2 models
> show #!7 models
> hide #!10 models
> show #!9 models
> show #!6 models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_174_v3.cxs"
——— End of log from Fri Jun 14 01:29:38 2024 ———
opened ChimeraX session
Showing emd_33479_7XV3.seg - 41 regions, 41 surfaces
> hide #!9 models
> hide #!7 models
> show #!7 models
> show #!9 models
> hide #!1 models
> hide #!4 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> ui mousemode right select
> select #7/R:501@CAH
1 atom, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
> false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
7 8izb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
> false intraRes false select true reveal true log true
Atom specifier selects no atoms
> cartoon style helix width 1.7 thickness 0.2
> cartoon style helix width 1.5 thickness 0.2
> cartoon style helix width 1.3 thickness 0.2
> select #7/N
973 atoms, 995 bonds, 128 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/A
1954 atoms, 1993 bonds, 1 pseudobond, 235 residues, 2 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> select #7/C
436 atoms, 442 bonds, 57 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/B
2622 atoms, 2669 bonds, 342 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> transparency 0 ribbons
> ui tool show "Side View"
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_8izb_overall_v2.png"
> width 3000 height 2304 supersample 3 transparentBackground true
> transparency 80 ribbons
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_8izb_binding_v2.png"
> width 2000 height 1536 supersample 3 transparentBackground true
> show #!1 models
> show #!6 models
> select ~sel & ##selected
Nothing selected
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_7xv3_binding_v2.png"
> width 2000 height 1536 supersample 3 transparentBackground true
> hide #!1 models
> hide #!6 models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_8izb_binding_v2.png"
> width 2000 height 1536 supersample 3 transparentBackground true
> show #!1 models
> hide #!7 models
> hide #!9 models
> show #!6 models
> transparency 0 ribbons
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_GPR174_7xv3_overall_v2.png"
> width 3000 height 2304 supersample 3 transparentBackground true
[Repeated 1 time(s)]
> show #!7 models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4D_174_v3.cxs"
——— End of log from Sun Jun 16 23:57:53 2024 ———
opened ChimeraX session
Showing emd_33479_7XV3.seg - 41 regions, 41 surfaces
> close session
> open 8X2K
Summary of feedback from opening 8X2K fetched from pdb
---
note | Fetching compressed mmCIF 8x2k from http://files.rcsb.org/download/8x2k.cif
8x2k title:
a lipid receptor complex structure [more info...]
Chain information for 8x2k #1
---
Chain | Description | UniProt
A | Soluble cytochrome b562,G-protein coupled receptor 3 | C562_ECOLX -105--1, GPR3_HUMAN 1-330
B | Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 26-394
C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
E | scfv16 |
Non-standard residues in 8x2k #1
---
5YM — (Z)-N-(2-hydroxyethyl)octadec-9-enamide
> select ~sel & ##selected
Nothing selected
> open 8WW2
Summary of feedback from opening 8WW2 fetched from pdb
---
note | Fetching compressed mmCIF 8ww2 from http://files.rcsb.org/download/8ww2.cif
8ww2 title:
GPR3/Gs complex [more info...]
Chain information for 8ww2 #2
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
N | Nb35 |
R | G-protein coupled receptor 3 | GPR3_HUMAN 1-330
Non-standard residues in 8ww2 #2
---
OLA — oleic acid
PLM — palmitic acid
Y01 — cholesterol hemisuccinate
> open 8U8F
Summary of feedback from opening 8U8F fetched from pdb
---
note | Fetching compressed mmCIF 8u8f from http://files.rcsb.org/download/8u8f.cif
8u8f title:
GPR3 Orphan G-coupled Protein Receptor in complex with Dominant Negative Gs.
[more info...]
Chain information for 8u8f #3
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 1-394
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 5-62
R | G-protein coupled receptor 3 | GPR3_HUMAN 2-330
Non-standard residues in 8u8f #3
---
PLM — palmitic acid
> style stick
Changed 30268 atom styles
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8x2k, chain C (#1) with 8ww2, chain B (#2), sequence alignment
score = 1641.5
RMSD between 337 pruned atom pairs is 0.626 angstroms; (across all 338 pairs:
0.643)
Matchmaker 8x2k, chain C (#1) with 8u8f, chain B (#3), sequence alignment
score = 1614.3
RMSD between 336 pruned atom pairs is 0.784 angstroms; (across all 337 pairs:
0.791)
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8x2k, chain C (#1) with 8ww2, chain B (#2), sequence alignment
score = 1641.5
RMSD between 337 pruned atom pairs is 0.626 angstroms; (across all 338 pairs:
0.643)
Matchmaker 8x2k, chain C (#1) with 8u8f, chain B (#3), sequence alignment
score = 1614.3
RMSD between 336 pruned atom pairs is 0.784 angstroms; (across all 337 pairs:
0.791)
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> show sel atoms
> select clear
[Repeated 2 time(s)]
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!3 models
> color #1 #fff39bff
> color #1 #b2ffa8ff
> color #2 #edba84ff
> color #2 #edd86aff
> color #2 #6bacedff
> color #3 #e581a5ff
> color #3 #e5728bff
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> color sel byhetero
> select clear
> cartoon style helix width 1.4 thickness 0.2
> cartoon style helix width 1.4 thickness 0.4
> select #1/D#2/G#3/G
1721 atoms, 1739 bonds, 169 residues, 3 models selected
> delete atoms sel
> delete bonds sel
> select #1/C#2/B#3/B
10266 atoms, 10407 bonds, 1016 residues, 3 models selected
> delete atoms sel
> delete bonds sel
> select #2/A#3/A
5608 atoms, 5678 bonds, 4 pseudobonds, 460 residues, 4 models selected
> delete atoms (#!2-3 & sel)
> delete bonds (#!2-3 & sel)
> select #1/B
1795 atoms, 1828 bonds, 4 pseudobonds, 218 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/E
1803 atoms, 1849 bonds, 1 pseudobond, 236 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #2/N
965 atoms, 987 bonds, 128 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
[Repeated 1 time(s)]
> ui tool show Matchmaker
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8x2k, chain A (#1) with 8ww2, chain R (#2), sequence alignment
score = 1513.5
RMSD between 254 pruned atom pairs is 0.631 angstroms; (across all 260 pairs:
0.821)
Matchmaker 8x2k, chain A (#1) with 8u8f, chain R (#3), sequence alignment
score = 1558.7
RMSD between 251 pruned atom pairs is 0.795 angstroms; (across all 259 pairs:
0.961)
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8x2k, chain A (#1) with 8ww2, chain R (#2), sequence alignment
score = 1513.5
RMSD between 254 pruned atom pairs is 0.631 angstroms; (across all 260 pairs:
0.821)
Matchmaker 8x2k, chain A (#1) with 8u8f, chain R (#3), sequence alignment
score = 1558.7
RMSD between 251 pruned atom pairs is 0.795 angstroms; (across all 259 pairs:
0.961)
> color #3 #eca5acff
> color #3 #ec626dff
> color #2 #4a8ff1ff
> color #2 #4c86f1ff
> color #2 #f1c847ff
> color #2 #38a8f1ff
> color #1 #fce991ff
> select clear
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> color sel byhetero
> select clear
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> select add #2
2118 atoms, 2158 bonds, 1 pseudobond, 275 residues, 4 models selected
> select subtract #2
70 atoms, 68 bonds, 2 residues, 2 models selected
> select add #3
4164 atoms, 4209 bonds, 1 pseudobond, 267 residues, 3 models selected
> select subtract #3
23 atoms, 22 bonds, 1 residue, 1 model selected
> color sel medium blue
> color sel byhetero
> color sel dim gray
> color sel byhetero
> select clear
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> select add #1
2041 atoms, 2076 bonds, 1 pseudobond, 267 residues, 4 models selected
> select subtract #1
120 atoms, 120 bonds, 4 residues, 2 models selected
> select add #3
4214 atoms, 4261 bonds, 1 pseudobond, 269 residues, 3 models selected
> select subtract #3
73 atoms, 74 bonds, 3 residues, 1 model selected
> color sel orange
> color sel byhetero
> select clear
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> select add #1
2041 atoms, 2076 bonds, 1 pseudobond, 267 residues, 4 models selected
> select subtract #1
120 atoms, 120 bonds, 4 residues, 2 models selected
> select add #2
2095 atoms, 2136 bonds, 1 pseudobond, 274 residues, 3 models selected
> select subtract #2
47 atoms, 46 bonds, 1 residue, 1 model selected
> color sel #fc6739ff
> color sel #fc6336ff
> color sel #fc6134ff
> color sel #fc5f32ff
> color sel #fc5529ff
> color sel #fc5328ff
> color sel #fc5227ff
> color sel #fc4f25ff
> color sel #fc4e24ff
> color sel #fc4d23ff
> color sel #fc4b1fff
> color sel #fc4a1eff
> color sel #fc4a1dff
[Repeated 1 time(s)]
> color sel #fc4a1cff
> color sel #fc4a1bff
> color sel #fc4919ff
> color sel #fc4917ff
> color sel #fc4812ff
> color sel #fc4811ff
> color sel #fc470fff
> color sel #fc460eff
> color sel #fc440bff
> color sel #fc4309ff
> color sel #fc4208ff
> color sel #fc3f04ff
> color sel #fc3e03ff
> color sel #fc3d02ff
[Repeated 2 time(s)]
> color sel #fc3c02ff
> color sel #fc3901ff
> color sel #fc3801ff
> color sel #fc3702ff
> color sel #fc3602ff
[Repeated 1 time(s)]
> color sel #fc3504ff
> color sel #fc3505ff
> color sel #fc3605ff
> color sel #fc3606ff
> color sel #fc3706ff
> color sel #fc3808ff
> color sel #fc3a0aff
> color sel #fc3d0cff
> color sel #fc3f0eff
> color sel #fc4211ff
> color sel #fc4613ff
> color sel #fc4916ff
> color sel #fc4c19ff
> color sel #fc4e1aff
> color sel #fc501bff
[Repeated 1 time(s)]
> color sel #fc501cff
> color sel #fc511cff
[Repeated 1 time(s)]
> color sel #fc511dff
[Repeated 2 time(s)]
> color sel #fc511eff
[Repeated 1 time(s)]
> color sel #fc511fff
> color sel #fc5323ff
> color sel #fc5424ff
> color sel #fc5426ff
> color sel #fc5528ff
> color sel #fc5629ff
> color sel #fc562aff
> color sel #fc562bff
> color sel #fc562dff
> color sel #fc562eff
> color sel #fc562fff
> color sel #fc552fff
[Repeated 1 time(s)]
> color sel #fc542fff
> color sel #fc532fff
[Repeated 1 time(s)]
> color sel #fc4f30ff
> color sel #fc4e31ff
> color sel #fc4a34ff
> color sel #fc4037ff
> color sel #fc3d38ff
> color sel #fc3b38ff
> color sel #fc3839ff
> color sel #fc3942ff
> color sel #fc3845ff
> color sel #fc3847ff
> color sel #fc3849ff
> color sel #fc384bff
> color sel #fc384dff
> color sel #fc3754ff
> color sel #fc3656ff
> color sel #fc3659ff
> color sel #fc365cff
> color sel #fc355dff
> color sel #fc355fff
> color sel #fc3463ff
> color sel #fc3364ff
> color sel #fc3366ff
> color sel #fc326aff
> color sel #fc326bff
> color sel #fc326dff
> color sel #fc316dff
[Repeated 1 time(s)]
> color sel #fc316eff
> color sel #fc326eff
[Repeated 1 time(s)]
> color sel #fc326fff
[Repeated 1 time(s)]
> color sel #fc3370ff
> color sel #fc3d80ff
> color sel #fc438aff
> color sel #fc4999ff
> color sel #fc4aa1ff
> color sel #fc4aa2ff
> color sel #fc49a5ff
> color sel #fc46afff
> color sel #fc44b3ff
> color sel #fc43b7ff
> color sel #fc3ebfff
> color sel #fc3ec0ff
[Repeated 1 time(s)]
> color sel #fc3dc2ff
[Repeated 1 time(s)]
> color sel #fc3dc3ff
> color sel #fc3dc5ff
> color sel #fc3dc7ff
> color sel #fc3dc9ff
> color sel #fc3dceff
> color sel #fc3ecfff
> color sel #fc3ed1ff
> color sel #fc3fd2ff
> color sel #fc3fd3ff
> color sel #fc40d6ff
> color sel #fc46dfff
> color sel #fc49e5ff
> color sel #fc4debff
> color sel #fc53f6ff
> color sel #fc53f7ff
[Repeated 1 time(s)]
> color sel #fc54f7ff
[Repeated 1 time(s)]
> color sel #fc55efff
> color sel #fc54e9ff
> color sel #fc53e3ff
> color sel #fc51dcff
> color sel #fc50d6ff
> color sel #fc4ed0ff
> color sel #fc4bcaff
> color sel #fc47c3ff
> color sel #fc3dacff
> color sel #fc39a5ff
> color sel #fc349bff
> color sel #fc3193ff
> color sel #fc3091ff
> color sel #fc2e8cff
> color sel #fc2c89ff
> color sel #fc267cff
> color sel #fc2478ff
> color sel #fc2272ff
> color sel #fc2171ff
> color sel #fc2373ff
> color sel #fc2776ff
> color sel #fc3988ff
> color sel #fc66b8ff
> color sel #fc95f0ff
> color sel #d6a9fcff
> color sel #cea9fcff
> color sel #caa8fcff
> color sel #c5a7fcff
> color sel #c0a6fcff
> color sel #b7a4fcff
> color sel #9999fcff
> color sel #959bfcff
> color sel #919cfcff
> color sel #869efcff
> color sel #859efcff
[Repeated 1 time(s)]
> color sel #859ffcff
> color sel #829ffcff
> color sel #78a0fcff
> color sel #719ffcff
> color sel #619efcff
> color sel #499dfcff
> color sel #469cfcff
> color sel #439cfcff
> color sel #3b9bfcff
> color sel #399bfcff
> color sel #389bfcff
[Repeated 2 time(s)]
> color sel #389cfcff
> color sel #3fabfcff
> color sel #43b6fcff
> color sel #48d4fcff
> color sel #48dafcff
> color sel #48defcff
> color sel #47e1fcff
> color sel #47e4fcff
> color sel #47e5fcff
> color sel #46e8fcff
> color sel #46eafcff
> color sel #45ecfcff
> color sel #44f9fcff
> color sel #43fcfcff
> color sel #43fcfaff
> color sel #42fcf5ff
> color sel #42fcf4ff
> color sel #42fcf2ff
> color sel #4efce4ff
> color sel #56fcddff
> color sel #5efcd5ff
> color sel #67fccdff
> color sel #6efcc4ff
> color sel #72fcbbff
> color sel #7cfca1ff
> color sel #7dfc9aff
> color sel #7cfc83ff
> color sel #78fc79ff
> color sel #76fc75ff
> color sel #75fc73ff
> color sel #71fc67ff
> color sel #70fc66ff
> color sel #70fc65ff
> color sel #70fc64ff
> color sel #6efc62ff
> color sel #6efc61ff
> color sel #6dfc5fff
> color sel #6dfc5dff
> color sel #6bfc58ff
> color sel #6bfc57ff
> color sel #6bfc56ff
> color sel #6cfc56ff
[Repeated 1 time(s)]
> color sel #6dfc55ff
[Repeated 2 time(s)]
> color sel #6ffc54ff
[Repeated 1 time(s)]
> color sel #70fc54ff
> color sel #70fc53ff
> color sel #71fc53ff
> color sel #72fc53ff
> color sel #74fc52ff
> color sel #75fc51ff
[Repeated 1 time(s)]
> color sel #75fc50ff
> color sel #6cfc49ff
> color sel #68fc47ff
> color sel #63fc44ff
> color sel #5ffc42ff
> color sel #57fc3dff
> color sel #54fc3cff
> color sel #51fc3bff
> color sel #4efc3aff
> color sel #4bfc39ff
> color sel #47fc38ff
> color sel #40fc35ff
> color sel #3ffc35ff
> color sel #3dfc35ff
> color sel #39fc33ff
[Repeated 1 time(s)]
> color sel #39fb33ff
> color sel #33e22eff
> color sel #30d72cff
> color sel #2fcf2aff
> color sel #2dc829ff
> color sel #2cc428ff
> color sel #2cc328ff
> color sel #2bc127ff
> color sel #2bc027ff
[Repeated 1 time(s)]
> color sel #2bbf27ff
> color sel #28b224ff
> color sel #27ad23ff
> color sel #26ab23ff
> color sel #26aa23ff
> color sel #26a922ff
> color sel #26a722ff
[Repeated 1 time(s)]
> color sel byhetero
> select clear
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> select add #1
2041 atoms, 2076 bonds, 1 pseudobond, 267 residues, 4 models selected
> select subtract #1
120 atoms, 120 bonds, 4 residues, 2 models selected
> select add #2
2095 atoms, 2136 bonds, 1 pseudobond, 274 residues, 3 models selected
> select subtract #2
47 atoms, 46 bonds, 1 residue, 1 model selected
> select H
2121 atoms, 266 residues, 1 model selected
> hide sel atoms
> select clear
> select ::name="HOH"
4 atoms, 4 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 4 atom styles
> color sel byhetero
> select clear
[Repeated 4 time(s)]
> select HOH
Expected an objects specifier or a keyword
> select HOH atoms
Expected an objects specifier or a keyword
> select ::name="HOH"
4 atoms, 4 residues, 2 models selected
> select add #2
2050 atoms, 2090 bonds, 1 pseudobond, 275 residues, 3 models selected
> select subtract #2
2 atoms, 2 residues, 1 model selected
> select ::name="HOH"
4 atoms, 4 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
> false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 8x2k
2 8ww2
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
8x2k #1/A HOH 501 O 8x2k #1/A TYR 280 OH no hydrogen 3.217 N/A
8ww2 #2/R HIS 96 NE2 8ww2 #2/R HOH 701 O no hydrogen 3.304 N/A
8ww2 #2/R TYR 280 OH 8ww2 #2/R HOH 702 O no hydrogen 2.982 N/A
8ww2 #2/R HOH 701 O 8ww2 #2/R HIS 96 NE2 no hydrogen 3.304 N/A
8ww2 #2/R HOH 701 O 8ww2 #2/R OLA 601 O2 no hydrogen 2.722 N/A
8ww2 #2/R HOH 702 O 8ww2 #2/R TYR 280 OH no hydrogen 2.982 N/A
8ww2 #2/R HOH 702 O 8ww2 #2/R OLA 601 O1 no hydrogen 2.993 N/A
8ww2 #2/R HOH 702 O 8ww2 #2/R OLA 601 O2 no hydrogen 3.443 N/A
8 hydrogen bonds found
> hbonds sel color #050308 radius 0.03 dashes 9 interModel false intraMol
> false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 8x2k
2 8ww2
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
8x2k #1/A HOH 501 O 8x2k #1/A TYR 280 OH no hydrogen 3.217 N/A
8ww2 #2/R HIS 96 NE2 8ww2 #2/R HOH 701 O no hydrogen 3.304 N/A
8ww2 #2/R TYR 280 OH 8ww2 #2/R HOH 702 O no hydrogen 2.982 N/A
8ww2 #2/R HOH 701 O 8ww2 #2/R HIS 96 NE2 no hydrogen 3.304 N/A
8ww2 #2/R HOH 701 O 8ww2 #2/R OLA 601 O2 no hydrogen 2.722 N/A
8ww2 #2/R HOH 702 O 8ww2 #2/R TYR 280 OH no hydrogen 2.982 N/A
8ww2 #2/R HOH 702 O 8ww2 #2/R OLA 601 O1 no hydrogen 2.993 N/A
8ww2 #2/R HOH 702 O 8ww2 #2/R OLA 601 O2 no hydrogen 3.443 N/A
8 hydrogen bonds found
> select clear
> select ::name="HOH"
4 atoms, 4 residues, 2 models selected
> style sel ball
Changed 4 atom styles
> select clear
[Repeated 2 time(s)]
> hide #!2 models
> hide #!3 models
> select clear
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> select add #3
4141 atoms, 4187 bonds, 1 pseudobond, 266 residues, 2 models selected
> select add #2
6189 atoms, 6277 bonds, 9 pseudobonds, 539 residues, 5 models selected
> select add #1
8110 atoms, 8233 bonds, 11 pseudobonds, 802 residues, 8 models selected
> select subtract #2
6062 atoms, 6143 bonds, 3 pseudobonds, 529 residues, 5 models selected
> select subtract #1
4141 atoms, 4187 bonds, 1 pseudobond, 266 residues, 2 models selected
> select subtract #3
Nothing selected
> select clear
> open /Users/dongju/Downloads/emd_38015_8X2K.map
Opened emd_38015_8X2K.map as #4, grid size 320,320,320, pixel 0.85, shown at
level 0.177, step 2, values float32
> volume #4 level 0.4238
> hide #!2 models
> hide #!3 models
> color #4 #bf8883ff models
> transparency 50
> volume #4 level 0.5886
> volume #4 level 0.465
> fitmap #1 inMap #4
Fit molecule 8x2k (#1) to map emd_38015_8X2K.map (#4) using 1921 atoms
average map value = 0.907, steps = 48
shifted from previous position = 0.015
rotated from previous position = 0.0873 degrees
atoms outside contour = 588, contour level = 0.465
Position of 8x2k (#1) relative to emd_38015_8X2K.map (#4) coordinates:
Matrix rotation and translation
0.99999891 -0.00055264 0.00136564 -0.14152221
0.00055318 0.99999977 -0.00038973 -0.02175877
-0.00136542 0.00039048 0.99999899 0.14489849
Axis 0.25597560 0.89601911 0.36280330
Axis point 106.88170121 0.00000000 103.12500396
Rotation angle (degrees) 0.08731843
Shift along axis -0.00315286
> volume #4 level 0.3963
> ui mousemode right "map eraser"
> volume erase #4 center 127.51,123.25,165.71 radius 18.278 outside true
Opened emd_38015_8X2K.map copy as #6, grid size 320,320,320, pixel 0.85, shown
at step 1, values float32
Window position QRect(1505,961 543x106) outside any known screen, using
primary screen
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600002333a20, name="P24h-2L") screenTo: QScreen(0x600002333a20,
name="P24h-2L") wdgScreen: QScreen(0x600002333a20, name="P24h-2L")
orgWdgScreen QScreen(0x0)
[Repeated 29 time(s)]
> volume erase #6 center 142,114.56,175.19 radius 8.024
> volume erase #6 center 136.19,104.28,165.16 radius 8.024
> volume erase #6 center 128.24,98.937,169.56 radius 8.024
> volume erase #6 center 126.39,104.21,161.15 radius 8.024
> volume erase #6 center 115.72,109.49,164.49 radius 8.024
> volume erase #6 center 132.54,123.1,182.79 radius 8.024
> volume erase #6 center 125.6,122.84,182.82 radius 8.024
> volume erase #6 center 129.85,131.24,173.66 radius 8.024
> volume erase #6 center 112.27,123.76,168.47 radius 8.024
> volume erase #6 center 115.5,115.26,169.04 radius 8.024
> undo
> ui mousemode right "map eraser"
Window position QRect(1505,961 543x106) outside any known screen, using
primary screen
QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x600002333a20, name="P24h-2L") screenTo: QScreen(0x600002333a20,
name="P24h-2L") wdgScreen: QScreen(0x600002333a20, name="P24h-2L")
orgWdgScreen QScreen(0x0)
[Repeated 31 time(s)]
> volume erase #6 center 116.48,128.87,176.5 radius 9.5658
> volume erase #6 center 123.67,132.4,168.66 radius 9.5658
> volume erase #6 center 123.1,126.91,155.3 radius 9.5658
> volume erase #6 center 125.01,117.12,159.44 radius 9.5658
> volume erase #6 center 136.08,107.51,167.69 radius 9.5658
> volume erase #6 center 123.64,103.8,167.02 radius 9.5658
> volume erase #6 center 136.62,115.75,158.76 radius 9.5658
> hide #!1 cartoons
> volume erase #6 center 130.23,127.73,158.64 radius 9.5658
> volume erase #6 center 131.66,131.14,153.87 radius 9.5658
> volume erase #6 center 140.88,132.78,176.18 radius 9.5658
> volume erase #6 center 142.88,137.99,164.91 radius 9.5658
> volume erase #6 center 129.75,139.75,165.34 radius 9.5658
> volume erase #6 center 128.93,134.45,168.38 radius 9.5658
> volume erase #6 center 134.52,113.7,179.21 radius 9.5658
> volume erase #6 center 132.74,109.33,180.49 radius 9.5658
> volume erase #6 center 132.82,122.81,156.79 radius 9.5658
> volume erase #6 center 122.17,117.24,157.44 radius 9.5658
> volume erase #6 center 120.58,131.5,164.85 radius 9.5658
> volume erase #6 center 115.75,128.65,163.98 radius 9.5658
> volume erase #6 center 139.63,135.19,156.83 radius 9.5658
> volume erase #6 center 136.82,136.03,161.61 radius 9.5658
> volume erase #6 center 135.65,122.9,180.03 radius 9.5658
> volume erase #6 center 127.19,136.49,183.98 radius 9.5658
> volume erase #6 center 126.46,115.47,154.19 radius 9.5658
> volume erase #6 center 141.41,122.41,149.22 radius 9.5658
> volume erase #6 center 140.71,109.81,171.26 radius 9.5658
> volume erase #6 center 131.13,114.42,168.7 radius 3.5872
> volume erase #6 center 129.51,115.56,167.48 radius 3.5872
> volume erase #6 center 143.93,119.91,165 radius 3.5872
> volume erase #6 center 147.72,123.04,164 radius 3.5872
> volume erase #6 center 141.43,120.71,170.51 radius 3.5872
> volume erase #6 center 139.15,121.13,170.31 radius 3.5872
> volume erase #6 center 139.59,120.06,162.9 radius 3.5872
> volume erase #6 center 144.6,126.91,169.16 radius 3.5872
> volume erase #6 center 142.9,123.29,172.77 radius 3.5872
> volume erase #6 center 135.18,116.13,148.01 radius 3.5872
> volume erase #6 center 127.53,122.57,149.89 radius 3.5872
> volume erase #6 center 142.81,125.98,172.3 radius 3.5872
> volume erase #6 center 125.5,111.69,182.44 radius 3.5872
> volume erase #6 center 119.49,113.64,177.23 radius 3.5872
> volume erase #6 center 141.1,118.59,171.25 radius 3.5872
> volume erase #6 center 119.87,112.45,173.34 radius 3.5872
> volume erase #6 center 121.27,112.17,169.3 radius 3.5872
> volume erase #6 center 122.64,117.8,167.35 radius 3.5872
> volume erase #6 center 140.15,123.5,171.95 radius 3.3695
> show #!1 cartoons
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_GPR3.cxs"
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8X2K_overall.png" width 3000
> height 1903 supersample 3 transparentBackground true
> hide #!1 models
> show #!1 models
> hide #!1 cartoons
> select add #6
2 models selected
> volume sel style mesh
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8X2K_ligand_mesh.png" width
> 2000 height 1269 supersample 3 transparentBackground true
> select add #6
2 models selected
> volume sel style surface
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8X2K_ligand_surface.png" width
> 2000 height 1269 supersample 3 transparentBackground true
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> select add #1
1921 atoms, 1956 bonds, 2 pseudobonds, 263 residues, 3 models selected
> show sel cartoons
> select clear
> show #!2 models
> hide #!1 models
> hide #!6 models
> open /Users/dongju/Downloads/emd_37881_8WW2.map
Opened emd_37881_8WW2.map as #5, grid size 256,256,256, pixel 1.1, shown at
level 0.322, step 1, values float32
> ui tool show "Volume Viewer"
> volume #5 level 1.109
> ui tool show "Fit in Map"
> fitmap #2 inMap #5
Fit molecule 8ww2 (#2) to map emd_37881_8WW2.map (#5) using 2048 atoms
average map value = 0.2273, steps = 108
shifted from previous position = 1.3
rotated from previous position = 5.34 degrees
atoms outside contour = 1882, contour level = 1.1093
Position of 8ww2 (#2) relative to emd_37881_8WW2.map (#5) coordinates:
Matrix rotation and translation
0.93399282 0.35338446 0.05269577 -53.98910026
-0.25181302 0.75569361 -0.60458033 160.37968845
-0.25347115 0.55140420 0.79479921 -8.76457449
Axis 0.86250634 0.22843810 -0.45155160
Axis point 0.00000000 104.61289764 225.25740459
Rotation angle (degrees) 42.07717898
Shift along axis -5.97145309
> select add #5
4 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-7.105,0,1,0,-3.3134,0,0,1,-1.3607
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.95945,0.0019066,-0.28188,36.818,-0.040684,0.99044,-0.13178,21.749,0.27893,0.13791,0.95036,-53.242
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.95945,0.0019066,-0.28188,42.412,-0.040684,0.99044,-0.13178,24.246,0.27893,0.13791,0.95036,-50.7
> view matrix models
> #5,0.95945,0.0019066,-0.28188,43.465,-0.040684,0.99044,-0.13178,19.488,0.27893,0.13791,0.95036,-49.071
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.94577,0.15382,-0.28611,24.668,-0.20098,0.96905,-0.14337,46.665,0.25521,0.1931,0.94741,-53.064
> view matrix models
> #5,0.9292,0.10856,-0.35328,42.518,-0.16119,0.97922,-0.12305,36.856,0.33258,0.17128,0.92739,-58.179
> view matrix models
> #5,0.92379,-0.065525,-0.37724,70.964,-0.13791,0.86218,-0.48747,99.73,0.35719,0.50235,0.78744,-88.974
> view matrix models
> #5,0.8279,0.50151,-0.25112,-12.256,-0.55781,0.68954,-0.46192,179.64,-0.058502,0.52251,0.85063,-41.831
> view matrix models
> #5,0.89237,0.36679,-0.26293,-0.83787,-0.44914,0.77876,-0.43797,148.54,0.044116,0.50892,0.85968,-55.627
> view matrix models
> #5,0.8829,0.3169,-0.3465,18.9,-0.44818,0.78885,-0.42053,144.61,0.14007,0.52658,0.83851,-68.738
> view matrix models
> #5,0.91961,0.31846,-0.23,-2.3946,-0.39005,0.80976,-0.43835,135.92,0.046645,0.49282,0.86888,-54.981
> view matrix models
> #5,0.95245,0.15168,-0.26425,21.041,-0.25161,0.88066,-0.40142,101.42,0.17183,0.44882,0.87695,-67.556
> view matrix models
> #5,0.96202,0.071376,-0.2635,30.853,-0.21539,0.79147,-0.57199,132.1,0.16773,0.60702,0.77678,-75.493
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.96202,0.071376,-0.2635,30.813,-0.21539,0.79147,-0.57199,138.5,0.16773,0.60702,0.77678,-71.707
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.95807,0.19822,-0.20693,5.8585,-0.28402,0.75269,-0.59396,156.61,0.038016,0.62783,0.77743,-56.428
> view matrix models
> #5,0.94976,0.24396,-0.19605,-0.87055,-0.31295,0.73323,-0.60368,164.74,-0.0035254,0.63471,0.77274,-50.899
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.94976,0.24396,-0.19605,-1.0075,-0.31295,0.73323,-0.60368,166.12,-0.0035254,0.63471,0.77274,-49.751
> fitmap #2 inMap #5
Fit molecule 8ww2 (#2) to map emd_37881_8WW2.map (#5) using 2048 atoms
average map value = 0.329, steps = 76
shifted from previous position = 1.39
rotated from previous position = 8.43 degrees
atoms outside contour = 1708, contour level = 1.1093
Position of 8ww2 (#2) relative to emd_37881_8WW2.map (#5) coordinates:
Matrix rotation and translation
0.91950152 0.12557835 0.37248763 -66.96689278
-0.16246606 0.98428326 0.06921873 17.35756690
-0.35794097 -0.12416333 0.92545218 75.38744531
Axis -0.23914600 0.90328481 -0.35621024
Axis point 170.94087250 0.00000000 213.61763802
Rotation angle (degrees) 23.84839592
Shift along axis 4.83991131
> view matrix models
> #5,0.94976,0.24396,-0.19605,-1.0108,-0.31295,0.73323,-0.60368,166.07,-0.0035254,0.63471,0.77274,-49.77
> select subtract #5
Nothing selected
> volume #5 level 1.488
> select add #5
4 models selected
> view matrix models
> #5,0.94976,0.24396,-0.19605,-0.8891,-0.31295,0.73323,-0.60368,166,-0.0035254,0.63471,0.77274,-49.393
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.90637,0.30351,-0.29389,10.083,-0.41806,0.74462,-0.52036,168.02,0.060903,0.5945,0.80178,-56.771
> view matrix models
> #5,0.92471,0.31681,-0.21105,-5.5286,-0.38013,0.79797,-0.46771,148.1,0.020234,0.51272,0.85832,-47.203
> view matrix models
> #5,0.87818,0.44033,-0.18683,-19.512,-0.47312,0.74212,-0.47477,169.99,-0.070402,0.50533,0.86005,-33.611
> view matrix models
> #5,0.96541,0.15763,-0.20769,10.555,-0.24143,0.84124,-0.48377,124.63,0.098463,0.51718,0.8502,-57.772
> volume #5 level 0.7885
> volume #5 step 2
> volume #5 step 1
> view matrix models
> #5,0.90157,0.39956,-0.16591,-21.23,-0.42572,0.75103,-0.5047,167.3,-0.077056,0.52565,0.8472,-33.228
> view matrix models
> #5,0.91439,0.404,0.025785,-48.997,-0.36846,0.85696,-0.36036,124.44,-0.16768,0.32001,0.93246,-1.1627
> view matrix models
> #5,0.90443,0.4027,-0.14084,-25.409,-0.41738,0.76692,-0.48747,161.49,-0.088297,0.49967,0.8617,-29.699
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.90443,0.4027,-0.14084,-26.413,-0.41738,0.76692,-0.48747,161.95,-0.088297,0.49967,0.8617,-32.605
> view matrix models
> #5,0.90443,0.4027,-0.14084,-25.849,-0.41738,0.76692,-0.48747,162.3,-0.088297,0.49967,0.8617,-32.466
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.92025,0.34341,-0.18765,-13.265,-0.39131,0.81279,-0.43157,144.43,0.0043142,0.47058,0.88235,-44.314
> fitmap #2 inMap #5
Fit molecule 8ww2 (#2) to map emd_37881_8WW2.map (#5) using 2048 atoms
average map value = 1.485, steps = 140
shifted from previous position = 4.53
rotated from previous position = 25.6 degrees
atoms outside contour = 546, contour level = 0.7885
Position of 8ww2 (#2) relative to emd_37881_8WW2.map (#5) coordinates:
Matrix rotation and translation
0.99999996 0.00012222 0.00026537 -0.07513565
-0.00012223 0.99999999 0.00004628 0.01029297
-0.00026536 -0.00004631 0.99999996 0.04239788
Axis -0.15650920 0.89709431 -0.41319083
Axis point 165.14679237 0.00000000 281.11680356
Rotation angle (degrees) 0.01694827
Shift along axis 0.00347477
> view matrix models
> #5,0.91866,0.34702,-0.18877,-13.418,-0.39502,0.81217,-0.42934,144.76,0.0043231,0.46899,0.88319,-44.193
> view matrix models
> #5,0.91891,0.34712,-0.18738,-13.651,-0.39446,0.81283,-0.42862,144.49,0.0035265,0.46777,0.88384,-43.985
> fitmap #2 inMap #5
Fit molecule 8ww2 (#2) to map emd_37881_8WW2.map (#5) using 2048 atoms
average map value = 1.485, steps = 44
shifted from previous position = 0.108
rotated from previous position = 0.247 degrees
atoms outside contour = 548, contour level = 0.7885
Position of 8ww2 (#2) relative to emd_37881_8WW2.map (#5) coordinates:
Matrix rotation and translation
0.99999993 -0.00012631 0.00036012 -0.04066985
0.00012642 0.99999995 -0.00030626 0.02288320
-0.00036008 0.00030630 0.99999989 -0.00138601
Axis 0.62591382 0.73589748 0.25823787
Axis point 2.55653855 0.00000000 97.33758639
Rotation angle (degrees) 0.02803672
Shift along axis -0.00897406
> ui mousemode right select
> select clear
> volume #5 level 0.8177
> volume #!5 style image
[Repeated 1 time(s)]
> volume #!5 style surface
> transparency #5.1 50
> volume #5 change image level -0.1034,0 level 0.3212,0.8 level 9.069,1
> volume #5 level 0.526
> ui mousemode right "map eraser"
> volume erase #5 center 129.08,126.26,175.65 radius 14.086 outside true
Opened emd_37881_8WW2.map copy as #8, grid size 256,256,256, pixel 1.1, shown
at step 1, values float32
> hide #!2 cartoons
> volume erase #8 center 132.73,134.06,181.07 radius 8.8704
> volume erase #8 center 123.22,143.01,175.92 radius 8.8704
> volume erase #8 center 126.34,138.23,176.54 radius 8.8704
> volume erase #8 center 123.1,136.44,172.4 radius 8.8704
> volume erase #8 center 133.5,118.49,184.72 radius 8.8704
> volume erase #8 center 130.68,114.11,180.62 radius 8.8704
> volume erase #8 center 133.71,110.82,173.85 radius 8.8704
> volume erase #8 center 139.97,119.37,181.39 radius 8.8704
> volume erase #8 center 128.97,125.27,186.28 radius 8.8704
> volume erase #8 center 138.92,115.29,172.66 radius 8.8704
> volume erase #8 center 126.08,128.57,164.84 radius 8.8704
> volume erase #8 center 131.88,123.79,163.63 radius 8.8704
> volume erase #8 center 131.8,119.64,171.9 radius 2.6752
> volume erase #8 center 127.99,116.9,169.62 radius 2.6752
> volume erase #8 center 127.72,114.89,165.99 radius 2.6752
> volume erase #8 center 125.74,117.48,172.43 radius 2.6752
> volume erase #8 center 124.41,115.77,170.2 radius 2.6752
> volume erase #8 center 124.9,114.59,173.59 radius 2.6752
> volume erase #8 center 126.71,114.11,171.83 radius 2.6752
> volume erase #8 center 122.83,114.96,172.56 radius 2.6752
> volume erase #8 center 124.04,114.17,173.93 radius 2.6752
> volume erase #8 center 123.28,117.16,179.85 radius 2.6752
> volume erase #8 center 119.13,117.47,182.77 radius 2.6752
> volume erase #8 center 119.63,118.49,183.56 radius 2.6752
> volume erase #8 center 120.36,122.2,181.63 radius 2.6752
> volume erase #8 center 120.12,126.6,185.16 radius 2.6752
> volume erase #8 center 120.53,131.8,185 radius 2.6752
> volume erase #8 center 119.62,130.25,185.06 radius 2.6752
> volume erase #8 center 118.43,127.92,184.85 radius 2.6752
> volume erase #8 center 122.49,133.78,183.77 radius 2.6752
> volume erase #8 center 115.19,130.14,180.01 radius 2.6752
> volume erase #8 center 113.75,128.84,180.2 radius 2.6752
> volume erase #8 center 115.67,132.32,180.14 radius 2.6752
> volume erase #8 center 115.13,127.99,176.33 radius 2.6752
> volume erase #8 center 117.62,127.49,170.29 radius 2.6752
> volume erase #8 center 121.06,128.17,173.73 radius 2.6752
> volume erase #8 center 118.41,127.89,171.18 radius 2.6752
> volume erase #8 center 118.46,129.16,172.58 radius 2.6752
> volume erase #8 center 118.1,126.3,171.9 radius 2.6752
> volume erase #8 center 116.68,121.64,172.99 radius 2.6752
> volume erase #8 center 119.78,122.6,168.51 radius 2.6752
> volume erase #8 center 119.32,117.8,168.12 radius 2.6752
> volume erase #8 center 125.46,123.88,170.24 radius 2.6752
> volume erase #8 center 123.18,120.41,167.11 radius 2.6752
> volume erase #8 center 121.58,116.58,167.74 radius 2.6752
> volume erase #8 center 125.47,119.8,170.75 radius 2.6752
> volume erase #8 center 120.87,116.15,178.38 radius 2.6752
> volume erase #8 center 138.19,128.06,185.02 radius 2.6752
> volume erase #8 center 126.82,126.58,178.55 radius 2.6752
> volume erase #8 center 125.47,127.68,175.58 radius 2.6752
> volume erase #8 center 125,127.48,174.51 radius 2.6752
> volume erase #8 center 123.46,129.67,180.61 radius 2.6752
> volume erase #8 center 124.49,129.56,182.67 radius 2.6752
> volume erase #8 center 126.72,124.17,178.91 radius 2.6752
> volume erase #8 center 115.36,123.16,169.06 radius 2.6752
> volume erase #8 center 137.76,130.39,167.52 radius 2.6752
> volume erase #8 center 137.44,133.42,169.51 radius 2.6752
> volume erase #8 center 134.92,135.56,168.98 radius 2.6752
> volume erase #8 center 131.73,135.74,167.68 radius 2.6752
> volume erase #8 center 134.23,134.44,164.63 radius 2.6752
> volume erase #8 center 136.07,137.48,172.31 radius 2.6752
> volume erase #8 center 133.32,132.73,171.21 radius 2.6752
> volume erase #8 center 132.66,129.88,171.79 radius 2.6752
> volume erase #8 center 136.37,131.27,172.58 radius 2.6752
> volume erase #8 center 139.33,134.06,173.1 radius 2.6752
> volume erase #8 center 137.19,130.43,169.86 radius 2.6752
> volume erase #8 center 141.58,131.99,171.85 radius 2.6752
> volume erase #8 center 140.33,131.13,174.85 radius 2.6752
> volume erase #8 center 143.02,125.79,175.07 radius 2.6752
> volume erase #8 center 142.74,124.1,167.11 radius 2.6752
> volume erase #8 center 140.07,127.39,178.97 radius 2.6752
> volume erase #8 center 141.7,129.37,175.9 radius 2.6752
> volume erase #8 center 139.07,133.03,177.52 radius 2.6752
> ui mousemode right select
> select clear
[Repeated 3 time(s)]
> show #!2 cartoons
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> select #8
2 models selected
Drag select of 24 atoms, 76 residues, 21 bonds, 7 pseudobonds, 8
emd_37881_8WW2.map copy
Drag select of 39 atoms, 144 residues, 35 bonds, 7 pseudobonds, 8
emd_37881_8WW2.map copy
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> select clear
[Repeated 4 time(s)]
> hide #!8 models
> hide #!2 cartoons
> select clear
[Repeated 9 time(s)]
> select ligand
143 atoms, 142 bonds, 5 residues, 3 models selected
> select clear
[Repeated 4 time(s)]
> show #!2 cartoons
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_GPR3_with maps.cxs"
> show #!8 models
> color #8 #ffd09280 models
> color #8 #ffd6ac80 models
> color #8 #ffeabc80 models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_GPR3_8WW2.png" width 3000
> height 1903 supersample 3 transparentBackground true
> hide #!2 cartoons
> color #8 #ffeabc41 models
> color #8 #ffeabc40 models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8WW2_surface.png" width 2000
> height 1269 supersample 3 transparentBackground true
> volume #!8 style mesh
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8WW2_mesh.png" width 2000
> height 1269 supersample 3 transparentBackground true
[Repeated 1 time(s)]
> volume #!8 style surface
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8WW2_surface.png" width 2000
> height 1269 supersample 3 transparentBackground true
> hide #!2 models
> show #!1 models
> hide #!8 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 cartoons
> volume #!6 style mesh
> color #6 #bf888342 models
> color #6 #bf888370 models
> hide #!6 models
> show #!6 models
> show #!1 cartoons
> select add #6
2 models selected
> volume sel style surface
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8X2K_overall.png" width 3000
> height 1903 supersample 3 transparentBackground true
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_GPR3_with maps.cxs"
——— End of log from Mon Jun 17 15:55:50 2024 ———
opened ChimeraX session
> show #!3 models
> hide #!1 models
> hide #!6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/R
Alignment identifier is 3/R
> select #3/R:96
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 17 atom styles
> show #!1 models
> show #!2 models
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show (sel-residues & sidechain) target ab
> ribbon suppressBackboneDisplay true
> ribbon sel suppressBackboneDisplay true
> ribbon sel suppressBackboneDisplay false
> ribbon sel suppressBackboneDisplay true
> ui mousemode right select
> select #3/R:280
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select H
2121 atoms, 266 residues, 1 model selected
> hide sel atoms
> select clear
> color #1-3 byhetero
> select clear
> hide #!2 models
> hide #!3 models
> select #1/A:96
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Side View"
> show #!6 models
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8X2K_overall_v2.png" width
> 3000 height 1949 supersample 3 transparentBackground true
> show #!4 models
> hide #!6 models
> volume #!4 style mesh
> volume #!4 style surface
> volume #!4 style image
> volume #!4 style surface
> transparency #4.1 50
> ui mousemode right "map eraser"
> volume erase #4 center 130.88,123.09,167.02 radius 18.278 outside true
Opened emd_38015_8X2K.map copy as #9, grid size 320,320,320, pixel 0.85, shown
at step 1, values float32
> volume erase #9 center 122.31,133.94,154.24 radius 18.224
> volume erase #9 center 130.45,95.963,162.54 radius 18.224
> volume erase #9 center 113.96,122.5,174.48 radius 5.032
> volume erase #9 center 117.33,126.37,181.13 radius 5.032
> volume erase #9 center 114.61,113.69,166.43 radius 5.032
> volume erase #9 center 114.43,117.27,169.78 radius 5.032
> volume erase #9 center 112.55,123.4,174.17 radius 5.032
> volume erase #9 center 113.05,123.04,170.37 radius 5.032
> volume erase #9 center 112.2,123.8,174.29 radius 5.032
> volume erase #9 center 115.88,113.27,169.86 radius 5.032
> volume erase #9 center 119.55,110.6,171.85 radius 5.032
> volume erase #9 center 114.48,125.87,179.79 radius 5.032
> volume erase #9 center 115.96,128.51,173.78 radius 5.032
> volume erase #9 center 112.94,123.39,172.63 radius 5.032
> volume erase #9 center 114.54,125.68,171.75 radius 5.032
> volume erase #9 center 116.25,119.68,169.12 radius 5.032
> volume erase #9 center 115.68,117.02,173.09 radius 5.032
> volume erase #9 center 116.7,111.14,166.69 radius 5.032
> volume erase #9 center 119.76,111.36,170.61 radius 5.032
> volume erase #9 center 128.92,112.06,178.21 radius 5.032
> volume erase #9 center 129.87,116.48,179.29 radius 5.032
> volume erase #9 center 129.72,114.86,178.03 radius 5.032
> volume erase #9 center 129.67,116,178.13 radius 5.032
> volume erase #9 center 134.38,135.13,171.54 radius 8.976
> volume erase #9 center 130.19,134.29,176.08 radius 8.976
> volume erase #9 center 140.54,122.46,178.15 radius 8.976
> show #!6 models
> select add #6
2 models selected
> volume sel style mesh
> select subtract #6
Nothing selected
> select add #6
2 models selected
> select subtract #6
Nothing selected
> select add #6
2 models selected
Can only have one displayed volume when erasing
[Repeated 5 time(s)]
> select add #9
5 models selected
Can only have one displayed volume when erasing
> hide #7 models
> show #7 models
> hide #!6 models
> select subtract #6
3 models selected
> volume erase #9 center 128.67,127.89,182.98 radius 8.976
> volume erase #9 center 135.16,122.88,184.6 radius 8.976
> volume erase #9 center 133.56,128.01,180.51 radius 8.976
> volume erase #9 center 144.06,134.86,172.66 radius 8.976
> volume erase #9 center 147.26,131.12,171.99 radius 8.976
> volume erase #9 center 142.66,112.71,164.07 radius 8.976
> volume erase #9 center 136.26,113.68,176.37 radius 8.976
> volume erase #9 center 122.49,118.9,180.94 radius 5.032
> volume erase #9 center 115.89,125.37,170.33 radius 5.032
> volume erase #9 center 113.13,124.28,164.48 radius 5.032
> volume erase #9 center 114.01,122.51,161.81 radius 5.032
> volume erase #9 center 112.22,124,172.46 radius 5.032
> volume erase #9 center 117.31,128.31,180.82 radius 5.032
> volume erase #9 center 116.07,129.07,178.69 radius 5.032
> volume erase #9 center 114.96,129.74,176.68 radius 5.032
> volume erase #9 center 116.6,130.62,177.6 radius 5.032
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!9 models
> show #!9 models
> hide #!4 models
> volume erase #9 center 118.75,129.42,176.96 radius 5.032
> volume erase #9 center 125.45,124.61,174.09 radius 2.04
> volume erase #9 center 128.33,124.58,172.93 radius 2.04
> volume erase #9 center 128.51,125.45,171.18 radius 2.72
> volume erase #9 center 118.93,117.37,166.13 radius 2.72
> volume erase #9 center 118.58,116.66,164.63 radius 2.72
> volume erase #9 center 117.38,111.67,162.72 radius 2.72
> volume erase #9 center 121.01,112.56,164.66 radius 2.72
> volume erase #9 center 123.99,112.79,165.74 radius 2.72
> volume erase #9 center 127.29,113.97,167.19 radius 2.72
> hide #!1 models
> volume erase #9 center 133.61,117.17,163.38 radius 5.032
> volume erase #9 center 136.77,116.29,160.24 radius 5.032
> volume erase #9 center 129.96,114.16,163.19 radius 5.032
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> volume erase #9 center 129.2,119.46,162.27 radius 5.032
> volume erase #9 center 127.03,121.47,166.53 radius 1.224
> volume erase #9 center 126.53,120.62,166.5 radius 1.224
[Repeated 1 time(s)]
> volume erase #9 center 126.44,120.3,166.88 radius 1.224
> show #!6 models
> hide #!9 models
> show #!9 models
> show #!1 models
> select add #1
1921 atoms, 1956 bonds, 2 pseudobonds, 263 residues, 5 models selected
> hide sel ribbons
Can only have one displayed volume when erasing
> select subtract #1
2 models selected
> select add #9
3 models selected
> select subtract #9
Nothing selected
> select add #9
3 models selected
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> hide #!6 models
> volume erase #9 center 127.8,120.24,167.11 radius 1.224
> volume erase #9 center 125.19,124.29,171.41 radius 1.224
> volume erase #9 center 125.08,124.08,170.24 radius 1.224
> volume erase #9 center 126.56,127.49,170.12 radius 1.224
> volume erase #9 center 124.92,124.39,170.78 radius 1.224
> volume erase #9 center 124.74,124.72,169.85 radius 1.224
> volume erase #9 center 127.29,123.4,175.53 radius 1.224
> volume erase #9 center 131.79,124.97,171.95 radius 2.312
> volume erase #9 center 130.89,116.38,173.27 radius 2.312
> volume erase #9 center 129.09,114.05,169.51 radius 2.312
> volume erase #9 center 129.32,114.2,169.61 radius 2.312
> volume erase #9 center 128.8,115.77,168.17 radius 2.312
> volume erase #9 center 134.3,114.04,168.46 radius 2.312
> volume erase #9 center 127.46,110.48,164.59 radius 2.312
> volume erase #9 center 125.58,111.26,168.38 radius 2.312
> volume erase #9 center 121,110.06,162.03 radius 2.312
> volume erase #9 center 119.25,109.36,159.33 radius 2.312
> volume erase #9 center 115.95,111.86,160.9 radius 2.312
> volume erase #9 center 117.47,113.27,160.44 radius 2.312
> volume erase #9 center 119.74,114.34,163.23 radius 2.312
> volume erase #9 center 125.52,115.68,165.69 radius 2.312
> volume erase #9 center 124.21,114.54,162.44 radius 2.312
> volume erase #9 center 120.24,114.83,161.49 radius 2.312
> volume erase #9 center 119.8,116.84,161.74 radius 2.312
> volume erase #9 center 122.34,116.24,160.05 radius 2.312
> volume erase #9 center 124.53,114.83,159.05 radius 2.312
> volume erase #9 center 121.96,115.22,155.5 radius 2.312
> volume erase #9 center 127.2,114.33,155.42 radius 2.312
> volume erase #9 center 128.19,114.83,154.14 radius 2.312
> volume erase #9 center 130.64,115.42,156.52 radius 2.312
> volume erase #9 center 135.89,121.73,159.88 radius 5.576
> volume erase #9 center 135.52,121.76,160.87 radius 5.576
> volume erase #9 center 135.22,117.93,152.41 radius 5.576
> volume erase #9 center 138.94,122.29,153.73 radius 5.576
> volume erase #9 center 145.1,119.1,156.14 radius 5.576
> volume erase #9 center 139.18,114.57,166.48 radius 5.576
[Repeated 1 time(s)]
> volume erase #9 center 140.34,118.64,167.69 radius 5.576
> volume erase #9 center 147.86,119.27,167.6 radius 5.576
> volume erase #9 center 150.46,124.56,165.65 radius 5.576
> volume erase #9 center 139.04,133.44,166.28 radius 5.576
> volume erase #9 center 128.35,128.21,165.71 radius 5.576
> volume erase #9 center 129.27,127.58,165.78 radius 5.576
> volume erase #9 center 137.2,131.35,160.79 radius 5.576
> volume erase #9 center 141.71,134.24,163.24 radius 5.576
> volume erase #9 center 142.69,133.06,162.59 radius 5.576
> volume erase #9 center 143.9,132.93,161 radius 5.576
> volume erase #9 center 141.89,131.71,158.06 radius 5.576
> volume erase #9 center 148.29,129.69,156.01 radius 5.576
> volume erase #9 center 145.13,130.71,154.65 radius 5.576
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> hide #7 models
> show #7 models
> hide #!6 models
> volume erase #9 center 147.87,123.94,162.78 radius 3.536
> volume erase #9 center 117.89,120.64,165.62 radius 3.536
> volume erase #9 center 125.65,117.5,168.53 radius 1.768
> volume erase #9 center 124.39,123.38,175.14 radius 1.768
> volume sel style mesh
> ui mousemode right select
> select clear
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #1/A
Alignment identifier is 1/A
Could not find virtual screen for QCocoaScreen(0x6000002f27e0, "DELL P2422H",
QRect(-1920,0 1920x1080), dpr=1, displayId=4128833, ) with displayId 4128833
> select #1/A:96
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:96
10 atoms, 10 bonds, 1 residue, 1 model selected
> ribbon sel suppressBackboneDisplay true
> hide sel ribbons
> ribbon sel suppressBackboneDisplay true
> select clear
> hide #!9 models
> select #1/A:96
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel ribbons
> select clear
> select #1/A:96@C
1 atom, 1 residue, 1 model selected
Drag select of 2 atoms, 1 bonds
Drag select of 2 atoms, 2 bonds
> hide sel atoms
Drag select of 2 atoms, 1 bonds
> hide sel atoms
> show #!9 models
> ui mousemode right "map eraser"
> volume erase #9 center 120.66,116.98,161.77 radius 3.5995
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8X2K_ligand_mesh_v2.png" width
> 2000 height 1299 supersample 3 transparentBackground true
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> ui mousemode right distance
> distance #1/A:96@NE2 #1/A:502@O
Distance between 8x2k #1/A HIS 96 NE2 and HOH 502 O: 4.321Å
> hide #7.1 models
> color #7 black models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8X2K_ligand_mesh_v3.png" width
> 2000 height 1299 supersample 3 transparentBackground true
> hide #!1 models
> hide #!9 models
> show #!2 models
> show #!5 models
> ui mousemode right "map eraser"
> volume erase #5 center 127.27,124.6,175.16 radius 14.985 outside true
Opened emd_37881_8WW2.map copy as #11, grid size 256,256,256, pixel 1.1, shown
at step 1, values float32
> select add #2
2050 atoms, 2091 bonds, 8 pseudobonds, 274 residues, 4 models selected
> hide sel ribbons
> select subtract #2
2 atoms, 1 bond, 1 residue, 1 model selected
> hide #!2 models
> show #!2 models
> show #!8 models
> hide #!11 models
> hide #10 models
> ui mousemode right select
Drag select of 44 atoms, 46 bonds
> hide sel atoms
Drag select of 9 atoms, 7 bonds
> hide sel atoms
> select add #8
9 atoms, 7 bonds, 1 residue, 3 models selected
> volume sel style mesh
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_8WW2_mesh_v2.png" width 2000
> height 1299 supersample 3 transparentBackground true
> hide #!2 models
> show #!3 models
> hide #!8 models
> hide #!7 models
> open /Users/dongju/Downloads/emd_42023.map.gz
File reader requires uncompressed file;
'/Users/dongju/Downloads/emd_42023.map.gz' is compressed
> open /Users/dongju/Downloads/emd_42023.map
Opened emd_42023.map as #10, grid size 256,256,256, pixel 0.86, shown at level
0.167, step 1, values float32
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #3 inMap #10
Fit molecule 8u8f (#3) to map emd_42023.map (#10) using 4141 atoms
average map value = 0.1101, steps = 192
shifted from previous position = 16.7
rotated from previous position = 9.16 degrees
atoms outside contour = 2995, contour level = 0.16691
Position of 8u8f (#3) relative to emd_42023.map (#10) coordinates:
Matrix rotation and translation
0.88449228 -0.43560265 -0.16710398 92.49693760
-0.33231245 -0.83960005 0.42969779 210.58389705
-0.32747801 -0.32453365 -0.88737594 304.93232510
Axis -0.96947337 0.20614143 0.13276707
Axis point 0.00000000 147.04753663 136.68586676
Rotation angle (degrees) 157.10831354
Shift along axis -5.77828007
> rename #10 emd_42023_8U8F.map
> undo
[Repeated 4 time(s)]
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!7 models
> show #!7 models
> show #7.1 models
> hide #7.1 models
> show #7.1 models
> hide #!8 models
> hide #!2 models
> show #!2 models
> show #!1 models
> show #!3 models
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4_GPR3_updated_no8U9F.cxs"
——— End of log from Mon Sep 23 15:26:47 2024 ———
opened ChimeraX session
Could not find virtual screen for QCocoaScreen(0x6000002f27e0, "DELL P2422H",
QRect(-1920,0 1920x1080), dpr=1, displayId=4128833, ) with displayId 4128833
[Repeated 1 time(s)]
> show #!10 models
> ui mousemode right translate
> select add #10
9 atoms, 7 bonds, 1 residue, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.91902,0.34695,-0.18716,-23.279,-0.3942,0.81275,-0.42901,138.04,0.0032674,0.46804,0.8837,-28.74,#10,1,0,0,-9.5979,0,1,0,-6.4832,0,0,1,15.236
> view matrix models
> #2,0.91902,0.34695,-0.18716,-28.621,-0.3942,0.81275,-0.42901,135.08,0.0032674,0.46804,0.8837,-20.164,#10,1,0,0,-14.94,0,1,0,-9.443,0,0,1,23.812
> view matrix models
> #2,0.91902,0.34695,-0.18716,-19.32,-0.3942,0.81275,-0.42901,147.7,0.0032674,0.46804,0.8837,-34.002,#10,1,0,0,-5.6394,0,1,0,3.1727,0,0,1,9.9738
> view matrix models
> #2,0.91902,0.34695,-0.18716,-22.6,-0.3942,0.81275,-0.42901,146.72,0.0032674,0.46804,0.8837,-28.615,#10,1,0,0,-8.9194,0,1,0,2.1914,0,0,1,15.361
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.55026,-0.35997,0.75342,101.56,-0.41995,0.89919,0.1229,66.698,-0.7217,-0.24877,-0.64595,338.13,#10,-0.7716,-0.39887,0.49552,170.44,-0.096972,0.84363,0.52809,-33.331,-0.62868,0.35942,-0.68962,247.26
> view matrix models
> #2,-0.4284,-0.60842,0.66806,117.88,-0.16046,0.77881,0.60639,-24.337,-0.88923,0.15258,-0.43127,297.28,#10,-0.72983,-0.61222,0.30419,209.76,0.0092519,0.43609,0.89986,-47.663,-0.68356,0.65956,-0.31261,178.86
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.4284,-0.60842,0.66806,127.97,-0.16046,0.77881,0.60639,12.444,-0.88923,0.15258,-0.43127,285.66,#10,-0.72983,-0.61222,0.30419,219.84,0.0092519,0.43609,0.89986,-10.883,-0.68356,0.65956,-0.31261,167.24
> ui mousemode right select
> select clear
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 1 maps.
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #3 inMap #10
Fit molecule 8u8f (#3) to map emd_42023_8U8F.map (#10) using 4141 atoms
average map value = 0.1039, steps = 140
shifted from previous position = 6.04
rotated from previous position = 13.2 degrees
atoms outside contour = 3150, contour level = 0.16691
Position of 8u8f (#3) relative to emd_42023_8U8F.map (#10) coordinates:
Matrix rotation and translation
-0.58378611 0.39230421 0.71083837 40.11433254
-0.81057672 -0.33172350 -0.48262294 278.52181831
0.04646678 -0.85793760 0.51164823 136.24670506
Axis -0.26347291 0.46639243 -0.84442888
Axis point 67.32370020 166.66693468 0.00000000
Rotation angle (degrees) 134.58210932
Shift along axis 4.28077393
> hide #!1 models
> hide #!2 models
> volume #10 level 0.3641
> ui mousemode right "translate selected models"
> select add #10
2 models selected
> view matrix models
> #10,-0.72983,-0.61222,0.30419,232.85,0.0092519,0.43609,0.89986,-3.0164,-0.68356,0.65956,-0.31261,178.23
> view matrix models
> #10,-0.72983,-0.61222,0.30419,239.92,0.0092519,0.43609,0.89986,-11.331,-0.68356,0.65956,-0.31261,177.48
> hide #!10 models
> show #!10 models
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.34978,-0.91732,-0.19019,203.67,-0.74194,-0.3952,0.54161,197.32,-0.572,-0.048329,-0.81883,292.62
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.34978,-0.91732,-0.19019,199.94,-0.74194,-0.3952,0.54161,195.51,-0.572,-0.048329,-0.81883,291.08
> view matrix models
> #10,0.34978,-0.91732,-0.19019,197.99,-0.74194,-0.3952,0.54161,193.99,-0.572,-0.048329,-0.81883,291.98
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.71492,-0.67613,-0.17814,131.3,-0.60499,-0.72591,0.32717,235.51,-0.35053,-0.12613,-0.92802,286.93
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.71492,-0.67613,-0.17814,132.86,-0.60499,-0.72591,0.32717,236.4,-0.35053,-0.12613,-0.92802,287.2
> view matrix models
> #10,0.71492,-0.67613,-0.17814,134.6,-0.60499,-0.72591,0.32717,236.6,-0.35053,-0.12613,-0.92802,287.56
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.71493,-0.67692,-0.17506,134.32,-0.6059,-0.72476,0.32805,236.49,-0.34894,-0.12846,-0.9283,287.64
> view matrix models
> #10,0.56403,-0.79822,-0.21144,167.64,-0.68901,-0.59607,0.41227,223.65,-0.45512,-0.086851,-0.88618,290.83
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.56403,-0.79822,-0.21144,167.91,-0.68901,-0.59607,0.41227,222.99,-0.45512,-0.086851,-0.88618,292.1
> view matrix models
> #10,0.56403,-0.79822,-0.21144,168.12,-0.68901,-0.59607,0.41227,222.47,-0.45512,-0.086851,-0.88618,292.89
> view matrix models
> #10,0.56403,-0.79822,-0.21144,167.68,-0.68901,-0.59607,0.41227,222.06,-0.45512,-0.086851,-0.88618,292.78
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.9451,-0.30826,-0.10842,64.336,-0.24932,-0.89473,0.37054,205.73,-0.21123,-0.32317,-0.92247,292.14
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.9451,-0.30826,-0.10842,64.792,-0.24932,-0.89473,0.37054,207.28,-0.21123,-0.32317,-0.92247,291.09
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.95406,-0.28402,-0.095414,59.891,-0.23096,-0.90001,0.36966,205.79,-0.19086,-0.33064,-0.92426,289.69
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.95406,-0.28402,-0.095414,54.61,-0.23096,-0.90001,0.36966,206.3,-0.19086,-0.33064,-0.92426,289.49
> ui mousemode right select
> select clear
> ui tool show "Fit in Map"
> fitmap #3 inMap #10
Fit molecule 8u8f (#3) to map emd_42023_8U8F.map (#10) using 4141 atoms
average map value = 0.1356, steps = 60
shifted from previous position = 2.97
rotated from previous position = 3.78 degrees
atoms outside contour = 3428, contour level = 0.36411
Position of 8u8f (#3) relative to emd_42023_8U8F.map (#10) coordinates:
Matrix rotation and translation
0.98885725 -0.13046063 0.07170335 9.70268642
0.11910430 0.98228692 0.14466024 -33.06462280
-0.08930573 -0.13450815 0.98687996 22.31914980
Axis -0.68489987 0.39501286 0.61227200
Axis point 0.00000000 170.70498206 232.97410918
Rotation angle (degrees) 11.75939778
Shift along axis -6.04092928
> select clear
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select add #10
2 models selected
> view matrix models
> #10,0.95406,-0.28402,-0.095414,60.021,-0.23096,-0.90001,0.36966,210.43,-0.19086,-0.33064,-0.92426,294.16
> view matrix models
> #10,0.95406,-0.28402,-0.095414,59.925,-0.23096,-0.90001,0.36966,210.25,-0.19086,-0.33064,-0.92426,294.21
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.95276,-0.26606,-0.1465,64.268,-0.21159,-0.92746,0.30831,217.85,-0.2179,-0.26274,-0.93994,292.51
> view matrix models
> #10,0.94455,-0.26808,-0.18966,70.424,-0.18725,-0.91414,0.35956,207.8,-0.26976,-0.30411,-0.91364,299.42
> view matrix models
> #10,0.96895,-0.23928,-0.062312,50.009,-0.21977,-0.94892,0.22637,230.41,-0.11329,-0.20564,-0.97205,278.71
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.96895,-0.23928,-0.062312,48.309,-0.21977,-0.94892,0.22637,229.48,-0.11329,-0.20564,-0.97205,277.8
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.96809,-0.24111,-0.068264,49.278,-0.22119,-0.95024,0.21935,230.58,-0.11775,-0.19725,-0.97326,277.64
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.96809,-0.24111,-0.068264,49.089,-0.22119,-0.95024,0.21935,230.35,-0.11775,-0.19725,-0.97326,277.49
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.9547,-0.29204,-0.057122,54.291,-0.27231,-0.93479,0.22806,233.68,-0.12,-0.20217,-0.97197,278.08
> view matrix models
> #10,0.95173,-0.29746,-0.075656,57.315,-0.27693,-0.9385,0.20621,237.11,-0.13234,-0.17531,-0.97558,277.29
> view matrix models
> #10,0.88769,-0.45987,0.022982,68.997,-0.4567,-0.873,0.17115,255.37,-0.058645,-0.16243,-0.98498,268.7
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.88769,-0.45987,0.022982,69.027,-0.4567,-0.873,0.17115,255.43,-0.058645,-0.16243,-0.98498,268.91
> view matrix models
> #10,0.88769,-0.45987,0.022982,69.188,-0.4567,-0.873,0.17115,255.62,-0.058645,-0.16243,-0.98498,268.99
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> select add #10
2 models selected
> view matrix models
> #10,0.88769,-0.45987,0.022982,71.124,-0.4567,-0.873,0.17115,254.25,-0.058645,-0.16243,-0.98498,269.49
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.91356,-0.40236,-0.059297,72.131,-0.38423,-0.90165,0.1985,245.57,-0.13333,-0.15856,-0.97831,276.88
> ui mousemode right select
> fitmap #3 inMap #10
Fit molecule 8u8f (#3) to map emd_42023_8U8F.map (#10) using 4141 atoms
average map value = 0.4117, steps = 48
shifted from previous position = 1.71
rotated from previous position = 1.6 degrees
atoms outside contour = 2121, contour level = 0.36411
Position of 8u8f (#3) relative to emd_42023_8U8F.map (#10) coordinates:
Matrix rotation and translation
0.99999902 0.00120173 0.00071855 -0.19601774
-0.00120458 0.99999135 0.00398280 -0.25695137
-0.00071375 -0.00398366 0.99999181 0.53913177
Axis -0.94341223 0.16961756 -0.28496185
Axis point 0.00000000 134.32444864 64.28382463
Rotation angle (degrees) 0.24191227
Shift along axis -0.01228992
> select clear
> transparency #10.1 50
> select add #3
4141 atoms, 4187 bonds, 1 pseudobond, 266 residues, 2 models selected
> hide sel ribbons
> select subtract #3
Nothing selected
> select add #10
2 models selected
> volume sel style mesh
> volume sel style surface
> select clear
> ui mousemode right "map eraser"
> volume erase #10 center 117.7,116.64,162.97 radius 15.055 outside true
Opened emd_42023_8U8F.map copy as #13, grid size 256,256,256, pixel 0.86,
shown at step 1, values float32
> volume erase #13 center 116.79,102.75,163.3 radius 7.9258
> volume erase #13 center 111.05,106.54,171.81 radius 7.9258
> volume erase #13 center 120.71,106.79,157.7 radius 7.9258
> volume erase #13 center 124.7,110.37,171.04 radius 7.9258
> volume erase #13 center 121.04,110.48,171.92 radius 7.9258
> volume erase #13 center 105.04,115.99,155.78 radius 7.9258
> volume erase #13 center 118.01,100.14,158.41 radius 7.9258
> volume erase #13 center 128.52,108.66,159.84 radius 7.9258
> volume erase #13 center 129.08,114.99,168.53 radius 7.9258
> volume erase #13 center 124.09,121.82,178.56 radius 7.9258
> volume erase #13 center 129.62,124.33,168.57 radius 7.9258
> volume erase #13 center 120.15,112.65,154.11 radius 7.9258
> volume erase #13 center 122.18,114.46,153.45 radius 7.9258
> volume erase #13 center 115.83,112.64,152.98 radius 7.9258
> volume erase #13 center 109.37,106.78,150.6 radius 7.9258
> volume erase #13 center 102.31,103.74,159.66 radius 7.9258
> volume erase #13 center 122.28,123.84,151.67 radius 7.9258
> volume erase #13 center 128.24,123.7,148.61 radius 7.9258
> volume erase #13 center 114.43,125.51,156.94 radius 7.9258
> volume erase #13 center 122.2,126.46,151.3 radius 7.9258
> volume erase #13 center 123.71,127.92,169 radius 7.9258
> volume erase #13 center 117.79,125.27,170.02 radius 7.9258
> volume erase #13 center 126.34,129.99,164.82 radius 7.9258
> volume erase #13 center 128.46,130.55,157.76 radius 7.9258
> volume erase #13 center 126.76,132.97,162.51 radius 7.9258
[Repeated 1 time(s)]
> volume erase #13 center 117.16,121.02,177.7 radius 3.0822
> volume erase #13 center 117.4,115.9,177.67 radius 3.0822
> volume erase #13 center 114.58,116,177.53 radius 3.0822
> volume erase #13 center 114.79,116.29,176.51 radius 3.0822
[Repeated 1 time(s)]
> volume erase #13 center 114.57,114.41,176.24 radius 3.0822
> volume erase #13 center 113.27,118.05,179.54 radius 3.0822
> volume erase #13 center 112.99,120.41,178.61 radius 3.0822
> volume erase #13 center 118.41,130.57,163.6 radius 3.0822
> volume erase #13 center 111.38,119.59,150.76 radius 3.0822
> volume erase #13 center 115.31,118.78,149.01 radius 3.0822
> volume erase #13 center 117.82,118,158.2 radius 3.0822
> volume erase #13 center 112.67,119.09,162.03 radius 3.0822
> volume erase #13 center 114.55,120.02,164.12 radius 3.0822
> volume erase #13 center 112.65,122.72,163.77 radius 3.0822
> volume erase #13 center 109.49,124.56,161.57 radius 3.0822
> volume erase #13 center 110.17,118.4,174.3 radius 3.0822
> volume erase #13 center 111.11,122.43,172.75 radius 3.0822
> volume erase #13 center 102.49,119.55,167.53 radius 3.0822
> volume erase #13 center 100.76,116.59,164.82 radius 3.0822
> volume erase #13 center 106.59,120.53,171.66 radius 3.0822
> volume erase #13 center 105.28,116.39,171.69 radius 3.0822
> volume erase #13 center 108.38,114.95,174.21 radius 3.0822
> volume erase #13 center 106.76,115.57,174.43 radius 3.0822
> hide #!13 models
> ui mousemode right select
Drag select of 2 atoms, 2 bonds
> hide sel atoms
Drag select of 1 atoms, 1 bonds
> hide sel atoms
Drag select of 4 atoms, 3 bonds
> hide sel atoms
> show #!13 models
Drag select of eraser sphere, 183 of 1000 triangles, 1 atoms, 13
emd_42023_8U8F.map copy
> select clear
> ui mousemode right "map eraser"
> volume erase #13 center 108.09,107.52,158.16 radius 3.0822
> volume erase #13 center 114.1,110.88,162.3 radius 1.431
> volume erase #13 center 108.99,109.31,166.7 radius 1.431
> volume erase #13 center 108.51,110.29,165.94 radius 1.431
> volume erase #13 center 107.82,110.35,165.37 radius 1.431
> volume erase #13 center 106.99,111.99,163.41 radius 1.431
> volume erase #13 center 109.81,113.95,164.24 radius 1.431
> volume erase #13 center 110.96,114.2,163.7 radius 1.431
> volume erase #13 center 102.18,117.15,164.89 radius 1.431
> volume erase #13 center 102.46,117.32,163.27 radius 1.431
> volume erase #13 center 104.77,125.58,165.01 radius 1.431
> volume erase #13 center 107.41,124.89,166.86 radius 3.4125
> volume erase #13 center 111.87,121.8,167.47 radius 3.4125
> volume erase #13 center 111.26,119.34,168.42 radius 1.8714
> volume erase #13 center 111.44,120.62,169.64 radius 1.8714
> volume erase #13 center 110.39,121.3,169.78 radius 1.8714
> volume erase #13 center 110.13,119.84,168.41 radius 1.8714
> volume erase #13 center 109.42,118.75,168.38 radius 1.8714
> volume erase #13 center 109.74,122.19,167.63 radius 1.8714
> volume erase #13 center 111.05,123.71,171.01 radius 1.8714
> volume erase #13 center 110.89,123.53,171.84 radius 1.8714
> volume erase #13 center 109.31,123.03,172.58 radius 1.8714
> volume erase #13 center 113.06,110.96,162.71 radius 1.8714
> volume erase #13 center 107.82,121.79,164.28 radius 1.8714
> volume erase #13 center 106.28,121.88,168.51 radius 1.8714
> volume erase #13 center 108.09,121.35,170.06 radius 1.8714
> volume erase #13 center 110.47,119.08,167.21 radius 1.8714
> select add #13
2 models selected
> volume sel style mesh
> ui mousemode right select
> select clear
> save "/Users/dongju/Desktop/Research projects-Monash/NSMB/Updated figures-
> chimera files and png files/Figure 4/Figure4F_GPR3_8U8F.cxs"
——— End of log from Mon Sep 23 15:58:13 2024 ———
opened ChimeraX session
> select add #3
4141 atoms, 4187 bonds, 1 pseudobond, 266 residues, 2 models selected
> show sel ribbons
> show #!1 models
> hide #!3 models
> hide #!7 models
> show #!9 models
> select add #1
6062 atoms, 6143 bonds, 4 pseudobonds, 529 residues, 6 models selected
> select subtract #3
1921 atoms, 1956 bonds, 3 pseudobonds, 263 residues, 4 models selected
> show sel ribbons
> hide #!13 models
> show #!4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #4 change image level -0.05594,0 level 0.1762,0.8 level 4.403,1
> volume #4 level 0.5696
> show #!4 models
> hide #!9 models
> hide #7.1 models
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #1 inMap #4
Fit molecule 8x2k (#1) to map emd_38015_8X2K.map (#4) using 1921 atoms
average map value = 0.907, steps = 28
shifted from previous position = 0.0179
rotated from previous position = 0.0166 degrees
atoms outside contour = 838, contour level = 0.56958
Position of 8x2k (#1) relative to emd_38015_8X2K.map (#4) coordinates:
Matrix rotation and translation
0.99999919 -0.00029728 0.00123779 -0.14813315
0.00029782 0.99999986 -0.00043551 0.03667520
-0.00123766 0.00043588 0.99999914 0.11830230
Axis 0.32381927 0.91991067 0.22114575
Axis point 93.36805511 0.00000000 122.85809050
Rotation angle (degrees) 0.07709056
Shift along axis 0.01193159
> hide #!1 models
> show #!1 models
> show #!6 models
> hide #!6 models
> show #!9 models
> volume #4 level 0.4363
> select subtract #1
Nothing selected
> volume #4 level 0.2497
> volume #4 level 0.3564
> hide #!4 models
> ui mousemode right select
> select #1/A:96@NE2
1 atom, 1 residue, 1 model selected
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hbonds sel color #000000 restrict cross select true reveal true
1 hydrogen bonds found
> hbonds sel color #000000 restrict cross select true reveal true
2 hydrogen bonds found
> hbonds sel color #000000 restrict cross select true reveal true
2 hydrogen bonds found
> hbonds sel color #000000 restrict cross select true reveal true
2 hydrogen bonds found
> select clear
> ui tool show H-Bonds
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hbonds sel color #000000 restrict cross distSlop 1.0 angleSlop 25.0 select
> true reveal true
Atom specifier selects no atoms
> select #1/A:280@OH
1 atom, 1 residue, 1 model selected
> select add #1/A:96@NE2
2 atoms, 1 bond, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 restrict cross distSlop 1.0 angleSlop 25.0 select
> true reveal true
5 hydrogen bonds found
> hbonds sel color #000000 restrict cross distSlop 1.0 angleSlop 30.0 select
> true reveal true
8 hydrogen bonds found
> hbonds sel color #000000 restrict cross distSlop 1.0 angleSlop 25.0 select
> true reveal true
6 hydrogen bonds found
> hbonds sel color #000000 restrict cross distSlop 1.0 angleSlop 25.0 select
> true reveal true
7 hydrogen bonds found
> select clear
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 3 days, 13 hours, 9 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Note:
See TracTickets
for help on using tickets.
