![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Last modified 10 months ago
#16617 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-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000323daf000 (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 0x0000000322da3000 (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 0x0000000321d97000 (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 0x0000000320d8b000 (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 0x000000031fd7f000 (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 0x000000031ed73000 (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 0x000000031dd67000 (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 0x000000031cd5b000 (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 0x000000031bd4f000 (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 0x000000031ad43000 (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 0x0000000319d37000 (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 0x0000000318d2b000 (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 0x0000000317d1f000 (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 0x0000000316d13000 (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 0x0000000315d07000 (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 0x00000001e9ed0f40 (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, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, lxml._elementpath, lxml.etree, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, 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, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 107)
{"app_name":"ChimeraX","timestamp":"2025-01-14 13:24:08.00 +0000","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"D4E63E48-D121-4E42-8F37-3478F73AD98C"}
{
"uptime" : 1200000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 242167,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2025-01-14 13:24:05.1895 +0000",
"codeSigningMonitor" : 1,
"incident" : "D4E63E48-D121-4E42-8F37-3478F73AD98C",
"pid" : 43803,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-13 10:06:49.2053 +0000",
"procStartAbsTime" : 30083938786137,
"procExitAbsTime" : 30924940853512,
"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":"24620DA0-5988-5B23-9E82-940A82D06194","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E13F26CC-2B73-1C1F-F7BF-9C3A2414B42E",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 13568,
"sleepWakeUUID" : "81BD1F33-43F8-4A7F-8D1A-2A508751098F",
"sip" : "enabled",
"vmRegionInfo" : "0x168 is not in any region. Bytes before following region: 4363124376\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104100000-104104000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000168","rawCodes":[1,360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000168"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":43803},
"vmregioninfo" : "0x168 is not in any region. Bytes before following region: 4363124376\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104100000-104104000 [ 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":1},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5369723544},{"value":99},{"value":95},{"value":2},{"value":0},{"value":14237422058713925516},{"value":14237422050797504716},{"value":14757395258967641293},{"value":4294967286},{"value":5369723473},{"value":0},{"value":49},{"value":4294967280},{"value":328},{"value":8394712296},{"value":0},{"value":11},{"value":8219594560,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8219594784,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4386211376,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8225169408,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":8225169408,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSCGSStatusItem._selectedContentFrame"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6476536864},"cpsr":{"value":1073745920},"fp":{"value":5369723616},"sp":{"value":5369723584},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6476305904,"matchesCrashFrame":1},"far":{"value":0}},"id":18968006,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":38384,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":240},{"imageOffset":27680,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":241},{"imageOffset":262624,"symbol":"raise","symbolLocation":32,"imageIndex":242},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":238},{"imageOffset":17796,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":243},{"imageOffset":343184,"imageIndex":170},{"imageOffset":343184,"imageIndex":170},{"imageOffset":380316,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":244,"imageIndex":244},{"imageOffset":11486732,"symbol":"-[NSWindow _postWindowDidChangeBackingPropertiesAndDisplayWindowForPreviousBackingScaleFactor:previousColorSpace:]","symbolLocation":192,"imageIndex":244},{"imageOffset":2095464,"symbol":"__67-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]_block_invoke","symbolLocation":448,"imageIndex":244},{"imageOffset":510204,"symbol":"NSPerformVisuallyAtomicChange","symbolLocation":108,"imageIndex":244},{"imageOffset":2095004,"symbol":"-[NSWindow _updateSettingsSendingScreenChangeNotificationToScreen:]","symbolLocation":96,"imageIndex":244},{"imageOffset":515532,"symbol":"-[NSWindow _setFrameCommon:display:fromServer:]","symbolLocation":1856,"imageIndex":244},{"imageOffset":11458836,"symbol":"-[NSWindow(NSScreenLayout) _setFrame:fromAdjustmentToScreen:anchorIfNeeded:animate:]","symbolLocation":592,"imageIndex":244},{"imageOffset":3274684,"symbol":"-[NSWindow _adjustWindowToScreen]","symbolLocation":1100,"imageIndex":244},{"imageOffset":3405156,"symbol":"-[NSWindow 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"uuid" : "aaa5636d-6f3f-3fa7-9f4a-cf966f0308fe",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
"base" : 6472040448,
"size" : 4214358016,
"uuid" : "bb3df3d3-38bd-304c-9233-e43de95f1903"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG image 1408K 75 \nColorSync 656K 31 \nCoreAnimation 4496K 246 \nCoreGraphics 64K 4 \nCoreServices 624K 2 \nCoreUI image data 5488K 54 \nDispatch continuations 96.0M 1 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 1.9G 255 \nMALLOC guard page 192K 12 \nMach message 64K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 1104K 69 \nStack 411.9M 70 \nStack Guard 56.0M 1 \nVM_ALLOCATE 360.5M 356 \nVM_ALLOCATE (reserved) 608.0M 4 reserved VM address space (unallocated)\n__AUTH 2211K 409 \n__AUTH_CONST 31.9M 627 \n__CTF 824 1 \n__DATA 25.1M 871 \n__DATA_CONST 44.1M 873 \n__DATA_DIRTY 2033K 235 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 568.0M 241 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2200K 1 \n__TEXT 995.4M 890 \ndyld private memory 592K 8 \nmapped file 585.4M 104 \nshared memory 3296K 34 \n=========== ======= ======= \nTOTAL 5.7G 5494 \nTOTAL, minus reserved VM space 5.1G 5494 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "6adeb57a55f13df3622dee06b3c3cc10cf749019",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "64b21a7351cbb02ce3442e4e",
"factorPackIds" : {
"REMINDERS_GROCERY" : "6647f0f7b6a75d3dc32993e7"
},
"deploymentId" : 240000042
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{
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/CondensedMap-
> State1.mrc format mrc
Opened CondensedMap-State1.mrc as #1, grid size 360,360,360, pixel 0.648,
shown at level 0.00859, step 2, values float32
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/SMARCA/M-32792/Prelim-DataQC.cxs format session
Opened cryosparc_P150_J139_005_volume_map.mrc gaussian as #4, grid size
360,360,360, pixel 0.648, shown at level 0.0206, step 1, values float32
Opened cryosparc_P150_J133_006_volume_map.mrc as #3, grid size 360,360,360,
pixel 0.648, shown at level 0.00704, step 2, values float32
Opened cryosparc_P150_J133_006_volume_map.mrc gaussian as #5, grid size
360,360,360, pixel 0.648, shown at level 0.0198, step 1, values float32
Opened E3_ligase_complex_AMPH-19559_final_map.mrc as #6, grid size
300,300,300, pixel 0.731, shown at level 0.136, step 2, values float32
Opened E3_ligase_complex_AMPH-19559_final_map.mrc gaussian as #7, grid size
300,300,300, pixel 0.731, shown at level 0.0455, step 1, values float32
Opened cryosparc_P150_J139_005_volume_map.mrc as #8, grid size 360,360,360,
pixel 0.648, shown at level 0.00757, step 2, values float32
opened ChimeraX session
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/SMARCA/M-19559/E3_ligase_complex_AMPH-19559_half1_map.mrc format mrc
No such file/path: /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
QC/DATA/SMARCA/M-19559/E3_ligase_complex_AMPH-19559_half1_map.mrc
> open /Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/CondensedMap-
> State1.mrc format mrc
Opened CondensedMap-State1.mrc as #10, grid size 360,360,360, pixel 0.648,
shown at level 0.00859, step 2, values float32
> toolshed show
Downloading bundle ChimeraX_LigandRecognizer-0.2-py3-none-any.whl
Installed ChimeraX-LigandRecognizer (0.2)
> close session
> open "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/TEAD/Second round_5A/12182027_Amphista_model_8S7E_8Q68_fit.pdb"
Chain information for 12182027_Amphista_model_8S7E_8Q68_fit.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
58 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/2grc.pdb
2grc.pdb title:
1.5 A structure of bromodomain from human BRG1 protein, A central atpase of
swi/SNF remodeling complex [more info...]
Chain information for 2grc.pdb #2
---
Chain | Description | UniProt
A | probable global transcription activator SNF2L4 | SMCA4_HUMAN 1448-1575
> close #2
> close #1
> open "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/TEAD/Second round_5A/12182024_Amphista_Glacios_3Dclass1.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_3Dclass2.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_3Dclass3.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_3Dclass4.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_3Drefine.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_deepEMhancer.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182024_Amphista_Glacios_postprocess.mrc"
> "/Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-QC/DATA/TEAD/Second
> round_5A/12182027_Amphista_model_8S7E_8Q68_fit.pdb"
Opened 12182024_Amphista_Glacios_3Dclass1.mrc as #1, grid size 160,160,160,
pixel 1.9, shown at level 1.02e-05, step 1, values float32
Opened 12182024_Amphista_Glacios_3Dclass2.mrc as #2, grid size 160,160,160,
pixel 1.9, shown at level 1.79e-06, step 1, values float32
Opened 12182024_Amphista_Glacios_3Dclass3.mrc as #3, grid size 160,160,160,
pixel 1.9, shown at level 1.11e-05, step 1, values float32
Opened 12182024_Amphista_Glacios_3Dclass4.mrc as #4, grid size 160,160,160,
pixel 1.9, shown at level 8.58e-06, step 1, values float32
Opened 12182024_Amphista_Glacios_3Drefine.mrc as #5, grid size 320,320,320,
pixel 0.95, shown at level 0.00115, step 2, values float32
Opened 12182024_Amphista_Glacios_deepEMhancer.mrc as #6, grid size
320,320,320, pixel 0.95, shown at level 0.00113, step 2, values float32
Opened 12182024_Amphista_Glacios_postprocess.mrc as #7, grid size 320,320,320,
pixel 0.95, shown at level 0.00895, step 2, values float32
Chain information for 12182027_Amphista_model_8S7E_8Q68_fit.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
58 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!8 models
> surface dust #7 size 9.5
> ui tool show "Map Statistics"
> measure mapstats #!7
Map 12182024_Amphista_Glacios_postprocess.mrc #7, step 2, minimum -0.07711,
maximum 0.1442, mean 2.224e-05, SD 0.003721, RMS 0.003721
> volume gaussian #7 bfactor 200
Opened 12182024_Amphista_Glacios_postprocess.mrc gaussian as #9, grid size
320,320,320, pixel 0.95, shown at step 1, values float32
> surface dust #9 size 9.5
> volume #9 level 0.03798
> show #!8 models
> color #8 #ffd70085
> color #8 gold
> color #9 #ffffb280 models
> color #9 #ffffb27c models
> color #9 #ffffb27a models
> volume #9 level 0.02755
> volume #7 level 0.04413
> volume #7 color #b2b2b283
> volume #7 color #b2b2b282
> transparency #7.1 0
> volume #!7 style surface
> transparency #7.1 50
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting simple
> volume #9 level 0.01287
> volume gaussian #7 bfactor 500
Opened 12182024_Amphista_Glacios_postprocess.mrc gaussian as #10, grid size
320,320,320, pixel 0.95, shown at step 1, values float32
> surface dust #9 size 9.5
> surface dust #10 size 9.5
> volume #10 level 0.00193
> volume #9 level 0.005044
> volume #9 level 0.007327
> volume #9 level 0.01059
> save /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/TEAD/TEAD-33353_QC_lowRes.cxs
> volume #9 level 0.02592
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> volume gaussian #7 bfactor 50
Opened 12182024_Amphista_Glacios_postprocess.mrc gaussian as #11, grid size
320,320,320, pixel 0.95, shown at step 1, values float32
> surface dust #11 size 9.5
> close #11
> volume #10 level 0.003282
> hide #!8 models
> show #!8 models
> hide #!10 models
> select add #8
9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,-7.0879,0,1,0,-95.424,0,0,1,15.923
> show #!9 models
> select subtract #8
Nothing selected
> 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 #8 inMap #9
Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms
average map value = 0.0001173, steps = 68
shifted from previous position = 2.63
rotated from previous position = 2.5 degrees
atoms outside contour = 9225, contour level = 0.025916
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:
Matrix rotation and translation
0.99907078 0.03464922 0.02563226 -13.95349461
-0.03448119 0.99938105 -0.00696877 -89.23650384
-0.02585786 0.00607847 0.99964715 20.46990590
Axis 0.14965739 0.59061371 -0.79295530
Axis point -1372.49318712 59.13081900 0.00000000
Rotation angle (degrees) 2.49833508
Shift along axis -71.02426682
Average map value = 0.0001173 for 9225 atoms, 9225 outside contour
> fitmap #8 inMap #9
Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms
average map value = 0.0001174, steps = 44
shifted from previous position = 0.00819
rotated from previous position = 0.0172 degrees
atoms outside contour = 9225, contour level = 0.025916
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:
Matrix rotation and translation
0.99906040 0.03488088 0.02572239 -13.99697307
-0.03471659 0.99937402 -0.00680628 -89.21845569
-0.02594369 0.00590689 0.99964595 20.50558129
Axis 0.14511744 0.58975483 -0.79443701
Axis point -1366.07525796 69.34971193 0.00000000
Rotation angle (degrees) 2.51053116
Shift along axis -70.93861284
> select add #8
9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected
> view matrix models
> #8,0.99906,0.034881,0.025722,-8.3619,-0.034717,0.99937,-0.0068063,-11.745,-0.025944,0.0059069,0.99965,-1.3901
> fitmap #8 inMap #9
Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms
average map value = 0.01963, steps = 152
shifted from previous position = 18.7
rotated from previous position = 3.15 degrees
atoms outside contour = 6156, contour level = 0.025916
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:
Matrix rotation and translation
0.99992934 -0.01142249 -0.00329146 2.27394680
0.01142241 0.99993476 -0.00004104 -1.74537512
0.00329171 0.00000344 0.99999458 -0.67996791
Axis 0.00187064 -0.27689963 0.96089703
Axis point 157.95429147 198.12642221 0.00000000
Rotation angle (degrees) 0.68110696
Shift along axis -0.16583167
> select subtract #8
Nothing selected
> select add #8
9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected
> view matrix models
> #8,0.99993,-0.011422,-0.0032915,-3.5695,0.011422,0.99993,-4.1036e-05,-62.845,0.0032917,3.4372e-06,0.99999,-2.4981
> fitmap #8 inMap #9
Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms
average map value = 1.363e-05, steps = 196
shifted from previous position = 19.4
rotated from previous position = 6 degrees
atoms outside contour = 9225, contour level = 0.025916
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:
Matrix rotation and translation
0.99431729 -0.05928567 -0.08842135 20.10376186
0.05599766 0.99766045 -0.03921596 -79.98971064
0.09053943 0.03404172 0.99531089 -29.43601181
Axis 0.32540047 -0.79491900 0.51207258
Axis point 635.65737995 0.00000000 -16.09347900
Rotation angle (degrees) 6.46322218
Shift along axis 55.05373958
> show #!6 models
> fitmap #8 inMap #6
Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_deepEMhancer.mrc (#6) using 9225 atoms
average map value = -2.05e-07, steps = 108
shifted from previous position = 2.8
rotated from previous position = 3.77 degrees
atoms outside contour = 9225, contour level = 0.0011304
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_deepEMhancer.mrc (#6) coordinates:
Matrix rotation and translation
0.98548173 -0.10928181 -0.12993553 37.97855608
0.10485094 0.99366348 -0.04048668 -86.45732218
0.13353665 0.02627502 0.99069551 -32.98473542
Axis 0.19294358 -0.76144356 0.61885093
Axis point 502.45375084 0.00000000 157.82069091
Rotation angle (degrees) 9.96277668
Shift along axis 52.74745576
> hide #!8 models
> show #!8 models
> hide #!6 models
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.96604,-0.25116,0.060748,329.53,-0.24323,0.96321,0.1143,-51.849,-0.087219,0.095641,-0.99159,288.6
> view matrix models
> #8,-0.93896,-0.34014,0.051598,339.78,-0.33368,0.93692,0.10412,-32.592,-0.083758,0.080546,-0.99323,290.52
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.93896,-0.34014,0.051598,336.16,-0.33368,0.93692,0.10412,15.724,-0.083758,0.080546,-0.99323,301.02
> fitmap #8 inMap #9
Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms
average map value = 0.01249, steps = 196
shifted from previous position = 26.1
rotated from previous position = 17.6 degrees
atoms outside contour = 7377, contour level = 0.025916
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:
Matrix rotation and translation
-0.99485298 -0.05640899 0.08417581 298.41439918
-0.05770550 0.99824838 -0.01304770 8.37561434
-0.08329235 -0.01783795 -0.99636549 322.22824158
Axis -0.02859139 0.99956123 -0.00773840
Axis point 156.08973708 0.00000000 154.88477744
Rotation angle (degrees) 175.19465315
Shift along axis -2.65367532
> select subtract #8
Nothing selected
> hide #!8 models
> show #!8 models
> undo
> ui mousemode right "rotate selected models"
> select add #8
9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected
> view matrix models
> #8,0.63145,-0.73347,-0.25158,198.47,0.74744,0.6621,-0.054305,-59.744,0.20641,-0.15375,0.96631,2.7575
> view matrix models
> #8,0.66766,-0.70845,-0.22876,185.82,0.72104,0.69184,-0.038128,-62.479,0.18528,-0.13949,0.97274,2.9451
> ui mousemode right "translate selected models"
> fitmap #8 inMap #9
Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 9225 atoms
average map value = 0.01963, steps = 224
shifted from previous position = 9.7
rotated from previous position = 47.5 degrees
atoms outside contour = 6156, contour level = 0.025916
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:
Matrix rotation and translation
0.99992784 -0.01156045 -0.00326680 2.29250872
0.01155956 0.99993314 -0.00029013 -1.73205577
0.00326994 0.00025235 0.99999462 -0.71324265
Axis 0.02257300 -0.27199657 0.96203343
Axis point 154.82316121 197.65867302 0.00000000
Rotation angle (degrees) 0.68849522
Shift along axis -0.16330125
> select subtract #8
Nothing selected
> open
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/Cluster0-TCF.pdb
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/FBXO22-cluster0_B.pdb
> /Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/SKP1-cluster0_A.pdb
Summary of feedback from opening
/Users/tarunnarwani/Documents/StructurePG_TJR/coordFiles/TEAD/Cluster0-TCF.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
6196 messages similar to the above omitted
Chain information for Cluster0-TCF.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
Chain information for FBXO22-cluster0_B.pdb #12
---
Chain | Description
B | No description available
Chain information for SKP1-cluster0_A.pdb #13
---
Chain | Description
A | No description available
> hide #11 models
> hide #13 models
> select add #12
6264 atoms, 6322 bonds, 403 residues, 1 model selected
> view matrix models #12,1,0,0,28.299,0,1,0,126.57,0,0,1,133.32
> view matrix models #12,1,0,0,74.356,0,1,0,168.28,0,0,1,152.09
> view matrix models #12,1,0,0,133.54,0,1,0,164.03,0,0,1,161.43
> view matrix models #12,1,0,0,169.31,0,1,0,154.78,0,0,1,157.95
> select subtract #12
Nothing selected
> select add #12
6264 atoms, 6322 bonds, 403 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #12 inMap #9
Fit molecule FBXO22-cluster0_B.pdb (#12) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 6264 atoms
average map value = 0.01064, steps = 248
shifted from previous position = 24.3
rotated from previous position = 31.5 degrees
atoms outside contour = 5083, contour level = 0.025916
Position of FBXO22-cluster0_B.pdb (#12) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:
Matrix rotation and translation
0.90868714 -0.41082603 0.07422710 166.52223980
0.41179179 0.85278525 -0.32122397 135.28017747
0.06866740 0.32245820 0.94408977 151.96432014
Axis 0.61623678 0.00532264 0.78754295
Axis point -278.21123987 132.65002846 0.00000000
Rotation angle (degrees) 31.48454427
Shift along axis 223.01560662
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> hide #12 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #12 models
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.77426,0.24415,0.58388,166.01,0.60207,0.00013087,-0.79844,136.29,-0.19501,0.96974,-0.14689,148.54
> view matrix models
> #12,-0.26602,0.63325,0.72679,161.77,0.90962,0.41448,-0.028195,138.15,-0.3191,0.6536,-0.68628,147.62
> view matrix models
> #12,-0.15284,0.67533,0.7215,162.15,0.93603,0.3331,-0.1135,138.22,-0.31698,0.658,-0.68305,147.63
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.15284,0.67533,0.7215,150.14,0.93603,0.3331,-0.1135,139.31,-0.31698,0.658,-0.68305,145.63
> fitmap #12 inMap #9
Fit molecule FBXO22-cluster0_B.pdb (#12) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 6264 atoms
average map value = 0.01432, steps = 92
shifted from previous position = 7.55
rotated from previous position = 14.3 degrees
atoms outside contour = 4754, contour level = 0.025916
Position of FBXO22-cluster0_B.pdb (#12) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:
Matrix rotation and translation
-0.32330010 0.51175524 0.79597966 145.55673879
0.87726895 0.47745562 0.04934891 143.14383578
-0.35479040 0.71424275 -0.60330844 141.25704059
Axis 0.48237030 0.83486605 0.26517460
Axis point 50.81561189 -0.00000000 39.28555144
Rotation angle (degrees) 136.43362582
Shift along axis 227.17595615
> select subtract #12
Nothing selected
> show #!8 models
> hide #!9 models
> hide #12 models
> hide #!8 models
> show #!9 models
> show #13 models
> select add #13
2536 atoms, 2559 bonds, 160 residues, 1 model selected
> view matrix models #13,1,0,0,169.68,0,1,0,134.62,0,0,1,100.38
> view matrix models #13,1,0,0,129.92,0,1,0,158.38,0,0,1,103.69
> view matrix models #13,1,0,0,125.66,0,1,0,170.68,0,0,1,115.53
> view matrix models #13,1,0,0,131.81,0,1,0,169.76,0,0,1,115.57
> fitmap #13 inMap #9
Fit molecule SKP1-cluster0_A.pdb (#13) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 2536 atoms
average map value = 0.0115, steps = 116
shifted from previous position = 4.35
rotated from previous position = 11 degrees
atoms outside contour = 2123, contour level = 0.025916
Position of SKP1-cluster0_A.pdb (#13) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:
Matrix rotation and translation
0.99400424 -0.10375006 0.03451810 132.62134676
0.10788845 0.98193472 -0.15544864 164.32868551
-0.01776672 0.15824072 0.98724071 117.10946969
Axis 0.82117189 0.13687051 0.55402453
Axis point 0.00000000 18.26009484 882.18276290
Rotation angle (degrees) 11.01120915
Shift along axis 196.27819317
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.16768,-0.76567,-0.62099,158.3,0.98541,-0.14877,-0.082648,136.5,-0.029107,-0.62579,0.77945,113.34
> view matrix models
> #13,-0.33663,-0.65511,-0.6764,163.2,0.93274,-0.3305,-0.14411,136.83,-0.12914,-0.67941,0.7223,115.58
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.33663,-0.65511,-0.6764,151.15,0.93274,-0.3305,-0.14411,134.13,-0.12914,-0.67941,0.7223,110.91
> view matrix models
> #13,-0.33663,-0.65511,-0.6764,151.93,0.93274,-0.3305,-0.14411,132.36,-0.12914,-0.67941,0.7223,109.65
> fitmap #13 inMap #9
Fit molecule SKP1-cluster0_A.pdb (#13) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) using 2536 atoms
average map value = 0.01541, steps = 156
shifted from previous position = 7.59
rotated from previous position = 25.6 degrees
atoms outside contour = 1886, contour level = 0.025916
Position of SKP1-cluster0_A.pdb (#13) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#9) coordinates:
Matrix rotation and translation
-0.49270313 -0.79679422 -0.34980366 152.17213174
0.85426248 -0.51945687 -0.02000428 128.10938210
-0.16576862 -0.30868031 0.93660943 122.14498317
Axis -0.17120156 -0.10914341 0.97917197
Axis point 48.46787857 117.27732412 0.00000000
Rotation angle (degrees) 122.53232085
Shift along axis 79.56654352
> hide #13 models
> show #!8 models
> color #9 #ffffb20d models
> color #9 #ffffb234 models
> color #9 #ffffb236 models
> lighting simple
> lighting soft
> lighting full
> color #8 gold
> show #!10 models
> hide #!9 models
> volume #10 level 0.02995
> volume #10 level 0.01517
> volume #10 level -0.004033
> volume #10 level 0.002368
> volume #10 level 0.003892
> volume #10 level 0.02294
> ui tool show "Ramachandran Plot"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/cbook.py", line 298, in process
func(*args, **kwargs)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 309, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 192, in step_to
self._new_camera_position(residue)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 281, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 266, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 425, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
^
UnboundLocalError: cannot access local variable 'o' where it is not associated
with a value
> ui tool show "Side View"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/cbook.py", line 298, in process
func(*args, **kwargs)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 309, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 192, in step_to
self._new_camera_position(residue)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 281, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 266, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 425, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
^
UnboundLocalError: cannot access local variable 'o' where it is not associated
with a value
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/cbook.py", line 298, in process
func(*args, **kwargs)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 309, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 192, in step_to
self._new_camera_position(residue)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 281, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 266, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 425, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
^
UnboundLocalError: cannot access local variable 'o' where it is not associated
with a value
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/cbook.py", line 298, in process
func(*args, **kwargs)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 309, in
on_pick
get_stepper(self.current_model).step_to(picked_rama.residue)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 192, in step_to
self._new_camera_position(residue)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 281, in _new_camera_position
interpolate_camera(session, 0, frames=1)
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 266, in interpolate_camera
ncp, fcp = _get_clip_points(session, dist)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/tarunnarwani/Library/Application
Support/ChimeraX/1.8/lib/python/site-packages/chimerax/isolde/navigate.py",
line 425, in _get_clip_points
return (o+vd*dist*0.5, o+vd*dist*1.5)
^
UnboundLocalError: cannot access local variable 'o' where it is not associated
with a value
> volume #10 level 0.0301
> 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 #8/B
Alignment identifier is 8/B
> select #8/B:26-36,38-47,49-62,82-92,130-139,202-209,236-245,298-312,339-349
1645 atoms, 1647 bonds, 100 residues, 1 model selected
> select #8/B:56
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #8/B:56
16 atoms, 15 bonds, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!10 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> view matrix models
> #8,0.99993,-0.01156,-0.0032668,2.3088,0.01156,0.99993,-0.00029013,-1.7053,0.0032699,0.00025235,0.99999,-0.7365
> select clear
> view
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!6 models
> volume gaussian #6 bfactor 100
Opened 12182024_Amphista_Glacios_deepEMhancer.mrc gaussian as #14, grid size
320,320,320, pixel 0.95, shown at step 1, values float32
> volume #10 level 0.02782
> volume #10 level -0.006166
> volume #10 level 0.005263
> volume #10 level 0.02386
> show #13 models
> ui mousemode right "translate selected models"
> select add #13
2536 atoms, 2559 bonds, 160 residues, 1 model selected
> view matrix models
> #13,-0.4927,-0.79679,-0.3498,165.94,0.85426,-0.51946,-0.020004,179.7,-0.16577,-0.30868,0.93661,169.79
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #11 to #8/A 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 12182027_Amphista_model_8S7E_8Q68_fit.pdb, chain A (#8) with
Cluster0-TCF.pdb, chain A (#11), sequence alignment score = 576
RMSD between 79 pruned atom pairs is 1.051 angstroms; (across all 128 pairs:
3.301)
> hide #13 models
> select #8/B:20
14 atoms, 13 bonds, 1 residue, 1 model selected
> ui mousemode right select
> select up
105 atoms, 105 bonds, 7 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #8/B:403
23 atoms, 22 bonds, 1 residue, 1 model selected
> select up
71 atoms, 70 bonds, 5 residues, 1 model selected
> select up
312 atoms, 315 bonds, 20 residues, 1 model selected
> select up
333 atoms, 335 bonds, 22 residues, 1 model selected
> select up
1803 atoms, 1822 bonds, 119 residues, 1 model selected
> select up
1858 atoms, 1876 bonds, 123 residues, 1 model selected
> select up
2222 atoms, 2242 bonds, 147 residues, 1 model selected
> select up
2236 atoms, 2255 bonds, 148 residues, 1 model selected
> select up
2650 atoms, 2673 bonds, 173 residues, 1 model selected
> select up
2717 atoms, 2740 bonds, 177 residues, 1 model selected
> select up
3722 atoms, 3757 bonds, 244 residues, 1 model selected
> select up
3748 atoms, 3782 bonds, 246 residues, 1 model selected
> select up
5189 atoms, 5236 bonds, 335 residues, 1 model selected
> show #!10 models
> ui mousemode right "rotate selected models"
> hide #!8 models
> show #!8 models
> select add #8
9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected
> select subtract #8
Nothing selected
> select add #8
9225 atoms, 9188 bonds, 8 pseudobonds, 826 residues, 2 models selected
> view matrix models
> #8,-0.050776,-0.98234,-0.1801,332.24,-0.9675,0.093113,-0.23511,316.58,0.24773,0.16231,-0.95514,231.81
> view matrix models
> #8,-0.40316,-0.91029,0.093985,334.57,-0.88572,0.36231,-0.29024,272.9,0.23015,-0.20026,-0.95233,287.18
> view matrix models
> #8,-0.40533,0.91417,-0.00064002,81.984,0.88635,0.39316,0.24456,-83.877,0.22382,0.098558,-0.96964,247
> view matrix models
> #8,0.63897,0.7332,0.23265,-86.807,0.72105,-0.67626,0.15088,112.15,0.26796,0.071341,-0.96079,242.88
> view matrix models
> #8,-0.86854,-0.49287,-0.052056,366.8,-0.49091,0.86998,-0.04636,101.34,0.068137,-0.014711,-0.99757,291.67
> view matrix models
> #8,-0.88027,-0.46419,-0.098213,371.34,-0.46362,0.88553,-0.029953,92.414,0.10087,0.019167,-0.99471,281.25
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.88027,-0.46419,-0.098213,371.21,-0.46362,0.88553,-0.029953,93.111,0.10087,0.019167,-0.99471,288.61
> view matrix models
> #8,-0.88027,-0.46419,-0.098213,383.15,-0.46362,0.88553,-0.029953,155.98,0.10087,0.019167,-0.99471,290.72
> view matrix models
> #8,-0.88027,-0.46419,-0.098213,383.74,-0.46362,0.88553,-0.029953,157.98,0.10087,0.019167,-0.99471,284.77
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.42759,0.86906,-0.2488,10.478,-0.90377,0.41684,-0.097187,304.24,0.019252,0.26642,0.96367,-33.182
> view matrix models
> #8,0.77352,0.60123,-0.20047,-10.647,-0.63227,0.75383,-0.17881,225.51,0.043614,0.26507,0.96324,-36.659
> volume #10 level 0.02553
> view matrix models
> #8,0.76877,0.63484,-0.077293,-33.348,-0.63567,0.7453,-0.20113,230.63,-0.070078,0.20376,0.97651,-12.231
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.76877,0.63484,-0.077293,-41.29,-0.63567,0.7453,-0.20113,160.36,-0.070078,0.20376,0.97651,-14.162
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.67531,0.73297,-0.081904,-40.626,-0.73298,0.65467,-0.1848,186.11,-0.081831,0.18483,0.97936,-10.016
> view matrix models
> #8,0.92495,0.34942,0.14956,-57.551,-0.33478,0.93529,-0.11468,73.385,-0.17995,0.056001,0.98208,23.493
> view matrix models
> #8,0.99272,-0.099665,0.067645,10.116,0.10567,0.99014,-0.091933,-5.6452,-0.057816,0.098412,0.99346,-3.1669
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.99272,-0.099665,0.067645,2.2475,0.10567,0.99014,-0.091933,-2.8917,-0.057816,0.098412,0.99346,-1.1003
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.98714,-0.15251,0.047811,13.821,0.15631,0.98363,-0.089662,-10.05,-0.033353,0.095982,0.99482,-4.7023
> 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 #8 inMap #10
Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_postprocess.mrc gaussian (#10) using 9225 atoms
average map value = 0.01841, steps = 108
shifted from previous position = 5.56
rotated from previous position = 10.6 degrees
atoms outside contour = 6516, contour level = 0.025532
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#10) coordinates:
Matrix rotation and translation
0.99999655 -0.00244054 -0.00097730 0.52642988
0.00244123 0.99999678 0.00070534 -0.49302841
0.00097557 -0.00070772 0.99999928 -0.11313285
Axis -0.25954042 -0.35868970 0.89664958
Axis point 211.23113280 208.89189162 0.00000000
Rotation angle (degrees) 0.15597247
Shift along axis -0.06122614
Average map value = 0.01841 for 9225 atoms, 6516 outside contour
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #4 inMap #10
Fit map 12182024_Amphista_Glacios_3Dclass4.mrc in map
12182024_Amphista_Glacios_postprocess.mrc gaussian using 36656 points
correlation = 0.8147, correlation about mean = 0.6883, overlap = 16.21
steps = 56, shift = 1.48, angle = 0.868 degrees
Position of 12182024_Amphista_Glacios_3Dclass4.mrc (#4) relative to
12182024_Amphista_Glacios_postprocess.mrc gaussian (#10) coordinates:
Matrix rotation and translation
0.99988562 0.00584419 -0.01394988 1.41668665
-0.00585547 0.99998256 -0.00076808 -0.07536794
0.01394514 0.00084968 0.99990240 -3.22359478
Axis 0.05340490 -0.92085783 -0.38622372
Axis point 193.32512548 0.00000000 94.64857300
Rotation angle (degrees) 0.86784733
Shift along axis 1.39008996
Correlation = 0.8147, Correlation about mean = 0.6883, Overlap = 16.21
> fitmap #8 inMap #4
Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_3Dclass4.mrc (#4) using 9225 atoms
average map value = 0.03868, steps = 56
shifted from previous position = 0.529
rotated from previous position = 0.463 degrees
atoms outside contour = 180, contour level = 8.5775e-06
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_3Dclass4.mrc (#4) coordinates:
Matrix rotation and translation
0.99985955 -0.00195433 0.01664564 -2.29841881
0.00198688 0.99999615 -0.00193912 0.76665025
-0.01664179 0.00197192 0.99985958 3.60031780
Axis 0.11589162 0.98637224 0.11678583
Axis point 208.72035729 0.00000000 146.17829889
Rotation angle (degrees) 0.96683567
Shift along axis 0.91030116
Average map value = 0.03868 for 9225 atoms, 180 outside contour
> fitmap #8 inMap #1
Fit molecule 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) to map
12182024_Amphista_Glacios_3Dclass1.mrc (#1) using 9225 atoms
average map value = 0.04031, steps = 52
shifted from previous position = 0.782
rotated from previous position = 0.702 degrees
atoms outside contour = 661, contour level = 1.0157e-05
Position of 12182027_Amphista_model_8S7E_8Q68_fit.pdb (#8) relative to
12182024_Amphista_Glacios_3Dclass1.mrc (#1) coordinates:
Matrix rotation and translation
0.99991779 -0.00315908 0.01242759 -1.22912133
0.00316312 0.99999496 -0.00030561 -0.01164305
-0.01242656 0.00034490 0.99992273 2.25993858
Axis 0.02535732 0.96882574 0.24644209
Axis point 171.03150715 0.00000000 101.08386603
Rotation angle (degrees) 0.73495019
Shift along axis 0.51449666
Average map value = 0.04031 for 9225 atoms, 661 outside contour
> hide #!8 models
> show #!8 models
> hide #!10 models
> show #!10 models
> volume #10 level 0.002087
> volume #10 level 0.002994
===== 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 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AY0010LB/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 86 days, 14 hours, 37 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL P2422H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
DELL P2422H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
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-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-LigandRecognizer: 0.2
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-maskChains: 1.4
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-QScore: 1.1
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-StarMap: 1.2.15
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
pyqtgraph: 0.13.7
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
Send2Trash: 1.8.3
SEQCROW: 1.8.12
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
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