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Opened 7 weeks ago
Closed 7 weeks ago
#18857 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9rc202411272016 (2024-11-27 20:16:15 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000032307f000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000322073000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000321067000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000032005b000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031f04f000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031e043000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031d037000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031c02b000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031b01f000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031a013000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000319007000 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000002072aa0c0 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mlp._mlp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 64)
{"app_name":"ChimeraX","timestamp":"2025-09-23 21:04:45.00 -0400","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.6.1 (24G90)","roots_installed":0,"name":"ChimeraX","incident_id":"7D32A524-BAEE-4A2E-A196-DD6147126ACB"}
{
"uptime" : 82000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 12387,
"osVersion" : {
"train" : "macOS 15.6.1",
"build" : "24G90",
"releaseType" : "User"
},
"captureTime" : "2025-09-23 21:04:32.9338 -0400",
"codeSigningMonitor" : 1,
"incident" : "7D32A524-BAEE-4A2E-A196-DD6147126ACB",
"pid" : 37741,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-23 10:17:32.8804 -0400",
"procStartAbsTime" : 1176309578896,
"procExitAbsTime" : 1971161620567,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9-rc2024.11.27.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D645BBC0-7ABF-53B9-A331-4E7B4D97625A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C9A6B6FC-0DC7-FC74-ADBC-3A1BBB8AAD37",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "43CB6B60-C7DF-4453-B41D-2AECA24BF2FF",
"wakeTime" : 5856,
"sleepWakeUUID" : "3CE3CABA-395C-4650-978F-F62DB66B153C",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4305305239\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1009dc000-1009e0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9-rc2024.11.27.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":37741},
"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" : "0x169 is not in any region. Bytes before following region: 4305305239\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1009dc000-1009e0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9-rc2024.11.27.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6161561976},{"value":99},{"value":95},{"value":0},{"value":1027},{"value":7786398920046486260},{"value":7786398928621109812},{"value":14757395258967641293},{"value":4294967286},{"value":6161561906},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8727303512},{"value":0},{"value":11},{"value":259},{"value":8710168992,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4328523312,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8671334400,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":8671334400,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6865123468},"cpsr":{"value":1073745920},"fp":{"value":6161562048},"sp":{"value":6161562016},"esr":{"value":1442840704,"description":" Address size 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},
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"path" : "\/Applications\/ChimeraX-1.9-rc2024.11.27.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-311-darwin.so",
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"uuid" : "d6494ba9-171e-39fc-b1aa-28ecf87975d1",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
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"name" : "AppKit",
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"name" : "CoreFoundation",
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"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
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},
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"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 5398624,
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"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
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"uuid" : "24ce0d89-4114-30c2-a81a-3db1f5931cff",
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"name" : "libdispatch.dylib"
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"CFBundleIdentifier" : "com.apple.HIToolbox",
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"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=3.9G written=57.9M(1%) resident=2618K(0%) swapped_out=55.3M(1%) unallocated=3.9G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 960K 57 \nColorSync 672K 33 \nCoreAnimation 6720K 172 \nCoreGraphics 64K 4 \nCoreServices 624K 2 \nCoreUI image data 5680K 44 \nFoundation 48K 2 \nKernel Alloc Once 1424K 4 \nMALLOC 3.1G 131 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.8M 51 \nStack 377.2M 51 \nVM_ALLOCATE 313.5M 471 \nVM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)\n__AUTH 5520K 696 \n__AUTH_CONST 77.4M 943 \n__CTF 824 1 \n__DATA 34.4M 1098 \n__DATA_CONST 37.2M 1116 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 649.3M 167 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1135 \n__TEXT (graphics) 32K 1 \n__TPRO_CONST 128K 2 \ndyld private memory 928K 10 \nmapped file 601.0M 116 \npage table in kernel 2618K 1 \nshared memory 3312K 28 \n=========== ======= ======= \nTOTAL 6.7G 6714 \nTOTAL, minus reserved VM space 6.6G 6714 \n",
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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: 1.9rc202411272016 (2024-11-27)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/briannaclose/Documents/Davey/Screening Compounds/Computation
> Screen sdf files/BC001-BC078_library.sdf"
PubChem entry 4038499
PubChem entry 4436450
PubChem entry 3495694
PubChem entry 17418473
PubChem entry 17399670
PubChem entry 17407526
PubChem entry 17421131
PubChem entry 4798163
PubChem entry 3281784
PubChem entry 16232152
PubChem entry 135872873
PubChem entry 135938954
PubChem entry 17433785
PubChem entry 3924279
PubChem entry 16352018
PubChem entry 1397748
PubChem entry 662319
PubChem entry 1416804
PubChem entry 663092
PubChem entry 1401038
PubChem entry 3693506
PubChem entry 1400206
PubChem entry 5124900
PubChem entry 1416605
PubChem entry 3824904
PubChem entry 6905027
PubChem entry 2128618
PubChem entry 3727625
PubChem entry 3706839
PubChem entry 3641147
PubChem entry 6876987
PubChem entry 6875154
PubChem entry 3427774
PubChem entry 1293582
PubChem entry 6301273
PubChem entry 62920
PubChem entry 9551410
PubChem entry 4887555
PubChem entry 6874016
PubChem entry 135645326
PubChem entry 7293325
PubChem entry 4184895
PubChem entry 17576436
PubChem entry 3761385
PubChem entry 2982720
PubChem entry 16191974
PubChem entry 2828232
PubChem entry 9665599
PubChem entry 2209575
PubChem entry 6890358
PubChem entry 6370397
PubChem entry 15988503
PubChem entry 9551712
PubChem entry 1251601
PubChem entry 1324653
PubChem entry 3242863
PubChem entry 3237928
PubChem entry 7579221
PubChem entry 1068748
PubChem entry 897624
PubChem entry 175540
PubChem entry 9599835
PubChem entry 703125
PubChem entry 15944743
PubChem entry 2214281
PubChem entry 16327529
PubChem entry 16310371
PubChem entry 4799556
PubChem entry 16249111
PubChem entry 5949904
PubChem entry 6904465
PubChem entry 2114184
PubChem entry 4857708
PubChem entry 4805360
PubChem entry 4881702
PubChem entry 6901783
PubChem entry 3877754
PubChem entry 5337380
> open "/Users/briannaclose/Documents/Davey/Screening Compounds/Computation
> Screen sdf files/output.json"
Failed opening file /Users/briannaclose/Documents/Davey/Screening
Compounds/Computation Screen sdf files/output.json:
expected str, bytes or os.PathLike object, not NoneType
> open "/Users/briannaclose/Documents/Davey/Screening Compounds/Computation
> Screen sdf files/output.json"
Failed opening file /Users/briannaclose/Documents/Davey/Screening
Compounds/Computation Screen sdf files/output.json:
expected str, bytes or os.PathLike object, not NoneType
> open "/Users/briannaclose/Documents/Davey/Screening Compounds/Computation
> Screen sdf files/output.json"
Failed opening file /Users/briannaclose/Documents/Davey/Screening
Compounds/Computation Screen sdf files/output.json:
expected str, bytes or os.PathLike object, not NoneType
> open "/Users/briannaclose/Desktop/Structures/GPC_binding site
> predictions.pdb"
Summary of feedback from opening
/Users/briannaclose/Desktop/Structures/GPC_binding site predictions.pdb
---
warnings | Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
Duplicate atom serial number found: 6
8085 messages similar to the above omitted
Chain information for GPC_binding site predictions.pdb #2
---
Chain | Description
A B C | No description available
a b c | No description available
> show cartoons
Computing secondary structure
> hide surfaces
> select add #1
3793 atoms, 3954 bonds, 78 residues, 79 models selected
> close #1
> select
9835 atoms, 10051 bonds, 1224 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> select clear
> ui tool show "Color Actions"
> open /Users/briannaclose/Desktop/Structures/various_data.json
Failed opening file /Users/briannaclose/Desktop/Structures/various_data.json:
JSON file "/Users/briannaclose/Desktop/Structures/various_data.json" is not
AlphaFold predicted aligned error data, expected a top level list
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
> ui mousemode right "next docked"
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Find Cavities"
> ui tool show ViewDockX
No suitable models found for ViewDockX
> kvfinder
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 67, in find_cavities
run(self.session, "kvfinder %s" % concise_model_spec(self.session, structures,
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 52, in cmd_kvfinder
num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices,
grid_spacing,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect
from _pyKVFinder import _detect, _detect_ladj
ImportError: dlopen(/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/briannaclose/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/briannaclose/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))
ImportError: dlopen(/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/briannaclose/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/briannaclose/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))
File "/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect
from _pyKVFinder import _detect, _detect_ladj
See log for complete Python traceback.
> close
> open "/Users/briannaclose/Documents/Davey/Manuscripts:Abstracts/ICAR
> 2025/Images/7PUY_Resistance mutations.cxs" format session
opened ChimeraX session
> select /a
1577 atoms, 1617 bonds, 192 residues, 1 model selected
> hide #1.1 models
> show #1.1 models
> select ~sel & ##selected
8818 atoms, 9042 bonds, 9 pseudobonds, 1074 residues, 2 models selected
> select ~sel
1577 atoms, 1617 bonds, 192 residues, 8 models selected
> select /a
1577 atoms, 1617 bonds, 192 residues, 1 model selected
> select ~sel & ##selected
8818 atoms, 9042 bonds, 9 pseudobonds, 1074 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> undo
> show sel surfaces
> select
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 9 models selected
> show sel surfaces
> close #1
> open "/Users/briannaclose/Documents/Davey/Escape Mutants/VSV-LASV-GP Escape
> mutants/LASV_GP with matri.cxs" format session
opened ChimeraX session
> select /a
1577 atoms, 1617 bonds, 192 residues, 1 model selected
Alignment identifier is 1/a
> open /Users/briannaclose/Desktop/Structures/new_7PUY.pdb
Chain information for new_7PUY.pdb #2
---
Chain | Description
A B C | No description available
a b c | No description available
> hide #!1 models
> show #!1 models
> hide #!1 target m
> select add #2
11417 atoms, 11682 bonds, 9 pseudobonds, 1416 residues, 4 models selected
> hide sel & #!2 atoms
> show sel & #!2 atoms
> show sel & #!2 surfaces
> hide sel & #!2 surfaces
> show sel & #!2 surfaces
> hide sel & #!2 cartoons
> show sel & #!2 cartoons
Computing secondary structure
> hide sel & #!2 atoms
> open "/Users/briannaclose/Documents/Davey/Screening Compounds/Computation
> Screen sdf files/output.sdf"
> select subtract #2
1577 atoms, 1617 bonds, 192 residues, 8 models selected
> select add #2
11417 atoms, 11682 bonds, 9 pseudobonds, 1416 residues, 4 models selected
> hide sel & #!2 surfaces
> select subtract #2
1577 atoms, 1617 bonds, 192 residues, 8 models selected
> hide #!2 models
> show #!1 models
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 3 models selected
> transparency (#!1 & sel) 50
> hide sel atoms
> show sel cartoons
> transparency (#!1 & sel) 70
> select clear
Drag select of 7puy_B SES surface, 94 of 251188 triangles, 7puy_b SES surface,
74 of 226210 triangles, 1 residues
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 3 models selected
> hide sel surfaces
> select clear
> interfaces #3.1-9#!1 & ~solvent
12 buried areas: #1/C #1/c 2681, #1/A #1/a 2653, #1/B #1/b 2653, #1/C #1/a
1234, #1/b #1/c 1218, #1/B #1/c 1214, #1/a #1/c 1213, #1/a #1/b 1204, #1/A
#1/b 1184, #1/B #1/C 1120, #1/A #1/B 1116, #1/A #1/C 1107
Ignoring fixed x limits to fulfill fixed data aspect with adjustable data
limits.
> hbonds #3.1-9#!1 reveal true
2875 hydrogen bonds found
Drag select of 2 residues
Drag select of 4 residues
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.75962,-0.40067,-0.51229,154.33,-0.077659,0.72617,-0.68311,138.96,0.64571,0.55869,0.5205,-95.156
> ui mousemode right rotate
> ui mousemode right pivot
> ui mousemode right rotate
> select clear
> select #1/b:441@CE1
1 atom, 1 residue, 1 model selected
Drag select of 100 atoms, 25 residues, 90 bonds, 20 pseudobonds
> hide sel atoms
> undo
> select add #1
10481 atoms, 10749 bonds, 964 pseudobonds, 1270 residues, 11 models selected
> hide sel atoms
> select clear
> undo
> select clear
> select add #1
10395 atoms, 10659 bonds, 960 pseudobonds, 1266 residues, 3 models selected
> hide sel atoms
> select clear
> select #1/b:441
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/b:443
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/b:442
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 6 residues, 2 pseudobonds
> select #1/c:444
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/b:443
14 atoms, 12 bonds, 2 residues, 2 models selected
> select subtract #1/c:444
8 atoms, 7 bonds, 1 residue, 3 models selected
> select subtract #1/b:443
1 model selected
> select add #1/b:443
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/b:442
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #1/b:441
28 atoms, 26 bonds, 3 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 28 atom styles
> select add #1/a:441
40 atoms, 38 bonds, 4 residues, 2 models selected
> select add #1/a:442
48 atoms, 45 bonds, 5 residues, 3 models selected
> select add #1/a:443
56 atoms, 52 bonds, 6 residues, 3 models selected
> select add #1/a:446
67 atoms, 63 bonds, 7 residues, 3 models selected
> show sel atoms
> style sel stick
Changed 67 atom styles
> select clear
> select add #1
10395 atoms, 10659 bonds, 960 pseudobonds, 1266 residues, 3 models selected
Ignoring fixed x limits to fulfill fixed data aspect with adjustable data
limits.
> show sel surfaces
> select clear
> select #3.4/?:1@C13
1 atom, 1 residue, 1 model selected
> select #3.4/?:1@C13
1 atom, 1 residue, 1 model selected
> select add #3.4
39 atoms, 42 bonds, 1 residue, 1 model selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 10 atomic
models, 0 maps.
> volume style surface
No volumes specified
> show sel surfaces
> transparency (#!3.4 & sel) 80
> select clear
> set bgColor white
> select #1/b:440@CB
1 atom, 1 residue, 1 model selected
> select #1/b:440@CB
1 atom, 1 residue, 1 model selected
> select clear
> ui mousemode right translate
> select add #1
10395 atoms, 10659 bonds, 960 pseudobonds, 1266 residues, 3 models selected
> surface hidePatches (#!1 & sel)
> select clear
> select add #1
10395 atoms, 10659 bonds, 960 pseudobonds, 1266 residues, 3 models selected
> ~hbonds
> select #3.4/?:1@C12
1 atom, 1 residue, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> select add #3.4/?:1@C19
2 atoms, 1 bond, 1 residue, 3 models selected
> select add #3.4/?:1@N3
3 atoms, 1 bond, 1 residue, 3 models selected
> select add #3.4
39 atoms, 43 bonds, 1 residue, 3 models selected
> select add #1/a:441
51 atoms, 54 bonds, 2 residues, 3 models selected
> hbonds sel reveal true
7 hydrogen bonds found
> select clear
> select add #1/b:444
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/b:445
14 atoms, 12 bonds, 2 residues, 2 models selected
> select add #1/b:446
25 atoms, 23 bonds, 3 residues, 2 models selected
> select add #1/b:447
33 atoms, 30 bonds, 4 residues, 2 models selected
> select add #1/b:448
43 atoms, 40 bonds, 5 residues, 2 models selected
> select add #1/b:443
51 atoms, 47 bonds, 6 residues, 2 models selected
> select add #1/b:442
59 atoms, 54 bonds, 7 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 59 atom styles
> select clear
> save "/Users/briannaclose/Desktop/Structures/BC073_GPC_Autodock Vina.cxs"
> open "/Users/briannaclose/Desktop/Structures/BC073_GPC_Autodock Vina.cxs"
opened ChimeraX session
> select add #2
9840 atoms, 10065 bonds, 9 pseudobonds, 1224 residues, 2 models selected
> close
> open "/Users/briannaclose/Desktop/Structures/BC073_GPC_Autodock Vina.cxs"
> format session
opened ChimeraX session
> close #2
> save "/Users/briannaclose/Desktop/Structures/BC073_GPC_Autodock Vina.cxs"
> hide #!3 models
> show #!3 models
> hide #3.1 models
> show #3.1 models
> hide #3.3 models
> show #3.3 models
> hide #3.3 models
> show #3.3 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> hide #3.4.1 models
> show #3.4.1 models
> hide #3.5 models
> show #3.5 models
> hide #3.5 models
> show #3.5 models
> hide #3.6 models
> show #3.6 models
> hide #3.6 models
> hide #3.5 models
> show #3.5 models
> show #3.6 models
> hide #3.6 models
> show #3.6 models
> hide #!3.4 models
> hide #3.3 models
> show #3.3 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> hide #3.3 models
> show #3.3 models
> hide #3.3 models
> show #3.3 models
> hide #3.3 models
> show #3.3 models
> hide #3.3 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> hide #3.2 models
> show #3.1 models
> show #3.2 models
> hide #3.2 models
> hide #3.1 models
> hide #3.7 models
> hide #3.8 models
> show #3.8 models
> show #3.7 models
> log metadata #3.7
The model has no metadata
> log chains #3.7
> log metadata #3.6
The model has no metadata
> log chains #3.6
> view #3.6 clip false
> select /A:435-448
Nothing selected
> select /A:435:448
Nothing selected
> select add #1/a:436
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1/a:443
19 atoms, 18 bonds, 2 residues, 2 models selected
> select clear
> select /a:435:448
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /a:435-448
119 atoms, 123 bonds, 2 pseudobonds, 14 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 119 atom styles
> select /a:435-448/b:435-448/c:435-448
357 atoms, 369 bonds, 2 pseudobonds, 42 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 357 atom styles
> select clear
> select add #3.8
39 atoms, 42 bonds, 1 residue, 1 model selected
> select add #3.7
78 atoms, 84 bonds, 2 residues, 2 models selected
> select add #3.6
117 atoms, 126 bonds, 3 residues, 3 models selected
> select add #3.5
156 atoms, 168 bonds, 4 residues, 4 models selected
> select add #3.4
195 atoms, 210 bonds, 5 residues, 5 models selected
> select add #3.3
234 atoms, 252 bonds, 6 residues, 7 models selected
> hbonds sel & #3.5-8#!3.4 reveal true
5 hydrogen bonds found
> select clear
> hide #3.5 models
> hide #3.7 models
> select /A:27-35/B:27-35/C:27-35
186 atoms, 183 bonds, 27 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 186 atom styles
> select clear
> select add #3.6
39 atoms, 42 bonds, 1 residue, 1 model selected
> select add #3.4
78 atoms, 84 bonds, 2 residues, 2 models selected
> select add #3.8
117 atoms, 126 bonds, 3 residues, 4 models selected
> select subtract #3.8
78 atoms, 84 bonds, 2 residues, 3 models selected
> select add #3.8
117 atoms, 126 bonds, 3 residues, 4 models selected
> select add #3.9
156 atoms, 168 bonds, 4 residues, 5 models selected
> select subtract #3.9
117 atoms, 126 bonds, 3 residues, 4 models selected
> hbonds sel reveal true
3 hydrogen bonds found
> select clear
> log metadata #3.6
The model has no metadata
> log chains #3.6
> ui mousemode right "mark maximum"
> undo
> select clear
> color bfactor #3.6,8-9#!1#!3.4
10551 atoms, 1270 residues, 7 surfaces, atom bfactor range 0 to 166
> undo
> interfaces #3.6,8-9#!1#!3.4 & ~solvent
12 buried areas: #1/C #1/c 2681, #1/A #1/a 2653, #1/B #1/b 2653, #1/C #1/a
1234, #1/b #1/c 1218, #1/B #1/c 1214, #1/a #1/c 1213, #1/a #1/b 1204, #1/A
#1/b 1184, #1/B #1/C 1120, #1/A #1/B 1116, #1/A #1/C 1107
Ignoring fixed x limits to fulfill fixed data aspect with adjustable data
limits.
> undo
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> mlp #3.6,8-9#!1#!3.4
Map values for surface "7puy_A SES surface": minimum -28.5, mean -3.01,
maximum 23.98
Map values for surface "7puy_B SES surface": minimum -27.55, mean -2.97,
maximum 23.07
Map values for surface "7puy_C SES surface": minimum -28.01, mean -2.956,
maximum 23.35
Map values for surface "7puy_a SES surface": minimum -25.67, mean -2.715,
maximum 23.71
Map values for surface "7puy_b SES surface": minimum -25.12, mean -2.738,
maximum 23.07
Map values for surface "7puy_c SES surface": minimum -25.72, mean -2.755,
maximum 24.63
To also show corresponding color key, enter the above mlp command and add key
true
Fetching compressed palette true from
https://www.colourlovers.com/api/palettes?keywords=true&format=json&numResults=100
Could not find palette true at COLOURlovers.com using keyword search
> mlp #3.6,8-9#!1#!3.4 key true
Map values for surface "7puy_A SES surface": minimum -28.5, mean -3.01,
maximum 23.98
Map values for surface "7puy_B SES surface": minimum -27.55, mean -2.97,
maximum 23.07
Map values for surface "7puy_C SES surface": minimum -28.01, mean -2.956,
maximum 23.35
Map values for surface "7puy_a SES surface": minimum -25.67, mean -2.715,
maximum 23.71
Map values for surface "7puy_b SES surface": minimum -25.12, mean -2.738,
maximum 23.07
Map values for surface "7puy_c SES surface": minimum -25.72, mean -2.755,
maximum 24.63
> key lipophilicity :-20 :0 :20 showTool true
> ui mousemode right "color key"
> undo
> ui mousemode right "mark maximum"
> hide #2 models
> close #2
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 2 models selected
> hide sel surfaces
> select subtract #1
6 models selected
> select add #3.4
39 atoms, 42 bonds, 1 residue, 1 model selected
> select add #3.6
78 atoms, 84 bonds, 2 residues, 3 models selected
> select add #3.8
117 atoms, 126 bonds, 3 residues, 4 models selected
> show sel surfaces
> transparency (#!3.4,6,8 & sel) 80
> ui tool show ViewDockX
Window position QRect(-1260,402 600x300) outside any known screen, using
primary screen
No suitable models found for ViewDockX
> select clear
> ui tool show Matchmaker
> select add #3.4
39 atoms, 42 bonds, 1 residue, 1 model selected
> select add #3.6
78 atoms, 84 bonds, 2 residues, 3 models selected
> select subtract #3.6
39 atoms, 42 bonds, 1 residue, 3 models selected
> select subtract #3.4
1 model selected
> select /A:27-35/B:27-35/C:27-35
186 atoms, 183 bonds, 27 residues, 1 model selected
> show sel surfaces
> select clear
> select /a:435-448/b:435-448/c:435-448
357 atoms, 369 bonds, 42 residues, 1 model selected
> show sel surfaces
> ui tool show "Side View"
> view orient
> ui mousemode right translate
> select clear
> select /a:435-448/b:435-448/c:435-448
357 atoms, 369 bonds, 42 residues, 1 model selected
> transparency (#!1 & sel) 50
> ui mousemode right "pick blobs"
> hide sel surfaces
> select /A:27-35/B:27-35/C:27-35
186 atoms, 183 bonds, 27 residues, 1 model selected
> hide sel surfaces
> select add #3.4
225 atoms, 225 bonds, 28 residues, 5 models selected
> select add #3.6
264 atoms, 267 bonds, 29 residues, 7 models selected
> select add #3.8
303 atoms, 309 bonds, 30 residues, 9 models selected
> select clear
> select #3.4
39 atoms, 42 bonds, 1 residue, 1 model selected
> select #3.4, #3.6, #3.8
Expected an objects specifier or a keyword
> select #3.4 #3.6 #3.8
117 atoms, 126 bonds, 3 residues, 3 models selected
> transparency (#!3.4,6,8 & sel) 50
> hide sel surfaces
> select clear
> 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
> undo
> toolshed show
> ui tool show "Find Cavities"
> kvfinder #1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 67, in find_cavities
run(self.session, "kvfinder %s" % concise_model_spec(self.session, structures,
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 52, in cmd_kvfinder
num_cavities, cavity_matrix = pyKVFinder.detect(struct_input, vertices,
grid_spacing,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect
from _pyKVFinder import _detect, _detect_ladj
ImportError: dlopen(/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/briannaclose/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/briannaclose/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))
ImportError: dlopen(/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so, 0x0002): tried:
'/Users/briannaclose/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib)),
'/System/Volumes/Preboot/Cryptexes/OS/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (no such file),
'/Users/briannaclose/Library/Application Support/ChimeraX/1.9/lib/python/site-
packages/_pyKVFinder.cpython-311-darwin.so' (missing LC_LOAD_DYLIB (must link
with at least libSystem.dylib))
File "/Users/briannaclose/Library/Application
Support/ChimeraX/1.9/lib/python/site-packages/pyKVFinder/grid.py", line 820,
in detect
from _pyKVFinder import _detect, _detect_ladj
See log for complete Python traceback.
> hide #3.4.1 models
> show #3.4.1 models
> ui tool show "Selection Inspector"
> select add #3.4.1
39 atoms, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> open "/Users/briannaclose/Documents/Davey/Screening Compounds/Computation
> Screen sdf files/output.json"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/__init__.py", line 129, in open
pae = alphafold_pae(session, file = path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1445, in alphafold_pae
structure = _guess_pae_associated_structure(session, file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1504, in
_guess_pae_associated_structure
structs = [m for m in session.models.list(type = AtomicStructure)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9-rc2024.11.27.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1505, in
if hasattr(m, 'filename') and dirname(m.filename) == dirname(pae_path)]
^^^^^^^^^^^^^^^^^^^
File "", line 152, in dirname
TypeError: expected str, bytes or os.PathLike object, not NoneType
TypeError: expected str, bytes or os.PathLike object, not NoneType
File "", line 152, in dirname
See log for complete Python traceback.
> log metadata #3.1
The model has no metadata
> log chains #3.1
> log metadata #3.1
The model has no metadata
> log chains #3.1
> open "/Users/briannaclose/Documents/Davey/Screening Compounds/Computation
> Screen sdf files/BC073 docking.sdf"
> select add #2
390 atoms, 378 bonds, 10 residues, 12 models selected
> ui tool show "Selection Inspector"
> log metadata #2.1
The model has no metadata
> log chains #2.1
> close #3
> hide #2.1 models
> hide #2.2 models
> undo
Undo failed, probably because structures have been modified.
> undo
> open "/Users/briannaclose/Desktop/Structures/BC073_GPC_Autodock Vina.cxs"
> format session
opened ChimeraX session
> help help:devel
> ui mousemode right translate
> open 9MHE fromDatabase pdb format mmcif
Summary of feedback from opening 9MHE fetched from pdb
---
notes | Fetching compressed mmCIF 9mhe from http://files.rcsb.org/download/9mhe.cif
Fetching CCD A1BK9 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/A1BK9/A1BK9.cif
Fetching CCD GAL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GAL/GAL.cif
Fetching CCD UNX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/UNX/UNX.cif
9mhe title:
Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0 [more
info...]
Chain information for 9mhe #2
---
Chain | Description | UniProt
A B C | Glycoprotein G1 | GLYC_LASSJ 1-259
D F H | 12.1F Heavy chain |
E G L | 12.1F Light chain |
a b c | Glycoprotein G2 | GLYC_LASSJ 260-491
Non-standard residues in 9mhe #2
---
A1BK9 — (4S)-3-(4-tert-
butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
UNX — unknown atom or ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #2
17594 atoms, 17091 bonds, 9 pseudobonds, 3015 residues, 2 models selected
> close
> open 9MHE format mmcif fromDatabase pdb
9mhe title:
Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0 [more
info...]
Chain information for 9mhe #1
---
Chain | Description | UniProt
A B C | Glycoprotein G1 | GLYC_LASSJ 1-259
D F H | 12.1F Heavy chain |
E G L | 12.1F Light chain |
a b c | Glycoprotein G2 | GLYC_LASSJ 260-491
Non-standard residues in 9mhe #1
---
A1BK9 — (4S)-3-(4-tert-
butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
UNX — unknown atom or ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 9MHE format mmcif fromDatabase pdb
9mhe title:
Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0 [more
info...]
Chain information for 9mhe #2
---
Chain | Description | UniProt
A B C | Glycoprotein G1 | GLYC_LASSJ 1-259
D F H | 12.1F Heavy chain |
E G L | 12.1F Light chain |
a b c | Glycoprotein G2 | GLYC_LASSJ 260-491
Non-standard residues in 9mhe #2
---
A1BK9 — (4S)-3-(4-tert-
butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
UNX — unknown atom or ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #2
> select /E/G/L
2537 atoms, 2514 bonds, 404 residues, 1 model selected
> hide target m
> undo
> hide sel atoms
> select /D/F/H
2994 atoms, 2964 bonds, 486 residues, 1 model selected
> hide sel atoms
> select ::name="A1BK9"
31 atoms, 34 bonds, 1 residue, 1 model selected
> select clear
> select add #1
17594 atoms, 17091 bonds, 9 pseudobonds, 3015 residues, 2 models selected
> cartoon (#!1 & sel)
> undo
> cartoon hide (#!1 & sel)
> hide (#!1 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!1 & sel-residues)
> show (#!1 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> undo
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select clear
> select ::name="A1BK9"
31 atoms, 34 bonds, 1 residue, 1 model selected
> show sel atoms
> hbonds sel reveal true
1 hydrogen bonds found
> select /c:422@CG
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> select /c:422@CB
1 atom, 1 residue, 1 model selected
> select /c:422@CB
1 atom, 1 residue, 1 model selected
> select /c:422
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> select /a:423
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> select /b:431
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select ::name="A1BK9"
31 atoms, 34 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> open /Users/briannaclose/Desktop/Structures/BC073_GNINA.sdf
PubChem entry 4857708
> close #2
> open "/Users/briannaclose/Documents/Davey/Escape Mutants/VSV-LASV-GP Escape
> mutants/7PUY_LASV_GP with matri.cxs" format session
opened ChimeraX session
> open /Users/briannaclose/Desktop/Structures/BC073_GNINA.sdf
PubChem entry 4857708
> select add #1
10395 atoms, 10659 bonds, 960 pseudobonds, 1266 residues, 4 models selected
> hide sel surfaces
> show sel atoms
> undo
> select add #1
10395 atoms, 10659 bonds, 960 pseudobonds, 1266 residues, 5 models selected
> hide sel surfaces
> show sel atoms
> style sel stick
Changed 10395 atom styles
> undo
> show sel cartoons
> hide sel atoms
> select clear
> set bgColor white
> select add #1
10395 atoms, 10659 bonds, 960 pseudobonds, 1266 residues, 4 models selected
> ~hbonds
> select clear
> select add #2.1
39 atoms, 42 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> select subtract #2.1
Nothing selected
> select add #2.7
39 atoms, 42 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> select #1/a:422
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> select #1/a:424
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/a:423
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/a:422
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/a:423
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> log metadata #2.7
The model has no metadata
> log chains #2.7
> open 9MHE fromDatabase pdb format mmcif
9mhe title:
Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0 [more
info...]
Chain information for 9mhe #4
---
Chain | Description | UniProt
A B C | Glycoprotein G1 | GLYC_LASSJ 1-259
D F H | 12.1F Heavy chain |
E G L | 12.1F Light chain |
a b c | Glycoprotein G2 | GLYC_LASSJ 260-491
Non-standard residues in 9mhe #4
---
A1BK9 — (4S)-3-(4-tert-
butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
UNX — unknown atom or ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> undo
> select add #4
17603 atoms, 17099 bonds, 9 pseudobonds, 3016 residues, 4 models selected
> close
> open /Users/briannaclose/Desktop/Structures/new_7PUY.pdb format pdb
Chain information for new_7PUY.pdb #1
---
Chain | Description
A B C | No description available
a b c | No description available
> select add #1
9840 atoms, 10065 bonds, 9 pseudobonds, 1224 residues, 2 models selected
> show sel cartoons
Computing secondary structure
> hide sel atoms
> open /Users/briannaclose/Desktop/Structures/BC073_GNINA.sdf
PubChem entry 4857708
> select clear
> open 9MHE fromDatabase pdb format mmcif
9mhe title:
Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0 [more
info...]
Chain information for 9mhe #3
---
Chain | Description | UniProt
A B C | Glycoprotein G1 | GLYC_LASSJ 1-259
D F H | 12.1F Heavy chain |
E G L | 12.1F Light chain |
a b c | Glycoprotein G2 | GLYC_LASSJ 260-491
Non-standard residues in 9mhe #3
---
A1BK9 — (4S)-3-(4-tert-
butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
UNX — unknown atom or ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #3
> view orient
> view
> view orient
> open 9MHE fromDatabase pdb format mmcif
9mhe title:
Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0 [more
info...]
Chain information for 9mhe #3
---
Chain | Description | UniProt
A B C | Glycoprotein G1 | GLYC_LASSJ 1-259
D F H | 12.1F Heavy chain |
E G L | 12.1F Light chain |
a b c | Glycoprotein G2 | GLYC_LASSJ 260-491
Non-standard residues in 9mhe #3
---
A1BK9 — (4S)-3-(4-tert-
butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
UNX — unknown atom or ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> volume planes z style image imageMode "full region"
No volumes specified
> view orient
> ui mousemode right "rotate slab"
> ui mousemode right "next docked"
> close #3
Drag select of 21 residues
Drag select of 133 residues
> select clear
> ui tool show Matchmaker
> open 9MHE fromDatabase pdb format mmcif
9mhe title:
Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0 [more
info...]
Chain information for 9mhe #3
---
Chain | Description | UniProt
A B C | Glycoprotein G1 | GLYC_LASSJ 1-259
D F H | 12.1F Heavy chain |
E G L | 12.1F Light chain |
a b c | Glycoprotein G2 | GLYC_LASSJ 260-491
Non-standard residues in 9mhe #3
---
A1BK9 — (4S)-3-(4-tert-
butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
UNX — unknown atom or ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!3 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker new_7PUY.pdb, chain A (#1) with 9mhe, chain A (#3), sequence
alignment score = 1042.7
RMSD between 168 pruned atom pairs is 0.882 angstroms; (across all 218 pairs:
2.703)
> show cartoons
> hide atoms
> hide #!2 models
> show #!2 models
> select add #2
351 atoms, 378 bonds, 9 residues, 10 models selected
> show sel atoms
> select subtract #2
Nothing selected
> select ::name="A1BK9"
31 atoms, 34 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right translate
> select add #2.7
70 atoms, 76 bonds, 2 residues, 2 models selected
> hbonds sel reveal true
2 hydrogen bonds found
> select #3/c:422@CA
1 atom, 1 residue, 1 model selected
> select #3/c:422
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> select #1/a:423@CA
1 atom, 1 residue, 1 model selected
> select #1/a:422
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/a:423
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> ui tool show "Side View"
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.8 models
> hide #2.9 models
> select clear
Drag select of 2 residues, 1 atoms
> view
> view sel
> view orient
> view sel
> hide #!3 models
> open "/Users/briannaclose/Desktop/Structures/BC073_GPC_Autodock Vina.cxs"
> format session
opened ChimeraX session
> ui mousemode right zoom
Drag select of 18 residues
Drag select of 3 residues
> select clear
> select add #3.8
39 atoms, 42 bonds, 1 residue, 1 model selected
> select add #3.6
78 atoms, 84 bonds, 2 residues, 2 models selected
> hbonds sel reveal true
2 hydrogen bonds found
> select #1/c:440
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/c:440
11 atoms, 11 bonds, 1 residue, 1 model selected
> select subtract #1/c:440
1 model selected
> select add #1/c:441
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> select add #3.4
51 atoms, 54 bonds, 2 residues, 3 models selected
> hbonds sel reveal true
5 hydrogen bonds found
> select clear
> open "/Users/briannaclose/Desktop/Structures/BC051_Autodock Vina.sdf"
> hide #!2 models
> show #!2 models
> hide #!3 models
> select add #3.1
39 atoms, 42 bonds, 1 residue, 1 model selected
> view sel
> hide #3.1 models
> show #3.1 models
> ui tool show "Side View"
> select clear
> view orient
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select add #2.1
29 atoms, 32 bonds, 1 residue, 1 model selected
> ui mousemode right select
> ui mousemode right translate
> hbonds sel reveal true
1 hydrogen bonds found
> select #1/B:144
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:256
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:257
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 3 models selected
> show sel surfaces
> select clear
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 2 models selected
> transparency (#!1 & sel) 30
> select clear
> select add #2.2
29 atoms, 32 bonds, 1 residue, 1 model selected
> view sel
> hbonds sel reveal true
0 hydrogen bonds found
> hide #2.3 models
> hide #2.4 models
> show #2.4 models
> hide #2.7 models
> select add #1
10424 atoms, 10691 bonds, 9 pseudobonds, 1267 residues, 15 models selected
> select subtract #2.2
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 20 models selected
> transparency (#!1 & sel) 0
> select /B:93
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 10 atom styles
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 15 models selected
> hide sel surfaces
> select /B:93
10 atoms, 10 bonds, 1 residue, 1 model selected
> show #2.3 models
> select add #2.3
39 atoms, 42 bonds, 2 residues, 3 models selected
> hide #2.2 models
> hbonds sel reveal true
4 hydrogen bonds found
> ~hbonds
> select add #1
10424 atoms, 10691 bonds, 9 pseudobonds, 1267 residues, 16 models selected
> select subtract #1
29 atoms, 32 bonds, 1 residue, 7 models selected
> hbonds sel reveal true
0 hydrogen bonds found
> select subtract #2.3
Nothing selected
> select add #2.4
29 atoms, 32 bonds, 1 residue, 1 model selected
> select add #1
10424 atoms, 10691 bonds, 9 pseudobonds, 1267 residues, 15 models selected
> select subtract #2.4
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 20 models selected
> show sel surfaces
> select clear
> ui mousemode right translate
> ui mousemode right zoom
> select clear
> view orient
> ui mousemode right translate
> select add #2.4
29 atoms, 32 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> select subtract #2.4
Nothing selected
> select add #2.5
29 atoms, 32 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
2 hydrogen bonds found
> select add #1
10424 atoms, 10691 bonds, 9 pseudobonds, 1267 residues, 7 models selected
> select subtract #2.5
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 12 models selected
> transparency (#!1 & sel) 50
> hide sel surfaces
> show sel surfaces
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 13 models selected
> select subtract #1
6 models selected
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 7 models selected
> select subtract #1
6 models selected
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 7 models selected
> select subtract #1
6 models selected
> select add #2.5
29 atoms, 32 bonds, 1 residue, 1 model selected
> hide #2.6 models
> hide #2.8 models
> select /c:256
Nothing selected
> select /c:356
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> select #1/c:387@CD1
1 atom, 1 residue, 1 model selected
> select #1/c:308@CD
1 atom, 1 residue, 1 model selected
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 9 models selected
> hide sel surfaces
> select clear
> hide #2.5 models
> show #2.6 models
> hbonds #2.1,3-4,6,9#!1 reveal true
976 hydrogen bonds found
> ~hbonds
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 8 models selected
> ~hbonds
> show sel cartoons
> hide sel atoms
> select clear
> select add #2.6
29 atoms, 32 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> select subtract #2.6
Nothing selected
> show #2.7 models
> select add #2.7
29 atoms, 32 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> select add #2
261 atoms, 288 bonds, 9 residues, 10 models selected
> hbonds sel & #2.1,3-4,6-7,9 reveal true
1 hydrogen bonds found
> show #2.5 models
> show #2.2 models
> show #2.8 models
> hbonds sel reveal true
3 hydrogen bonds found
> hide #!2 models
> show #!2 models
> select subtract #2
Nothing selected
> hide #2.5 models
> hide #2.7 models
> hide #2.8 models
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 8 models selected
> show sel surfaces
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 13 models selected
> select subtract #1
6 models selected
> select add #2.6
29 atoms, 32 bonds, 1 residue, 1 model selected
> select subtract #2.6
Nothing selected
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 7 models selected
> transparency (#!1 & sel) 20
> select clear
> select ::name="XYS"
57 atoms, 57 bonds, 6 residues, 1 model selected
> show sel atoms
> select ::name="BDP"
36 atoms, 36 bonds, 3 residues, 1 model selected
> show sel atoms
> select clear
> select add #2.1
29 atoms, 32 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> select add #2.9
58 atoms, 64 bonds, 2 residues, 2 models selected
> select subtract #2.9
29 atoms, 32 bonds, 1 residue, 1 model selected
> select subtract #2.1
Nothing selected
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 2 models selected
> transparency (#!1 & sel) 70
> select clear
> select add #2.9
29 atoms, 32 bonds, 1 residue, 1 model selected
> select subtract #2.9
Nothing selected
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> select clear
> open /Users/briannaclose/Desktop/Structures/BC051_GNINA.sdf
PubChem entry 6370397
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #5.1
29 atoms, 32 bonds, 1 residue, 1 model selected
> hide #2.6 models
> show #2.6 models
> hide #2.6 models
> show #2.6 models
> hide #2.6 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> hide #2.3 models
> hide #!2 models
> hide #5.2 models
> hide #5.3 models
> show #5.3 models
> hide #5.3 models
> show #5.3 models
> hide #5.4 models
> show #5.4 models
> hide #5.4 models
> hide #5.5 models
> show #5.5 models
> hide #5.5 models
> show #5.5 models
> hide #5.6 models
> show #5.6 models
> hide #5.7 models
> show #5.7 models
> hide #5.8 models
> show #5.8 models
> hide #5.9 models
> hbonds sel reveal true
0 hydrogen bonds found
> select add #5.2
58 atoms, 64 bonds, 2 residues, 2 models selected
> show #5.2 models
> hide #5.1 models
> select subtract #5.1
29 atoms, 32 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> show #5.4 models
> show #5.1 models
> select add #5
261 atoms, 288 bonds, 9 residues, 10 models selected
> show #5.9 models
> hbonds sel reveal true
5 hydrogen bonds found
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #5.1 models
> show #5.1 models
> hide #5.2 models
> hide #5.4 models
> show #5.4 models
> hide #5.1 models
> select subtract #5
Nothing selected
> select add #5.3
29 atoms, 32 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:234
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> select #1/a:362
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/a:362
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /a:363
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> select clear
> select ::name="NAG"
462 atoms, 471 bonds, 33 residues, 1 model selected
> hide sel atoms
> hide #5.6 models
> show #5.6 models
> select add #5.3
491 atoms, 503 bonds, 34 residues, 2 models selected
> hbonds sel reveal true
68 hydrogen bonds found
> undo
> select add #1
10395 atoms, 10659 bonds, 72 pseudobonds, 1266 residues, 3 models selected
> select subtract #1
6 models selected
> select add #5.6
29 atoms, 32 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> select subtract #5.6
Nothing selected
> select clear
> select add #3
351 atoms, 378 bonds, 9 residues, 10 models selected
> select subtract #4
351 atoms, 378 bonds, 9 residues, 11 models selected
> ~hbonds
> hide #5.3-9#!1 atoms
> select ::name="XYS"
57 atoms, 57 bonds, 6 residues, 1 model selected
> select ::name="BDP"
36 atoms, 36 bonds, 3 residues, 1 model selected
> show sel atoms
> select ::name="XYS"
57 atoms, 57 bonds, 6 residues, 1 model selected
> show sel atoms
> select clear
> hide #!5 models
> show #!5 models
> select add #5
261 atoms, 288 bonds, 9 residues, 10 models selected
> show sel & #5.3-9 atoms
> show #!2 models
> select clear
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 2 models selected
> show sel surfaces
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #2.1
29 atoms, 32 bonds, 1 residue, 1 model selected
> show sel surfaces
> open /Users/briannaclose/Desktop/Structures/BC038_GNINA.sdf
PubChem entry 4887555
> hide #!2 models
> select add #2
261 atoms, 288 bonds, 9 residues, 11 models selected
> select subtract #2
1 model selected
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 8 models selected
> hide sel surfaces
> select clear
> hide #!5 models
> select add #4.1
32 atoms, 36 bonds, 1 residue, 1 model selected
> select subtract #4.1
Nothing selected
> select add #4.1
32 atoms, 36 bonds, 1 residue, 1 model selected
> select add #4.2
64 atoms, 72 bonds, 2 residues, 2 models selected
> select subtract #4.1
32 atoms, 36 bonds, 1 residue, 1 model selected
> select add #4.3
64 atoms, 72 bonds, 2 residues, 2 models selected
> select subtract #4.3
32 atoms, 36 bonds, 1 residue, 1 model selected
> select add #4.4
64 atoms, 72 bonds, 2 residues, 2 models selected
> select subtract #4.4
32 atoms, 36 bonds, 1 residue, 1 model selected
> select add #4.5
64 atoms, 72 bonds, 2 residues, 2 models selected
> select subtract #4.5
32 atoms, 36 bonds, 1 residue, 1 model selected
> select add #4.6
64 atoms, 72 bonds, 2 residues, 2 models selected
> select subtract #4.6
32 atoms, 36 bonds, 1 residue, 1 model selected
> select add #4.7
64 atoms, 72 bonds, 2 residues, 2 models selected
> select subtract #4.7
32 atoms, 36 bonds, 1 residue, 1 model selected
> select add #4.8
64 atoms, 72 bonds, 2 residues, 2 models selected
> select subtract #4.8
32 atoms, 36 bonds, 1 residue, 1 model selected
> select add #4.9
64 atoms, 72 bonds, 2 residues, 2 models selected
> select subtract #4.9
32 atoms, 36 bonds, 1 residue, 1 model selected
> select add #4
288 atoms, 324 bonds, 9 residues, 10 models selected
> hbonds sel reveal true
19 hydrogen bonds found
> select subtract #4
Nothing selected
> hide #!4 models
> open /Users/briannaclose/Desktop/Structures/BC073_GNINA.sdf
PubChem entry 4857708
> select add #7.7
39 atoms, 42 bonds, 1 residue, 1 model selected
> select add #7
351 atoms, 378 bonds, 9 residues, 10 models selected
> select subtract #7
Nothing selected
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 8 models selected
> hide sel atoms
> select subtract #1
6 models selected
> select add #7.7
39 atoms, 42 bonds, 1 residue, 1 model selected
> select add #7.1
78 atoms, 84 bonds, 2 residues, 2 models selected
> select subtract #7.1
39 atoms, 42 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> open 9MHE format mmcif fromDatabase pdb
9mhe title:
Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0 [more
info...]
Chain information for 9mhe #8
---
Chain | Description | UniProt
A B C | Glycoprotein G1 | GLYC_LASSJ 1-259
D F H | 12.1F Heavy chain |
E G L | 12.1F Light chain |
a b c | Glycoprotein G2 | GLYC_LASSJ 260-491
Non-standard residues in 9mhe #8
---
A1BK9 — (4S)-3-(4-tert-
butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
UNX — unknown atom or ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close
> open 9MHE format mmcif fromDatabase pdb
9mhe title:
Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0 [more
info...]
Chain information for 9mhe #1
---
Chain | Description | UniProt
A B C | Glycoprotein G1 | GLYC_LASSJ 1-259
D F H | 12.1F Heavy chain |
E G L | 12.1F Light chain |
a b c | Glycoprotein G2 | GLYC_LASSJ 260-491
Non-standard residues in 9mhe #1
---
A1BK9 — (4S)-3-(4-tert-
butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
UNX — unknown atom or ion
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> save /Users/briannaclose/Desktop/Structures/9MHE.pdb relModel #1
Residue names longer than 4 characters; truncating
> close
> open /Users/briannaclose/Downloads/rank_1.pdb format pdb
Chain information for rank_1.pdb #1
---
Chain | Description
A B C | No description available
a b c | No description available
> select add #1
19547 atoms, 19783 bonds, 1225 residues, 1 model selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
> select subtract #1
Nothing selected
> select ::name="UNK"
51 atoms, 54 bonds, 1 residue, 1 model selected
> show sel atoms
> close
> open "/Users/briannaclose/Documents/Davey/Escape Mutants/VSV-LASV-GP Escape
> mutants/LASV_GP with matri.cxs" format session
> set bgColor transparent
opened ChimeraX session
> set bgColor white
> set bgColor #ffffff00
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide sel surfaces
> undo
> select add #1
10395 atoms, 10659 bonds, 9 pseudobonds, 1266 residues, 2 models selected
> show sel surfaces
> select subtract #1
6 models selected
> select add #1.1
9 pseudobonds, 1 model selected
> ui tool show "Build Structure"
> toolshed show
> ui tool show "Modeller Comparative"
Populating font family aliases took 75 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> delete solvent
> open "/Users/briannaclose/Desktop/Structures/BC051_Autodock Vina.sdf"
> "/Users/briannaclose/Desktop/Structures/BC073_GPC_Autodock Vina.cxs"
opened ChimeraX session
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411272016 (2024-11-27)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 2 days, 10 hours, 55 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LEN L27m-28:
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: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9rc202411272016
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.11
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.4
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
narwhals: 1.32.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.4
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 6.0.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.3
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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