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Opened 4 months ago
Closed 4 months ago
#18046 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-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x000000031b7db000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031a7cf000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003197c3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003187b7000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003177ab000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031679f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000315793000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000314787000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031377b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031276f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000311763000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f08c9f00 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, 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._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, PIL._imagingmath (total: 124)
{"app_name":"ChimeraX","timestamp":"2025-06-21 22:46:56.00 -0500","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.5 (24F74)","roots_installed":0,"name":"ChimeraX","incident_id":"9D385268-48F4-48ED-9EBB-3142D328F9D0"}
{
"uptime" : 320000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir10,1",
"coalitionID" : 4868,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-06-21 22:46:29.2389 -0500",
"codeSigningMonitor" : 1,
"incident" : "9D385268-48F4-48ED-9EBB-3142D328F9D0",
"pid" : 16571,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-21 19:06:23.8030 -0500",
"procStartAbsTime" : 7435389773775,
"procExitAbsTime" : 7750787958776,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"57A90D80-F304-5878-AA3D-33EE15DFFA9E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C26E1A6D-208C-0431-BC9F-D1252B1481C3",
"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" : "E8DBF600-6B0F-4813-9F99-AF230E8CEDBE",
"wakeTime" : 3,
"sleepWakeUUID" : "9C194F45-36EF-4AAC-AF70-89D1BB2D3F63",
"sip" : "enabled",
"vmRegionInfo" : "0x168 is not in any region. Bytes before following region: 4341087896\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102bfc000-102c00000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.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":16571},
"vmregioninfo" : "0x168 is not in any region. Bytes before following region: 4341087896\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102bfc000-102c00000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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{
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"size" : 98304,
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"path" : "\/Users\/USER\/Library\/Application Support\/ChimeraX\/*\/_map_mask.cpython-311-darwin.so",
"name" : "_map_mask.cpython-311-darwin.so"
},
{
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"name" : "contour_thread.cpython-311-darwin.so"
},
{
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"uuid" : "8abbdcef-1901-3d4b-9e6b-a38214b79214",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
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"name" : "libsystem_platform.dylib"
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"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.60.5"
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"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
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"size" : 288576,
"uuid" : "8bf83cda-8db1-3d46-94b0-d811bd77e078",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
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===== Log before crash start =====
Startup Messages
---
warning | Registration file '/Users/kjyeol/Library/Application Support/ChimeraX/registration' has expired
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kjyeol/Desktop/Jason McLellan Lab/KSHV
> gB/250616_KSHV_gB_Trimer_refinement_isolde_5.pdb"
Chain information for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb #1
---
Chain | Description
A B C | No description available
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> set bgColor white
> graphics silhouettes true
> ui tool show "Side View"
> lighting soft
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C
Alignment identifier is 1
> select add #1
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 2 models selected
> surface (#!1 & sel)
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_A SES
surface #1.2: minimum, -14.82, mean 0.35, maximum 18.91
Coulombic values for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_B SES
surface #1.3: minimum, -17.29, mean 0.34, maximum 19.78
Coulombic values for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_C SES
surface #1.4: minimum, -15.02, mean 0.36, maximum 15.22
To also show corresponding color key, enter the above coulombic command and
add key true
> 25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
Unknown command: 25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
> selcte #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
Unknown command: selcte #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411,
539, 593, 669
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
573 atoms, 573 bonds, 33 residues, 1 model selected
> show sel cartoons
> surface hidePatches (#!1 & sel)
> select add #1
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 5 models selected
> select subtract #1
3 models selected
> select add #1
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 2 models selected
> color sel byhetero
> style sel stick
Changed 27591 atom styles
> surface style solid
> cartoon (#!1 & sel)
> transparency (#!1 & sel) 100
> ui mousemode right select
> select clear
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
573 atoms, 573 bonds, 33 residues, 1 model selected
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
573 atoms, 573 bonds, 33 residues, 1 model selected
> color sel yellow
> select clear
> zone #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
> distance 8
Expected a keyword
> zone #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
Must specify a single residue, 33 specified
> zone #1:93
Must specify a single residue, 3 specified
> zone #1:93
Must specify a single residue, 3 specified
> zone #1:93
Must specify a single residue, 3 specified
> zone :100 distance 8
Expected a keyword
> zone :93 distance 8
Expected a keyword
> zone :#1:93 distance 8
Expected an atoms specifier or a keyword
> select #1:100 show sel target a
> select /C:282@O
1 atom, 1 residue, 1 model selected
> show sel target a
> show sel atoms
> close
> open "/Users/kjyeol/Desktop/Jason McLellan Lab/KSHV
> gB/250616_KSHV_gB_Trimer_refinement_isolde_5.pdb" format pdb
Chain information for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb #1
---
Chain | Description
A B C | No description available
> lighting soft
> select /A:102
22 atoms, 21 bonds, 1 residue, 1 model selected
> zone 100
Expected an atoms specifier or a keyword
> zone :100
Must specify a single residue, 3 specified
> show #1:100 show :100 show #1:100 select zone :100 5 residues true
Selected 897 atoms
> select zone :100 5 residues true
Selected 897 atoms
> show sel atoms
> color sel byhetero
> select add #1
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 2 models selected
> show sel atoms
> select clear
> undo
> select zone :25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669 5
> residues true
Selected 6615 atoms
> select zone :25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669 5
> residues true:show sel atoms
Invalid "residues" argument: Expected true or false (or 1 or 0)
> select zone :25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669 5
> residues true
Selected 6615 atoms
> show sel atoms
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
573 atoms, 573 bonds, 33 residues, 1 model selected
> color select yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
573 atoms, 573 bonds, 33 residues, 1 model selected
> color sel yellow
> show sel atoms
> select clear
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_A SES
surface #1.2: minimum, -14.82, mean 0.35, maximum 18.91
Coulombic values for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_B SES
surface #1.3: minimum, -17.29, mean 0.34, maximum 19.78
Coulombic values for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_C SES
surface #1.4: minimum, -15.02, mean 0.36, maximum 15.22
To also show corresponding color key, enter the above coulombic command and
add key true
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
573 atoms, 573 bonds, 33 residues, 1 model selected
> color sel yellow
> undo
> surface hidePatches (#!1 & sel)
> undo
> select add #1
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 5 models selected
> surface hidePatches (#!1 & sel)
> select clear
> select /A:396
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:395
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:398
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:103
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> open "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Data/cyro-
> EM/cryosparc_P986_J84_map_sharp__DeepEMhancer_tightmask.mrc"
Opened cryosparc_P986_J84_map_sharp__DeepEMhancer_tightmask.mrc as #2, grid
size 384,384,384, pixel 0.933, shown at level 0.000107, step 2, values float32
> volume #2 level 0.09834
> volume #2 step 1
> surface dust #2 size 9.33
> transparency sel 50
> transparency sel 0
> select add #1
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 3 models selected
> select add #2
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 7 models selected
> select subtract #1
5 models selected
> transparency sel 50
> select clear
> volume #2 level 0.06262
> volume #2 level 0.04178
> zoom #1:93
Expected a number > 0 or a keyword
> zoom :93
Expected a number > 0 or a keyword
> select add #1
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 2 models selected
> zoom :93
Expected a number > 0 or a keyword
> zoom :93
Expected a number > 0 or a keyword
> zoom :93
Expected a number > 0 or a keyword
> zoom :#1:93
Expected a number > 0 or a keyword
> zoom :100
Expected a number > 0 or a keyword
> zoom :100
Expected a number > 0 or a keyword
> zoom :100
Expected a number > 0 or a keyword
> view #1:100
> view #93
No objects specified.
> select clear
> view #1:93
> select #1:93
51 atoms, 51 bonds, 3 residues, 1 model selected
> hide #!2 models
> select /C:481
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /C:477
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /C:93
17 atoms, 17 bonds, 1 residue, 1 model selected
> show #!2 models
> volume #2 step 2
> hide #!2 models
> select /C:477
15 atoms, 14 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> select /C:474
17 atoms, 16 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> select /C:481
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/C
9197 atoms, 9307 bonds, 1 pseudobond, 583 residues, 2 models selected
> coulombic sel
Coulombic values for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_C SES
surface #1.4: minimum, -15.02, mean 0.36, maximum 15.22
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_C SES surface,
1271 of 785520 triangles, cap far, 49 of 11591 triangles, 7 atoms, 6 residues,
7 bonds
> select clear
> undo
> select add #1
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 5 models selected
> surface hidePatches (#!1 & sel)
> select clear
> select /A:85
10 atoms, 9 bonds, 1 residue, 1 model selected
Drag select of 1 atoms, 4 residues
> select clear
Drag select of 1 residues
> select clear
> close
> open "/Users/kjyeol/Desktop/Jason McLellan Lab/KSHV
> gB/250616_KSHV_gB_Trimer_refinement_isolde_5.pdb" format pdb
Chain information for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb #1
---
Chain | Description
A B C | No description available
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
573 atoms, 573 bonds, 33 residues, 1 model selected
> color sel yellow
> show sel atoms
> select clear
> select zone :25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669 5
> residues true
Selected 6615 atoms
> show sel atoms
> select clear
> select /A:91
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:469
24 atoms, 23 bonds, 1 residue, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_A SES
surface #1.2: minimum, -14.82, mean 0.35, maximum 18.91
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_A SES surface,
1782 of 782632 triangles, 389 atoms, 115 residues, 358 bonds
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_A SES
surface #1.2: minimum, -14.82, mean 0.35, maximum 18.91
Coulombic values for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_B SES
surface #1.3: minimum, -17.29, mean 0.34, maximum 19.78
Coulombic values for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb_C SES
surface #1.4: minimum, -15.02, mean 0.36, maximum 15.22
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #1
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 5 models selected
> select subtract #1
3 models selected
> select add #1
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 2 models selected
> select subtract #1
3 models selected
> select add #1
27591 atoms, 27921 bonds, 3 pseudobonds, 1749 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> select clear
> select /B:474
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
573 atoms, 573 bonds, 33 residues, 1 model selected
> hbonds sel reveal true
66 hydrogen bonds found
> select clear
> select /B:669
21 atoms, 21 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
2 hydrogen bonds found
> select /B:651
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671
561 atoms, 561 bonds, 33 residues, 1 model selected
> color (#!1 & sel) yellow
> hbonds sel reveal true
66 hydrogen bonds found
> select /B:671
17 atoms, 17 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
2 hydrogen bonds found
> select /C:586
14 atoms, 13 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> hbonds sel reveal true
1 hydrogen bonds found
> select /B:671@CB
1 atom, 1 residue, 1 model selected
> select clear
> select /B:671
17 atoms, 17 bonds, 1 residue, 1 model selected
> select /C:586
14 atoms, 13 bonds, 1 residue, 1 model selected
> open "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Data/cyro-
> EM/cryosparc_P986_J84_map_sharp__DeepEMhancer_tightmask.mrc"
Opened cryosparc_P986_J84_map_sharp__DeepEMhancer_tightmask.mrc as #2, grid
size 384,384,384, pixel 0.933, shown at level 0.000107, step 2, values float32
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> surface dust #2 size 9.33
> transparency sel 50
> select add #1
27591 atoms, 27921 bonds, 4 pseudobonds, 1749 residues, 4 models selected
> select subtract #1
3 models selected
> select add #2
2 models selected
> transparency sel 50
> volume #2 level 0.07155
> hide #!1 models
> show #!1 models
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb
---
Chain | Description
1.2/A 1.2/B 1.2/C | No description available
ISOLDE: created disulfide bonds between the following residues:
A191-C635; A635-B191; B635-C191; A105-C628; A628-B105; B628-C105
> clipper associate #2 toModel #1
Opened cryosparc_P986_J84_map_sharp__DeepEMhancer_tightmask.mrc as #1.1.1.1,
grid size 384,384,384, pixel 0.933, shown at step 1, values float32
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671
561 atoms, 561 bonds, 33 residues, 1 model selected
> isolde sim start /C:586
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> close
> open "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Data/cyro-
> EM/cryosparc_P986_J84_map_sharp__DeepEMhancer_tightmask.mrc"
Opened cryosparc_P986_J84_map_sharp__DeepEMhancer_tightmask.mrc as #1, grid
size 384,384,384, pixel 0.933, shown at level 0.000107, step 2, values float32
> surface dust #1 size 9.33
> open "/Users/kjyeol/Desktop/Jason McLellan Lab/KSHV
> gB/250616_KSHV_gB_Trimer_refinement_isolde_5.pdb"
Chain information for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb #2
---
Chain | Description
A B C | No description available
> surface dust #1 size 9.33
> transparency 50
> volume #1 level 0.04178
> hide #!2 models
> select add #1
2 models selected
> select subtract #1
Nothing selected
> show #!2 models
> hide #!1 models
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669
Nothing selected
> color select yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671
Nothing selected
> color select yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671
Nothing selected
> select #2:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671
561 atoms, 561 bonds, 33 residues, 1 model selected
> select #2:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671
561 atoms, 561 bonds, 33 residues, 1 model selected
> color select yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #2:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671
561 atoms, 561 bonds, 33 residues, 1 model selected
> color sel yellow
> show sel atoms
> hbonds sel reveal true
66 hydrogen bonds found
> show sel atoms
> select zone :25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671 5
Selected 3509 atoms, 1 surfaces
> select zone :25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671 5
> residues true
Selected 6780 atoms, 1 surfaces
> show sel atoms
> ui mousemode right select
> select clear
> lighting soft
> view
> select clear
> show #!1 models
> hide #!1 models
> select /C:88
14 atoms, 13 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select /A:91
22 atoms, 21 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> select /B:484
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /B:336
17 atoms, 17 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
2 hydrogen bonds found
> select zone :276
Missing or invalid "range" argument: Expected a number
> view #1:276
No objects specified.
> view #2:276
> select #2:276
51 atoms, 51 bonds, 3 residues, 1 model selected
> select /C:90
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:336@CA
1 atom, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> select /A:549
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:586
14 atoms, 13 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> hbonds sel relax true
1 hydrogen bonds found
> select /C:671
17 atoms, 17 bonds, 1 residue, 1 model selected
> hbonds sel relax true
2 hydrogen bonds found
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb
---
Chain | Description
2.2/A 2.2/B 2.2/C | No description available
ISOLDE: created disulfide bonds between the following residues:
A628-B105; B635-C191; B628-C105; A191-C635; A105-C628; A635-B191
> clipper associate #1 toModel #2
Opened cryosparc_P986_J84_map_sharp__DeepEMhancer_tightmask.mrc as #2.1.1.1,
grid size 384,384,384, pixel 0.933, shown at step 1, values float32
> isolde sim start /A:586
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:549-551,583-589
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hbonds sel reveal true
23 hydrogen bonds found
> hbonds sel reveal true
0 hydrogen bonds found
> isolde sim start /C:671
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hbonds sel reveal true
13 hydrogen bonds found
> isolde sim start /C:668-674
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:665-677
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hbonds sel reveal true
1 hydrogen bonds found
> hbonds sel reveal true
0 hydrogen bonds found
> isolde sim start /A:85
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:336
ISOLDE: started sim
> hbonds sel reveal true
14 hydrogen bonds found
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #2:593
51 atoms, 51 bonds, 3 residues, 1 model selected
> select #2:593
51 atoms, 51 bonds, 3 residues, 1 model selected
> view sel
> hbonds sel reveal true
6 hydrogen bonds found
> select #2:593
51 atoms, 51 bonds, 3 residues, 1 model selected
> view sel
> hbonds sel reveal true
0 hydrogen bonds found
> close
> open "/Users/kjyeol/Desktop/Jason McLellan Lab/KSHV
> gB/250616_KSHV_gB_Trimer_refinement_isolde_5.pdb" format pdb
Chain information for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb #1
---
Chain | Description
A B C | No description available
> lighting soft
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671
561 atoms, 561 bonds, 33 residues, 1 model selected
> color sel yellow
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671
561 atoms, 561 bonds, 33 residues, 1 model selected
> color sel yellow
> show sel atoms
> select #1:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671
561 atoms, 561 bonds, 33 residues, 1 model selected
> color sel yellow
> show sel atoms
> hbonds sel reveal true
66 hydrogen bonds found
> select zone :25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 671 5
Selected 3509 atoms
> residues true;show sel atoms
Unknown command: residues true;show sel atoms
> undo
> select zone :25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669 5
Selected 3553 atoms
> residues true;show sel atoms
Unknown command: residues true;show sel atoms
> select zone:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669 5
Expected an objects specifier or a keyword
> select zone:25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669 5
Expected an objects specifier or a keyword
> select zone :25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669 5
Selected 3553 atoms
> select zone :25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669 5
Selected 3553 atoms
> show sel atoms
> ui mousemode right select
> select clear
> view
> select add #1
27591 atoms, 27921 bonds, 69 pseudobonds, 1749 residues, 3 models selected
> view
> select clear
> select /A:477
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:478
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:481
24 atoms, 23 bonds, 1 residue, 1 model selected
> select zone :25, 93, 108, 150, 276, 331, 336, 382, 392, 411, 539, 593, 669 5
> residues true
Selected 6615 atoms
> show sel atoms
> select clear
> select /A:88
14 atoms, 13 bonds, 1 residue, 1 model selected
> select clear
> select /C:586
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> hbonds sel reveal true
1 hydrogen bonds found
Drag select of 26 residues
> select /C:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> select clear
> select /C:129
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /C:128
24 atoms, 23 bonds, 1 residue, 1 model selected
> select zone :129 5 residues true
Selected 261 atoms
> show sel atoms
> select zone :129 10 residues true
Selected 729 atoms
> show sel atoms
> select clear
> select /A:689
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /A:690
25 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select /B:690
25 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /C:690
25 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> open "/Users/kjyeol/Library/CloudStorage/Box-Box/McLellan Lab/Manuscripts/In
> Progress/KSHV_gB/Data/cyro-
> EM/cryosparc_P167_J111_007_volume_map_deepemhancer.mrc"
Opened cryosparc_P167_J111_007_volume_map_deepemhancer.mrc as #2, grid size
384,384,384, pixel 0.933, shown at level 0.00141, step 2, values float32
> surface dust #2 size 9.33
> transparency 50
> volume #2 step 1
> volume #2 level 0.1668
> volume #2 level 0.08919
> select clear
> volume #2 level 0.06893
> open /Users/kjyeol/Library/CloudStorage/Box-
> Box/JeongRyeolKim/project/KSHVgB/AF3/250426_KSHV_gB_FL_Trimer_a604a_2/250426_KSHV_gB_FL_Trimer_a604a_2_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
250426_KSHV_gB_FL_Trimer_a604a_2_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#3
---
Chain | Description
A B C | No description available
Computing secondary structure
> hide #!2 models
> hide #!1 models
> select #3:731
30 atoms, 30 bonds, 3 residues, 1 model selected
> show sel atoms
> show #!1 models
> hide #3 models
> select add #3
19827 atoms, 20250 bonds, 2535 residues, 1 model selected
> select #1/C:308
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/C:108
17 atoms, 17 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
3 hydrogen bonds found
===== Log before crash end =====
Log:
Startup Messages
---
warning | Registration file '/Users/kjyeol/Library/Application Support/ChimeraX/registration' has expired
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kjyeol/Desktop/Jason McLellan Lab/KSHV
> gB/250616_KSHV_gB_Trimer_refinement_isolde_5.pdb"
Chain information for 250616_KSHV_gB_Trimer_refinement_isolde_5.pdb #1
---
Chain | Description
A B C | No description available
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1
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 Air
Model Identifier: MacBookAir10,1
Model Number: MGN63KH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 5 days, 11 hours, 53 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LF27T35:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Television: Yes
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.24.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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
more-itertools: 10.3.0
msgpack: 1.0.8
narwhals: 1.35.0
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: 2.2.5
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
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
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 4 months 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 , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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