![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Closed 11 months ago
#16328 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-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070001e31d000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001d31a000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001c317000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001b314000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001a311000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001930e000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001830b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700017308000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700016305000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700015302000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000142ff000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff85982ffc0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.dssp._dssp, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 58)
{"app_name":"ChimeraX","timestamp":"2024-11-18 20:04:27.00 -0600","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.5 (23F79)","roots_installed":0,"name":"ChimeraX","incident_id":"7C79743C-CA85-4F62-8FA1-3FA00ACEED3C"}
{
"uptime" : 99000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 3792,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-11-18 20:04:20.5890 -0600",
"codeSigningMonitor" : 0,
"incident" : "7C79743C-CA85-4F62-8FA1-3FA00ACEED3C",
"pid" : 81482,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-18 16:49:57.1100 -0600",
"procStartAbsTime" : 87815028991255,
"procExitAbsTime" : 99478312351489,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"E60D1225-B5CF-5D41-ACC9-083031FCBA76","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "90E39C74-BFE4-E0B0-E0AF-7936AEE17B24",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 16664,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "1EAB7FBF-145A-4A35-866E-583E9E70CB79",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4301398016\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100622000-100626000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":81482},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4301398016\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100622000-100626000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"queue":"com.apple.main-thread","instructionState":{"instructionStream":{"bytes":[139,69,192,72,133,192,116,20,240,131,40,1,117,14,72,139,125,192,232,215,158,2,0,235,3,72,137,195,72,141,125,232,232,7,148,2,0,72,137,223,232,119,139,2,0,102,46,15,31,132,0,0,0,0,0,15,31,0,85,72,137,229,65,87,65,86,83,72,131,236,88,73,137,255,72,139,5,1,27,5,0,72,139,12,7,139,73,4,72,139,124,7,8,72,139,7,255,144,104,1,0,0,242,15,17,69,176,232,122,247,251,255,138,72,16,246,193,1,117,12,76,139,53,139,9,5,0,233,56,1,0,0,72,139,64,8,199,69,144,2,0,0,0,15,87,192,15,17,69,148,199,69,164,0,0,0,0,72,137,69,168,72,141,125,216,72,141,117,144,232,32,151,2,0,72,139,93,216,72,141,21,230,13,3,0,72,141,125,184,190,8,0],"offset":96}},"frames":[{"imageOffset":33098,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":154},{"imageOffset":24253,"symbol":"pthread_kill","symbolLocation":262,"imageIndex":155},{"imageOffset":282792,"symbol":"raise","symbolLocation":24,"imageIndex":156},{"imageOffset":2540852,"symbol":"faulthandler_fatal_error","symbolLocation":388,"imageIndex":152},{"imageOffset":16349,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":157},{"imageOffset":0,"imageIndex":158},{"imageOffset":374118,"imageIndex":84},{"imageOffset":418292,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":394,"imageIndex":159},{"imageOffset":12933256,"symbol":"-[NSWindow 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===== Log before crash start =====
> set bgColor white
> cd
Current working directory is: /Users/elizabethmcfadden
> cd Desktop
Current working directory is: /Users/elizabethmcfadden/Desktop
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/elizabethmcfadden/Desktop/GnHGcfit-coot-2.pdb
Summary of feedback from opening /Users/elizabethmcfadden/Desktop/GnHGcfit-
coot-2.pdb
---
warnings | Start residue of secondary structure not found: SHEET 45 4545 PHE B 991 THR B1000 0
Cannot find LINK/SSBOND residue CYS (995 )
Cannot find LINK/SSBOND residue CYS (1048 )
Cannot find LINK/SSBOND residue CYS (1087 )
Chain information for GnHGcfit-coot-2.pdb #1
---
Chain | Description
A B | No description available
> color bychain
> open /Users/elizabethmcfadden/Desktop/GnBtet.cif
Summary of feedback from opening /Users/elizabethmcfadden/Desktop/GnBtet.cif
---
warnings | Unknown polymer entity '1' on line 36
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for GnBtet.cif #2
---
Chain | Description
A | No description available
> open /Users/elizabethmcfadden/Desktop/GnBtetfit.pdb
Summary of feedback from opening
/Users/elizabethmcfadden/Desktop/GnBtetfit.pdb
---
warning | Ignored bad PDB record found on line 784
Chain information for GnBtetfit.pdb #3
---
Chain | Description
A | No description available
> close #2
> dssp
> select #3/A:465
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel red
> show sel
> style sel sphere
Changed 32 atom styles
> select #3/A:466-500
520 atoms, 532 bonds, 72 residues, 1 model selected
> delete sel
> open /Users/elizabethmcfadden/Downloads/cryosparc_P8_J771_005_volume_map.mrc
Opened cryosparc_P8_J771_005_volume_map.mrc as #2, grid size 448,448,448,
pixel 0.832, shown at level 0.0235, step 2, values float32
> surface dust #2 size 8.32
> volume #2 level 0.05361
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #2 step 1
> volume #2 level 0.05583
> hide #!1 models
> hide #!2 models
> close #3
> show #!2 models
> show #!1 models
> hide atoms
> show atoms
> show cartoons
> ui tool show "Color Zone"
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule GnHGcfit-coot-2.pdb (#1) to map
cryosparc_P8_J771_005_volume_map.mrc (#2) using 6034 atoms
average map value = 0.1358, steps = 72
shifted from previous position = 1.89
rotated from previous position = 0.078 degrees
atoms outside contour = 1220, contour level = 0.055825
Position of GnHGcfit-coot-2.pdb (#1) relative to
cryosparc_P8_J771_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99999916 0.00004355 0.00129372 -0.22022671
-0.00004300 0.99999991 -0.00042150 0.01210849
-0.00129373 0.00042144 0.99999907 2.08939644
Axis 0.30960068 0.95033516 -0.03178856
Axis point 1611.88540793 0.00000000 141.81400268
Rotation angle (degrees) 0.07799884
Shift along axis -0.12309413
> color #2 #b2b2b278 models
> volume #2 level 0.0703
> hide #!2 models
> select #1/B:1039
4 atoms, 3 bonds, 1 residue, 1 model selected
> show #!2 models
> ui tool show "Side View"
> select #1/B:10181039
Nothing selected
> select #1/B:1018-1039
144 atoms, 143 bonds, 1 pseudobond, 21 residues, 2 models selected
> delete sel
> select #1/B:1091-1092
20 atoms, 21 bonds, 2 residues, 1 model selected
> delete sel
> volume #2 level 0.1028
> hide #!2 models
> select #1/B:982-990
57 atoms, 58 bonds, 9 residues, 1 model selected
> delete sel
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #1/B:962-976
116 atoms, 117 bonds, 15 residues, 1 model selected
> delete sel
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/B:694-702
70 atoms, 70 bonds, 9 residues, 1 model selected
> select #1/B:694-704
84 atoms, 84 bonds, 11 residues, 1 model selected
> select #1/B:694-703
76 atoms, 76 bonds, 10 residues, 1 model selected
> delete sel
> show #!2 models
> hide #!2 models
> show #!2 models
> fitmap #1 inMap #2
Fit molecule GnHGcfit-coot-2.pdb (#1) to map
cryosparc_P8_J771_005_volume_map.mrc (#2) using 5621 atoms
average map value = 0.1416, steps = 36
shifted from previous position = 0.0278
rotated from previous position = 0.0547 degrees
atoms outside contour = 1963, contour level = 0.10276
Position of GnHGcfit-coot-2.pdb (#1) relative to
cryosparc_P8_J771_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99999939 -0.00057084 0.00094622 -0.03726409
0.00057185 0.99999927 -0.00106370 -0.04355887
-0.00094561 0.00106424 0.99999899 1.86955978
Axis 0.69358343 0.61662222 0.37245007
Axis point 0.00000000 -1531.85551450 -412.99896532
Rotation angle (degrees) 0.08789297
Shift along axis 0.64361255
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #1/B:993-994
15 atoms, 14 bonds, 2 residues, 1 model selected
> delete sel
> show #!2 models
> open 6yrb
6yrb title:
Crystal structure of the tetramerization domain of the glycoprotein Gn (Andes
virus) at pH 7.5 [more info...]
Chain information for 6yrb #3
---
Chain | Description | UniProt
A B | Envelope polyprotein | Q9E006_9VIRU 375-484
C D | RNA (5'-D(*())-R(P*UP*UP*UP*())-3') |
Non-standard residues in 6yrb #3
---
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)
IOD — iodide ion
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)
6yrb mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open /Users/elizabethmcfadden/Desktop/GnBtet.cif
Summary of feedback from opening /Users/elizabethmcfadden/Desktop/GnBtet.cif
---
warnings | Unknown polymer entity '1' on line 36
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for GnBtet.cif #4
---
Chain | Description
A | No description available
> hide #!4 models
> show #!4 models
> close #4
> open /Users/elizabethmcfadden/Desktop/GnBtetfit.pdb
Summary of feedback from opening
/Users/elizabethmcfadden/Desktop/GnBtetfit.pdb
---
warning | Ignored bad PDB record found on line 784
Chain information for GnBtetfit.pdb #4
---
Chain | Description
A | No description available
> mmaker #3 to #4
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 GnBtetfit.pdb, chain A (#4) with 6yrb, chain A (#3), sequence
alignment score = 508
RMSD between 100 pruned atom pairs is 0.001 angstroms; (across all 100 pairs:
0.001)
> mmaker #3 to #4/A
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 GnBtetfit.pdb, chain A (#4) with 6yrb, chain A (#3), sequence
alignment score = 508
RMSD between 100 pruned atom pairs is 0.001 angstroms; (across all 100 pairs:
0.001)
> select #4/A:379-483
3012 atoms, 3059 bonds, 5 pseudobonds, 400 residues, 2 models selected
> select #4/A:379-483
3012 atoms, 3059 bonds, 5 pseudobonds, 400 residues, 2 models selected
> hide #!4 models
> select add #4
3016 atoms, 3062 bonds, 5 pseudobonds, 401 residues, 2 models selected
> select subtract #4
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> ui mousemode right select
Drag select of 123 atoms, 99 residues, 1 pseudobonds, 115 bonds
> delete sel
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #3 inMap #2
Fit molecule 6yrb (#3) to map cryosparc_P8_J771_005_volume_map.mrc (#2) using
927 atoms
average map value = 0.1335, steps = 60
shifted from previous position = 1.9
rotated from previous position = 0.269 degrees
atoms outside contour = 389, contour level = 0.10276
Position of 6yrb (#3) relative to cryosparc_P8_J771_005_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.99133360 -0.13114939 0.00758470 186.63562754
0.13112260 0.99135837 0.00392992 186.59675038
-0.00803456 -0.00290134 0.99996351 223.40848682
Axis -0.02599161 0.05942829 0.99789414
Axis point -1217.12034028 1548.92322160 0.00000000
Rotation angle (degrees) 7.55123629
Shift along axis 229.17618381
> show #!2 models
> show #!1 models
> select add #3
927 atoms, 893 bonds, 1 pseudobond, 168 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.32163,0.94431,0.069575,169.95,-0.94633,0.32305,-0.0098605,194.85,-0.031787,-0.062669,0.99753,225.3
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.32163,0.94431,0.069575,179.38,-0.94633,0.32305,-0.0098605,184.83,-0.031787,-0.062669,0.99753,225.73
> fitmap #3 inMap #2
Fit molecule 6yrb (#3) to map cryosparc_P8_J771_005_volume_map.mrc (#2) using
927 atoms
average map value = 0.04322, steps = 112
shifted from previous position = 5.45
rotated from previous position = 9.84 degrees
atoms outside contour = 723, contour level = 0.10276
Position of 6yrb (#3) relative to cryosparc_P8_J771_005_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.33784617 0.93911498 -0.06263415 178.57681797
-0.93432360 0.34266423 0.09808487 190.69106642
0.11357545 0.02538296 0.99320508 227.58200055
Axis -0.03860734 -0.09357366 -0.99486353
Axis point 204.17680110 -35.86791148 0.00000000
Rotation angle (degrees) 70.31445439
Shift along axis -251.15106868
> view matrix models
> #3,0.33785,0.93911,-0.062634,179.29,-0.93432,0.34266,0.098085,191.07,0.11358,0.025383,0.99321,226.24
> fitmap #3 inMap #2
Fit molecule 6yrb (#3) to map cryosparc_P8_J771_005_volume_map.mrc (#2) using
927 atoms
average map value = 0.0432, steps = 56
shifted from previous position = 1.58
rotated from previous position = 0.0177 degrees
atoms outside contour = 726, contour level = 0.10276
Position of 6yrb (#3) relative to cryosparc_P8_J771_005_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.33802452 0.93905311 -0.06259945 178.55907715
-0.93428867 0.34283131 0.09783348 190.68847263
0.11333188 0.02541584 0.99323206 227.58796521
Axis -0.03845910 -0.09343250 -0.99488254
Axis point 204.23402678 -35.89127082 0.00000000
Rotation angle (degrees) 70.30312282
Shift along axis -251.10701557
> view matrix models
> #3,0.33802,0.93905,-0.062599,181.91,-0.93429,0.34283,0.097833,189.43,0.11333,0.025416,0.99323,226.75
> fitmap #3 inMap #2
Fit molecule 6yrb (#3) to map cryosparc_P8_J771_005_volume_map.mrc (#2) using
927 atoms
average map value = 0.04628, steps = 152
shifted from previous position = 1.98
rotated from previous position = 1.96 degrees
atoms outside contour = 707, contour level = 0.10276
Position of 6yrb (#3) relative to cryosparc_P8_J771_005_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.32143689 0.94417985 -0.07213002 182.94578249
-0.93604979 0.32833449 0.12651984 190.21189000
0.14314026 0.02684915 0.98933816 225.14589114
Axis -0.05259291 -0.11359096 -0.99213461
Axis point 198.70046645 -36.77759390 0.00000000
Rotation angle (degrees) 71.36399847
Shift along axis -254.60303241
> view matrix models
> #3,0.32144,0.94418,-0.07213,180.24,-0.93605,0.32833,0.12652,188.2,0.14314,0.026849,0.98934,225.38
> fitmap #3 inMap #2
Fit molecule 6yrb (#3) to map cryosparc_P8_J771_005_volume_map.mrc (#2) using
927 atoms
average map value = 0.04882, steps = 92
shifted from previous position = 1.46
rotated from previous position = 2.62 degrees
atoms outside contour = 699, contour level = 0.10276
Position of 6yrb (#3) relative to cryosparc_P8_J771_005_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.28798475 0.95361628 -0.08764009 180.49629117
-0.94183139 0.29860120 0.15424321 188.01699502
0.17325827 0.03812250 0.98413833 224.81088034
Axis -0.06057925 -0.13610861 -0.98884003
Axis point 186.97243676 -33.23088714 0.00000000
Rotation angle (degrees) 73.41950351
Shift along axis -258.82705886
> view matrix models
> #3,0.28798,0.95362,-0.08764,185.21,-0.94183,0.2986,0.15424,170.41,0.17326,0.038122,0.98414,227.15
> view matrix models
> #3,0.28798,0.95362,-0.08764,186.85,-0.94183,0.2986,0.15424,187.9,0.17326,0.038122,0.98414,221.09
> view matrix models
> #3,0.28798,0.95362,-0.08764,187.2,-0.94183,0.2986,0.15424,186.14,0.17326,0.038122,0.98414,224.65
> fitmap #3 inMap #2
Fit molecule 6yrb (#3) to map cryosparc_P8_J771_005_volume_map.mrc (#2) using
927 atoms
average map value = 0.1335, steps = 96
shifted from previous position = 3.31
rotated from previous position = 14.4 degrees
atoms outside contour = 389, contour level = 0.10276
Position of 6yrb (#3) relative to cryosparc_P8_J771_005_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.13115007 0.99135482 0.00390940 186.59452581
-0.99132960 0.13117684 -0.00763364 186.09788078
-0.00808047 -0.00287435 0.99996323 223.40715346
Axis 0.00240038 0.00604716 -0.99997883
Axis point 200.50176195 -13.03373727 0.00000000
Rotation angle (degrees) 82.46423377
Shift along axis -221.82916351
> select subtract #3
Nothing selected
> fitmap #3 inMap #2
Fit molecule 6yrb (#3) to map cryosparc_P8_J771_005_volume_map.mrc (#2) using
927 atoms
average map value = 0.1335, steps = 48
shifted from previous position = 0.00423
rotated from previous position = 0.00163 degrees
atoms outside contour = 389, contour level = 0.10276
Position of 6yrb (#3) relative to cryosparc_P8_J771_005_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.13114049 0.99135617 0.00388894 186.59459397
-0.99133103 0.13116704 -0.00761638 186.09501000
-0.00806065 -0.00285641 0.99996344 223.40441352
Axis 0.00240072 0.00602684 -0.99997896
Axis point 200.49656836 -13.03648053 0.00000000
Rotation angle (degrees) 82.46478763
Shift along axis -221.83018711
> open
> /Users/elizabethmcfadden/Downloads/cryosparc_P8_J615_004_volume_map_sharp.mrc
Opened cryosparc_P8_J615_004_volume_map_sharp.mrc as #5, grid size
448,448,448, pixel 0.832, shown at level 0.033, step 2, values float32
> volume #5 level 0.04646
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #5 step 1
> volume #5 level 0.05871
> surface dust #2 size 8.32
> surface dust #5 size 8.32
> hide #!5 models
> show #!1,3 atoms
> hide #!1,3 atoms
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/elizabethmcfadden/Desktop/ANDVGnBase_single_fit.pdb models #3
> relModel #2
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/elizabethmcfadden/Desktop/GnGcfit.pdb models #1 relModel #2
> hide #!2 models
> open /Users/elizabethmcfadden/Desktop/ANDV_GnGc-singleprotfit-coot-3.pdb
Chain information for ANDV_GnGc-singleprotfit-coot-3.pdb #6
---
Chain | Description
A | No description available
B | No description available
> hide #!3 models
> hide #!1 models
> color #6 #bade86ff
> color bychain
> close #6
> open /Users/elizabethmcfadden/Desktop/ANDV_GnGc-singleprotfit-coot-3.pdb
Chain information for ANDV_GnGc-singleprotfit-coot-3.pdb #6
---
Chain | Description
A | No description available
B | No description available
> show #!5 models
> hide #!5 models
> show #!2 models
> volume #2 level 0.08563
> volume #2 level 0.02282
> ui tool show "Side View"
> color #6 #a48ad3ff
> hide #!2 models
> graphics silhouettes true
> open /Users/elizabethmcfadden/Desktop/ANDVtet_Ecto_renum.pdb
Chain information for ANDVtet_Ecto_renum.pdb #7
---
Chain | Description
A C E G | No description available
> close #7
> open
> "/Users/elizabethmcfadden/Library/Containers/net.whatsapp.WhatsApp/Data/tmp/documents/03F29F08-273F-486A-B042-112F9CBDB5B5/ANDV
> tetramer renumbered.pdb"
Chain information for ANDV tetramer renumbered.pdb #7
---
Chain | Description
A B C D | No description available
> mmaker #7 to #8
No 'to' model specified
> mmaker #7 to #6
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 ANDV_GnGc-singleprotfit-coot-3.pdb, chain A (#6) with ANDV tetramer
renumbered.pdb, chain A (#7), sequence alignment score = 2357.6
RMSD between 352 pruned atom pairs is 0.544 angstroms; (across all 473 pairs:
6.958)
> color #7 #7ca0d4ff
> hide #!6 models
> show #!6 models
> select #7/A:19-1138
8636 atoms, 8831 bonds, 1120 residues, 1 model selected
> select ~sel
41976 atoms, 42862 bonds, 15 pseudobonds, 5495 residues, 13 models selected
> select subtract #1
36370 atoms, 37113 bonds, 11 pseudobonds, 4771 residues, 11 models selected
> select subtract #2
36370 atoms, 37113 bonds, 11 pseudobonds, 4771 residues, 9 models selected
> select subtract #3
35443 atoms, 36220 bonds, 10 pseudobonds, 4603 residues, 7 models selected
> select subtract #4
32427 atoms, 33158 bonds, 5 pseudobonds, 4202 residues, 5 models selected
> select subtract #5
32427 atoms, 33158 bonds, 5 pseudobonds, 4202 residues, 3 models selected
> select subtract #6
25908 atoms, 26493 bonds, 3360 residues, 1 model selected
> delete sel
> mmaker #7 to #6
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 ANDV_GnGc-singleprotfit-coot-3.pdb, chain A (#6) with ANDV tetramer
renumbered.pdb, chain A (#7), sequence alignment score = 2357.6
RMSD between 352 pruned atom pairs is 0.544 angstroms; (across all 473 pairs:
6.958)
> select #7/A:1-374
2733 atoms, 2790 bonds, 356 residues, 1 model selected
> delete sel
> select #7/A:600-1088
3757 atoms, 3848 bonds, 489 residues, 1 model selected
> select #7/A:700-1088
2965 atoms, 3036 bonds, 389 residues, 1 model selected
> delete sel
> select #7/A:650-699
383 atoms, 392 bonds, 50 residues, 1 model selected
> delete sel
> select down
Nothing selected
> select #7/A:380-450
546 atoms, 553 bonds, 71 residues, 1 model selected
> mmaker sel to #6
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 ANDV_GnGc-singleprotfit-coot-3.pdb, chain A (#6) with ANDV tetramer
renumbered.pdb, chain A (#7), sequence alignment score = 309
RMSD between 66 pruned atom pairs is 0.400 angstroms; (across all 67 pairs:
0.560)
> select add #7
2555 atoms, 2609 bonds, 1 pseudobond, 325 residues, 2 models selected
> select subtract #7
Nothing selected
> show #!6-7 atoms
> color byhetero
> hide #!7 models
> select #6/A:481-497
128 atoms, 132 bonds, 17 residues, 1 model selected
> mmaker #7 to #6
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 ANDV_GnGc-singleprotfit-coot-3.pdb, chain A (#6) with ANDV tetramer
renumbered.pdb, chain A (#7), sequence alignment score = 1877
RMSD between 102 pruned atom pairs is 0.599 angstroms; (across all 119 pairs:
1.895)
> mmaker #7 to sel
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 ANDV_GnGc-singleprotfit-coot-3.pdb, chain A (#6) with ANDV tetramer
renumbered.pdb, chain A (#7), sequence alignment score = 91.3
RMSD between 16 pruned atom pairs is 0.469 angstroms; (across all 17 pairs:
1.077)
> show #!7 models
> select add #6
6519 atoms, 6665 bonds, 5 pseudobonds, 842 residues, 2 models selected
> select subtract #6
Nothing selected
> select #7/A:495-526
253 atoms, 259 bonds, 32 residues, 1 model selected
> select ~sel
18370 atoms, 18717 bonds, 16 pseudobonds, 2428 residues, 14 models selected
> select subtract #6
11851 atoms, 12052 bonds, 11 pseudobonds, 1586 residues, 12 models selected
> select subtract #5
11851 atoms, 12052 bonds, 11 pseudobonds, 1586 residues, 10 models selected
> select subtract #3
10924 atoms, 11159 bonds, 10 pseudobonds, 1418 residues, 8 models selected
> select subtract #4
7908 atoms, 8097 bonds, 5 pseudobonds, 1017 residues, 6 models selected
> select subtract #2
7908 atoms, 8097 bonds, 5 pseudobonds, 1017 residues, 4 models selected
> select subtract #1
2302 atoms, 2348 bonds, 1 pseudobond, 293 residues, 2 models selected
> delete sel
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/elizabethmcfadden/Desktop/GnTMAFfit.pdb models #7 relModel #2
> show #!2 models
> graphics silhouettes false
Window position QRect(1243,969 575x201) outside any known screen, using
primary screen
> volume #2 level 0.05609
> select add #7
253 atoms, 259 bonds, 32 residues, 1 model selected
> view matrix models
> #7,0.72089,0.22421,-0.65578,191.23,0.66966,0.018357,0.74244,176.85,0.1785,-0.97437,-0.13691,194.02
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.39309,0.59407,-0.70182,218.06,0.59671,0.4159,0.68627,197.81,0.69958,-0.68855,-0.191,192.91
> fitmap #7 inMap #2
Fit molecule ANDV tetramer renumbered.pdb (#7) to map
cryosparc_P8_J771_005_volume_map.mrc (#2) using 253 atoms
average map value = 0.04474, steps = 384
shifted from previous position = 4.12
rotated from previous position = 35.8 degrees
atoms outside contour = 185, contour level = 0.056093
Position of ANDV tetramer renumbered.pdb (#7) relative to
cryosparc_P8_J771_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.82594789 0.43965136 -0.35286933 202.96152863
0.40376300 -0.02450977 0.91453524 180.29066299
0.39342792 -0.89783403 -0.19775875 190.36314111
Axis -0.92451818 -0.38069801 -0.01830722
Axis point 0.00000000 130.47526160 57.15881694
Rotation angle (degrees) 101.42939997
Shift along axis -259.76294072
> view matrix models
> #7,0.70198,0.53804,-0.46663,209.6,0.52361,0.054221,0.85023,179.9,0.48276,-0.84118,-0.24366,190
> fitmap #7 inMap #2
Fit molecule ANDV tetramer renumbered.pdb (#7) to map
cryosparc_P8_J771_005_volume_map.mrc (#2) using 253 atoms
average map value = 0.04474, steps = 160
shifted from previous position = 0.386
rotated from previous position = 11.2 degrees
atoms outside contour = 185, contour level = 0.056093
Position of ANDV tetramer renumbered.pdb (#7) relative to
cryosparc_P8_J771_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.82587577 0.43953993 -0.35317682 202.95117731
0.40387634 -0.02405339 0.91449731 180.31006879
0.39346298 -0.89790093 -0.19738489 190.36783249
Axis -0.92446075 -0.38084301 -0.01819114
Axis point 0.00000000 130.52159281 57.16387921
Rotation angle (degrees) 101.40724286
Shift along axis -259.75323502
> view matrix models
> #7,0.77776,0.46132,-0.42693,204.27,0.45499,0.055435,0.88877,182.45,0.43368,-0.8855,-0.16678,190.32
> view matrix models
> #7,0.79416,0.46034,-0.39673,204.21,0.43648,0.022165,0.89944,181.47,0.42284,-0.88747,-0.18332,190.28
> fitmap #7 inMap #2
Fit molecule ANDV tetramer renumbered.pdb (#7) to map
cryosparc_P8_J771_005_volume_map.mrc (#2) using 253 atoms
average map value = 0.04473, steps = 128
shifted from previous position = 0.147
rotated from previous position = 3.72 degrees
atoms outside contour = 186, contour level = 0.056093
Position of ANDV tetramer renumbered.pdb (#7) relative to
cryosparc_P8_J771_005_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.82668511 0.43885252 -0.35213661 202.91595756
0.40330864 -0.02577066 0.91470105 180.23721319
0.39234407 -0.89818948 -0.19829724 190.37573896
Axis -0.92488554 -0.37981301 -0.01813349
Axis point 0.00000000 130.52057315 57.11136857
Rotation angle (degrees) 101.46044578
Shift along axis -259.58264855
> select subtract #7
Nothing selected
> select #7/A:495
6 atoms, 5 bonds, 1 residue, 1 model selected
> open
> "/Users/elizabethmcfadden/Library/Containers/net.whatsapp.WhatsApp/Data/tmp/documents/03F29F08-273F-486A-B042-112F9CBDB5B5/ANDV
> tetramer renumbered.pdb"
Chain information for ANDV tetramer renumbered.pdb #8
---
Chain | Description
A B C D | No description available
> delete #8/B/C/D
> mmaker #8 to #7
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 ANDV tetramer renumbered.pdb, chain A (#7) with ANDV tetramer
renumbered.pdb, chain A (#8), sequence alignment score = 4268.5
RMSD between 32 pruned atom pairs is 0.000 angstroms; (across all 32 pairs:
0.000)
> show sel atoms
> select add #7
253 atoms, 259 bonds, 32 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #8
8636 atoms, 8831 bonds, 1120 residues, 1 model selected
> show sel atoms
> select subtract #8
Nothing selected
> show #!5 models
> volume #5 level 0.03371
> hide #!5 models
> open
> /Users/elizabethmcfadden/Downloads/cryosparc_P8_J771_005_volume_map_half_A.mrc
Opened cryosparc_P8_J771_005_volume_map_half_A.mrc as #9, grid size
448,448,448, pixel 0.832, shown at level 0.154, step 2, values float32
> surface dust #2 size 8.32
> surface dust #9 size 8.32
> surface dust #2 size 8.32
> surface dust #9 size 8.32
> hide #!7 models
> hide #!6 models
> hide #8 models
> hide #!2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #9 step 1
> volume #9 level 0.09359
> close #9
> show #!2 models
> show #8 models
> hide #8 models
> show #!7 models
> show #!6 models
> show #8 models
> hide #!2 models
> select #8/A:522-625
833 atoms, 847 bonds, 104 residues, 1 model selected
> delete sel
> select #8/A:1-522
3856 atoms, 3937 bonds, 503 residues, 1 model selected
> delete sel
> show #!2 models
> hide #!2 models
> select #8/A:628
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/B:700
Nothing selected
> select #6/B:662
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!8 models
> select add #6
6519 atoms, 6665 bonds, 5 pseudobonds, 842 residues, 2 models selected
> select subtract #6
Nothing selected
> open /Users/elizabethmcfadden/Desktop/ANDV_GnGc-singleprotfit-coot-6.pdb
Chain information for ANDV_GnGc-singleprotfit-coot-6.pdb #9
---
Chain | Description
A | No description available
B | No description available
> hide #!6 models
> show #!6 models
> hide #!6-7,9 atoms
> show #!8 models
> hide #!8 models
===== Log before crash end =====
Log:
> set bgColor white
> cd
Current working directory is: /Users/elizabethmcfadden
> cd Desktop
Current working directory is: /Users/elizabethmcfadden/Desktop
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 5 days, 10 hours, 43 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 11 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 , 11 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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