id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16328	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
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"",
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  ""faultingThread"" : 0,
  ""threads"" : 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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
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX