![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7137 closed defect (can't reproduce)
Crash while user closing window
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000031479a000 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000316f9f000 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x0000000202ceb600 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2022-06-20 23:48:15.00 +0100","app_version":"1.3.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.3.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.3.1 (21E258)","incident_id":"93679404-B58D-40C3-835A-9D25F733449C","name":"ChimeraX"}
{
"uptime" : 2700000,
"procLaunch" : "2022-06-20 23:30:51.6142 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"procStartAbsTime" : 66994718364011,
"coalitionID" : 187786,
"osVersion" : {
"train" : "macOS 12.3.1",
"build" : "21E258",
"releaseType" : "User"
},
"captureTime" : "2022-06-20 23:48:12.7405 +0100",
"incident" : "93679404-B58D-40C3-835A-9D25F733449C",
"bug_type" : "309",
"pid" : 87920,
"procExitAbsTime" : 67019704717824,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"747C3F2E-A655-5C1F-A8FC-C212BAFBB3C9","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "CA582E41-11B6-6235-261E-4B953049E08A",
"wakeTime" : 46311,
"sleepWakeUUID" : "AD5C3827-F0D9-4245-8A8E-F389F41E1C01",
"sip" : "enabled",
"vmRegionInfo" : "0xc is not in any region. Bytes before following region: 4341108724\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102c01000-102c02000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x000000000000000c","rawCodes":[1,12],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000000c"},
"vmregioninfo" : "0xc is not in any region. Bytes before following region: 4341108724\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102c01000-102c02000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"asi" : {"AppKit":["Calling windowShouldClose: on the delegate for the QNSPanel 0x7fc7d3035df0"]},
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/cryosparc_P8_J39__localfilter.mrc
> format mrc
Opened cryosparc_P8_J39__localfilter.mrc as #1, grid size 128,128,128, pixel
1.96, shown at level 0.694, step 1, values float32
> set bgColor white
> lighting flat
> transparency 50
> open
> "/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Pta1/Pta1
> 1-322 AlphaFold.pdb" format pdb
Chain information for Pta1 1-322 AlphaFold.pdb #2
---
Chain | Description
A | No description available
> open
> "/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Swd2.2
> AlphaFold.pdb" format pdb
Swd2.2 AlphaFold.pdb title:
Alphafold V2.0 prediction for uncharacterized WD repeat-containing protein
C824.04 (Q9UT39) [more info...]
Chain information for Swd2.2 AlphaFold.pdb #3
---
Chain | Description | UniProt
A | uncharacterized WD repeat-containing protein C824.04 | YIQ4_SCHPO
> open
> "/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Ssu72
> AlphaFold.pdb" format pdb
Ssu72 AlphaFold.pdb title:
Alphafold V2.0 prediction for RNA polymerase II subunit A C-terminal domain
phosphatase SSU72 (O42868) [more info...]
Chain information for Ssu72 AlphaFold.pdb #4
---
Chain | Description | UniProt
A | RNA polymerase II subunit A C-terminal domain phosphatase SSU72 |
SSU72_SCHPO
> color #2 #42ec39 transparency 0
> color #3 #dd5de1 transparency 0
> color #4 #4f54ec transparency 0
> select #2
2563 atoms, 2608 bonds, 322 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,2.0204,0,1,0,124.02,0,0,1,123.79
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.17529,0.34208,0.92318,-3.7042,-0.66034,0.65465,-0.36796,122.1,-0.73023,-0.6741,0.11114,122.37
> view matrix models
> #2,-0.0021576,0.9985,-0.054758,0.084184,-0.60437,-0.044928,-0.79543,122.29,-0.7967,0.031378,0.60356,121.99
> view matrix models
> #2,0.90916,0.41595,-0.020325,2.3393,-0.19456,0.3811,-0.90383,124.56,-0.3682,0.82568,0.42741,125
> view matrix models
> #2,0.39483,0.90693,-0.14693,1.5433,-0.56486,0.1135,-0.81734,122.7,-0.7246,0.40571,0.5571,122.88
> view matrix models
> #2,0.83736,0.46915,-0.28058,2.768,-0.4161,0.21414,-0.88375,123.51,-0.35453,0.85676,0.37452,125.22
> view matrix models
> #2,-0.02707,0.99958,0.010577,-0.15178,-0.67212,-0.010368,-0.74037,121.98,-0.73995,-0.02715,0.67211,121.95
> view matrix models
> #2,0.6955,0.33015,-0.63819,2.9083,-0.64409,-0.10722,-0.7574,121.98,-0.31848,0.93782,0.13807,126
> view matrix models
> #2,0.47568,-0.85098,-0.22261,-0.48011,-0.65194,-0.17119,-0.73869,121.82,0.5905,0.49651,-0.63623,130.32
> view matrix models
> #2,0.857,0.46264,0.22694,1.6522,0.29906,-0.087889,-0.95018,125.72,-0.41965,0.88218,-0.21368,126.39
> view matrix models
> #2,-0.087521,0.94096,-0.32701,0.33752,-0.045813,-0.33173,-0.94226,124.16,-0.99511,-0.067486,0.072141,122.39
> view matrix models
> #2,0.58844,0.65253,-0.47742,2.62,0.038845,-0.61261,-0.78943,123.71,-0.80761,0.44599,-0.38583,124.83
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.58844,0.65253,-0.47742,2.3458,0.038845,-0.61261,-0.78943,115.82,-0.80761,0.44599,-0.38583,115.79
> view matrix models
> #2,0.58844,0.65253,-0.47742,75.15,0.038845,-0.61261,-0.78943,111.83,-0.80761,0.44599,-0.38583,52.946
> view matrix models
> #2,0.58844,0.65253,-0.47742,84.331,0.038845,-0.61261,-0.78943,126.58,-0.80761,0.44599,-0.38583,99.057
> view matrix models
> #2,0.58844,0.65253,-0.47742,116.55,0.038845,-0.61261,-0.78943,126.34,-0.80761,0.44599,-0.38583,93.831
> view matrix models
> #2,0.58844,0.65253,-0.47742,118.57,0.038845,-0.61261,-0.78943,129.65,-0.80761,0.44599,-0.38583,100.32
> ui tool show "Fit in Map"
Fit molecule Pta1 1-322 AlphaFold.pdb (#2) to map
cryosparc_P8_J39__localfilter.mrc (#1) using 2563 atoms
average map value = 0.9097, steps = 116
shifted from previous position = 1.61
rotated from previous position = 23.3 degrees
atoms outside contour = 684, contour level = 0.69429
Position of Pta1 1-322 AlphaFold.pdb (#2) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.34551033 0.82457607 -0.44799209 120.51797266
-0.15330928 -0.42137975 -0.89383185 128.59654208
-0.92580715 0.37750948 -0.01917589 102.60597416
Axis 0.75965297 0.28550447 -0.58430690
Axis point 0.00000000 -9.07352477 136.47947536
Rotation angle (degrees) 123.19722247
Shift along axis 68.31334455
> select #3
2716 atoms, 2788 bonds, 341 residues, 1 model selected
> view matrix models #3,1,0,0,-42.171,0,1,0,31.068,0,0,1,56.616
> view matrix models #3,1,0,0,119.27,0,1,0,129.74,0,0,1,168.14
> view matrix models #3,1,0,0,127.94,0,1,0,121.43,0,0,1,160.79
Fit molecule Swd2.2 AlphaFold.pdb (#3) to map
cryosparc_P8_J39__localfilter.mrc (#1) using 2716 atoms
average map value = 1.045, steps = 112
shifted from previous position = 4.98
rotated from previous position = 33.1 degrees
atoms outside contour = 498, contour level = 0.69429
Position of Swd2.2 AlphaFold.pdb (#3) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.88911050 0.43694405 -0.13624393 128.98728126
-0.36911474 0.86054295 0.35102726 122.89220580
0.27062303 -0.26181238 0.92640027 159.09373573
Axis -0.56159007 -0.37284215 -0.73865102
Axis point 83.79311509 29.09245924 0.00000000
Rotation angle (degrees) 33.06765611
Shift along axis -235.77212005
> select #4
1588 atoms, 1620 bonds, 197 residues, 1 model selected
> view matrix models #4,1,0,0,17.166,0,1,0,70.353,0,0,1,129
> view matrix models #4,1,0,0,110.16,0,1,0,118.73,0,0,1,142.6
> view matrix models #4,1,0,0,115.05,0,1,0,126.38,0,0,1,119.81
Fit molecule Ssu72 AlphaFold.pdb (#4) to map cryosparc_P8_J39__localfilter.mrc
(#1) using 1588 atoms
average map value = 1.119, steps = 168
shifted from previous position = 25.6
rotated from previous position = 57.4 degrees
atoms outside contour = 186, contour level = 0.69429
Position of Ssu72 AlphaFold.pdb (#4) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.55205240 0.75234070 -0.35947409 123.08233438
-0.80489991 0.59338242 0.00578293 139.88487803
0.21765634 0.28614819 0.93313715 99.68389577
Axis 0.16646343 -0.34266410 -0.92459247
Axis point 168.27263558 -89.87417745 0.00000000
Rotation angle (degrees) 57.36495427
Shift along axis -119.61179857
> view matrix models
> #4,0.55205,0.75234,-0.35947,120.51,-0.8049,0.59338,0.0057829,101.5,0.21766,0.28615,0.93314,103.82
Fit molecule Ssu72 AlphaFold.pdb (#4) to map cryosparc_P8_J39__localfilter.mrc
(#1) using 1588 atoms
average map value = 1.042, steps = 100
shifted from previous position = 7.56
rotated from previous position = 37.3 degrees
atoms outside contour = 376, contour level = 0.69429
Position of Ssu72 AlphaFold.pdb (#4) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.66729888 0.72873398 0.15381478 125.31053396
-0.64519000 0.66877250 -0.36942279 98.20808870
-0.37207803 0.14727566 0.91644302 108.61780077
Axis 0.33137988 0.33727660 -0.88115372
Axis point 207.73205515 -86.69392086 0.00000000
Rotation angle (degrees) 51.22547749
Shift along axis -21.06030018
> ~select #4
Nothing selected
> ui tool show XMAS
Unsupported evidence file format
Traceback (most recent call last):
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 285, in
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 443, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 456, in map_crosslinks
evidence = Evidence(evidence_file)
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'
File "/Users/alexau/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 38, in __init__
self.peptide_pairs = evidence.peptide_pairs
See log for complete Python traceback.
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/reports
2/uniprot-Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides.csv
Unique peptide pairs: 82 out of 82
Unique peptide pairs with pseudobonds: 21
Pseudobonds are stored in /Users/alexau/Downloads/reports 2/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_2,3,4.pb
Mapping information is stored in /Users/alexau/Downloads/reports 2/uniprot-
Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross-
linked_peptides_2,3,4.tsv
Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1).csv
Unique peptide pairs: 199 out of 199
Unique peptide pairs with pseudobonds: 23
Pseudobonds are stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1)_2,3,4.pb
Mapping information is stored in /Users/alexau/Downloads/uniprot-
Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides
(1)_2,3,4.tsv
> select #3
2716 atoms, 2788 bonds, 341 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.9093,0.40377,-0.10069,129.04,-0.34219,0.86319,0.37122,122.9,0.2368,-0.3031,0.92307,159.13
> view matrix models
> #3,0.57749,-0.39251,-0.71585,130.04,0.78483,0.50839,0.35438,124.06,0.22484,-0.76647,0.60164,159.81
> view matrix models
> #3,-0.38311,-0.71693,-0.58245,129.91,0.83931,-0.5335,0.10461,125.57,-0.38573,-0.44878,0.80611,158.99
> view matrix models
> #3,-0.79746,-0.54254,-0.26403,129.38,0.45729,-0.25797,-0.85108,125.1,0.39363,-0.79944,0.45382,159.98
> view matrix models
> #3,-0.86121,-0.23872,0.44869,128.82,0.064908,-0.92726,-0.36876,125.73,0.50408,-0.28846,0.81406,159.28
> view matrix models
> #3,-0.8612,-0.27344,0.42845,128.87,0.13223,-0.93446,-0.3306,125.77,0.49077,-0.22805,0.84092,159.19
Fit molecule Swd2.2 AlphaFold.pdb (#3) to map
cryosparc_P8_J39__localfilter.mrc (#1) using 2716 atoms
average map value = 1.012, steps = 60
shifted from previous position = 5.63
rotated from previous position = 4.08 degrees
atoms outside contour = 641, contour level = 0.69429
Position of Swd2.2 AlphaFold.pdb (#3) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
-0.83562147 -0.32038454 0.44619560 124.39440282
0.19000742 -0.93073393 -0.31246044 128.10443049
0.51539688 -0.17631818 0.83861669 161.44276676
Axis 0.25554584 -0.12989426 0.95803121
Axis point 30.03552555 80.73068953 0.00000000
Rotation angle (degrees) 164.55130269
Shift along axis 169.81565159
> view matrix models
> #3,-0.79267,-0.41969,0.4422,124.56,0.35771,-0.90752,-0.22011,128.16,0.49368,-0.016292,0.86949,161.2
> view matrix models
> #3,-0.70213,-0.23434,0.67239,124.32,-0.47551,-0.54856,-0.68773,127.24,0.53001,-0.8026,0.27373,162.4
> view matrix models
> #3,-0.66154,-0.37285,0.65065,124.54,0.28503,-0.92754,-0.24172,128.15,0.69363,0.025547,0.71988,161.28
> view matrix models
> #3,-0.62479,-0.43285,0.64982,124.65,0.4132,-0.88947,-0.19521,128.16,0.6625,0.14654,0.73459,161.09
> view matrix models
> #3,-0.22364,-0.81451,0.53531,125.43,-0.11979,-0.52209,-0.84444,127.43,0.96728,-0.25298,0.019189,161.93
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.22364,-0.81451,0.53531,132.33,-0.11979,-0.52209,-0.84444,127.83,0.96728,-0.25298,0.019189,158.79
Fit molecule Swd2.2 AlphaFold.pdb (#3) to map
cryosparc_P8_J39__localfilter.mrc (#1) using 2716 atoms
average map value = 1.071, steps = 88
shifted from previous position = 5.5
rotated from previous position = 34.7 degrees
atoms outside contour = 424, contour level = 0.69429
Position of Swd2.2 AlphaFold.pdb (#3) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
-0.01209748 -0.95321880 0.30203902 129.26106747
-0.55594668 -0.24465855 -0.79439631 121.79582858
0.83112992 -0.17752778 -0.52697907 158.62449314
Axis 0.68192911 -0.58489366 0.43917207
Axis point 0.00000000 95.19080151 67.91524617
Rotation angle (degrees) 153.10886839
Shift along axis 86.57272350
> select #2
2563 atoms, 2608 bonds, 20 pseudobonds, 322 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.53094,0.28132,-0.79935,121.21,0.70776,-0.66596,0.23573,128.62,-0.46602,-0.69091,-0.5527,103.93,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.53094,0.28132,-0.79935,125.56,0.70776,-0.66596,0.23573,147.28,-0.46602,-0.69091,-0.5527,107.6,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #2,0.53094,0.28132,-0.79935,113.68,0.70776,-0.66596,0.23573,142.28,-0.46602,-0.69091,-0.5527,102.71,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
Fit molecule Pta1 1-322 AlphaFold.pdb (#2) to map
cryosparc_P8_J39__localfilter.mrc (#1) using 2563 atoms
average map value = 0.9097, steps = 196
shifted from previous position = 11.3
rotated from previous position = 92.4 degrees
atoms outside contour = 684, contour level = 0.69429
Position of Pta1 1-322 AlphaFold.pdb (#2) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.34556411 0.82473498 -0.44765796 120.51990922
-0.15322066 -0.42105490 -0.89400011 128.59508978
-0.92580175 0.37752480 -0.01913502 102.60732002
Axis 0.75963812 0.28565405 -0.58425311
Axis point -0.00000000 -9.10711489 136.48340437
Rotation angle (degrees) 123.18286155
Shift along axis 68.33657980
> select #4
1588 atoms, 1620 bonds, 11 pseudobonds, 197 residues, 3 models selected
> view matrix models
> #4,0.6673,0.72873,0.15381,123.7,-0.64519,0.66877,-0.36942,94.797,-0.37208,0.14728,0.91644,112.43,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.67875,0.72387,0.12376,123.64,-0.59754,0.64235,-0.47993,94.582,-0.4269,0.2518,0.86854,112.14,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #4,0.99322,0.087684,-0.07633,124.35,-0.11612,0.77927,-0.61583,93.672,0.0054826,0.62052,0.78417,110.88,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #4,0.59842,-0.79276,0.11589,126.92,-0.64453,-0.56227,-0.5181,97.105,0.47589,0.23535,-0.84743,107.86,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #4,0.66152,-0.63887,0.39273,127.14,-0.74476,-0.62107,0.24416,98.948,0.087922,-0.45401,-0.88665,109.51,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0
Fit molecule Ssu72 AlphaFold.pdb (#4) to map cryosparc_P8_J39__localfilter.mrc
(#1) using 1588 atoms
average map value = 1.105, steps = 108
shifted from previous position = 2.5
rotated from previous position = 56.4 degrees
atoms outside contour = 319, contour level = 0.69429
Position of Ssu72 AlphaFold.pdb (#4) relative to
cryosparc_P8_J39__localfilter.mrc (#1) coordinates:
Matrix rotation and translation
0.64939981 -0.06208153 0.75790881 127.55306239
-0.07828310 -0.99682460 -0.01457611 102.01548721
0.75640706 -0.04986573 -0.65219765 108.84418931
Axis -0.90812078 0.03864516 -0.41692109
Axis point -0.00000000 53.95325634 24.56384825
Rotation angle (degrees) 178.88667145
Shift along axis -157.27062038
> ~select #4
Nothing selected
> ui tool show "Side View"
> hide #5 models
> show #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #5 models
> show #5 models
> hide #6 models
> hide #5 models
> show #5 models
> show #6 models
> ui mousemode right distance
> color #5 black models transparency 0
> color #5 #807d29 models transparency 0
> color #5 #bdba3d models transparency 0
> color #5 black models transparency 0
> color #5 #62601f models transparency 0
> color #5 #fffb52 models transparency 0
> color #5 black models transparency 0
> color #6 black models transparency 0
> color #5 #88862c models transparency 0
> color #5 #9f9c33 models transparency 0
> color #5 black models transparency 0
> hide #5 models
> hide #6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:136
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:173
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:173
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> ui mousemode right label
> ui mousemode right distance
> ui tool show Distances
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
> select #2/A:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:166
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 9 atom styles
> select #2/A:173
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:173
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 9 atom styles
> select #2/A:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 9 atom styles
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: AppleHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 16 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 12.3.1 (21E258)
Kernel Version: Darwin 21.4.0
Time since boot: 72 days 7:03
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-XMAS: 1.1.1
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
et-xmlfile: 1.1.0
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openpyxl: 3.0.10
openvr: 1.16.801
packaging: 21.0
pandas: 1.4.2
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
QtRangeSlider: 0.1.5
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
seaborn: 0.11.2
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash while user closing window |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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