![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#6512 closed defect (duplicate)
Calling _cpp_modified failed
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| 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: 1.4.dev202203290305 (2022-03-29 03:05:53 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x000070001099e000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001172d2600 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 1407 in delete
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 124 in delete
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/models.py", line 898 in close
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/std_commands/close.py", line 32 in close
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/model_panel/tool.py", line 397 in close
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/model_panel/tool.py", line 87 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 340000,
"procLaunch" : "2022-03-31 13:02:41.1959 +0200",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro11,4",
"procStartAbsTime" : 340427172121612,
"coalitionID" : 41687,
"osVersion" : {
"train" : "macOS 12.2.1",
"build" : "21D62",
"releaseType" : "User"
},
"captureTime" : "2022-03-31 13:15:40.7914 +0200",
"incident" : "176A7C55-0DC0-47CD-8903-F94B83F07303",
"bug_type" : "309",
"pid" : 25793,
"procExitAbsTime" : 341206790438662,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"E83DAE97-A2F9-5898-A533-DC761BE11870","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E94387A5-3CA6-D3D5-989B-BC34744961E8",
"wakeTime" : 15679,
"sleepWakeUUID" : "D630726B-E513-4652-9E60-A3ADB090EB79",
"sip" : "enabled",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"asi" : {"libsystem_c.dylib":["abort() called"],"libc++abi.dylib":["terminating with uncaught exception of type std::runtime_error: Calling [C++: N10atomstruct5ChainE] _cpp_demotion failed."]},
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"source" : "P",
"arch" : "x86_64",
"base" : 140703501537280,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15278080,
"uuid" : "9d3ab204-4858-3120-b002-5c38b02edec4",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113.30.116"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4604682240,
"size" : 63488000,
"uuid" : "10431d8f-5e3b-3bbc-abd5-81f6a73a5269",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4524081152,
"CFBundleShortVersionString" : "3.9.6, (c) 2001-2019 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2510848,
"uuid" : "7fdc4a6b-e70b-3c9e-a72e-cd15ddf0d90f",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.6"
}
],
"sharedCache" : {
"base" : 140703453495296,
"size" : 15216836608,
"uuid" : "0939015d-8308-3e69-b095-bd928f835202"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=1.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 776K 48 \nColorSync 240K 28 \nCoreAnimation 1100K 42 \nCoreGraphics 20K 4 \nCoreUI image data 5260K 51 \nFoundation 44K 2 \nKernel Alloc Once 8K 1 \nMALLOC 662.7M 684 \nMALLOC guard page 32K 7 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 100K 25 \nStack 163.7M 26 \nStack Guard 56.0M 1 \nVM_ALLOCATE 154.2M 109 \n__DATA 44.6M 647 \n__DATA_CONST 29.9M 341 \n__DATA_DIRTY 1616K 211 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 670.8M 133 \n__OBJC_RO 81.8M 1 \n__OBJC_RW 3136K 2 \n__TEXT 751.2M 652 \n__UNICODE 588K 1 \ndyld private memory 1184K 3 \nmapped file 187.5M 50 \nshared memory 2968K 24 \n=========== ======= ======= \nTOTAL 2.9G 3113 \nTOTAL, minus reserved VM space 2.8G 3113 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "607844aa04477260f58a8077",
"factorPackIds" : {
"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
},
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "602ad4dac86151000cf27e46",
"factorPackIds" : {
"SIRI_DICTATION_ASSETS" : "6193d03f2171a2330e561dfc"
},
"deploymentId" : 240000305
},
{
"rolloutId" : "601d9415f79519000ccd4b69",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
},
"deploymentId" : 240000414
},
{
"rolloutId" : "5fc94383418129005b4e9ae0",
"factorPackIds" : {
},
"deploymentId" : 240000302
},
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000128
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202203290305 (2022-03-29)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett Davis/Koehn/Barrett/zz_Eva/asdf.mol2"
Chain information for combination #1
---
Chain | Description
B | No description available
Opened asdf.mol2 containing 1 structures (6284 atoms, 6336 bonds)
> save "/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett Davis/Koehn/Barrett/zz_Eva/turboid_pdp1.cif"
> relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> open "/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett Davis/Koehn/Barrett/zz_Eva/turboid_pdp1.cif"
Summary of feedback from opening /Users/barrettdavis/Library/CloudStorage/Box-
Box/TKU_Lab/Lab_Members/Barrett Davis/Koehn/Barrett/zz_Eva/turboid_pdp1.cif
---
warnings | Unknown polymer entity '1' near line 114
Atom H is not in the residue template for SER /B:1
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for turboid_pdp1.cif #2
---
Chain | Description
B | ?
> close #1
> rainbow
> open 7PNN
7pnn title:
mVenus released from fusion protein. [more info...]
Chain information for 7pnn #1
---
Chain | Description | UniProt
A | mVenus | GFP_AEQVI
Non-standard residues in 7pnn #1
---
CL — chloride ion
CR2 —
{(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic
acid (chromophore (gly-tyr-gly))
> matchmaker #1 to #2
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 turboid_pdp1.cif, chain B (#2) with 7pnn, chain A (#1), sequence
alignment score = 147.9
RMSD between 29 pruned atom pairs is 0.620 angstroms; (across all 29 pairs:
0.620)
> select #1:36-end
3390 atoms, 3152 bonds, 471 residues, 1 model selected
> select #2:36-end
5733 atoms, 5781 bonds, 368 residues, 1 model selected
> select #2:40-end
5676 atoms, 5723 bonds, 364 residues, 1 model selected
> ui mousemode right "translate selected atoms"
> select #2:48-end
5599 atoms, 5646 bonds, 356 residues, 1 model selected
> undo
> ui tool show Matchmaker
> matchmaker #2 to #1 showAlignment true
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 7pnn, chain A (#1) with turboid_pdp1.cif, chain B (#2), sequence
alignment score = 147.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7pnn #1/A, turboid_pdp1.cif
#2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 29 pruned atom pairs is 0.620 angstroms; (across all 29 pairs:
0.620)
> select #1/A:229
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:229 #2/B:29
28 atoms, 26 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 7pnn, chain A..turboid_pdp1.cif, chain B
[229] RMSD: 1.557
> select #1/A:201
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:201-229 #2/B:1-29
922 atoms, 928 bonds, 58 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 7pnn, chain A..turboid_pdp1.cif, chain B
[201-229] RMSD: 0.620
> select #1/A:229
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:229 #2/B:29
28 atoms, 26 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 7pnn, chain A..turboid_pdp1.cif, chain B
[229] RMSD: 1.557
> select #2/B:28
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/B:13-28
257 atoms, 258 bonds, 16 residues, 1 model selected
> select #2/B:30-31
26 atoms, 25 bonds, 2 residues, 1 model selected
> select #2/B:30-40
153 atoms, 153 bonds, 11 residues, 1 model selected
> select #1/A:229
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:201-229
460 atoms, 463 bonds, 29 residues, 1 model selected
> select #2/B:29
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:201-229 #2/B:1-29
922 atoms, 928 bonds, 58 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 7pnn, chain A..turboid_pdp1.cif, chain B
[201-229] RMSD: 0.620
> select #2/B:29
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/B:11-29
300 atoms, 301 bonds, 19 residues, 1 model selected
> select #2/B:11-end
6122 atoms, 6172 bonds, 393 residues, 1 model selected
> select #2/B:1-29
462 atoms, 465 bonds, 29 residues, 1 model selected
> Del #2/B:1-29
Unknown command: Del #2/B:1-29
> delete #2/B:1-29
> combine #1 #2
Associated combination chain B to turboid_pdp1.cif, chain B with 0 mismatches
Associated combination chain A to 7pnn, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: 7pnn #1/A, turboid_pdp1.cif
#2/B, combination #3/A
> hide #1 models
> hide #2 models
> select #3/B:30
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3/B:30 #3/A:229
33 atoms, 31 bonds, 2 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> color sel wihte
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color sel white
> color sel byhetero
> select #3/B:30 #3/A:229@c
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/B:30@n #3/A:229@c
2 atoms, 2 residues, 1 model selected
> ui tool show Matchmaker
> ui tool show "Build Structure"
> bond sel
Created 0 bonds
> select #3/A
3899 atoms, 3665 bonds, 506 residues, 1 model selected
> select #3/B:30@n #3/A:229@c
2 atoms, 2 residues, 1 model selected
> select #3/A
3899 atoms, 3665 bonds, 506 residues, 1 model selected
> select #3/B:30@n #3/A:229@c
2 atoms, 2 residues, 1 model selected
> bond sel
Created 1 bond
> select all
19442 atoms, 19071 bonds, 1760 residues, 3 models selected
> hide sel & #3 atoms
> show sel & #3 cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py", line 200, in _atomic_changes_cb
self.reevaluate()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py", line 112, in reevaluate
by_struct.setdefault(chain.structure, []).append(chain)
AttributeError: 'Sequence' object has no attribute 'structure'
Populating font family aliases took 1109 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py", line 112, in reevaluate
by_struct.setdefault(chain.structure, []).append(chain)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py", line 200, in _atomic_changes_cb
self.reevaluate()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py", line 112, in reevaluate
by_struct.setdefault(chain.structure, []).append(chain)
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/rmsd.py", line 112, in reevaluate
by_struct.setdefault(chain.structure, []).append(chain)
See log for complete Python traceback.
> close #1-2
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 458, in _delay_disassoc
self._notify_observers(self.NOTE_DEL_ASSOC, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 681, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 431, in
alignment_notification
self.notify_alignment(self.alignment.NOTE_HDR_RELEVANCE)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 152, in
notify_alignment
self.alignment.notify(note_name, note_data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 549, in notify
if hdr.shown and not hdr.relevant:
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 441, in relevant
return len(set([x.structure
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 441, in
return len(set([x.structure
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes done":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 441, in
return len(set([x.structure
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 458, in _delay_disassoc
self._notify_observers(self.NOTE_DEL_ASSOC, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 681, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 431, in
alignment_notification
self.notify_alignment(self.alignment.NOTE_HDR_RELEVANCE)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 152, in
notify_alignment
self.alignment.notify(note_name, note_data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/alignment.py", line 549, in notify
if hdr.shown and not hdr.relevant:
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 441, in relevant
return len(set([x.structure
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 441, in
return len(set([x.structure
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes done":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_headers/header_sequence.py", line 441, in
return len(set([x.structure
See log for complete Python traceback.
> save "/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett
> Davis/Koehn/Barrett/zz_Eva/mvenus_turboid_pdp1.mol2"
> open "/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett
> Davis/Koehn/Barrett/zz_Eva/mvenus_turboid_pdp1.mol2"
Chain information for combination #1
---
Chain | Description
A | No description available
Opened mvenus_turboid_pdp1.mol2 containing 1 structures (9721 atoms, 9536
bonds)
> hide #3 models
> show #3 models
> hide #1 models
> show #1 models
> hide #3 models
> close #3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4.dev202203290305 (2022-03-29)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/barrettdavis/Library/CloudStorage/Box-
> Box/TKU_Lab/Lab_Members/Barrett
> Davis/Koehn/Barrett/zz_Eva/mvenus_turboid_pdp1.mol2"
Chain information for combination #1
---
Chain | Description
A | No description available
Opened mvenus_turboid_pdp1.mol2 containing 1 structures (9721 atoms, 9536
bonds)
OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.9.6
Locale: UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro11,4
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 428.60.3.0.0
OS Loader Version: 540.80.2~11
SMC Version (system): 2.29f24
Software:
System Software Overview:
System Version: macOS 12.2.1 (21D62)
Kernel Version: Darwin 21.3.0
Time since boot: 6 days 21:27
Graphics/Displays:
Intel Iris Pro:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0d26
Revision ID: 0x0008
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
E2411:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 107NDEZ58868
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
E2411:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 107NDQA58884
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.5.30
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.36.3
ChimeraX-AtomicLibrary: 6.1.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
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: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202203290305
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-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: 1.1.5
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
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: 1.8
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
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: 2.5
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: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.16.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
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-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.31.2
funcparserlib: 1.0.0a0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.9.2
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.4
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.28
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.7
PyQt6-commercial: 6.2.3
PyQt6-sip: 13.2.0
PyQt6-WebEngine-commercial: 6.2.1
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 22.3.0
qtconsole: 5.3.0
QtPy: 2.0.1
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Calling _cpp_modified failed |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Barrett,
--Eric