![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 22 months ago
Closed 22 months ago
#10433 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | pett | |
| 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: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff84b450340 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.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":"2024-01-05 08:58:12.00 -0500","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.3.1 (22E772610a)","roots_installed":0,"name":"ChimeraX","incident_id":"C36E1379-F61E-4E51-8F68-B6E326723392"}
{
"uptime" : 610000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 98578,
"osVersion" : {
"train" : "macOS 13.3.1",
"build" : "22E772610a",
"releaseType" : "User"
},
"captureTime" : "2024-01-05 08:58:08.8900 -0500",
"incident" : "C36E1379-F61E-4E51-8F68-B6E326723392",
"pid" : 46166,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-12-30 15:44:50.1233 -0500",
"procStartAbsTime" : 487586934954910,
"procExitAbsTime" : 615777919820110,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7CCB1FA2-64AC-5556-8F32-B50F9EEAA107","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "A72F2F73-3BEC-1BC6-8419-A88B1E886275",
"throttleTimeout" : 2147483647,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 535,
"bridgeVersion" : {"build":"20P4252","train":"7.4"},
"sleepWakeUUID" : "571A665D-7BDF-4DF3-97E4-CA6C4551F1BF",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486663656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe63000-7fffffe64000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737486663656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe63000-7fffffe64000 [ 4K] r-x\/r-x SM=SHM ",
"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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===== Log before crash start =====
> color name grey80 #333333
Color 'grey80' is opaque: gray(20%) hex: #333333
> color name grey65 #595959
Color 'grey65' is opaque: gray(34.9%) hex: #595959
> color name grey40 #999999
Color 'grey40' is opaque: gray(60%) hex: #999999
> color name grey20 #CCCCCC
Color 'grey20' is opaque: gray(80%) hex: #cccccc
> color name grey10 #E6E6E6
Color 'grey10' is opaque: gray(90.2%) hex: #e6e6e6
> color name grey3 #F7F7F7
Color 'grey3' is opaque: gray(96.9%) hex: #f7f7f7
> color name spartan #18453B
Color 'spartan' is opaque: rgb(9.41%, 27.1%, 23.1%) hex: #18453b
> color name msu_yellow #E6BF5C
Color 'msu_yellow' is opaque: rgb(90.2%, 74.9%, 36.1%) hex: #e6bf5c
> color name teal_light #49B0AB
Color 'teal_light' is opaque: rgb(28.6%, 69%, 67.1%) hex: #49b0ab
> color name teal_dark #1C7B81
Color 'teal_dark' is opaque: rgb(11%, 48.2%, 50.6%) hex: #1c7b81
> color name msu_blue #004583
Color 'msu_blue' is opaque: rgb(0%, 27.1%, 51.4%) hex: #004583
> color name excel #0B9A6D
Color 'excel' is opaque: rgb(4.31%, 60.4%, 42.7%) hex: #0b9a6d
> preset Ball-Stick-Endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open smiles:O=C1C=C2CCC3C4CCC(C(=O)CO)C4(C)CC(O)C3C2(C)CC1
Translated SMILES to 3D structure via NCI web service (SMILES:
O=C1C=C2CCC3C4CCC(C(=O)CO)C4(C)CC(O)C3C2(C)CC1)
> close #*
> open
> smiles:CC(N1CCCCC1(/C=C/S(=O)(C2=CC=CC=C2)=O)/C=C/S(=O)(C3=CC=CC=C3)=O)=O
> format smiles fromDatabase smiles
Translated SMILES to 3D structure via NCI web service (SMILES:
CC(N1CCCCC1(/C=C/S(=O)(C2=CC=CC=C2)=O)/C=C/S(=O)(C3=CC=CC=C3)=O)=O)
> ui mousemode right "structure eraser"
> ui mousemode right "change element"
no element selected; shift-click to set element
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
no element selected; shift-click to set element
> ui mousemode right "structure eraser"
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> ui tool show "Build QM Input"
job started: local ORCA job "piperidine-vinyl-sulfone-radical-opt-hf3c"
> ui tool show "Job Queue"
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-opt-hf3c
> Sat Dec 30 17.31.08 2023/piperidine-vinyl-sulfone-radical-opt-hf3c.out"
> format out
Opened piperidine-vinyl-sulfone-radical-opt-hf3c.out as an ORCA output file
> close #2
> ui tool show "Job Queue"
killing local ORCA job "piperidine-vinyl-sulfone-radical-opt-hf3c"...
local ORCA job "piperidine-vinyl-sulfone-radical-opt-hf3c" might finish an in-
progess calculation step before exiting
job finished: local ORCA job "piperidine-vinyl-sulfone-radical-opt-hf3c"
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-opt-hf3c
> Sat Dec 30 17.31.08 2023/piperidine-vinyl-sulfone-radical-opt-hf3c.out"
> format out
Opened piperidine-vinyl-sulfone-radical-opt-hf3c.out as an ORCA output file
> hide #2 models
> close #2
> ui tool show "Build QM Input"
job started: local ORCA job "piperidine-vinyl-sulfone-radical-opt-hf3c"
> ui tool show "Job Queue"
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-opt-hf3c
> Sat Dec 30 17.36.34 2023/piperidine-vinyl-sulfone-radical-opt-hf3c.out"
> format out
Opened piperidine-vinyl-sulfone-radical-opt-hf3c.out as an ORCA output file
> hide #1 models
> close #2
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-opt-hf3c
> Sat Dec 30 17.36.34 2023/piperidine-vinyl-sulfone-radical-opt-hf3c.out"
> format out
Opened piperidine-vinyl-sulfone-radical-opt-hf3c.out as an ORCA output file
> close #2
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-opt-hf3c
> Sat Dec 30 17.36.34 2023/piperidine-vinyl-sulfone-radical-opt-hf3c.out"
> format out
Opened piperidine-vinyl-sulfone-radical-opt-hf3c.out as an ORCA output file
> close #2
job finished: local ORCA job "piperidine-vinyl-sulfone-radical-opt-hf3c"
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-opt-hf3c
> Sat Dec 30 17.36.34 2023/piperidine-vinyl-sulfone-radical-opt-hf3c.out"
> format out
Opened piperidine-vinyl-sulfone-radical-opt-hf3c.out as an ORCA output file
> close #2
> ui tool show "Job Queue"
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-opt-hf3c
> Sat Dec 30 17.36.34 2023/piperidine-vinyl-sulfone-radical-opt-hf3c.out"
> format out
Opened piperidine-vinyl-sulfone-radical-opt-hf3c.out as an ORCA output file
> preset seqcrow "index labels"
Using preset: SEQCROW / Index Labels
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> distance #2@C3,C9
Distance between piperidine-vinyl-sulfone-radical-opt-hf3c #2/a UNK 1 C3 and
C9: 3.314Å
> ui tool show "Build QM Input"
job started: local ORCA job "piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1"
> close #3
> ui tool show "Job Queue"
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> close #3
> close #4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> hide #2.1 models
> hide #!2 models
> distance #3@C3,C9
Distance between piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1
#3/a UNK 1 C3 and C9: 3.400Å
> close #4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> close #4
> close #3
> show #!2 models
> hide #!2 models
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> distance #3@C3,C9
Distance between piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1
#3/a UNK 1 C3 and C9: 3.200Å
> close #3
> close #3-4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> close #3-4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> distance #3@C3,C9
Distance between piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1
#3/a UNK 1 C3 and C9: 2.800Å
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> show #!1 models
> hide #!1 models
> hide #3 models
> hide #!4 models
> hide #4.1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!4 models
> show #3 models
> hide #!2 models
> close #3-4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> distance #3@C3,C9
Distance between piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1
#3/a UNK 1 C3 and C9: 2.600Å
> close #3-4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> distance #3@C3,C9
Distance between piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1
#3/a UNK 1 C3 and C9: 2.600Å
> hide #3 models
> close #3-4
> show #!2 models
> ui mousemode right select
> select #2/a:1@H8
1 atom, 1 residue, 1 model selected
> select add #2/a:1@C5
2 atoms, 1 residue, 1 model selected
> select add #2/a:1@H9
3 atoms, 1 residue, 1 model selected
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,-0.080574,0,1,0,-0.28252,0,0,1,0.10832
> ui mousemode right "translate selected atoms"
> ui mousemode right select
Drag select of 1 atoms
> select #2/a:1@H6
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"
> undo
> ui mousemode right select
> select #2/a:1@H10
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"
> ui mousemode right select
> select #2/a:1@H11
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"
> ui mousemode right select
> select #2/a:1@H7
1 atom, 1 residue, 1 model selected
> select clear
> select #2/a:1@H7
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"
> ui mousemode right select
> select #2/a:1@C5
1 atom, 1 residue, 1 model selected
> select add #2/a:1@H8
2 atoms, 1 residue, 1 model selected
> select add #2/a:1@H9
3 atoms, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"
> ui mousemode right select
> select #2/a:1@H10
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected atoms"
> ui tool show "Build QM Input"
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> hide #!2 models
> distance #3@C3,C9
Distance between piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1
#3/a UNK 1 C3 and C9: 2.400Å
> close #3-4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> select up
38 atoms, 39 bonds, 1 residue, 1 model selected
> distance #3@C3,C9
Distance between piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1
#3/a UNK 1 C3 and C9: 1.800Å
> select up
114 atoms, 118 bonds, 1 pseudobond, 3 residues, 4 models selected
> close #3-4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> select up
114 atoms, 118 bonds, 3 residues, 3 models selected
> close #3-4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> close #3-4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.002.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.008.gbw
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.densities
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.009.gbw
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.003.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.001.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.010.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.004.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.relaxscanact.dat
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.005.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.011.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.007.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1_property.txt
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1_trj.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.006.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.opt
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.allxyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.gbw
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.relaxscanscf.dat
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.001.gbw
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.008.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.002.gbw
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.003.gbw
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.009.xyz
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.007.gbw
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.006.gbw
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.004.gbw
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.010.gbw
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.011.gbw
deleting /Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-sulfone-
radical-scan-3p4-1p4-11steps-hf3c-1.005.gbw
job finished: local ORCA job "piperidine-vinyl-sulfone-radical-
scan-3p4-1p4-11steps-hf3c-1"
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
job started: local ORCA job "piperidine-vinyl-sulfone-radical-boat-opt-hf3c"
> close #3-4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-
> scan-3p4-1p4-11steps-hf3c-1 Sat Dec 30 18.01.36 2023/piperidine-vinyl-
> sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out" format out
Opened piperidine-vinyl-sulfone-radical-scan-3p4-1p4-11steps-hf3c-1.out as an
ORCA output file
> select up
114 atoms, 118 bonds, 3 residues, 3 models selected
> select up
114 atoms, 118 bonds, 3 residues, 3 models selected
> close #3-4
> ui tool show "Job Queue"
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-boat-opt-
> hf3c Sat Dec 30 19.15.58 2023/piperidine-vinyl-sulfone-radical-boat-opt-
> hf3c.out" format out
Opened piperidine-vinyl-sulfone-radical-boat-opt-hf3c.out as an ORCA output
file
> close #3-4
> ui tool show "Job Queue"
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-boat-opt-
> hf3c Sat Dec 30 19.15.58 2023/piperidine-vinyl-sulfone-radical-boat-opt-
> hf3c.out" format out
Opened piperidine-vinyl-sulfone-radical-boat-opt-hf3c.out as an ORCA output
file
> close #3-4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-boat-opt-
> hf3c Sat Dec 30 19.15.58 2023/piperidine-vinyl-sulfone-radical-boat-opt-
> hf3c.out" format out
Opened piperidine-vinyl-sulfone-radical-boat-opt-hf3c.out as an ORCA output
file
> select down
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 297, in forward_keystroke
run(self.session, 'select down')
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/select.py", line 138, in select_down
session.selection.demote(session)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/selection.py", line 64, in demote
self._promotion.demote_selection()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/selection.py", line 200, in demote_selection
p.demote()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/selection.py", line 229, in demote
m.selected = False # This may clear child drawing selections.
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 777, in set_selected
self.atoms.selected = sel
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
job finished: local ORCA job "piperidine-vinyl-sulfone-radical-boat-opt-hf3c"
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-boat-opt-
> hf3c Sat Dec 30 19.15.58 2023/piperidine-vinyl-sulfone-radical-boat-opt-
> hf3c.out" format out
Opened piperidine-vinyl-sulfone-radical-boat-opt-hf3c.out as an ORCA output
file
> select up
152 atoms, 156 bonds, 4 residues, 4 models selected
> select up
152 atoms, 156 bonds, 4 residues, 4 models selected
> close #3-4
> open "/Users/joe/SEQCROW_SCRATCH/piperidine-vinyl-sulfone-radical-boat-opt-
> hf3c Sat Dec 30 19.15.58 2023/piperidine-vinyl-sulfone-radical-boat-opt-
> hf3c.out" format out
Opened piperidine-vinyl-sulfone-radical-boat-opt-hf3c.out as an ORCA output
file
> select up
114 atoms, 117 bonds, 3 residues, 3 models selected
> select up
114 atoms, 117 bonds, 3 residues, 3 models selected
> select up
114 atoms, 117 bonds, 3 residues, 3 models selected
> select up
114 atoms, 117 bonds, 3 residues, 3 models selected
> distance #3@C3,C9
Distance between piperidine-vinyl-sulfone-radical-boat-opt-hf3c #3/a UNK 1 C3
and C9: 3.616Å
> close #*
> ui tool show "2D Builder"
Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.
> ui mousemode right "bond rotation"
> torsion /a:1@C1,C2,C3,H4 123.16
> ui tool show "Build QM Input"
> preset seqcrow "index labels"
Using preset: SEQCROW / Index Labels
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
job started: local ORCA job "but-1-ene-scan-1-359-37steps-hf3c"
job finished: local ORCA job "but-1-ene-scan-1-359-37steps-hf3c"
> open "/Users/joe/SEQCROW_SCRATCH/but-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.27.50 2023/but-1-ene-scan-1-359-37steps-hf3c.out" format out
Summary of feedback from opening /Users/joe/SEQCROW_SCRATCH/but-1-ene-
scan-1-359-37steps-hf3c Sun Dec 31 14.27.50 2023/but-1-ene-scan-1-359-37steps-
hf3c.out
---
errors | could not open but-1-ene-scan-1-359-37steps-hf3c.out
LookupError('Could not find atom: [] on\nbut-1-ene-scan-1-359-37steps-
hf3c.out\n0')
SEQCROW failed to open but-1-ene-scan-1-359-37steps-hf3c.out
> ui tool show "Build QM Input"
job started: local ORCA job "but-1-ene-scan-1-359-37steps-hf3c"
> ui tool show "Job Queue"
> open "/Users/joe/SEQCROW_SCRATCH/but-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.29.51 2023/but-1-ene-scan-1-359-37steps-hf3c.out" format out
Opened but-1-ene-scan-1-359-37steps-hf3c.out as an ORCA output file
> close #2
> open "/Users/joe/SEQCROW_SCRATCH/but-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.29.51 2023/but-1-ene-scan-1-359-37steps-hf3c.out" format out
Opened but-1-ene-scan-1-359-37steps-hf3c.out as an ORCA output file
> hide #!1 models
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
job finished: local ORCA job "but-1-ene-scan-1-359-37steps-hf3c"
> open "/Users/joe/SEQCROW_SCRATCH/but-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.29.51 2023/but-1-ene-scan-1-359-37steps-hf3c.out" format out
Opened but-1-ene-scan-1-359-37steps-hf3c.out as an ORCA output file
> hide #2 models
> close #*
> ui tool show "2D Builder"
Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.
> torsion /a:1@H6,C3,C1,C2 2.58
> preset seqcrow "index labels"
Using preset: SEQCROW / Index Labels
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> torsion /a:1@H6,C3,C1,C2 130.49
> torsion /a:1@H6,C3,C1,C2 -108.05
> torsion /a:1@H6,C3,C1,C2 -114.75
> ui tool show "Build QM Input"
job started: local ORCA job "prop-1-ene-scan-1-359-37steps-hf3c"
job finished: local ORCA job "prop-1-ene-scan-1-359-37steps-hf3c"
> open "/Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.50.57 2023/prop-1-ene-scan-1-359-37steps-hf3c.out" format out
Summary of feedback from opening /Users/joe/SEQCROW_SCRATCH/prop-1-ene-
scan-1-359-37steps-hf3c Sun Dec 31 14.50.57 2023/prop-1-ene-
scan-1-359-37steps-hf3c.out
---
errors | could not open prop-1-ene-scan-1-359-37steps-hf3c.out
LookupError('Could not find atom: [] on\nprop-1-ene-scan-1-359-37steps-
hf3c.out\n0')
SEQCROW failed to open prop-1-ene-scan-1-359-37steps-hf3c.out
> ui tool show "Build QM Input"
job started: local ORCA job "prop-1-ene-scan-1-359-37steps-hf3c"
> ui tool show "Job Queue"
> open "/Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.out" format out
Opened prop-1-ene-scan-1-359-37steps-hf3c.out as an ORCA output file
> close #2
> open "/Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.out" format out
Opened prop-1-ene-scan-1-359-37steps-hf3c.out as an ORCA output file
> close #2
> hide #!1 models
> open "/Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.out" format out
Opened prop-1-ene-scan-1-359-37steps-hf3c.out as an ORCA output file
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.001.gbw
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.allxyz
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.008.xyz
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.002.gbw
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.003.gbw
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.009.xyz
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.xyz
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.SHARK.K.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.007.gbw
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.006.gbw
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.004.gbw
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.005.gbw
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.S.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.2.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c_property.txt
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.E.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.3.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.1.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.ginp.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.T.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.V.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.ghess.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.PDAT.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.EIJ.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.en.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.K.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.grad.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.H.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.SP12.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.002.xyz
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.008.gbw
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.opt
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.009.gbw
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.003.xyz
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.001.xyz
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.int.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.SM12.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.004.xyz
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.densities
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.005.xyz
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.SHARKINP.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.gbw
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.007.xyz
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.fsv.tmp
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c_trj.xyz
deleting /Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.006.xyz
job finished: local ORCA job "prop-1-ene-scan-1-359-37steps-hf3c"
> open "/Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.53.17 2023/prop-1-ene-scan-1-359-37steps-hf3c.out" format out
Opened prop-1-ene-scan-1-359-37steps-hf3c.out as an ORCA output file
> hide #2 models
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset seqcrow "index labels"
Using preset: SEQCROW / Index Labels
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> close #2
> close #3
> show #!1 models
> ui tool show "Build QM Input"
job started: local ORCA job "prop-1-ene-scan-1-359-37steps-hf3c"
> ui tool show "Job Queue"
> open "/Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.56.11 2023/prop-1-ene-scan-1-359-37steps-hf3c.out" format out
Opened prop-1-ene-scan-1-359-37steps-hf3c.out as an ORCA output file
> hide #!1 models
> close #2
job finished: local ORCA job "prop-1-ene-scan-1-359-37steps-hf3c"
> open "/Users/joe/SEQCROW_SCRATCH/prop-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.56.11 2023/prop-1-ene-scan-1-359-37steps-hf3c.out" format out
Opened prop-1-ene-scan-1-359-37steps-hf3c.out as an ORCA output file
> open "/Users/joe/SEQCROW_SCRATCH/but-1-ene-scan-1-359-37steps-hf3c Sun Dec
> 31 14.29.51 2023/but-1-ene-scan-1-359-37steps-hf3c.out"
Opened but-1-ene-scan-1-359-37steps-hf3c.out as an ORCA output file
> hide #2 models
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset seqcrow "index labels"
Using preset: SEQCROW / Index Labels
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> view
> torsion #3@C1,C2,C3,C4
Torsion angle for atoms but-1-ene-scan-1-359-37steps-hf3c #3/a UNK 1 C1 C2 C3
C4 is 0.100002°
> torsion #3@C1,C2,C3,C4
Torsion angle for atoms but-1-ene-scan-1-359-37steps-hf3c #3/a UNK 1 C1 C2 C3
C4 is 0.100002°
> torsion #3@C1,C2,C3,C4
Torsion angle for atoms but-1-ene-scan-1-359-37steps-hf3c #3/a UNK 1 C1 C2 C3
C4 is 120.033°
> open smiles:[H][C@@]12CCCC[C@]1([H])CCCC2
Translated SMILES to 3D structure via NCI web service (SMILES:
[H][C@@]12CCCC[C@]1([H])CCCC2)
> hide #!3 models
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> view
> ui tool show "Conformer Search"
job started: local CREST job "cis-decalin"
job finished: local CREST job "cis-decalin"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/joe/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/managers/job_manager.py", line 313, in job_finished
job.open_structure()
File "/Users/joe/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/jobs.py", line 837, in open_structure
fr.all_geom[i] = (*fr.all_geom[i], {"energy": float(comment)})
ValueError: could not convert string to float: 'comment'
Error processing trigger "job finished":
ValueError: could not convert string to float: 'comment'
File "/Users/joe/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/jobs.py", line 837, in open_structure
fr.all_geom[i] = (*fr.all_geom[i], {"energy": float(comment)})
See log for complete Python traceback.
> hide #4 models
> open "/Users/joe/SEQCROW_SCRATCH/cis-decalin Sun Dec 31 16.23.20
> 2023/crest_conformers.xyz"
opened crest_conformers.xyz as an XYZ coordinate file
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> coordset
Missing or invalid "structures" argument: empty atom specifier
> coordset #5
> coordset slider #5
> close #5
> ui tool show "Conformer Search"
job started: local CREST job "cis-decalin-xtb2"
> show #4 models
job finished: local CREST job "cis-decalin-xtb2"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
File "/Users/joe/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/managers/job_manager.py", line 313, in job_finished
job.open_structure()
File "/Users/joe/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/jobs.py", line 837, in open_structure
fr.all_geom[i] = (*fr.all_geom[i], {"energy": float(comment)})
ValueError: could not convert string to float: 'comment'
Error processing trigger "job finished":
ValueError: could not convert string to float: 'comment'
File "/Users/joe/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/jobs.py", line 837, in open_structure
fr.all_geom[i] = (*fr.all_geom[i], {"energy": float(comment)})
See log for complete Python traceback.
> open "/Users/joe/SEQCROW_SCRATCH/cis-decalin-xtb2 Sun Dec 31 16.26.27
> 2023/crest_conformers.xyz"
opened crest_conformers.xyz as an XYZ coordinate file movie
> close #4
> close #5
> ui tool show "2D Builder"
Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.
> close #*
> hide #3 models
> hide #1 models
> ui mousemode right "change element"
> ui mousemode right "structure eraser"
> ui mousemode right "change element"
> ui mousemode right "structure eraser"
> ui mousemode right "change element"
> close #*
> open
> smiles:O[C@@H]1CC[C@]2(C)[C@@]3([H])C[C@H](O)[C@]4(C)[C@@H]([C@H](C)CCC(O)=O)CC[C@@]4([H])[C@]3([H])CC[C@@]([H])2C1
Translated SMILES to 3D structure via NCI web service (SMILES:
O[C@@H]1CC[C@]2(C)[C@@]3([H])C[C@H](O)[C@]4(C)[C@@H]([C@H](C)CCC(O)=O)CC[C@@]4([H])[C@]3([H])CC[C@@]([H])2C1)
> open
> smiles:O[C@@H](C[C@@](CC[C@@]1([H])[C@]2([H])CC[C@@H]([C@]23C)[C@H](C)CCC(O)=O)4[H])CC[C@]4(C)C1([H])=CC3=O
Translated SMILES to 3D structure via NCI web service (SMILES:
O[C@@H](C[C@@](CC[C@@]1([H])[C@]2([H])CC[C@@H]([C@]23C)[C@H](C)CCC(O)=O)4[H])CC[C@]4(C)C1([H])=CC3=O)
> hide #1 models
> close #2
> open
> smiles:O[C@@H](C[C@@](CC[C@@]1([H])[C@]2([H])CC[C@@H]([C@]23C)[C@H](C)CCC(O)=O)4[H])CC[C@]4(C)C1=CC3=O
Translated SMILES to 3D structure via NCI web service (SMILES:
O[C@@H](C[C@@](CC[C@@]1([H])[C@]2([H])CC[C@@H]([C@]23C)[C@H](C)CCC(O)=O)4[H])CC[C@]4(C)C1=CC3=O)
> close #2
> open
> smiles:[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@@H]([C@]34C)[C@H](C)CCC(O)=O)C[C@H](O5)CC[C@]1(C)[C@]52CC4=O
Translated SMILES to 3D structure via NCI web service (SMILES:
[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@@H]([C@]34C)[C@H](C)CCC(O)=O)C[C@H](O5)CC[C@]1(C)[C@]52CC4=O)
> view
> close #2
> open
> smiles:[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@@H]([C@]34C)[C@H](C)CCC(O)=O)C[C@H](O5)CC[C@]1(C)[C@]52CC4=O
Translated SMILES to 3D structure via NCI web service (SMILES:
[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@@H]([C@]34C)[C@H](C)CCC(O)=O)C[C@H](O5)CC[C@]1(C)[C@]52CC4=O)
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> hide H
> show H
> close #2
> open
> smiles:[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@@H]([C@]34C)[C@H](C)CCC(O)=O)C[C@H](O5)CC[C@]1(C)[C@]52CC4=O
Translated SMILES to 3D structure via NCI web service (SMILES:
[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@@H]([C@]34C)[C@H](C)CCC(O)=O)C[C@H](O5)CC[C@]1(C)[C@]52CC4=O)
> close #2
> open
> smiles:[H][C@@]12C[C@H](O3)CC[C@@](C)1[C@@]43C=C[C@]5(C)[C@@H]([C@H](C)CCC(O)=O)CC[C@@]5([H])[C@]4([H])CC2
Translated SMILES to 3D structure via NCI web service (SMILES:
[H][C@@]12C[C@H](O3)CC[C@@](C)1[C@@]43C=C[C@]5(C)[C@@H]([C@H](C)CCC(O)=O)CC[C@@]5([H])[C@]4([H])CC2)
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> hide #2 models
> show #1 models
> view
> hide #1 models
> open
> smiles:[H][C@@]12C[C@H](O3)CC[C@@](C)1[C@@]43[C@@H](Br)[C@H](Br)[C@]5(C)[C@@H]([C@H](C)CCC(O)=O)CC[C@@]5([H])[C@]4([H])CC2
Translated SMILES to 3D structure via NCI web service (SMILES:
[H][C@@]12C[C@H](O3)CC[C@@](C)1[C@@]43[C@@H](Br)[C@H](Br)[C@]5(C)[C@@H]([C@H](C)CCC(O)=O)CC[C@@]5([H])[C@]4([H])CC2)
> view
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> open
> smiles:[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@@H]([C@]3(C4)C)[C@H](C)CCC(O)=O)C[C@H](O5)CC[C@@](C)1[C@]52C4=O
Translated SMILES to 3D structure via NCI web service (SMILES:
[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@@H]([C@]3(C4)C)[C@H](C)CCC(O)=O)C[C@H](O5)CC[C@@](C)1[C@]52C4=O)
> hide #3 models
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset seqcrow vdw
Using preset: SEQCROW / VDW
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> close #*
> open
> smiles:O=C(C=C1CC[C@@]2([H])[C@]3([H])CC[C@@](O)([C@]3(C4)C)C(CO)=O)CC[C@]1(C)[C@@]2([H])C4=O
Translated SMILES to 3D structure via NCI web service (SMILES:
O=C(C=C1CC[C@@]2([H])[C@]3([H])CC[C@@](O)([C@]3(C4)C)C(CO)=O)CC[C@]1(C)[C@@]2([H])C4=O)
> rename #1 cortisone
> open /Users/joe/Desktop/generic_movie.cxc
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> color name grey80 #333333
Color 'grey80' is opaque: gray(20%) hex: #333333
> color name spartan #18453B
Color 'spartan' is opaque: rgb(9.41%, 27.1%, 23.1%) hex: #18453b
> color name msu_blue #004583
Color 'msu_blue' is opaque: rgb(0%, 27.1%, 51.4%) hex: #004583
> color name excel #0B9A6D
Color 'excel' is opaque: rgb(4.31%, 60.4%, 42.7%) hex: #0b9a6d
> color #* grey80 target b halfbond false
> color #*@C* grey40 atoms
> color #*@N* msu_blue atoms
> color H grey10
> color #* grey80 target b
> style H ball
Changed 28 atom styles
> size ballScale 0.6
Changed 1 ball scales
> size atomRadius 0.5
Changed 54 atom radii
> size #*@H* atomRadius 0.35
Changed 28 atom radii
> size stickRadius 0.08
Changed 57 bond radii
> hide #*
> show #1
> view orient
> zoom 0.5
executed generic_movie.cxc
> set bgColor white
> hide H
> show H
> open /Users/joe/Desktop/generic_movie.cxc
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> set bgColor white
> color name grey80 #333333
Color 'grey80' is opaque: gray(20%) hex: #333333
> color name grey65 #595959
Color 'grey65' is opaque: gray(34.9%) hex: #595959
> color name grey40 #999999
Color 'grey40' is opaque: gray(60%) hex: #999999
> color name grey20 #CCCCCC
Color 'grey20' is opaque: gray(80%) hex: #cccccc
> color name grey10 #E6E6E6
Color 'grey10' is opaque: gray(90.2%) hex: #e6e6e6
> color name grey3 #F7F7F7
Color 'grey3' is opaque: gray(96.9%) hex: #f7f7f7
> color name spartan #18453B
Color 'spartan' is opaque: rgb(9.41%, 27.1%, 23.1%) hex: #18453b
> color name msu_blue #004583
Color 'msu_blue' is opaque: rgb(0%, 27.1%, 51.4%) hex: #004583
> color name msu_red #D24C4A
Color 'msu_red' is opaque: rgb(82.4%, 29.8%, 29%) hex: #d24c4a
> color name excel #0B9A6D
Color 'excel' is opaque: rgb(4.31%, 60.4%, 42.7%) hex: #0b9a6d
> color #* grey80 target b halfbond false
> color #*@C* grey40 atoms
> color #*@N* msu_blue atoms
> color #*@O* msu_red atoms
> color H grey10
> color #* grey80 target b
> style H ball
Changed 28 atom styles
> size ballScale 0.6
Changed 1 ball scales
> size atomRadius 0.5
Changed 54 atom radii
> size #*@H* atomRadius 0.35
Changed 28 atom radii
> size stickRadius 0.08
Changed 57 bond radii
> hide #*
> show #1
> view orient
> zoom 0.5
executed generic_movie.cxc
> zoom 1.2
> ui mousemode right translate
> hide H
> select down
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 297, in forward_keystroke
run(self.session, 'select down')
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/select.py", line 138, in select_down
session.selection.demote(session)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/selection.py", line 64, in demote
self._promotion.demote_selection()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/selection.py", line 200, in demote_selection
p.demote()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/selection.py", line 229, in demote
m.selected = False # This may clear child drawing selections.
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 777, in set_selected
self.atoms.selected = sel
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 163, in get_prop
vcount = getattr(self, value_count)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> show H
> hide H
> open smiles:CC(CNC)CC1=CC=CC=C1
Translated SMILES to 3D structure via NCI web service (SMILES:
CC(CNC)CC1=CC=CC=C1)
> rename #2 meth
> hide #1 models
> open /Users/joe/Desktop/generic_movie.cxc
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> set bgColor white
> color name grey80 #333333
Color 'grey80' is opaque: gray(20%) hex: #333333
> color name grey65 #595959
Color 'grey65' is opaque: gray(34.9%) hex: #595959
> color name grey40 #999999
Color 'grey40' is opaque: gray(60%) hex: #999999
> color name grey20 #CCCCCC
Color 'grey20' is opaque: gray(80%) hex: #cccccc
> color name grey10 #E6E6E6
Color 'grey10' is opaque: gray(90.2%) hex: #e6e6e6
> color name grey3 #F7F7F7
Color 'grey3' is opaque: gray(96.9%) hex: #f7f7f7
> color name spartan #18453B
Color 'spartan' is opaque: rgb(9.41%, 27.1%, 23.1%) hex: #18453b
> color name msu_blue #004583
Color 'msu_blue' is opaque: rgb(0%, 27.1%, 51.4%) hex: #004583
> color name msu_red #D24C4A
Color 'msu_red' is opaque: rgb(82.4%, 29.8%, 29%) hex: #d24c4a
> color name excel #0B9A6D
Color 'excel' is opaque: rgb(4.31%, 60.4%, 42.7%) hex: #0b9a6d
> color #* grey80 target b halfbond false
> color #*@C* grey40 atoms
> color #*@N* msu_blue atoms
> color #*@O* msu_red atoms
> color H grey10
> color #* grey80 target b
> style H ball
Changed 45 atom styles
> size ballScale 0.6
Changed 2 ball scales
> size atomRadius 0.5
Changed 83 atom radii
> size #*@H* atomRadius 0.35
Changed 45 atom radii
> size stickRadius 0.08
Changed 86 bond radii
> hide #*
> show #1
> view orient
> zoom 0.5
executed generic_movie.cxc
> show #2
> hide H
> show H
> zoom 1.2
> close #2
> open smiles:CNC(C)CC1=CC=CC=C1
Translated SMILES to 3D structure via NCI web service (SMILES:
CNC(C)CC1=CC=CC=C1)
> open /Users/joe/Desktop/generic_movie.cxc
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> set bgColor white
> color name grey80 #333333
Color 'grey80' is opaque: gray(20%) hex: #333333
> color name grey65 #595959
Color 'grey65' is opaque: gray(34.9%) hex: #595959
> color name grey40 #999999
Color 'grey40' is opaque: gray(60%) hex: #999999
> color name grey20 #CCCCCC
Color 'grey20' is opaque: gray(80%) hex: #cccccc
> color name grey10 #E6E6E6
Color 'grey10' is opaque: gray(90.2%) hex: #e6e6e6
> color name grey3 #F7F7F7
Color 'grey3' is opaque: gray(96.9%) hex: #f7f7f7
> color name spartan #18453B
Color 'spartan' is opaque: rgb(9.41%, 27.1%, 23.1%) hex: #18453b
> color name msu_blue #004583
Color 'msu_blue' is opaque: rgb(0%, 27.1%, 51.4%) hex: #004583
> color name msu_red #D24C4A
Color 'msu_red' is opaque: rgb(82.4%, 29.8%, 29%) hex: #d24c4a
> color name excel #0B9A6D
Color 'excel' is opaque: rgb(4.31%, 60.4%, 42.7%) hex: #0b9a6d
> color #* grey80 target b halfbond false
> color #*@C* grey40 atoms
> color #*@N* msu_blue atoms
> color #*@O* msu_red atoms
> color H grey10
> color #* grey80 target b
> style H ball
Changed 43 atom styles
> size ballScale 0.6
Changed 2 ball scales
> size atomRadius 0.5
Changed 80 atom radii
> size #*@H* atomRadius 0.35
Changed 43 atom radii
> size stickRadius 0.08
Changed 83 bond radii
> hide #*
> show #1
> view orient
> zoom 0.5
executed generic_movie.cxc
> show #2
> ui mousemode right "bond rotation"
> torsion #2/?:1@N1,C2,C4,C5 73.65
> torsion #2/?:1@N1,C2,C4,C5 162.08
> torsion #2/?:1@C1,N1,C2,C3 99.60
> torsion #2/?:1@N1,C2,C4,C5 162.08
> ui mousemode right select
> select #2/?:1@C5
1 atom, 1 residue, 1 model selected
> select add #2/?:1@C4
2 atoms, 1 residue, 1 model selected
> select add #2/?:1@C2
3 atoms, 1 residue, 1 model selected
> select add #2/?:1@N1
4 atoms, 1 residue, 1 model selected
> torsion sel
Torsion angle for atoms smiles:CNC(C)CC1=CC=CC=C1 #2/? UNL 1 C5 C4 C2 N1 is
162.08°
> torsion sel 180
> select #2/?:1@C4
1 atom, 1 residue, 1 model selected
> select add #2/?:1@C2
2 atoms, 1 residue, 1 model selected
> select add #2/?:1@N1
3 atoms, 1 residue, 1 model selected
> select add #2/?:1@C1
4 atoms, 1 residue, 1 model selected
> select up
26 atoms, 26 bonds, 1 residue, 1 model selected
> select down
4 atoms, 1 residue, 1 model selected
> torsion sel
Torsion angle for atoms smiles:CNC(C)CC1=CC=CC=C1 #2/? UNL 1 C1 N1 C2 C4 is
-140.403°
> torsion sel 180
> select add #2
26 atoms, 26 bonds, 1 residue, 1 model selected
> select subtract #2
Nothing selected
> view
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
> color name grey80 #333333
Color 'grey80' is opaque: gray(20%) hex: #333333
> color name grey65 #595959
Color 'grey65' is opaque: gray(34.9%) hex: #595959
> color name grey40 #999999
Color 'grey40' is opaque: gray(60%) hex: #999999
> color name grey20 #CCCCCC
Color 'grey20' is opaque: gray(80%) hex: #cccccc
> color name grey10 #E6E6E6
Color 'grey10' is opaque: gray(90.2%) hex: #e6e6e6
> color name grey3 #F7F7F7
Color 'grey3' is opaque: gray(96.9%) hex: #f7f7f7
> color name spartan #18453B
Color 'spartan' is opaque: rgb(9.41%, 27.1%, 23.1%) hex: #18453b
> color name msu_yellow #E6BF5C
Color 'msu_yellow' is opaque: rgb(90.2%, 74.9%, 36.1%) hex: #e6bf5c
> color name teal_light #49B0AB
Color 'teal_light' is opaque: rgb(28.6%, 69%, 67.1%) hex: #49b0ab
> color name teal_dark #1C7B81
Color 'teal_dark' is opaque: rgb(11%, 48.2%, 50.6%) hex: #1c7b81
> color name msu_blue #004583
Color 'msu_blue' is opaque: rgb(0%, 27.1%, 51.4%) hex: #004583
> color name excel #0B9A6D
Color 'excel' is opaque: rgb(4.31%, 60.4%, 42.7%) hex: #0b9a6d
> preset Ball-Stick-Endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.10.12
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
OS Loader Version: 577~129
Software:
System Software Overview:
System Version: macOS 13.3.1 (a) (22E772610a)
Kernel Version: Darwin 22.4.0
Time since boot: 38 days, 22 hours, 27 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
Send2Trash: 1.8.2
SEQCROW: 1.8.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (3)
comment:1 by , 22 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 22 months ago
comment:3 by , 22 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi Joe,
--Eric