![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 19 months ago
Closed 19 months ago
#14960 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (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 0x00007ff8591b1100 (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
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{
"uptime" : 300000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 15457,
"osVersion" : {
"train" : "macOS 14.4",
"build" : "23E214",
"releaseType" : "User"
},
"captureTime" : "2024-04-10 16:16:25.0666 +0200",
"codeSigningMonitor" : 0,
"incident" : "B9DD7586-DA21-49FC-BDF1-F1412FE6BE2E",
"pid" : 43304,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-04-10 10:28:22.5487 +0200",
"procStartAbsTime" : 284349418614153,
"procExitAbsTime" : 305231559260544,
"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":"5475C0C3-039C-53E8-89A6-F12B7B37AE6A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "69F1B9D9-604E-01D5-03EF-91F38D4674EF",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 94698,
"bridgeVersion" : {"build":"21P4222","train":"8.4"},
"sleepWakeUUID" : "764D7C72-E7D4-4182-9888-FDCC71073DD8",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4459876328\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 109d45000-109d46000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":43304},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4459876328\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 109d45000-109d46000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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 /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Laba/Data/NOA1/IP_cryoEM/sessions/noa1-final-classes-
> extended.cxs format session
Opened 7pua-ban-middle as #39, grid size 360,360,360, pixel 1.39, shown at
level 0.021, step 2, values float32
Opened 7pub-ban-late as #40, grid size 360,360,360, pixel 1.39, shown at level
0.054, step 2, values float32
Opened 7pub-ban-late gaussian as #43, grid size 360,360,360, pixel 1.39, shown
at level 0.0315, step 1, values float32
Opened 7pub-ban-late gaussian as #44, grid size 360,360,360, pixel 1.39, shown
at level 0.0266, step 1, values float32
Opened 7pub-ban-late gaussian as #45, grid size 360,360,360, pixel 1.39, shown
at level 0.0365, step 1, values float32
Opened 7pub-ban-late gaussian as #46, grid size 360,360,360, pixel 1.39, shown
at level 0.0419, step 1, values float32
Opened 7pub-ban-late gaussian as #47, grid size 360,360,360, pixel 1.39, shown
at level 0.0426, step 1, values float32
Opened 7pub-ban-late gaussian as #48, grid size 360,360,360, pixel 1.39, shown
at level 0.0426, step 1, values float32
opened ChimeraX session
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> hide atoms
> show cartoons
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 5272997 atom styles
> style ringFill thin
Changed 375880 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
> NatCom/figures/figure 1 - overview classes"
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
NatCom/figures/figure 1 - overview classes
> view orig
> show #!22 models
> align #22/V toAtoms #22/V matchNumbering true
RMSD between 2946 atom pairs is 0.000 angstroms
> color #22 goldenrod
> color #22/A light gray
> hide #22/9 cartoons
> show #22/9 surfaces
> color #22/9 #f54242
> color #22 goldenrod
> color #22/A light gray
> hide #22/5 cartoons
> show #22/5 surfaces
> color #22/5 #FA8072
> color #22 goldenrod
> color #22/A light gray
> hide #22/7 cartoons
> show #22/7 surfaces
> color #22/7 #FF00FF
> color #22 goldenrod
> color #22/A light gray
> hide #22/a cartoons
> show #22/a surfaces
> color #22/a #FF69B4
> color #22 goldenrod
> color #22/A light gray
> hide #22/8 cartoons
> show #22/8 surfaces
> color #22/8 #964B00
> save 8csp-like.png transparentBackground true
> hide #!22 models
> show #!23 models
> align #23/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #23 goldenrod
> color #23/A light gray
> hide #23/9 cartoons
> show #23/9 surfaces
> color #23/9 #f54242
> color #23 goldenrod
> color #23/A light gray
> hide #23/a cartoons
> show #23/a surfaces
> color #23/a #ff00ffff
> save noa1-rbfa-in.png transparentBackground true
> hide #!23 models
> show #!18 models
> align #18/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #18 goldenrod
> color #18/A light gray
> hide #18/9 cartoons
> show #18/9 surfaces
> color #18/9 #f54242
> color #18 goldenrod
> color #18/A light gray
> hide #18/2 cartoons
> show #18/2 surfaces
> color #18/2 #009000ff
> color #18/A:1492-1556 #ff8800ff
> save noa1-new-ms37.png transparentBackground true
> hide #!18 models
> show #!20 models
> align #20/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #20 goldenrod
> color #20/A light gray
> hide #20/a cartoons
> show #20/a surfaces
> color #20/a #ff00ffff
> color #20 goldenrod
> color #20/A light gray
> hide #20/b cartoons
> show #20/b surfaces
> color #20/b #12ffffff
> color #20/A:1492-1556 #ff8800ff
> save m15-rbfa-in.png transparentBackground true
> hide #!20 models
> show #!17 models
> align #17/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #17 goldenrod
> color #17/A light gray
> hide #17/a cartoons
> show #17/a surfaces
> color #17/a #ff00ffff
> color #17 goldenrod
> color #17/A light gray
> hide #17/b cartoons
> show #17/b surfaces
> color #17/b #12ffffff
> color #17 goldenrod
> color #17/A light gray
> hide #17/7 cartoons
> show #17/7 surfaces
> color #17/7 #1200ffff
> color #17/A:1492-1556 #ff8800ff
> save m15-if2-rbfa-in.png transparentBackground true
> hide #!17 models
> show #!28 models
> align #28/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #28 goldenrod
> color #28/A light gray
> hide #28/b cartoons
> show #28/b surfaces
> color #28/b #12ffffff
> color #28 goldenrod
> color #28/A light gray
> hide #28/2 cartoons
> show #28/2 surfaces
> color #28/2 #009000ff
> color #28/A:1492-1556 #ff8800ff
> save m15-ms37.png transparentBackground true
> hide #!28 models
> show #!25 models
> align #25/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #25 goldenrod
> color #25/A light gray
> hide #25/a cartoons
> show #25/a surfaces
> color #25/a #ff00ffff
> color #25 goldenrod
> color #25/A light gray
> hide #25/b cartoons
> show #25/b surfaces
> color #25/b #feff00ff
> color #25/A:1492-1556 #ff8800ff
> save rbfa-if3.png transparentBackground true
> hide #!25 models
> show #!26 models
> align #26/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #26 goldenrod
> color #26/A light gray
> hide #26/2 cartoons
> show #26/2 surfaces
> color #26/2 #009000ff
> color #26 goldenrod
> color #26/A light gray
> hide #26/8 cartoons
> show #26/8 surfaces
> color #26/8 #feff00ff
> color #26/A:1492-1556 #ff8800ff
> save ms37-if3.png transparentBackground true
> hide #!26 models
> show #!21 models
> align #21/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #21 goldenrod
> color #21/A light gray
> hide #21/2 cartoons
> show #21/2 surfaces
> color #21/2 #009000ff
> color #21 goldenrod
> color #21/A light gray
> hide #21/8 cartoons
> show #21/8 surfaces
> color #21/8 #feff00ff
> color #21 goldenrod
> color #21/A light gray
> hide #21/7 cartoons
> show #21/7 surfaces
> color #21/7 #1200ffff
> color #21/A:1492-1556 #ff8800ff
> save if2-if3-ms37.png transparentBackground true
> hide #!21 models
> show #!59 models
> align #59/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 0.941 angstroms
> color #59 goldenrod
> color #59/A light gray
> hide #59/9 cartoons
> show #59/9 surfaces
> color #59/9 #ab7afcff
> color #59 goldenrod
> color #59/A light gray
> hide #59/5 cartoons
> show #59/5 surfaces
> color #59/5 #3fff2eff
> color #59/A:1492-1556 #ff8800ff
> save noa1-tfb1m.png transparentBackground true
> hide #!59 models
> show #!60 models
> align #60/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 0.966 angstroms
> color #60 goldenrod
> color #60/A light gray
> hide #60/9 cartoons
> show #60/9 surfaces
> color #60/9 #ab7afcff
> color #60/A:1492-1556 #ff8800ff
> save noa1-without-tfb1m.png transparentBackground true
> hide #!60 models
> show #!62 models
> align #62/V toAtoms #22/V matchNumbering true
Pairing dropped 0 atoms and 2946 reference atoms
Traceback (most recent call last):
File "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py",
line 62, in
execute(commands)
File "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py",
line 26, in execute
run(session, command)
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/align.py", line 98, in align
raise UserError('No atoms paired for alignment')
chimerax.core.errors.UserError: No atoms paired for alignment
Error opening python file
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> show #!19 models
> open /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Laba/Data/NOA1/IP_cryoEM/sessions/Models/if2-if3-trna/if2_trna_rsfed_after_readyset.pdb
Chain information for if2_trna_rsfed_after_readyset.pdb #62
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
t | No description available
> hide #62 atoms
> show #62 cartoons
> select add #62
137676 atoms, 141274 bonds, 22 pseudobonds, 7508 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #62,0.66389,0.15262,-0.73209,272.41,-0.45863,-0.69014,-0.55979,829.07,-0.59068,0.7074,-0.38818,372.94
> view matrix models
> #62,0.8146,0.34716,-0.46466,86.911,-0.51595,0.067713,-0.85394,699.22,-0.26499,0.93536,0.23428,18.417
> view matrix models
> #62,0.61515,-0.046669,-0.78703,365.26,-0.30371,-0.93523,-0.18193,745.61,-0.72756,0.35095,-0.58948,584.73
> view matrix models
> #62,0.61189,-0.073943,-0.78748,374.83,-0.27941,-0.95164,-0.12775,727.21,-0.73995,0.2982,-0.60296,608.83
> view matrix models
> #62,0.37058,0.17723,-0.91174,407.64,-0.32021,-0.89707,-0.30453,775.18,-0.87186,0.4048,-0.27568,519.14
> view matrix models
> #62,0.75146,-0.22668,-0.61961,329.71,-0.28236,-0.95927,0.0084979,690.09,-0.5963,0.16857,-0.78486,658.98
> view matrix models
> #62,0.87409,-0.37341,-0.3107,246.11,-0.32958,-0.92575,0.18538,641.72,-0.35686,-0.059634,-0.93225,700.14
> view matrix models
> #62,0.89331,-0.40103,-0.20291,216.84,-0.3534,-0.9057,0.23414,628.34,-0.27767,-0.13745,-0.95079,705.53
> view matrix models
> #62,0.90382,-0.42165,-0.072893,181.48,-0.38608,-0.87702,0.28597,614.08,-0.18451,-0.23033,-0.95546,707.2
> view matrix models
> #62,0.92317,-0.36549,-0.11906,171.87,-0.35196,-0.92823,0.12049,668.55,-0.15455,-0.069325,-0.98555,657.14
> view matrix models
> #62,0.93365,-0.32931,-0.14087,163.93,-0.32959,-0.94387,0.022032,695.74,-0.14022,0.02586,-0.98978,624.56
> select clear
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3687787 atom styles
> style ringFill thin
Changed 383388 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
> NatCom/figures/figure 1 - overview classes"
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
NatCom/figures/figure 1 - overview classes
> view orig
> hide 62 atoms
Traceback (most recent call last):
File "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py",
line 62, in
execute(commands)
File "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py",
line 26, in execute
run(session, command)
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 2862, in run
raise UserError(self._error)
chimerax.core.errors.UserError: Expected a collection of one of 'atoms',
'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or
'surfaces' or a keyword
Error opening python file
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3624047 atom styles
> style ringFill thin
Changed 383388 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
> NatCom/figures/figure 1 - overview classes"
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
NatCom/figures/figure 1 - overview classes
> view orig
> hide 62 atoms
Traceback (most recent call last):
File "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py",
line 66, in
execute('hide {0} atoms'.format(model_id))
File "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py",
line 25, in execute
run(session, command)
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 2862, in run
raise UserError(self._error)
chimerax.core.errors.UserError: Expected a collection of one of 'atoms',
'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or
'surfaces' or a keyword
Error opening python file
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3624047 atom styles
> style ringFill thin
Changed 383388 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
> NatCom/figures/figure 1 - overview classes"
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
NatCom/figures/figure 1 - overview classes
> view orig
> hide #62 atoms
> show #62 cartoons
> align #62/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.157 angstroms
> color #62 goldenrod
> color #62/A light gray
> hide #62/2 cartoons
> show #62/2 surfaces
> color #62/2 009000ff
Traceback (most recent call last):
File "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py",
line 100, in
execute('color #{0}/{1} {2}'.format(
File "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py",
line 25, in execute
run(session, command)
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 2862, in run
raise UserError(self._error)
chimerax.core.errors.UserError: Expected a color or one of 'byatom',
'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide',
'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a
keyword
Error opening python file
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> ui mousemode right "tape measure"
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3624047 atom styles
> style ringFill thin
Changed 383388 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
> NatCom/figures/figure 1 - overview classes"
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
NatCom/figures/figure 1 - overview classes
> view orig
> hide #62 atoms
> show #62 cartoons
> align #62/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.157 angstroms
> color #62 goldenrod
> color #62/A light gray
> hide #62/2 cartoons
> show #62/2 surfaces
> color #62/2 #009000ff
> color #62 goldenrod
> color #62/A light gray
> hide #62/5 cartoons
> show #62/5 surfaces
> color #62/5 #ff6b85ff
> color #62 goldenrod
> color #62/A light gray
> hide #62/7 cartoons
> show #62/7 surfaces
> color #62/7 #1200ffff
> color #62/A:1492-1556 ff8800ff
Traceback (most recent call last):
File "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py",
line 128, in
execute('color #{0}/A:{1}-{2} {3}'.format(
File "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py",
line 25, in execute
run(session, command)
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 2862, in run
raise UserError(self._error)
chimerax.core.errors.UserError: Expected a color or one of 'byatom',
'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide',
'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a
keyword
Error opening python file
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3624047 atom styles
> style ringFill thin
Changed 383388 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd "/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
> NatCom/figures/figure 1 - overview classes"
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Laba/Papers/Planned/2023 NOA1 IP structure -
NatCom/figures/figure 1 - overview classes
> view orig
> hide #62 atoms
> show #62 cartoons
> align #62/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.157 angstroms
> color #62 goldenrod
> color #62/A light gray
> hide #62/2 cartoons
> show #62/2 surfaces
> color #62/2 #009000ff
> color #62 goldenrod
> color #62/A light gray
> hide #62/5 cartoons
> show #62/5 surfaces
> color #62/5 #ff6b85ff
> color #62 goldenrod
> color #62/A light gray
> hide #62/7 cartoons
> show #62/7 surfaces
> color #62/7 #1200ffff
> color #62/A:1492-1556 #ff8800ff
> save if2-ms37-trna.png transparentBackground true
> hide #!62 models
> hide #19 atoms
> show #19 cartoons
> align #19/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #19 goldenrod
> color #19/A light gray
> hide #19/c cartoons
> show #19/c surfaces
> color #19/c #ff00ffff
> color #19 goldenrod
> color #19/A light gray
> hide #19/b cartoons
> show #19/b surfaces
> color #19/b #12ffffff
> color #19 goldenrod
> color #19/A light gray
> hide #19/a cartoons
> show #19/a surfaces
> color #19/a #79ffa0ff
> color #19/A:1492-1556 #ff8800ff
> save m15-rbfa-in-pus1.png transparentBackground true
> hide #!19 models
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3624047 atom styles
> style ringFill thin
Changed 383388 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
> view orig
> hide #19 atoms
> show #19 cartoons
> align #19/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #19 goldenrod
> color #19/A light gray
> hide #19/c cartoons
> show #19/c surfaces
> color #19/c #ff00ffff
> color #19 goldenrod
> color #19/A light gray
> hide #19/b cartoons
> show #19/b surfaces
> color #19/b #12ffffff
> color #19 goldenrod
> color #19/A light gray
> hide #19/a cartoons
> show #19/a surfaces
> color #19/a #79ffa0ff
> color #19/A:1492-1556 #ff8800ff
> save m15-rbfa-in-pus1.png transparentBackground true
> hide #!19 models
> show #19 cartoons
> show #19
> show #!19
> show #!19 models
> hide #!19 models
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3624047 atom styles
> style ringFill thin
Changed 383388 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
> view orig
> show #!19 models
> hide #19 atoms
> show #19 cartoons
> align #19/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #19 goldenrod
> color #19/A light gray
> hide #19/c cartoons
> show #19/c surfaces
> color #19/c #ff00ffff
> color #19 goldenrod
> color #19/A light gray
> hide #19/b cartoons
> show #19/b surfaces
> color #19/b #12ffffff
> color #19 goldenrod
> color #19/A light gray
> hide #19/a cartoons
> show #19/a surfaces
> color #19/a #79ffa0ff
> color #19/A:1492-1556 #ff8800ff
> save m15-rbfa-in-pus1.png transparentBackground true
> hide #!19 models
> hide #!47 models
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3624047 atom styles
> style ringFill thin
Changed 383388 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
> view orig
> show #!22 models
> hide #22 atoms
> show #22 cartoons
> align #22/V toAtoms #22/V matchNumbering true
RMSD between 2946 atom pairs is 0.000 angstroms
> color #22 goldenrod
> color #22/A light gray
> hide #22/9 cartoons
> show #22/9 surfaces
> color #22/9 #f54242
> color #22 goldenrod
> color #22/A light gray
> hide #22/5 cartoons
> show #22/5 surfaces
> color #22/5 #FA8072
> color #22 goldenrod
> color #22/A light gray
> hide #22/7 cartoons
> show #22/7 surfaces
> color #22/7 #FF00FF
> color #22 goldenrod
> color #22/A light gray
> hide #22/a cartoons
> show #22/a surfaces
> color #22/a #FF69B4
> color #22 goldenrod
> color #22/A light gray
> hide #22/8 cartoons
> show #22/8 surfaces
> color #22/8 #964B00
> save 8csp-like.png transparentBackground true
> hide #!22 models
> show #!23 models
> hide #23 atoms
> show #23 cartoons
> align #23/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #23 goldenrod
> color #23/A light gray
> hide #23/9 cartoons
> show #23/9 surfaces
> color #23/9 #f54242
> color #23 goldenrod
> color #23/A light gray
> hide #23/a cartoons
> show #23/a surfaces
> color #23/a #ff00ffff
> save noa1-rbfa-in.png transparentBackground true
> hide #!23 models
> show #!18 models
> hide #18 atoms
> show #18 cartoons
> align #18/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #18 goldenrod
> color #18/A light gray
> hide #18/9 cartoons
> show #18/9 surfaces
> color #18/9 #f54242
> color #18 goldenrod
> color #18/A light gray
> hide #18/2 cartoons
> show #18/2 surfaces
> color #18/2 #009000ff
> color #18/A:1492-1556 #ff8800ff
> save noa1-new-ms37.png transparentBackground true
> hide #!18 models
> show #!20 models
> hide #20 atoms
> show #20 cartoons
> align #20/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #20 goldenrod
> color #20/A light gray
> hide #20/a cartoons
> show #20/a surfaces
> color #20/a #ff00ffff
> color #20 goldenrod
> color #20/A light gray
> hide #20/b cartoons
> show #20/b surfaces
> color #20/b #12ffffff
> color #20/A:1492-1556 #ff8800ff
> save m15-rbfa-in.png transparentBackground true
> hide #!20 models
> show #!17 models
> hide #17 atoms
> show #17 cartoons
> align #17/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #17 goldenrod
> color #17/A light gray
> hide #17/a cartoons
> show #17/a surfaces
> color #17/a #ff00ffff
> color #17 goldenrod
> color #17/A light gray
> hide #17/b cartoons
> show #17/b surfaces
> color #17/b #12ffffff
> color #17 goldenrod
> color #17/A light gray
> hide #17/7 cartoons
> show #17/7 surfaces
> color #17/7 #1200ffff
> color #17/A:1492-1556 #ff8800ff
> save m15-if2-rbfa-in.png transparentBackground true
> hide #!17 models
> show #!28 models
> hide #28 atoms
> show #28 cartoons
> align #28/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #28 goldenrod
> color #28/A light gray
> hide #28/b cartoons
> show #28/b surfaces
> color #28/b #12ffffff
> color #28 goldenrod
> color #28/A light gray
> hide #28/2 cartoons
> show #28/2 surfaces
> color #28/2 #009000ff
> color #28/A:1492-1556 #ff8800ff
> save m15-ms37.png transparentBackground true
> hide #!28 models
> show #!25 models
> hide #25 atoms
> show #25 cartoons
> align #25/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #25 goldenrod
> color #25/A light gray
> hide #25/a cartoons
> show #25/a surfaces
> color #25/a #ff00ffff
> color #25 goldenrod
> color #25/A light gray
> hide #25/b cartoons
> show #25/b surfaces
> color #25/b #feff00ff
> color #25/A:1492-1556 #ff8800ff
> save rbfa-if3.png transparentBackground true
> hide #!25 models
> show #!26 models
> hide #26 atoms
> show #26 cartoons
> align #26/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #26 goldenrod
> color #26/A light gray
> hide #26/2 cartoons
> show #26/2 surfaces
> color #26/2 #009000ff
> color #26 goldenrod
> color #26/A light gray
> hide #26/8 cartoons
> show #26/8 surfaces
> color #26/8 #feff00ff
> color #26/A:1492-1556 #ff8800ff
> save ms37-if3.png transparentBackground true
> hide #!26 models
> show #!21 models
> hide #21 atoms
> show #21 cartoons
> align #21/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #21 goldenrod
> color #21/A light gray
> hide #21/2 cartoons
> show #21/2 surfaces
> color #21/2 #009000ff
> color #21 goldenrod
> color #21/A light gray
> hide #21/8 cartoons
> show #21/8 surfaces
> color #21/8 #feff00ff
> color #21 goldenrod
> color #21/A light gray
> hide #21/7 cartoons
> show #21/7 surfaces
> color #21/7 #1200ffff
> color #21/A:1492-1556 #ff8800ff
> save if2-if3-ms37.png transparentBackground true
> hide #!21 models
> show #!59 models
> hide #59 atoms
> show #59 cartoons
> align #59/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 0.941 angstroms
> color #59 goldenrod
> color #59/A light gray
> hide #59/9 cartoons
> show #59/9 surfaces
> color #59/9 #ab7afcff
> color #59 goldenrod
> color #59/A light gray
> hide #59/5 cartoons
> show #59/5 surfaces
> color #59/5 #3fff2eff
> color #59/A:1492-1556 #ff8800ff
> save noa1-tfb1m.png transparentBackground true
> hide #!59 models
> show #!60 models
> hide #60 atoms
> show #60 cartoons
> align #60/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 0.966 angstroms
> color #60 goldenrod
> color #60/A light gray
> hide #60/9 cartoons
> show #60/9 surfaces
> color #60/9 #ab7afcff
> color #60/A:1492-1556 #ff8800ff
> save noa1-without-tfb1m.png transparentBackground true
> hide #!60 models
> show #!62 models
> hide #62 atoms
> show #62 cartoons
> align #62/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.157 angstroms
> color #62 goldenrod
> color #62/A light gray
> hide #62/2 cartoons
> show #62/2 surfaces
> color #62/2 #009000ff
> color #62 goldenrod
> color #62/A light gray
> hide #62/5 cartoons
> show #62/5 surfaces
> color #62/5 #ff6b85ff
> color #62 goldenrod
> color #62/A light gray
> hide #62/7 cartoons
> show #62/7 surfaces
> color #62/7 #1200ffff
> color #62/A:1492-1556 #ff8800ff
> save if2-ms37-trna.png transparentBackground true
> hide #!62 models
> show #!19 models
> hide #19 atoms
> show #19 cartoons
> align #19/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #19 goldenrod
> color #19/A light gray
> hide #19/c cartoons
> show #19/c surfaces
> color #19/c #ff00ffff
> color #19 goldenrod
> color #19/A light gray
> hide #19/b cartoons
> show #19/b surfaces
> color #19/b #12ffffff
> color #19 goldenrod
> color #19/A light gray
> hide #19/a cartoons
> show #19/a surfaces
> color #19/a #79ffa0ff
> color #19/A:1492-1556 #ff8800ff
> save m15-rbfa-in-pus1.png transparentBackground true
> hide #!19 models
> show #!22 models
> color #22/9 #f54242
> hide #!22 models
> show #!22 models
> hide #22 atoms
> show #22 cartoons
> color #22 goldenrod
> hide #!22 models
> show #!22 models
> hide #!22 models
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3624047 atom styles
> style ringFill thin
Changed 383388 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
> view orig
> show #!22 models
> hide #22 atoms
> show #22 cartoons
> align #22/V toAtoms #22/V matchNumbering true
RMSD between 2946 atom pairs is 0.000 angstroms
> color #22 goldenrod
> color #22/A light gray
> hide #22/9 cartoons
> show #22/9 surfaces
> color #22/9 #f54242
> hide #22/5 cartoons
> show #22/5 surfaces
> color #22/5 #FA8072
> hide #22/7 cartoons
> show #22/7 surfaces
> color #22/7 #FF00FF
> hide #22/a cartoons
> show #22/a surfaces
> color #22/a #FF69B4
> hide #22/8 cartoons
> show #22/8 surfaces
> color #22/8 #964B00
> save 8csp-like.png transparentBackground true
> hide #!22 models
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3624047 atom styles
> style ringFill thin
Changed 383388 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
> view orig
> show #!22 models
> hide #22 atoms
> show #22 cartoons
> align #22/V toAtoms #22/V matchNumbering true
RMSD between 2946 atom pairs is 0.000 angstroms
> color #22 goldenrod
> color #22/A light gray
> hide #22/9 cartoons
> show #22/9 surfaces
> color #22/9 #f54242
> hide #22/5 cartoons
> show #22/5 surfaces
> color #22/5 #FA8072
> hide #22/7 cartoons
> show #22/7 surfaces
> color #22/7 #FF00FF
> hide #22/a cartoons
> show #22/a surfaces
> color #22/a #FF69B4
> hide #22/8 cartoons
> show #22/8 surfaces
> color #22/8 #964B00
> save 8csp-like.png transparentBackground true
> hide #!22 models
> show #!23 models
> hide #23 atoms
> show #23 cartoons
> align #23/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #23 goldenrod
> color #23/A light gray
> hide #23/9 cartoons
> show #23/9 surfaces
> color #23/9 #f54242
> hide #23/a cartoons
> show #23/a surfaces
> color #23/a #ff00ffff
> save noa1-rbfa-in.png transparentBackground true
> hide #!23 models
> show #!18 models
> hide #18 atoms
> show #18 cartoons
> align #18/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #18 goldenrod
> color #18/A light gray
> hide #18/9 cartoons
> show #18/9 surfaces
> color #18/9 #f54242
> hide #18/2 cartoons
> show #18/2 surfaces
> color #18/2 #009000ff
> color #18/A:1492-1556 #ff8800ff
> save noa1-new-ms37.png transparentBackground true
> hide #!18 models
> show #!20 models
> hide #20 atoms
> show #20 cartoons
> align #20/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #20 goldenrod
> color #20/A light gray
> hide #20/a cartoons
> show #20/a surfaces
> color #20/a #ff00ffff
> hide #20/b cartoons
> show #20/b surfaces
> color #20/b #12ffffff
> color #20/A:1492-1556 #ff8800ff
> save m15-rbfa-in.png transparentBackground true
> hide #!20 models
> show #!17 models
> hide #17 atoms
> show #17 cartoons
> align #17/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #17 goldenrod
> color #17/A light gray
> hide #17/a cartoons
> show #17/a surfaces
> color #17/a #ff00ffff
> hide #17/b cartoons
> show #17/b surfaces
> color #17/b #12ffffff
> hide #17/7 cartoons
> show #17/7 surfaces
> color #17/7 #1200ffff
> color #17/A:1492-1556 #ff8800ff
> save m15-if2-rbfa-in.png transparentBackground true
> hide #!17 models
> show #!28 models
> hide #28 atoms
> show #28 cartoons
> align #28/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #28 goldenrod
> color #28/A light gray
> hide #28/b cartoons
> show #28/b surfaces
> color #28/b #12ffffff
> hide #28/2 cartoons
> show #28/2 surfaces
> color #28/2 #009000ff
> color #28/A:1492-1556 #ff8800ff
> save m15-ms37.png transparentBackground true
> hide #!28 models
> show #!25 models
> hide #25 atoms
> show #25 cartoons
> align #25/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #25 goldenrod
> color #25/A light gray
> hide #25/a cartoons
> show #25/a surfaces
> color #25/a #ff00ffff
> hide #25/b cartoons
> show #25/b surfaces
> color #25/b #feff00ff
> color #25/A:1492-1556 #ff8800ff
> save rbfa-if3.png transparentBackground true
> hide #!25 models
> show #!26 models
> hide #26 atoms
> show #26 cartoons
> align #26/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #26 goldenrod
> color #26/A light gray
> hide #26/2 cartoons
> show #26/2 surfaces
> color #26/2 #009000ff
> hide #26/8 cartoons
> show #26/8 surfaces
> color #26/8 #feff00ff
> color #26/A:1492-1556 #ff8800ff
> save ms37-if3.png transparentBackground true
> hide #!26 models
> show #!21 models
> hide #21 atoms
> show #21 cartoons
> align #21/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #21 goldenrod
> color #21/A light gray
> hide #21/2 cartoons
> show #21/2 surfaces
> color #21/2 #009000ff
> hide #21/8 cartoons
> show #21/8 surfaces
> color #21/8 #feff00ff
> hide #21/7 cartoons
> show #21/7 surfaces
> color #21/7 #1200ffff
> color #21/A:1492-1556 #ff8800ff
> save if2-if3-ms37.png transparentBackground true
> hide #!21 models
> show #!59 models
> hide #59 atoms
> show #59 cartoons
> align #59/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 0.941 angstroms
> color #59 goldenrod
> color #59/A light gray
> hide #59/9 cartoons
> show #59/9 surfaces
> color #59/9 #ab7afcff
> hide #59/5 cartoons
> show #59/5 surfaces
> color #59/5 #3fff2eff
> color #59/A:1492-1556 #ff8800ff
> save noa1-tfb1m.png transparentBackground true
> hide #!59 models
> show #!60 models
> hide #60 atoms
> show #60 cartoons
> align #60/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 0.966 angstroms
> color #60 goldenrod
> color #60/A light gray
> hide #60/9 cartoons
> show #60/9 surfaces
> color #60/9 #ab7afcff
> color #60/A:1492-1556 #ff8800ff
> save noa1-without-tfb1m.png transparentBackground true
> hide #!60 models
> show #!62 models
> hide #62 atoms
> show #62 cartoons
> align #62/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.157 angstroms
> color #62 goldenrod
> color #62/A light gray
> hide #62/2 cartoons
> show #62/2 surfaces
> color #62/2 #009000ff
> hide #62/5 cartoons
> show #62/5 surfaces
> color #62/5 #ff6b85ff
> hide #62/7 cartoons
> show #62/7 surfaces
> color #62/7 #1200ffff
> color #62/A:1492-1556 #ff8800ff
> save if2-ms37-trna.png transparentBackground true
> hide #!62 models
> show #!19 models
> hide #19 atoms
> show #19 cartoons
> align #19/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #19 goldenrod
> color #19/A light gray
> hide #19/c cartoons
> show #19/c surfaces
> color #19/c #ff00ffff
> hide #19/b cartoons
> show #19/b surfaces
> color #19/b #12ffffff
> hide #19/a cartoons
> show #19/a surfaces
> color #19/a #79ffa0ff
> color #19/A:1492-1556 #ff8800ff
> save m15-rbfa-in-pus1.png transparentBackground true
> hide #!19 models
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3624047 atom styles
> style ringFill thin
Changed 383388 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
> view orig
> show #!22 models
> hide #22 atoms
> show #22 cartoons
> align #22/V toAtoms #22/V matchNumbering true
RMSD between 2946 atom pairs is 0.000 angstroms
> color #22 goldenrod
> color #22/A light gray
> hide #22/9 cartoons
> show #22/9 surfaces
> color #22/9 #f54242
> hide #22/5 cartoons
> show #22/5 surfaces
> color #22/5 #FA8072
> hide #22/7 cartoons
> show #22/7 surfaces
> color #22/7 #FF00FF
> hide #22/a cartoons
> show #22/a surfaces
> color #22/a #FF69B4
> hide #22/8 cartoons
> show #22/8 surfaces
> color #22/8 #964B00
> save 8csp-like.png transparentBackground true
> hide #!22 models
> show #!59 models
> hide #59 atoms
> show #59 cartoons
> align #59/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 0.941 angstroms
> color #59 goldenrod
> color #59/A light gray
> hide #59/9 cartoons
> show #59/9 surfaces
> color #59/9 #f54242
> hide #59/5 cartoons
> show #59/5 surfaces
> color #59/5 #FA8072
> color #59/A:1492-1556 #ff8800ff
> save noa1-tfb1m.png transparentBackground true
> hide #!59 models
> show #!60 models
> hide #60 atoms
> show #60 cartoons
> align #60/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 0.966 angstroms
> color #60 goldenrod
> color #60/A light gray
> hide #60/9 cartoons
> show #60/9 surfaces
> color #60/9 #f54242
> color #60/A:1492-1556 #ff8800ff
> save noa1-without-tfb1m.png transparentBackground true
> hide #!60 models
> show #!23 models
> hide #23 atoms
> show #23 cartoons
> align #23/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #23 goldenrod
> color #23/A light gray
> hide #23/9 cartoons
> show #23/9 surfaces
> color #23/9 #f54242
> hide #23/a cartoons
> show #23/a surfaces
> color #23/a #ff00ffff
> save noa1-rbfa-in.png transparentBackground true
> hide #!23 models
> show #!18 models
> hide #18 atoms
> show #18 cartoons
> align #18/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #18 goldenrod
> color #18/A light gray
> hide #18/9 cartoons
> show #18/9 surfaces
> color #18/9 #f54242
> hide #18/2 cartoons
> show #18/2 surfaces
> color #18/2 #009000ff
> color #18/A:1492-1556 #ff8800ff
> save noa1-new-ms37.png transparentBackground true
> hide #!18 models
> show #!20 models
> hide #20 atoms
> show #20 cartoons
> align #20/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #20 goldenrod
> color #20/A light gray
> hide #20/a cartoons
> show #20/a surfaces
> color #20/a #ff00ffff
> hide #20/b cartoons
> show #20/b surfaces
> color #20/b #12ffffff
> color #20/A:1492-1556 #ff8800ff
> save m15-rbfa-in.png transparentBackground true
> hide #!20 models
> show #!17 models
> hide #17 atoms
> show #17 cartoons
> align #17/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #17 goldenrod
> color #17/A light gray
> hide #17/a cartoons
> show #17/a surfaces
> color #17/a #ff00ffff
> hide #17/b cartoons
> show #17/b surfaces
> color #17/b #12ffffff
> hide #17/7 cartoons
> show #17/7 surfaces
> color #17/7 #1200ffff
> color #17/A:1492-1556 #ff8800ff
> save m15-if2-rbfa-in.png transparentBackground true
> hide #!17 models
> show #!28 models
> hide #28 atoms
> show #28 cartoons
> align #28/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #28 goldenrod
> color #28/A light gray
> hide #28/b cartoons
> show #28/b surfaces
> color #28/b #12ffffff
> hide #28/2 cartoons
> show #28/2 surfaces
> color #28/2 #009000ff
> color #28/A:1492-1556 #ff8800ff
> save m15-ms37.png transparentBackground true
> hide #!28 models
> show #!25 models
> hide #25 atoms
> show #25 cartoons
> align #25/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #25 goldenrod
> color #25/A light gray
> hide #25/a cartoons
> show #25/a surfaces
> color #25/a #ff00ffff
> hide #25/b cartoons
> show #25/b surfaces
> color #25/b #feff00ff
> color #25/A:1492-1556 #ff8800ff
> save rbfa-if3.png transparentBackground true
> hide #!25 models
> show #!26 models
> hide #26 atoms
> show #26 cartoons
> align #26/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #26 goldenrod
> color #26/A light gray
> hide #26/2 cartoons
> show #26/2 surfaces
> color #26/2 #009000ff
> hide #26/8 cartoons
> show #26/8 surfaces
> color #26/8 #feff00ff
> color #26/A:1492-1556 #ff8800ff
> save ms37-if3.png transparentBackground true
> hide #!26 models
> show #!21 models
> hide #21 atoms
> show #21 cartoons
> align #21/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #21 goldenrod
> color #21/A light gray
> hide #21/2 cartoons
> show #21/2 surfaces
> color #21/2 #009000ff
> hide #21/8 cartoons
> show #21/8 surfaces
> color #21/8 #feff00ff
> hide #21/7 cartoons
> show #21/7 surfaces
> color #21/7 #1200ffff
> color #21/A:1492-1556 #ff8800ff
> save if2-if3-ms37.png transparentBackground true
> hide #!21 models
> show #!62 models
> hide #62 atoms
> show #62 cartoons
> align #62/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.157 angstroms
> color #62 goldenrod
> color #62/A light gray
> hide #62/2 cartoons
> show #62/2 surfaces
> color #62/2 #009000ff
> hide #62/5 cartoons
> show #62/5 surfaces
> color #62/5 #ff6b85ff
> hide #62/7 cartoons
> show #62/7 surfaces
> color #62/7 #1200ffff
> color #62/A:1492-1556 #ff8800ff
> save if2-ms37-trna.png transparentBackground true
> hide #!62 models
> show #!19 models
> hide #19 atoms
> show #19 cartoons
> align #19/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #19 goldenrod
> color #19/A light gray
> hide #19/c cartoons
> show #19/c surfaces
> color #19/c #ff00ffff
> hide #19/b cartoons
> show #19/b surfaces
> color #19/b #12ffffff
> hide #19/a cartoons
> show #19/a surfaces
> color #19/a #79ffa0ff
> color #19/A:1492-1556 #ff8800ff
> save m15-rbfa-in-pus1.png transparentBackground true
> hide #!19 models
> show #!22 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!62 models
> color #62/3 teal
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> show #!19 models
> marker segment #63 position 310.4,315.2,373.2 toPosition 369.4,326.8,457.8
> color yellow radius 0.1 label 103.8 labelHeight 10.38 labelColor yellow
> marker segment #63 position 327.9,309.8,348.2 toPosition 348.7,306.3,374.7
> color yellow radius 0.1 label 33.81 labelHeight 3.381 labelColor yellow
> marker delete #63
> hide #!62 models
> hide #!19 models
> show #!21 models
> show #!19 models
> hide #!19 models
> hide #!21 models
> show #!26 models
> show #!25 models
> hide #!26 models
> show #!28 models
> hide #!25 models
> hide #!28 models
> show #!28 models
> show #!17 models
> hide #!28 models
> show #!20 models
> hide #!20 models
> hide #!17 models
> show #!20 models
> hide #!20 models
> show #!18 models
> hide #!18 models
> show #!22 models
> show #!23 models
> hide #!22 models
> marker segment #63 position 320.3,326.1,368.5 toPosition 323.2,252.1,332.3
> color yellow radius 0.1 label 82.46 labelHeight 8.246 labelColor yellow
> show #!28 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!63 models
> ui mousemode right "tape measure"
> ui mousemode right "rotate selected models"
> ui mousemode right translate
> ui mousemode right zoom
> show #!60 models
> hide #!28 models
> show #!59 models
> hide #!60 models
> runscript /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/noa1_fig1_vivek_style.py
> graphics silhouettes true width 1
> set bgColor white
> lighting soft shadows false depthCue true depthCueStart 0.5
> lighting depthCueEnd 1.5 ambientIntensity 1.25 fillIntensity 0.2 intensity
> 0.1
> material ambientReflectivity 0.8
> windowsize 1800 1490
> style all stick
Changed 3624049 atom styles
> style ringFill thin
Changed 383390 residue ring styles
> transparency 20 cartoons
> delete H
> cartoon style modeHelix tube radius 1.4
> cd /Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
Current working directory is:
/Users/dmitrii.shiriaev/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/Code/lab/chimerax_scripting/noa1_figures/figures
> view orig
> show #!22 models
> hide #22 atoms
> show #22 cartoons
> align #22/V toAtoms #22/V matchNumbering true
RMSD between 2946 atom pairs is 0.000 angstroms
> color #22 goldenrod
> color #22/A light gray
> hide #22/9 cartoons
> show #22/9 surfaces
> color #22/9 #f54242
> hide #22/5 cartoons
> show #22/5 surfaces
> color #22/5 #FA8072
> hide #22/7 cartoons
> show #22/7 surfaces
> color #22/7 #FF00FF
> hide #22/a cartoons
> show #22/a surfaces
> color #22/a #FF69B4
> hide #22/8 cartoons
> show #22/8 surfaces
> color #22/8 #964B00
> save 8csp-like.png transparentBackground true
> hide #!22 models
> show #!59 models
> hide #59 atoms
> show #59 cartoons
> align #59/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 0.941 angstroms
> color #59 goldenrod
> color #59/A light gray
> hide #59/9 cartoons
> show #59/9 surfaces
> color #59/9 #f54242
> hide #59/5 cartoons
> show #59/5 surfaces
> color #59/5 #FA8072
> color #59/A:1492-1556 #ff8800ff
> save noa1-tfb1m.png transparentBackground true
> hide #!59 models
> show #!60 models
> hide #60 atoms
> show #60 cartoons
> align #60/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 0.966 angstroms
> color #60 goldenrod
> color #60/A light gray
> hide #60/9 cartoons
> show #60/9 surfaces
> color #60/9 #f54242
> color #60/A:1492-1556 #ff8800ff
> save noa1-without-tfb1m.png transparentBackground true
> hide #!60 models
> show #!23 models
> hide #23 atoms
> show #23 cartoons
> align #23/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #23 goldenrod
> color #23/A light gray
> hide #23/9 cartoons
> show #23/9 surfaces
> color #23/9 #f54242
> hide #23/a cartoons
> show #23/a surfaces
> color #23/a #ff00ffff
> save noa1-rbfa-in.png transparentBackground true
> hide #!23 models
> show #!18 models
> hide #18 atoms
> show #18 cartoons
> align #18/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #18 goldenrod
> color #18/A light gray
> hide #18/9 cartoons
> show #18/9 surfaces
> color #18/9 #f54242
> hide #18/2 cartoons
> show #18/2 surfaces
> color #18/2 #009000ff
> hide #18/3 cartoons
> show #18/3 surfaces
> color #18/3 #008080
> color #18/A:1492-1556 #ff8800ff
> save noa1-new-ms37.png transparentBackground true
> hide #!18 models
> show #!20 models
> hide #20 atoms
> show #20 cartoons
> align #20/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #20 goldenrod
> color #20/A light gray
> hide #20/a cartoons
> show #20/a surfaces
> color #20/a #ff00ffff
> hide #20/b cartoons
> show #20/b surfaces
> color #20/b #12ffffff
> hide #20/3 cartoons
> show #20/3 surfaces
> color #20/3 #008080
> color #20/A:1492-1556 #ff8800ff
> save m15-rbfa-in.png transparentBackground true
> hide #!20 models
> show #!17 models
> hide #17 atoms
> show #17 cartoons
> align #17/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #17 goldenrod
> color #17/A light gray
> hide #17/a cartoons
> show #17/a surfaces
> color #17/a #ff00ffff
> hide #17/b cartoons
> show #17/b surfaces
> color #17/b #12ffffff
> hide #17/7 cartoons
> show #17/7 surfaces
> color #17/7 #1200ffff
> hide #17/3 cartoons
> show #17/3 surfaces
> color #17/3 #008080
> color #17/A:1492-1556 #ff8800ff
> save m15-if2-rbfa-in.png transparentBackground true
> hide #!17 models
> show #!28 models
> hide #28 atoms
> show #28 cartoons
> align #28/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #28 goldenrod
> color #28/A light gray
> hide #28/b cartoons
> show #28/b surfaces
> color #28/b #12ffffff
> hide #28/2 cartoons
> show #28/2 surfaces
> color #28/2 #009000ff
> hide #28/3 cartoons
> show #28/3 surfaces
> color #28/3 #008080
> color #28/A:1492-1556 #ff8800ff
> save m15-ms37.png transparentBackground true
> hide #!28 models
> show #!25 models
> hide #25 atoms
> show #25 cartoons
> align #25/V toAtoms #22/V matchNumbering true
Pairing dropped 24 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.124 angstroms
> color #25 goldenrod
> color #25/A light gray
> hide #25/a cartoons
> show #25/a surfaces
> color #25/a #ff00ffff
> hide #25/b cartoons
> show #25/b surfaces
> color #25/b #feff00ff
> hide #25/3 cartoons
> show #25/3 surfaces
> color #25/3 #008080
> color #25/A:1492-1556 #ff8800ff
> save rbfa-if3.png transparentBackground true
> hide #!25 models
> show #!26 models
> hide #26 atoms
> show #26 cartoons
> align #26/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #26 goldenrod
> color #26/A light gray
> hide #26/2 cartoons
> show #26/2 surfaces
> color #26/2 #009000ff
> hide #26/8 cartoons
> show #26/8 surfaces
> color #26/8 #feff00ff
> hide #26/3 cartoons
> show #26/3 surfaces
> color #26/3 #008080
> color #26/A:1492-1556 #ff8800ff
> save ms37-if3.png transparentBackground true
> hide #!26 models
> show #!21 models
> hide #21 atoms
> show #21 cartoons
> align #21/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #21 goldenrod
> color #21/A light gray
> hide #21/2 cartoons
> show #21/2 surfaces
> color #21/2 #009000ff
> hide #21/8 cartoons
> show #21/8 surfaces
> color #21/8 #feff00ff
> hide #21/7 cartoons
> show #21/7 surfaces
> color #21/7 #1200ffff
> hide #21/3 cartoons
> show #21/3 surfaces
> color #21/3 #008080
> color #21/A:1492-1556 #ff8800ff
> save if2-if3-ms37.png transparentBackground true
> hide #!21 models
> show #!62 models
> hide #62 atoms
> show #62 cartoons
> align #62/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.157 angstroms
> color #62 goldenrod
> color #62/A light gray
> hide #62/2 cartoons
> show #62/2 surfaces
> color #62/2 #009000ff
> hide #62/5 cartoons
> show #62/5 surfaces
> color #62/5 #ff6b85ff
> hide #62/7 cartoons
> show #62/7 surfaces
> color #62/7 #1200ffff
> hide #62/3 cartoons
> show #62/3 surfaces
> color #62/3 #008080
> color #62/A:1492-1556 #ff8800ff
> save if2-ms37-trna.png transparentBackground true
> hide #!62 models
> show #!19 models
> hide #19 atoms
> show #19 cartoons
> align #19/V toAtoms #22/V matchNumbering true
Pairing dropped 23 atoms and 0 reference atoms
RMSD between 2946 atom pairs is 1.308 angstroms
> color #19 goldenrod
> color #19/A light gray
> hide #19/c cartoons
> show #19/c surfaces
> color #19/c #ff00ffff
> hide #19/b cartoons
> show #19/b surfaces
> color #19/b #12ffffff
> hide #19/a cartoons
> show #19/a surfaces
> color #19/a #79ffa0ff
> hide #19/3 cartoons
> show #19/3 surfaces
> color #19/3 #008080
> color #19/A:1492-1556 #ff8800ff
> save m15-rbfa-in-pus1.png transparentBackground true
> hide #!19 models
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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-5.5.17
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: 64 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0)
OS Loader Version: 580~1678
Software:
System Software Overview:
System Version: macOS 14.4 (23E214)
Kernel Version: Darwin 23.4.0
Time since boot: 2 hours, 57 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: No
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: 2022.2.22
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
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 (2)
comment:1 by , 19 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Dmitrii,
windowing toolkit that ChimeraX uses that has to do with waking from sleep
on a Mac when multiple displays are connected. In the 1.7 release we have
switched to a different version of the Qt toolkit that does not have that
problem, so if you use that release then you won't get these crashes
anymore.
--Eric