id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14960 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 dmitrii.shiriaev@… Eric Pettersen "{{{ 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 {""app_name"":""ChimeraX"",""timestamp"":""2024-04-10 16:16:42.00 +0200"",""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 14.4 (23E214)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""B9DD7586-DA21-49FC-BDF1-F1412FE6BE2E""} { ""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. 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""rolloutId"" : ""6434420a89ec2e0a7a38bf5a"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ ] } } ===== 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 }}} " defect closed normal Window Toolkit duplicate Tom Goddard all ChimeraX