id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10059 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… 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 0x00007ff859b4a640 (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"":""2023-10-24 17:14:11.00 +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 13.4.1 (22F770820d)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""D26681C4-6AC9-4DAF-B068-6194C367761B""} { ""uptime"" : 55000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 7336, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,2"", ""coalitionID"" : 1202, ""osVersion"" : { ""train"" : ""macOS 13.4.1"", ""build"" : ""22F770820d"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-10-24 17:14:08.1325 +0200"", ""incident"" : ""D26681C4-6AC9-4DAF-B068-6194C367761B"", ""pid"" : 79345, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-10-24 10:22:01.2834 +0200"", ""procStartAbsTime"" : 31100993267776, ""procExitAbsTime"" : 55827016569167, ""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"":""1545732F-3ECF-5423-8838-9536F50DE789"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""E8834526-84A6-79EE-EAB6-12A98E7DF4C1"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 24806, ""bridgeVersion"" : {""build"":""20P5060"",""train"":""7.5""}, ""sleepWakeUUID"" : ""A31B1434-0BFC-4ECD-8858-666C3C0028C0"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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""com.apple.main-thread"" } }, ""logWritingSignature"" : ""f8251187cc95cc0bd904e3737f2acf0a8a81fe39"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62699e1ec1ff2978b47f6c3b"", ""factorPackIds"" : { ""SIRI_FIND_MY_CONFIGURATION_FILES"" : ""652805151bce5442b8d752e1"" }, ""deploymentId"" : 240000031 }, { ""rolloutId"" : ""6391cacc75b0720ff1f8c695"", ""factorPackIds"" : { ""COREOS_ICD"" : ""63957f508061fa721c8edc4a"" }, ""deploymentId"" : 240000007 } ], ""experiments"" : [ { ""treatmentId"" : ""a092db1b-c401-44fa-9c54-518b7d69ca61"", ""experimentId"" : ""64a844035c85000c0f42398a"", ""deploymentId"" : 400000019 }, { ""treatmentId"" : ""d28d100b-301c-49ae-b6c9-57930102d4d4"", ""experimentId"" : ""64466b09a3b9440a82a18c34"", ""deploymentId"" : 400000002 } ] } } ===== Log before crash start ===== 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/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_ISOLDE/6Flagellin_3.1A-PP- > WholeSimSettled.cxs format session No such file/path: /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_ISOLDE/6Flagellin_3.1A-PP- WholeSimSettled.cxs > open > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_ISOLDE/6Flagellin_3.1A-PP- > WholeSimSettled.cxs format session Opened Rhom_single_Map_3.1A.mrc as #2, grid size 62,90,171, pixel 0.94,0.94,0.94, shown at level 0.0155, step 1, values float32 Opened Rhom_Flagella_Map_2RingMasked.mrc as #3.1.1.1, grid size 200,201,275, pixel 0.94,0.94,0.94, shown at level 0.0186, step 1, values float32 Opened run_class001.mrc as #4, grid size 384,384,384, pixel 0.94, shown at level 0.00773, step 2, values float32 Opened postprocess_masked.mrc as #5, grid size 384,384,384, pixel 0.94, shown at level 0.0178, step 2, values float32 opened ChimeraX session > hide cartoons > select #3/C 4139 atoms, 4151 bonds, 1 pseudobond, 273 residues, 2 models selected > show sel cartoons > hide all > show #3/C > isolde start > set selectionWidth 4 > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 > select #3/C 4139 atoms, 4151 bonds, 1 pseudobond, 273 residues, 2 models selected > isolde sim start /C ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde set simFidelityMode Lowest/Fastest ISOLDE: setting sim fidelity mode to Lowest/Fastest nonbonded_cutoff_distance = 0.900000 use_gbsa = False > isolde set simFidelityMode Lowest/Fastest ISOLDE: setting sim fidelity mode to Lowest/Fastest nonbonded_cutoff_distance = 0.900000 use_gbsa = False > isolde sim start /C ISOLDE: started sim > ui tool show ""Ramachandran Plot"" > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > isolde sim start /C:81 ISOLDE: started sim > isolde pepflip /C:81 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:388 ISOLDE: started sim > isolde pepflip /C:388 > isolde sim resume > select clear > isolde sim resume > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:42 ISOLDE: started sim > isolde pepflip /C:42 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:42 ISOLDE: started sim > isolde pepflip /C:42 > isolde pepflip #!3.2/C:42 > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:40 ISOLDE: started sim > isolde pepflip /C:40 > isolde pepflip /C:39 > isolde pepflip /C:40 > isolde pepflip /C:38 > isolde pepflip /C:42 Unable to flip peptide bond after 50 rounds. Giving up. > isolde pepflip /C:42 > isolde pepflip /C:43 > isolde pepflip #!3.2/C:42 > isolde pepflip /C:42 > isolde pepflip /C:41 > isolde pepflip /C:42 Traceback (most recent call last): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 138, in invoke return self._func(self._name, data) File ""/Users/mbell/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/delayed_reaction.py"", line 81, in callback self.ff(*self.ff_args) File ""/Users/mbell/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1531, in _update_coordinates_and_repeat self.atoms.coords = th.coords File ""/Users/mbell/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 101, in coords return self.current_coords RuntimeError: Particle coordinate is NaN. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan Error processing trigger ""new frame"": RuntimeError: Particle coordinate is NaN. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan File ""/Users/mbell/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 101, in coords return self.current_coords See log for complete Python traceback. > isolde sim pause > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:40 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:138 ISOLDE: started sim > isolde pepflip /C:138 > isolde pepflip /C:140 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select clear > isolde sim start /C:378 ISOLDE: started sim > isolde pepflip /C:378 > isolde pepflip /C:379 > isolde pepflip /C:378 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:398 ISOLDE: started sim > isolde pepflip /C:398 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:405 ISOLDE: started sim > select clear > isolde pepflip /C:405 > isolde cisflip /C:405 > isolde pepflip /C:405 Unable to flip peptide bond after 50 rounds. Giving up. > isolde cisflip /C:405 > isolde pepflip /C:406 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:383 ISOLDE: started sim > isolde pepflip /C:383 > isolde pepflip /C:384 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:408 ISOLDE: started sim > isolde sim resume > isolde pepflip /C:408 > isolde sim resume > isolde pepflip #!3.2/C:406 > isolde pepflip /C:408 > isolde pepflip /C:407 > select clear > isolde sim resume > select clear > isolde pepflip /C:406 > isolde pepflip /C:408 > isolde cisflip /C:408 > isolde pepflip /C:408 Unable to flip peptide bond after 50 rounds. Giving up. > isolde pepflip /C:408 Unable to flip peptide bond after 50 rounds. Giving up. > isolde sim resume > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:42 ISOLDE: started sim > isolde pepflip /C:42 > isolde pepflip /C:40 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:441 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:479 ISOLDE: started sim > isolde sim resume > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:493 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:123 ISOLDE: started sim > isolde sim resume > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_ISOLDE/Current.cxs Taking snapshot of stepper: 6_Flagellin_Selection_ForMask.pdb > show #3/C > select #3/C 4139 atoms, 4151 bonds, 1 pseudobond, 273 residues, 2 models selected > isolde sim start /C ISOLDE: started sim > isolde pepflip /C:42 > isolde pepflip /C:383 > isolde pepflip /C:398 > isolde pepflip /C:116 > isolde pepflip /C:140 > isolde pepflip /C:141 > isolde pepflip /C:472 > isolde pepflip /C:408 > isolde pepflip /C:117 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 6 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:28 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:469 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:469 ISOLDE: started sim > show #3/D > select clear > isolde pepflip /C:472 > select clear > isolde sim resume > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:388 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:454 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:3 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:120 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:75 ISOLDE: started sim > isolde sim resume > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:5 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:502 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:103 ISOLDE: started sim > isolde cisflip /C:100 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #!3.2/C:100 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:92 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:41 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:488 ISOLDE: started sim > isolde pepflip #!3.2/C:488 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > isolde sim start /C:31 ISOLDE: started sim > show #3/E > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #3.2 to IUPAC-IUB standards. ISOLDE: stopped sim > hide #3/E > isolde sim start /C:388 ISOLDE: started sim > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:417 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_ISOLDE/Current.cxs Taking snapshot of stepper: 6_Flagellin_Selection_ForMask.pdb > select clear > isolde sim start /C:504 ISOLDE: started sim > isolde pepflip /C:504 > isolde pepflip /C:505 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:39 ISOLDE: started sim > isolde pepflip /C:39 > isolde pepflip /C:36 > isolde pepflip /C:42 > isolde pepflip /C:41 > isolde pepflip /C:40 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:40 ISOLDE: started sim > select clear > isolde pepflip /C:40 > isolde pepflip /C:39 > isolde pepflip /C:41 > show #3/A > hide #3/A > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:117 ISOLDE: started sim > select clear > isolde pepflip /C:117 > isolde pepflip /C:116 > isolde sim resume > isolde pepflip /C:116 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:99 ISOLDE: started sim > isolde pepflip /C:99 > isolde pepflip /C:98 > isolde pepflip /C:97 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:99 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:501 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:39 ISOLDE: started sim > isolde pepflip /C:39 > isolde pepflip /C:40 > isolde pepflip /C:41 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:418 ISOLDE: started sim > isolde pepflip /C:418 > isolde pepflip /C:415 > select clear > isolde pepflip /C:415 > isolde pepflip /C:414 > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:99 ISOLDE: started sim > isolde pepflip /C:99 > isolde pepflip /C:98 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:36 ISOLDE: started sim > isolde pepflip /C:36 > isolde pepflip /C:37 > isolde pepflip /C:38 > select clear > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_ISOLDE/Current.cxs Taking snapshot of stepper: 6_Flagellin_Selection_ForMask.pdb > stop Unknown command: isolde stop > Incomplete command: isolde > isolde start > set selectionWidth 4 > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 > stop Unknown command: isolde stop Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: 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 INTEL-20.6.1 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel 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: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5060.0.0,0) OS Loader Version: 577~170 Software: System Software Overview: System Version: macOS 13.4.1 (c) (22F770820d) Kernel Version: Darwin 22.5.0 Time since boot: 1 day, 23 hours, 32 minutes Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2415: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 7MT0197I2H9S Mirror: Off Online: Yes Rotation: Supported 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-Clipper: 0.21.0 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-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 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