id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9838 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 klara.blascitz@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.4.1-arm64-arm-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. this error happens often if I just put my laptop on standby while I take a break Fatal Python error: Segmentation fault Current thread 0x00000001ed255e00 (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"":""2023-09-25 12:27:37.00 +0200"",""app_version"":""1.6.1"",""slice_uuid"":""a5992708-d5b4-36ec-ac0a-e525f6105b56"",""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"":""96F4E8B5-0470-4E38-8F3D-F5345038DFC9""} { ""uptime"" : 170000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookAir10,1"", ""coalitionID"" : 1764, ""osVersion"" : { ""train"" : ""macOS 13.4.1"", ""build"" : ""22F770820d"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-09-25 12:27:24.8101 +0200"", ""incident"" : ""96F4E8B5-0470-4E38-8F3D-F5345038DFC9"", ""pid"" : 39315, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-09-25 09:28:30.6428 +0200"", ""procStartAbsTime"" : 3922686433562, ""procExitAbsTime"" : 4160989376269, ""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"":""1B20862E-6908-5E11-9F81-BDEDD50F43C6"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""92D3BFCB-074E-98D7-0094-F2BDA68A1B13"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 1381, ""sleepWakeUUID"" : ""7EE3A33A-7677-447E-8E26-B81334106764"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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""factorPackIds"" : { }, ""deploymentId"" : 240000010 } ], ""experiments"" : [ { ""treatmentId"" : ""3a3cf641-8471-4e4e-9ad4-81d0ede970fd"", ""experimentId"" : ""64a84dae90d82611a0bd7d3d"", ""deploymentId"" : 400000010 }, { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000017 } ] } } ===== 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 > cd /Users/klarab/Library/CloudStorage/OneDrive- > UniversiteitLeiden/BPS/RP2/Cryo Current working directory is: /Users/klarab/Library/CloudStorage/OneDrive- UniversiteitLeiden/BPS/RP2/Cryo > open /Users/klarab/Library/CloudStorage/OneDrive- > UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/117_open_map_A.mrc Opened 117_open_map_A.mrc as #1, grid size 512,512,512, pixel 0.976, shown at level 0.0329, step 2, values float32 > open /Users/klarab/Library/CloudStorage/OneDrive- > UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/117_open_map_B.mrc Opened 117_open_map_B.mrc as #2, grid size 512,512,512, pixel 0.976, shown at level 0.0329, step 2, values float32 > open /Users/klarab/Library/CloudStorage/OneDrive- > UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/22.09_7sxt_spike_without_Fab_rotameres_1.pdb Chain information for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available > open /Users/klarab/Library/CloudStorage/OneDrive- > UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/117_open_map_sharp.mrc Opened 117_open_map_sharp.mrc as #4, grid size 512,512,512, pixel 0.976, shown at level 0.118, step 2, values float32 > open /Users/klarab/Library/CloudStorage/OneDrive- > UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/117_open_local_sharp.mrc Opened 117_open_local_sharp.mrc as #5, grid size 512,512,512, pixel 0.976, shown at level 0.0325, step 2, values float32 > open /Users/klarab/Library/CloudStorage/OneDrive- > UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/117_RBD_fitted.pdb Chain information for 117_RBD_fitted.pdb #6 --- Chain | Description D | No description available H | No description available L | No description available > mousemode rightMode zoom > mousemode middleMode translate > mousemode shift middleMode clip > volume #1 level 0.139 > volume #1 step 1 > transparency #1 50 > volume #2 level 0.1 > volume #2 step 1 > volume #2 style mesh > transparency #2 50 > volume #4 level 0.223 > volume #4 step 1 > volume #4 style mesh > transparency #4 50 > volume #5 level 0.211 > volume #5 step 1 > transparency #5 50 > show #3 cartoons > set bgColor white > isolde start > set selectionWidth 4 > clipper associate #1 toModel #3 Opened 117_open_map_A.mrc as #1.1.1.1, grid size 512,512,512, pixel 0.976, shown at level 0.282, step 1, values float32 Chain information for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available > addh Summary of feedback from adding hydrogens to multiple structures --- notes | No usable SEQRES records for 117_RBD_fitted.pdb (#6) chain D; guessing termini instead No usable SEQRES records for 117_RBD_fitted.pdb (#6) chain H; guessing termini instead No usable SEQRES records for 117_RBD_fitted.pdb (#6) chain L; guessing termini instead Chain-initial residues that are actual N termini: 117_RBD_fitted.pdb #6/D ASN 331, 117_RBD_fitted.pdb #6/H LEU 4, 117_RBD_fitted.pdb #6/L ILE 2 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 117_RBD_fitted.pdb #6/D LYS 529, 117_RBD_fitted.pdb #6/H ALA 119, 117_RBD_fitted.pdb #6/L ARG 108 251 hydrogen bonds 117_RBD_fitted.pdb #6/D LYS 529 is not terminus, removing H atom from 'C' 117_RBD_fitted.pdb #6/H ALA 119 is not terminus, removing H atom from 'C' 117_RBD_fitted.pdb #6/L ARG 108 is not terminus, removing H atom from 'C' No usable SEQRES records for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb (#1.2) chain C; guessing termini instead Chain-initial residues that are actual N termini: 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A GLN 14, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B GLN 14, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C GLN 14 Chain-initial residues that are not actual N termini: 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A LYS 77, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A MET 153, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A ASN 185, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A GLY 257, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A SER 530, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A ASN 641, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A SER 691, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A ASN 856, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B LYS 77, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B MET 153, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B ASN 185, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B GLY 257, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B ASN 641, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B SER 691, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B ALA 855, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C LYS 77, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C MET 153, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C ASN 185, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C GLY 257, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C ASN 641, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C SER 691, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C ASN 856 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A SER 1147, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A HIS 69, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A TYR 145, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A LEU 176, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A SER 247, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A ILE 332, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A VAL 620, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A GLN 675, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A THR 827, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B SER 1147, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B HIS 69, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B TYR 145, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B LEU 176, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B SER 247, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B VAL 620, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B GLN 675, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B THR 827, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C SER 1147, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C HIS 69, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C TYR 145, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C LEU 176, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C SER 247, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C VAL 620, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C GLN 675, 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C THR 827 2224 hydrogen bonds 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A SER 1147 is not terminus, removing H atom from 'C' 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B SER 1147 is not terminus, removing H atom from 'C' 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C SER 1147 is not terminus, removing H atom from 'C' 3153 hydrogens added > isolde restrain ligands #1 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > 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 > hide #!2 models > hide #!4 models > hide #!5 models > hide #6 models > show #!5 models > select clear > hide #!5 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select clear Window position QRect(1985,901 575x202) outside any known screen, using primary screen > open /Users/klarab/Library/CloudStorage/OneDrive- > UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/22.09_7sxt_spike_without_Fab_rotameres_1.pdb Chain information for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available > hide #!1 models > color #3 bychain > select clear > open ""/Users/klarab/Library/CloudStorage/OneDrive- > UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/22.09_7sxt_spike_without_Fab_rotameres_1 > copy.pdb"" Chain information for 22.09_7sxt_spike_without_Fab_rotameres_1 copy.pdb #7 --- Chain | Description A | No description available B | No description available C | No description available > close #7 > hide #!3 models > open /Users/klarab/Library/CloudStorage/OneDrive- > UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/25.09_7sxt_A_done_copying_B&C.pdb Summary of feedback from opening /Users/klarab/Library/CloudStorage/OneDrive- UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/25.09_7sxt_A_done_copying_B&C.pdb --- warnings | Duplicate atom serial number found: 7303 Duplicate atom serial number found: 7304 Duplicate atom serial number found: 7305 Duplicate atom serial number found: 7306 Duplicate atom serial number found: 7307 11397 messages similar to the above omitted CONECT record to nonexistent atom: (23239, 23557) CONECT record for nonexistent atom: 23557 note | Combining 2 symmetry atoms into SER /B:750 H Chain information for 25.09_7sxt_A_done_copying_B&C.pdb #7 --- Chain | Description A | No description available B C | No description available > color #7 bychain > select clear > hide #7 chain A Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select clear > ui mousemode right select > select #7/C:192 20 atoms, 20 bonds, 1 residue, 1 model selected > ui mousemode right zoom > select up 183 atoms, 184 bonds, 10 residues, 1 model selected > select up 1056 atoms, 1069 bonds, 63 residues, 1 model selected > select up 1403 atoms, 1421 bonds, 87 residues, 1 model selected > select up 9536 atoms, 9669 bonds, 611 residues, 1 model selected > select up 9566 atoms, 9698 bonds, 613 residues, 1 model selected > select up 10389 atoms, 10528 bonds, 670 residues, 1 model selected > cofr sel > ui mousemode right select > select #7/B:723 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 189 atoms, 190 bonds, 12 residues, 1 model selected > select up 853 atoms, 859 bonds, 59 residues, 1 model selected > select up 1011 atoms, 1016 bonds, 68 residues, 1 model selected > select up 8189 atoms, 8289 bonds, 536 residues, 1 model selected > select up 8330 atoms, 8429 bonds, 545 residues, 1 model selected > select up 13701 atoms, 13863 bonds, 891 residues, 1 model selected > select up 14290 atoms, 14462 bonds, 928 residues, 1 model selected > select up 16090 atoms, 16290 bonds, 1040 residues, 1 model selected > select up 45182 atoms, 45736 bonds, 2923 residues, 1 model selected > select down 16090 atoms, 16290 bonds, 1040 residues, 1 model selected > select #7/C:643 20 atoms, 20 bonds, 1 residue, 1 model selected > select up 53 atoms, 53 bonds, 3 residues, 1 model selected > select up 6091 atoms, 6173 bonds, 399 residues, 1 model selected > select up 6203 atoms, 6284 bonds, 406 residues, 1 model selected > select up 8000 atoms, 8101 bonds, 521 residues, 1 model selected > select up 8393 atoms, 8498 bonds, 546 residues, 1 model selected > select up 11633 atoms, 11785 bonds, 748 residues, 1 model selected > select up 11654 atoms, 11805 bonds, 750 residues, 1 model selected > select up 16089 atoms, 16290 bonds, 1040 residues, 1 model selected > select up 45182 atoms, 45736 bonds, 2923 residues, 1 model selected > select down 16089 atoms, 16290 bonds, 1040 residues, 1 model selected > select #7 /B:750-1147 5701 atoms, 5762 bonds, 1 pseudobond, 370 residues, 2 models selected Drag select of 14 residues > select #7 /B:750-1147 5701 atoms, 5762 bonds, 1 pseudobond, 370 residues, 2 models selected > ui mousemode right zoom > turn x -1 > turn x 1 > turn z 1 sel Expected 'forever' or an integer >= 1 or a keyword > turn sel z 1 Expected an axis vector or a keyword > turn z sel 1 Expected a number or a keyword > cofr sel > turn z 1 > turn z -1 > rotate z -1 Unknown command: rotate z -1 > rotate z -1 coordinateSystem #7 sel Unknown command: rotate z -1 coordinateSystem #7 sel > turn z -1 coordinateSystem #7 sel Expected a keyword > turn z -1 coordinateSystem #7 /B:750-1147 > turn z -10 coordinateSystem #7 /B:750-1147 > turn z -10 coordinateSystem #7/B:750-1147 > turn z -10 coordinateSystem #7/C:750-1147 > rotate z -10 coordinateSystem #7/C:750-1147 Unknown command: rotate z -10 coordinateSystem #7/C:750-1147 > turn z -10 coordinateSystem #7 /C > turn z -10 coordinateSystem #7 sel Expected a keyword > turn z -10 coordinateSystem #7 sel Expected a keyword > turn z -10 coordinateSystem #7 sel Expected a keyword > turn z -10 coordinateSystem #7 sel Expected a keyword > show #!2 models > hide #!2 models > show #!2 models > volume #2 style surface > hide #!2 models > ui mousemode right ""rotate selected models"" > view matrix models > #7,1,-0.0010422,-0.0026379,0.92232,0.0010368,1,-0.002071,0.27634,0.00264,0.0020682,0.99999,-1.1348 > view matrix models > #7,0.9998,0.019087,-0.0057994,-2.9834,-0.019133,0.99978,-0.0080887,6.8087,0.0056437,0.0081981,0.99995,-3.3098 > ui mousemode right rotate > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.75212,0.63779,-0.16595,-47.698,-0.65287,0.75543,-0.055607,232.07,0.0899,0.15017,0.98456,-53.609 > view matrix models > #7,0.42951,0.86503,-0.2593,1.4733,-0.89321,0.44923,0.019098,344.3,0.13301,0.22341,0.96561,-76.651 > select #7 /B 16090 atoms, 16290 bonds, 9 pseudobonds, 1040 residues, 2 models selected > view matrix models > #7,-0.41577,-0.85066,-0.32174,630.48,0.86217,-0.48126,0.15829,98.681,-0.2895,-0.21158,0.9335,138.01 > close #7 > open /Users/klarab/Library/CloudStorage/OneDrive- > UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/25.09_7sxt_A_done_copying_B&C.pdb Summary of feedback from opening /Users/klarab/Library/CloudStorage/OneDrive- UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/25.09_7sxt_A_done_copying_B&C.pdb --- warnings | Duplicate atom serial number found: 7303 Duplicate atom serial number found: 7304 Duplicate atom serial number found: 7305 Duplicate atom serial number found: 7306 Duplicate atom serial number found: 7307 11397 messages similar to the above omitted CONECT record to nonexistent atom: (23239, 23557) CONECT record for nonexistent atom: 23557 note | Combining 2 symmetry atoms into SER /B:750 H Chain information for 25.09_7sxt_A_done_copying_B&C.pdb #7 --- Chain | Description A | No description available B C | No description available > color #7 bychain > view all > select #7 /B 16090 atoms, 16290 bonds, 9 pseudobonds, 1040 residues, 2 models selected > turn z 1 coordinateSystem system #7 /B:750-1147 Invalid ""coordinateSystem"" argument: invalid coordinate-system > turn z 1 coordinateSystem #7 /B:750-1147 > view matrix models > #7,0.99407,0.02141,0.1066,-30.882,-0.038572,0.9861,0.16164,-28.605,-0.10166,-0.16479,0.98108,68.74 > turn z 1 coordinateSystem #7 /B:750-1147 > turn z 1 coordinateSystem #7 sel Expected a keyword > turn z 1 coordinateSystem #7 select Expected a keyword > turn z 1 coordinateSystem #7 selected Expected a keyword 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 Metal - 83.1 OpenGL renderer: Apple M1 OpenGL vendor: Apple 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 Air Model Identifier: MacBookAir10,1 Model Number: MGN63D/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 8422.121.1 OS Loader Version: 8422.121.1 Software: System Software Overview: System Version: macOS 13.4.1 (c) (22F770820d) Kernel Version: Darwin 22.5.0 Time since boot: 10 days, 23 hours, 39 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal EV2780: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz 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: 2022.2.22 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