id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9705 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 Thread 0x00000003259ad000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003249aa000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003239a7000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003229a4000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003219a1000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000032099e000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031f99b000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031e998000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031d995000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031c992000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031b98f000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031a98c000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000319989000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x0000000204a25280 (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"", 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""ACA44488-D3F7-4068-9BEC-E8D9D49AF336"", ""pid"" : 56774, ""translated"" : true, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-09-01 14:34:41.9701 +0200"", ""procStartAbsTime"" : 4045640534165, ""procExitAbsTime"" : 4566808230122, ""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"":""B9F9C638-D31C-5FD4-A86B-35A3B758CD97"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""2F1583CC-662F-F391-31B1-BF000E50A7D5"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, 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""deploymentId"" : 400000019 } ] } } ===== Log before crash start ===== You can double click a model's Name or ID in the model panel to edit those fields 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/rlinares/Desktop/p142_papier/p143/p143_AF_fit.pdb > /Users/rlinares/Desktop/p142_papier/p143/p143_flexiblefit.pdb Chain information for p143_AF_fit.pdb #1 --- Chain | Description A | No description available Chain information for p143_flexiblefit.pdb #2 --- Chain | Description A | No description available > open > /Users/rlinares/Desktop/p142_papier/p143/Cartes_box200/mask_p143monomer_box200.mrc > /Users/rlinares/Desktop/p142_papier/p143/Cartes_box200/p143_map.mrc Opened mask_p143monomer_box200.mrc as #3.1, grid size 200,200,200, pixel 1.36, shown at level 1, step 1, values float32 Opened p143_map.mrc as #3.2, grid size 200,200,200, pixel 1.36, shown at level 0.0245, step 1, values float32 > turn x 90 > turn y 90 > hide #2 models > hide #1 models > volume #3.2 level 0.01504 > show #1 models > color bfactor #1 palette alphafold key true > key alphafold :0 :50 :70 :90 :100 showTool true > ui mousemode right ""color key"" 3981 atoms, 255 residues, atom bfactor range 31.6 to 89.4 > key numericLabelSpacing equal > key labelColor default > key labelColor black > transparency #3 50 > ui mousemode right translate > color #3 #ffb2b2ff models > color #3 #ffffb2ff models > color #3 white models > color #3 #ffffff6d models > graphics silhouettes true > lighting simple > lighting soft > lighting simple > lighting full > lighting simple > lighting flat > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > graphics silhouettes false > graphics silhouettes true > open /Users/rlinares/Downloads/7zhj(1).cif 7zhj(1).cif title: Tail tip of siphophage T5 : tip proteins [more info...] Chain information for 7zhj(1).cif #5 --- Chain | Description | UniProt A B C D E F | Tail tube protein | TUBE_BPT5 1-464 G H I | Minor tail protein | TAIL1_BPT5 1-298 J K L M N O P Q R S T U | L-shaped tail fiber protein p132 | FIBL2_BPT5 1-140 V W X Y Z a | Distal tail protein | DIT_BPT5 1-204 b c d | Probable baseplate hub protein | BPPB3_BPT5 1-949 e f g | Pore-forming tail tip protein pb2 | Q7Y5E2_BPT5 1-1219 > hide #!3.2 models > hide #4 models > hide #5 models > show #5 models > show #4 models > hide #4 models > show #2 models > show #!3.2 models > select add #5 74346 atoms, 75777 bonds, 9528 residues, 1 model selected > hide #1 models > hide #2 models > hide #!3 models > hide #!3.1 models > hide #!3.2 models > show #!3.2 models > hide #!3.2 models > show #!3.2 models > show #1 models > show #2 models > fitin map #5 #3.250 Unknown command: fitin map #5 #3.250 > fitinmap #5 #3.250 Unknown command: fitinmap #5 #3.250 > fitmap #5 #3.250 Missing required ""in_map"" argument > fitmap #5 inMap #3.2 Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms average map value = -5.916e-05, steps = 204 shifted from previous position = 7.95 rotated from previous position = 13.1 degrees atoms outside contour = 74120, contour level = 0.015036 Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates: Matrix rotation and translation 0.97427484 0.03701817 0.22230203 -40.23333919 -0.04114622 0.99905553 0.01396531 15.19506856 -0.22157510 -0.02275294 0.97487783 59.25025831 Axis -0.08119914 0.98159479 -0.17285358 Axis point 250.12648893 0.00000000 207.02962675 Rotation angle (degrees) 13.06756936 Shift along axis 7.94069343 > fitmap #5 inMap #3.2 Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms average map value = -5.912e-05, steps = 80 shifted from previous position = 0.0121 rotated from previous position = 0.00905 degrees atoms outside contour = 74120, contour level = 0.015036 Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates: Matrix rotation and translation 0.97426543 0.03688920 0.22236470 -40.20313144 -0.04100736 0.99906174 0.01392967 15.17587928 -0.22164221 -0.02268979 0.97486404 59.25237659 Axis -0.08096759 0.98172292 -0.17223345 Axis point 250.05239899 0.00000000 206.84289544 Rotation angle (degrees) 13.06972163 Shift along axis 7.94841759 > fitmap #5 inMap #3.2 Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms average map value = -5.911e-05, steps = 64 shifted from previous position = 0.00142 rotated from previous position = 0.00086 degrees atoms outside contour = 74120, contour level = 0.015036 Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates: Matrix rotation and translation 0.97426734 0.03687571 0.22235856 -40.19973278 -0.04099377 0.99906227 0.01393135 15.17357478 -0.22163632 -0.02268817 0.97486542 59.25108487 Axis -0.08097064 0.98173207 -0.17217983 Axis point 250.05480159 0.00000000 206.83092907 Rotation angle (degrees) 13.06923748 Shift along axis 7.94954171 > fitmap #5 inMap #3.2 Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms average map value = -5.916e-05, steps = 80 shifted from previous position = 0.0194 rotated from previous position = 0.00524 degrees atoms outside contour = 74120, contour level = 0.015036 Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates: Matrix rotation and translation 0.97427557 0.03691185 0.22231651 -40.21249872 -0.04101203 0.99906261 0.01385310 15.17403842 -0.22159677 -0.02261439 0.97487613 59.22104120 Axis -0.08064930 0.98173187 -0.17233175 Axis point 249.95688838 0.00000000 206.92391673 Rotation angle (degrees) 13.06679563 Shift along axis 7.93428107 > show #!3.1 models > hide #!3.2 models > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > show #!3.2 models > hide #!3.1 models > ui mousemode right ""move picked models"" > view matrix models > #5,0.97428,0.036912,0.22232,-29.135,-0.041012,0.99906,0.013853,-94.154,-0.2216,-0.022614,0.97488,-64.023 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #5,0.97428,0.036912,0.22232,-30.135,-0.041012,0.99906,0.013853,-81.743,-0.2216,-0.022614,0.97488,-56.104 > fitmap #5 inMap #3.2 Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms average map value = 0.004884, steps = 460 shifted from previous position = 114 rotated from previous position = 24.4 degrees atoms outside contour = 62783, contour level = 0.015036 Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates: Matrix rotation and translation 0.79707552 0.17904412 0.57672681 -161.56622262 -0.20567972 0.97842531 -0.01948761 -40.36204889 -0.56777325 -0.10308791 0.81670461 148.95265937 Axis -0.06907272 0.94561537 -0.31786872 Axis point 114.40803191 0.00000000 329.30371724 Rotation angle (degrees) 37.24046536 Shift along axis -74.35454670 > view matrix models > #5,0.79708,0.17904,0.57673,-161,-0.20568,0.97843,-0.019488,-43.171,-0.56777,-0.10309,0.8167,144.04 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.96226,0.26648,-0.05509,-93.698,-0.26897,0.96214,-0.044061,-19.624,0.041263,0.057216,0.99751,-72.258 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.96226,0.26648,-0.05509,-91.163,-0.26897,0.96214,-0.044061,-14.109,0.041263,0.057216,0.99751,-126.71 > fitmap #5 inMap #3.2 Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms average map value = 0.01629, steps = 352 shifted from previous position = 43 rotated from previous position = 14.3 degrees atoms outside contour = 43749, contour level = 0.015036 Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates: Matrix rotation and translation 0.99934057 0.02175343 -0.02907263 -90.75244437 -0.02327652 0.99831678 -0.05312076 -78.81777772 0.02786813 0.05376244 0.99816480 -125.16904318 Axis 0.82723654 -0.44070043 -0.34851519 Axis point 0.00000000 2254.73809000 -1527.94261998 Rotation angle (degrees) 3.70403387 Shift along axis 3.28460370 > fitmap #5 inMap #3.2 Fit molecule 7zhj(1).cif (#5) to map p143_map.mrc (#3.2) using 74346 atoms average map value = 0.01629, steps = 144 shifted from previous position = 0.00899 rotated from previous position = 0.00769 degrees atoms outside contour = 43748, contour level = 0.015036 Position of 7zhj(1).cif (#5) relative to p143_map.mrc (#3.2) coordinates: Matrix rotation and translation 0.99934437 0.02175097 -0.02894341 -90.78307278 -0.02326612 0.99831893 -0.05308488 -78.82815505 0.02774010 0.05372348 0.99817046 -125.13328168 Axis 0.82780804 -0.43932012 -0.34890067 Axis point 0.00000000 2256.70651611 -1530.43284215 Rotation angle (degrees) 3.69887762 Shift along axis 3.13892188 > hide #5 models > ui tool show ""Side View"" > show #5 models > hide #!3.2 models > select #5.b-d Expected an objects specifier or a keyword > select #5.b-d Expected an objects specifier or a keyword > select #5/b-d 22731 atoms, 23226 bonds, 2847 residues, 1 model selected > color #5/b-d yelloz Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #5/b-d yellow > show sel cartoons > hide sel atoms > color #5/V-W-X-Y-Z-a orange > color #5/V,W,X,Y,Z,a orange > select #5/V,W,X,Y,Z,a, b, c, d 32391 atoms, 33120 bonds, 4071 residues, 1 model selected > invert selection Unknown command: invert selection > select ~sel 47891 atoms, 48645 bonds, 5967 residues, 9 models selected > hide #2 models > hide #1 models > hide #!3 models > select #5/V,W,X,Y,Z,a, b, c, d 32391 atoms, 33120 bonds, 4071 residues, 1 model selected > show #2 models > hide #2 models > select ~sel 47891 atoms, 48645 bonds, 5967 residues, 9 models selected > show #!3.2 models > hide #!3.2 models > show #4 models > show #!3.2 models > select clear > hide #!3 models > hide #4 models > hide #!3.2 models > select #5/V,W,X,Y,Z,a, b, c, d 32391 atoms, 33120 bonds, 4071 residues, 1 model selected > select ~sel 47891 atoms, 48645 bonds, 5967 residues, 9 models selected > show #!3.2 models > hide #!3.2 models > show #4 models > hide #4 models > show #4 models > select clear > show #!3.2 models > select #5/V,W,X,Y,Z,a, b, c, d 32391 atoms, 33120 bonds, 4071 residues, 1 model selected > select #5/A-U 41169 atoms, 41865 bonds, 5352 residues, 1 model selected > delete atoms sel > delete bonds sel > select #5/V,W,X,Y,Z,a, b, c, d 32391 atoms, 33120 bonds, 4071 residues, 1 model selected > show sel cartoons > hide sel atoms > select clear > ui tool show ""Color Zone"" > ui tool show ""Surface Color"" > show #2 models > show #1 models > hide #2 models > show #2 models > hide #2 models > transparency #3 30 > transparency #3 70 > show #!3.1 models > hide #!3.1 models > select #5/e,f,g 786 atoms, 792 bonds, 105 residues, 1 model selected > color #5/e,f,g red > hide sel atoms > show sel cartoons > select clear > save /Users/rlinares/Desktop/p142_papier/230901.cxs > color zone #3.2 near #5 range 5 Expected a keyword > color zone #3.2 near #5 distance 5 > transparency #3 70 > hide #4 models > show #4 models > hide #5 models > transparency #3 50 > show #5 models > hide #5 models > save img22.tiff width 2000 height 2000 supersample 3 transparentBackground > true > hide #4 models > show #4 models > hide #!3.2 models > show #!3.2 models > hide #1 models > save img22.tiff width 2000 height 2000 supersample 3 transparentBackground > true > show #!3.1 models > hide #!3.1 models > show #1 models > save img23.tiff width 2000 height 2000 supersample 3 transparentBackground > true > hide #1 models > show #2 models > color #2 #00ceebff > color #2 #0000ebff > color #2 blue > transparency #3 70 > save img24.tiff width 2000 height 2000 supersample 3 transparentBackground > true > color #2 blue > background white Unknown command: background white > set background white Expected a keyword > bgColor white Unknown command: bgColor white > set bgColor white > transparency #3 50 > hide #2 models > save img22.tiff width 2000 height 2000 supersample 3 transparentBackground > true > show #2 models > save img23.tiff width 2000 height 2000 supersample 3 transparentBackground > true > show #1 models > hide #2 models > save img24.tiff width 2000 height 2000 supersample 3 transparentBackground > true > turn x 90 > color zone #3.2 near #5 distance 5 > transparency #3 50 > save img25.tiff width 2000 height 2000 supersample 3 transparentBackground > true > show #2 models > hide #1 models > color zone #3.2 near #5 distance 5 > transparency #3 50 > save img26.tiff width 2000 height 2000 supersample 3 transparentBackground > true > turn x 180 > color zone #3.2 near #5 distance 5 > transparency #3 50 > save img27.tiff width 2000 height 2000 supersample 3 transparentBackground > true > show #1 models > hide #2 models > color zone #3.2 near #5 distance 5 > transparency #3 50 > save img28.tiff width 2000 height 2000 supersample 3 transparentBackground > true > turn x 180 > turn x 90 > color zone #3.2 near #5 distance 5 > transparency #3 70 > transparency #3 30 > hide #1 models > save tip_p143_side.tiff width 2000 height 2000 supersample 3 > transparentBackground true > color zone #3.2 near #5 distance 5 > transparency #3 80 > transparency #3 20 > save tip_p143_side.tiff width 2000 height 2000 supersample 3 > transparentBackground true > save tip_p143_side.tiff width 1200 height 1200 supersample 3 > transparentBackground true > save tip_p143_side.tiff width 1400 height 1400 supersample 3 > transparentBackground true > show #2 models 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 M2 Pro 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: Mac Model Identifier: Mac14,9 Model Number: Z17G00197FN/A Chip: Unknown Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8422.121.1 OS Loader Version: 8422.121.1 Software: System Software Overview: System Version: macOS 13.4 (22F66) Kernel Version: Darwin 22.5.0 Time since boot: 9 days, 9 hours, 56 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: EV3285: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 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