id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8339 Crash in color chooser chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.3-arm64-arm-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x00000002c4807000 (most recent call first): File ""/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/private/var/folders/ht/62vn9s5906l37_519kbwyf_r0000gn/T/AppTranslocation/2F052660-B889-46C0-B9A0-22CFE4F70BA7/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File 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\nStack Guard 56.0M 1 \nVM_ALLOCATE 225.9M 406 \nVM_ALLOCATE (reserved) 224.0M 3 reserved VM address space (unallocated)\n__AUTH 2620K 313 \n__AUTH_CONST 20.6M 513 \n__DATA 23.2M 641 \n__DATA_CONST 27.4M 651 \n__DATA_DIRTY 1822K 221 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 611.5M 137 \n__OBJC_CONST 3690K 284 \n__OBJC_RO 82.9M 1 \n__OBJC_RW 3152K 1 \n__TEXT 719.3M 669 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 512.9M 77 \nshared memory 3328K 33 \n=========== ======= ======= \nTOTAL 6.1G 4937 \nTOTAL, minus reserved VM space 4.8G 4937 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 }, { ""rolloutId"" : ""6112dda2fc54bc3389840642"", ""factorPackIds"" : { ""SIRI_DICTATION_ASSETS"" : ""631730a28520965d1cba0681"" }, ""deploymentId"" : 240000145 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6CO8 format mmcif fromDatabase pdb 6co8 title: Structure of Zika virus at a resolution of 3.1 Angstrom [more info...] Chain information for 6co8 #1 --- Chain | Description | UniProt A C E | E protein | POLG_ZIKVF B D F | M protein | POLG_ZIKVF Non-standard residues in 6co8 #1 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose 6co8 mmCIF Assemblies --- 1| complete icosahedral assembly 2| icosahedral asymmetric unit 3| icosahedral pentamer 4| icosahedral 23 hexamer 5| icosahedral asymmetric unit, std point frame > nucleotides atoms > style nucleic stick Changed 0 atom styles > style sphere Changed 13248 atom styles > style sphere Changed 13248 atom styles > style sphere Changed 13248 atom styles > style stick Changed 13248 atom styles > style stick Changed 13248 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > hide surfaces > select add #1 13248 atoms, 13536 bonds, 1734 residues, 1 model selected > view clip false > show sel atoms > show sel cartoons > hide sel atoms > hide #1 models > show #1 models > select subtract #1 Nothing selected > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > set bgColor white > lighting simple Alignment identifier is 1 Alignment identifier is 2 > select /A,C,E:1-2 57 atoms, 54 bonds, 6 residues, 1 model selected > select /A,C,E:1-13 312 atoms, 312 bonds, 39 residues, 1 model selected > select /B,D,F:72-75 91 atoms, 94 bonds, 12 residues, 1 model selected > select /B,D,F 1800 atoms, 1845 bonds, 225 residues, 1 model selected > color sel orange > color sel orange red > color sel orange > select /A,C,E:1-2 57 atoms, 54 bonds, 6 residues, 1 model selected > select /A,C,E:1-4 99 atoms, 96 bonds, 12 residues, 1 model selected > select /B,D,F:75 19 atoms, 16 bonds, 3 residues, 1 model selected > select /B,D,F 1800 atoms, 1845 bonds, 225 residues, 1 model selected > color sel orange red > select /A,C,E:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select /A,C,E:1-51 1128 atoms, 1140 bonds, 153 residues, 1 model selected > color sel red > select /A,C,E:52 24 atoms, 21 bonds, 3 residues, 1 model selected > select /A,C,E:52 24 atoms, 21 bonds, 3 residues, 1 model selected > select /A,C,E:52-53 48 atoms, 45 bonds, 6 residues, 1 model selected > select /A,C,E:52-135 1908 atoms, 1938 bonds, 252 residues, 1 model selected > color sel yellow > select /A,C,E:136-137 63 atoms, 63 bonds, 6 residues, 1 model selected > select /A,C,E:136-194 1335 atoms, 1356 bonds, 177 residues, 1 model selected > color sel red > select /A,C,E:130-132 72 atoms, 72 bonds, 9 residues, 1 model selected > select /A,C,E:27-132 2370 atoms, 2406 bonds, 318 residues, 1 model selected > select /A,C,E:190 18 atoms, 15 bonds, 3 residues, 1 model selected > select /A,C,E:190-191 45 atoms, 42 bonds, 6 residues, 1 model selected > select /A,C,E:193 33 atoms, 30 bonds, 3 residues, 1 model selected > select /A,C,E:193 33 atoms, 30 bonds, 3 residues, 1 model selected > select /A,C,E:194 21 atoms, 18 bonds, 3 residues, 1 model selected > select /A,C,E:194 21 atoms, 18 bonds, 3 residues, 1 model selected > select /A,C,E:195 12 atoms, 9 bonds, 3 residues, 1 model selected > select /A,C,E:195-288 2214 atoms, 2283 bonds, 282 residues, 1 model selected > select /A,C,E:285 18 atoms, 15 bonds, 3 residues, 1 model selected > select /A,C,E:195-285 2154 atoms, 2220 bonds, 273 residues, 1 model selected > color sel yellow > select /A,C,E:300 24 atoms, 21 bonds, 3 residues, 1 model selected > select /A,C,E:285-300 387 atoms, 387 bonds, 48 residues, 1 model selected > select /A,C,E:286-287 30 atoms, 27 bonds, 6 residues, 1 model selected > select /A,C,E:286-300 369 atoms, 369 bonds, 45 residues, 1 model selected > color sel red > select /A,C,E:301-302 39 atoms, 36 bonds, 6 residues, 1 model selected > select /A,C,E:301-400 2262 atoms, 2313 bonds, 300 residues, 1 model selected > color sel blue > select /A,C,E:401 30 atoms, 30 bonds, 3 residues, 1 model selected > select /A,C,E:401-402 63 atoms, 63 bonds, 6 residues, 1 model selected > color sel blue > select /A,C,E:403 18 atoms, 15 bonds, 3 residues, 1 model selected > select /A,C,E:403-501 2145 atoms, 2184 bonds, 297 residues, 1 model selected > color sel cornflower blue > select /A,C,E:402 33 atoms, 30 bonds, 3 residues, 1 model selected > select /A,C,E:401-402 63 atoms, 63 bonds, 6 residues, 1 model selected > select clear > view > lighting full > set bgColor black > select /E 3790 atoms, 3870 bonds, 501 residues, 1 model selected > select /E 3790 atoms, 3870 bonds, 501 residues, 1 model selected > select /A 3787 atoms, 3867 bonds, 501 residues, 1 model selected > select /C 3787 atoms, 3867 bonds, 501 residues, 1 model selected > select clear > select /C 3787 atoms, 3867 bonds, 501 residues, 1 model selected > hide sel target a > cartoon hide sel > select /E 3790 atoms, 3870 bonds, 501 residues, 1 model selected > cartoon hide sel > select /D 600 atoms, 615 bonds, 75 residues, 1 model selected > cartoon hide sel > select /F 601 atoms, 616 bonds, 75 residues, 1 model selected > cartoon hide sel > select /D 600 atoms, 615 bonds, 75 residues, 1 model selected > cartoon sel > select /B 599 atoms, 614 bonds, 75 residues, 1 model selected > cartoon hide sel > select /F 601 atoms, 616 bonds, 75 residues, 1 model selected > cartoon sel > select /A 3787 atoms, 3867 bonds, 501 residues, 1 model selected > cartoon hide sel > select /C 3787 atoms, 3867 bonds, 501 residues, 1 model selected > cartoon sel > select /B 599 atoms, 614 bonds, 75 residues, 1 model selected > select /D 600 atoms, 615 bonds, 75 residues, 1 model selected > select /B 599 atoms, 614 bonds, 75 residues, 1 model selected > cartoon sel > select /A 3787 atoms, 3867 bonds, 501 residues, 1 model selected > select /C 3787 atoms, 3867 bonds, 501 residues, 1 model selected > select /D 600 atoms, 615 bonds, 75 residues, 1 model selected > select /A 3787 atoms, 3867 bonds, 501 residues, 1 model selected > select /C 3787 atoms, 3867 bonds, 501 residues, 1 model selected > select /B 599 atoms, 614 bonds, 75 residues, 1 model selected > select /B 599 atoms, 614 bonds, 75 residues, 1 model selected > select /D 600 atoms, 615 bonds, 75 residues, 1 model selected > select /D 600 atoms, 615 bonds, 75 residues, 1 model selected > select /F 601 atoms, 616 bonds, 75 residues, 1 model selected > select /B 599 atoms, 614 bonds, 75 residues, 1 model selected > cartoon hide sel > select /D 600 atoms, 615 bonds, 75 residues, 1 model selected > cartoon hide sel > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view sel > view matrix models #1,1,0,0,-1.4792,0,1,0,6.2175,0,0,1,-2.4054 > set bgColor white > lighting simple > view > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting shadows false > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting simple > lighting soft > lighting full > lighting simple > lighting flat > lighting shadows true intensity 0.5 > lighting flat > lighting shadows true intensity 0.5 > lighting flat > lighting shadows true intensity 0.5 > lighting flat > lighting simple > graphics silhouettes false > lighting shadows true > lighting simple > lighting shadows true > graphics silhouettes true > graphics silhouettes false > select /A,C,E:1-2 57 atoms, 54 bonds, 6 residues, 1 model selected > select /A,C,E:1-8 174 atoms, 171 bonds, 24 residues, 1 model selected > select /B,D,F:1 14 atoms, 11 bonds, 3 residues, 1 model selected > select /B,D,F:1-7 149 atoms, 152 bonds, 21 residues, 1 model selected > select /B,D,F:7 30 atoms, 30 bonds, 3 residues, 1 model selected > graphics silhouettes true > graphics silhouettes false > show sel atoms > select /B 599 atoms, 614 bonds, 75 residues, 1 model selected > delete atoms sel > delete bonds sel > select /F 601 atoms, 616 bonds, 75 residues, 1 model selected > select /D 600 atoms, 615 bonds, 75 residues, 1 model selected > delete atoms sel > delete bonds sel > select /F:7 10 atoms, 10 bonds, 1 residue, 1 model selected > select /F:7 10 atoms, 10 bonds, 1 residue, 1 model selected > select /F:10 11 atoms, 10 bonds, 1 residue, 1 model selected > select /F:10 11 atoms, 10 bonds, 1 residue, 1 model selected > style sel stick Changed 11 atom styles > show sel atoms > select /F:15 11 atoms, 10 bonds, 1 residue, 1 model selected > select /F:15 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 11 atom styles > select /F:10 11 atoms, 10 bonds, 1 residue, 1 model selected > select /F:10 11 atoms, 10 bonds, 1 residue, 1 model selected > style sel ball Changed 11 atom styles > select /F:7 10 atoms, 10 bonds, 1 residue, 1 model selected > select /F:7 10 atoms, 10 bonds, 1 residue, 1 model selected > style sel ball Changed 10 atom styles > select /F:19 14 atoms, 15 bonds, 1 residue, 1 model selected > select /F:19 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 14 atom styles > select /F:23 11 atoms, 10 bonds, 1 residue, 1 model selected > select /F:23 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 11 atom styles > select /F:19 14 atoms, 15 bonds, 1 residue, 1 model selected > select /F:19 14 atoms, 15 bonds, 1 residue, 1 model selected > select /F:23 11 atoms, 10 bonds, 1 residue, 1 model selected > select /F:23 11 atoms, 10 bonds, 1 residue, 1 model selected > select /F:24 9 atoms, 8 bonds, 1 residue, 1 model selected > select /F:24 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 9 atom styles > select /F:25 12 atoms, 12 bonds, 1 residue, 1 model selected > select /F:25 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 12 atom styles > select /F:28 10 atoms, 10 bonds, 1 residue, 1 model selected > select /F:28 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 10 atom styles > select /F:35 14 atoms, 15 bonds, 1 residue, 1 model selected > select /F:35 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 14 atom styles > select /F:38 11 atoms, 10 bonds, 1 residue, 1 model selected > select /F:38 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 11 atom styles > select /F:51 14 atoms, 15 bonds, 1 residue, 1 model selected > select /F:51 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 14 atom styles > select /A-E:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select /A-E:1-26 591 atoms, 597 bonds, 78 residues, 1 model selected > select /A-E:26-27 57 atoms, 57 bonds, 6 residues, 1 model selected > select /A-E:26-27 57 atoms, 57 bonds, 6 residues, 1 model selected > select /A-E:26 27 atoms, 24 bonds, 3 residues, 1 model selected > select /A-E:26 27 atoms, 24 bonds, 3 residues, 1 model selected > show sel atoms > style sel ball Changed 27 atom styles > select /A 3787 atoms, 3867 bonds, 501 residues, 1 model selected > hide sel target a > select /C 3787 atoms, 3867 bonds, 501 residues, 1 model selected > select /C 3787 atoms, 3867 bonds, 501 residues, 1 model selected > select /E 3790 atoms, 3870 bonds, 501 residues, 1 model selected > hide sel target a > select /A-E:73 33 atoms, 30 bonds, 3 residues, 1 model selected > select /A-E:73 33 atoms, 30 bonds, 3 residues, 1 model selected > show sel atoms > style sel ball Changed 33 atom styles > select /A 3787 atoms, 3867 bonds, 501 residues, 1 model selected > delete atoms sel > delete bonds sel > select /C 3787 atoms, 3867 bonds, 501 residues, 1 model selected > select /E 3790 atoms, 3870 bonds, 501 residues, 1 model selected > delete atoms sel > delete bonds sel > select /C:93 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C:93 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 9 atom styles > select /C:203 12 atoms, 12 bonds, 1 residue, 1 model selected > select /C:203 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 12 atom styles > select /C:210 10 atoms, 10 bonds, 1 residue, 1 model selected > select /C:210 10 atoms, 10 bonds, 1 residue, 1 model selected > style sel ball Changed 10 atom styles > show sel atoms > style sel ball Changed 10 atom styles > select /C:212 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:211-212 22 atoms, 23 bonds, 2 residues, 1 model selected > select /C:211 14 atoms, 15 bonds, 1 residue, 1 model selected > select /C:211 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 14 atom styles > select /C:214 10 atoms, 10 bonds, 1 residue, 1 model selected > select /C:214 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 10 atom styles > select /C:216-217 23 atoms, 24 bonds, 2 residues, 1 model selected > select /C:216-217 23 atoms, 24 bonds, 2 residues, 1 model selected > select /C:216 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C:216 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 9 atom styles > select /C:219 10 atoms, 10 bonds, 1 residue, 1 model selected > select /C:219 10 atoms, 10 bonds, 1 residue, 1 model selected > select /C:220 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:220 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 8 atom styles > select /C:244 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C:244 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 9 atom styles > select /C:249 10 atoms, 10 bonds, 1 residue, 1 model selected > select /C:249 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 10 atom styles > select /C:266 10 atoms, 10 bonds, 1 residue, 1 model selected > select /C:266 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 10 atom styles > select /C:269 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:269 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 8 atom styles > select /C:274 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C:274 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 9 atom styles > select /C:420-421 19 atoms, 18 bonds, 2 residues, 1 model selected > select /C:420-421 19 atoms, 18 bonds, 2 residues, 1 model selected > select /C:420 11 atoms, 10 bonds, 1 residue, 1 model selected > select /C:420 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 11 atom styles > select /C:449 11 atoms, 11 bonds, 1 residue, 1 model selected > select /C:449 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 11 atom styles > select > /C:131-133,148-152,197-200,214-219,238-241,261-270,391-395,405-424,426-431,441-455,461-466,469-475,481-496 822 atoms, 830 bonds, 107 residues, 1 model selected > select /C:462 14 atoms, 15 bonds, 1 residue, 1 model selected > select /C:462 14 atoms, 15 bonds, 1 residue, 1 model selected > select /C:462 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 14 atom styles > select /C:474 14 atoms, 15 bonds, 1 residue, 1 model selected > select /C:474 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 14 atom styles > view matrix models #1,1,0,0,0.75112,0,1,0,-18.316,0,0,1,-5.5584 > select clear > show cartoons > hide cartoons > show cartoons > set bgColor white > lighting simple > lighting soft > lighting full > lighting simple > lighting soft > lighting full > lighting shadows false > lighting shadows true > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting simple > save ""/Users/sydney/Desktop/ZIKV Publication Fall 2022 updated > 10.05.22/mature chimera C6O8.cxs"" > save ""/Users/sydney/Desktop/ZIKV Publication Fall 2022 updated > 10.05.22/mature chimera C6O8.jpg"" width 1288 height 903 supersample 3 > lighting simple > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting simple > graphics silhouettes false > lighting shadows true > select /C:52 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:52-91 312 atoms, 316 bonds, 40 residues, 1 model selected > select /C:52 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:52-128 581 atoms, 590 bonds, 77 residues, 1 model selected > select > /C:9-12,20-23,30-33,41-50,58-65,69-73,90-95,98-99,109-110,112-124,128-129,135-143,164-169,175-180,184-189,202-205,210-211,225-226,243-247,253-257,282-283,291-294,312-314,319-320,326-327,329-333,339-340,344-345,364-365,371-375,384-388,397-401 1171 atoms, 1166 bonds, 144 residues, 1 model selected > select /C:135 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:52-135 636 atoms, 646 bonds, 84 residues, 1 model selected > color sel #f6fff1ff > color sel #f6fff0ff > color sel #f5ffeeff > color sel #f6ffeaff > color sel #f7ffe6ff > color sel #f8ffe1ff > color sel #f8ffdcff > color sel #f9ffd8ff > color sel #f9ffd5ff > color sel #f8ffd3ff > color sel #f9ffcfff > color sel #f9ffcaff > color sel #faffc5ff > color sel #faffbfff > color sel #fbffb9ff > color sel #fbffb3ff > color sel #fbffacff > color sel #fbffa5ff > color sel #fbff9fff > color sel #fcff98ff > color sel #fcff96ff > color sel #feff8fff > color sel #ffff8cff > color sel #fffc84ff > color sel #fff97dff > color sel #fff879ff > color sel #fff571ff > color sel #fff36aff > color sel #fff164ff > color sel #ffef5fff > color sel #ffed59ff > color sel #ffec56ff > color sel #ffea50ff > color sel #ffe74bff > color sel #ffe645ff > color sel #ffe542ff > color sel #ffe43eff > color sel #ffe439ff > color sel #ffe432ff > color sel #ffe430ff > color sel #ffe52bff > color sel #ffe624ff > color sel #ffe621ff > color sel #ffe71eff > color sel #ffe71aff > color sel #ffe717ff > color sel #ffe712ff > color sel #ffe70eff > color sel #ffe709ff > color sel #ffe606ff > color sel #ffe500ff > color sel #ffe200ff > color sel #ffe101ff > color sel #ffde00ff > color sel #ffda00ff > color sel #ffd700ff > color sel #ffd500ff > color sel #ffd300ff > color sel #ffd100ff > color sel #ffcf00ff > color sel #ffcd00ff > color sel #ffca00ff > color sel #ffca02ff > color sel #ffcc04ff > color sel #ffcf07ff > color sel #ffd50dff > color sel #ffd80fff > color sel #ffe015ff > color sel #ffe91cff > color sel #ffef1fff > color sel #fff420ff > color sel #fff821ff > color sel #fffa21ff > color sel #fffa22ff > color sel #fffb22ff > color sel #fffb21ff > color sel #fffa21ff > color sel #fff920ff > color sel #fff019ff > color sel #ffea14ff > color sel #ffe711ff > color sel #ffde09ff > color sel #ffd905ff > color sel #ffd300ff > color sel #ffd100ff > color sel #ffcf00ff > color sel #ffcd00ff > color sel #ffca00ff > color sel #ffc801ff > color sel #ffc600ff > color sel #ffc100ff > color sel #ffbf01ff > color sel #ffbd00ff > color sel #ffbf01ff > color sel #ffc100ff > color sel #ffc401ff > color sel #ffc600ff > color sel #ffc801ff > color sel #ffca00ff > color sel #ffcd00ff > color sel #ffcf00ff > color sel #ffd100ff > color sel #ffd300ff > color sel #ffd100ff > color sel #ffcf00ff > color sel #ffcd00ff > color sel #ffca00ff > color sel #ffc801ff > color sel #ffca00ff > color sel #ffcd00ff > color sel #ffcf00ff > color sel #ffcd00ff > color sel #ffcf00ff > color sel #ffd100ff > color sel #ffcf00ff > color sel #ffcd00ff > color sel #ffca00ff > color sel #ffcd00ff > color sel #ffcf00ff > color sel #ffd100ff > color sel #ffd300ff > color sel #ffd500ff > color sel #ffd700ff > color sel #ffda00ff > color sel #ffde00ff > color sel #ffe105ff > color sel #ffe60bff > color sel #ffe80eff > color sel #ffec13ff > color sel #fff11bff > color sel #fff522ff > color sel #fff829ff > color sel #fffa2eff > color sel #fffa30ff > color sel #fffb32ff > color sel #fffb34ff > color sel #fffc36ff > color sel #fffc38ff > color sel #fffc3aff > color sel #fffc3bff > color sel #fffc3cff > color sel #fffd3dff > color sel #fffc3eff > color sel #fffd3fff > color sel #fffc3fff > color sel #fffd3fff > color sel #fffd3eff > color sel #fffd39ff > color sel #fffb33ff > color sel #fff92bff > color sel #fff827ff > color sel #fff61fff > color sel #fff419ff > color sel #fff211ff > color sel #fff10dff > color sel #ffee05ff > color sel #ffee00ff > color sel #ffec01ff > color sel #ffe900ff > color sel #ffec01ff > color sel #ffee00ff > color sel #fff000ff > color sel #ffee00ff > color sel #fff000ff > color sel #fff200ff > color sel #fff400ff > color sel #fff900ff > color sel #fffb00ff > color sel #fffd00ff > color sel #feff00ff > color sel #fcff00ff > color sel #faff00ff > color sel #f7ff00ff > color sel #faff00ff > color sel #fcff00ff > color sel #feff00ff > color sel #fffd00ff > color sel #fffb00ff > color sel #fff400ff > color sel #fff200ff > color sel #fff000ff > color sel #ffee00ff > color sel #ffe900ff > color sel #ffe700ff > color sel #ffe500ff > color sel #ffe200ff > color sel #ffe101ff > color sel #ffde00ff > color sel #ffda00ff > color sel #ffd500ff > color sel #ffd300ff > color sel #ffd100ff > color sel #ffcf00ff > color sel #ffcd00ff > color sel #ffca00ff > color sel #ffc801ff > color sel #ffc600ff ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 7459.101.2 OS Loader Version: 7459.101.2 Software: System Software Overview: System Version: macOS 12.3 (21E230) Kernel Version: Darwin 21.4.0 Time since boot: 103 days 16:19 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 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: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 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: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 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-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 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 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 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: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect closed normal Platform duplicate Tom Goddard all ChimeraX