id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18307 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x0000000200bbdf00 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=9.4G written=5192K(0%) resident=5192K(0%) swapped_out=0K(0%) unallocated=9.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 576K 27 \nColorSync 656K 33 \nCoreAnimation 1760K 108 \nCoreGraphics 48K 3 \nCoreUI image data 5904K 51 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 8.7G 181 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 848K 53 \nStack 170.9M 54 \nStack Guard 56.0M 1 \nVM_ALLOCATE 322.9M 201 \nVM_ALLOCATE (reserved) 256.0M 2 reserved VM address space (unallocated)\n__AUTH 5521K 697 \n__AUTH_CONST 77.4M 944 \n__CTF 824 1 \n__DATA 34.3M 1087 \n__DATA_CONST 36.9M 1103 \n__DATA_DIRTY 2778K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 647.0M 153 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1123 \n__TPRO_CONST 128K 2 \ndyld private memory 800K 8 \nmapped file 289.5M 61 \npage table in kernel 5192K 1 \nshared memory 3744K 26 \n=========== ======= ======= \nTOTAL 11.9G 6298 \nTOTAL, minus reserved VM space 11.7G 6298 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""9d2e6a3fb7cc2b480554b18eb93ad1c9b8090fb6"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""67d07cd6a7affa169ae21f45"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""6425c75e4327780c10cc4252"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_INTENT_SELECTION_CACHE"" : ""642600a457e7664b1698eb32"" }, ""deploymentId"" : 240000004 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 9guq 9guq title: 30S PIC (Pre-Initiation complex) [more info...] Chain information for 9guq #1 --- Chain | Description | UniProt A | 16S ribosomal RNA | B | 30S ribosomal protein S1 | RS1_ECOLI 1-557 C | 30S ribosomal protein S2 | RS2_ECOLI 1-241 D | Small ribosomal subunit protein uS3 | RS3_ECOLI 1-233 E | Small ribosomal subunit protein uS4 | RS4_ECOLI 1-206 F | 30S ribosomal protein S5 | RS5_ECOLI 10-165 G | Small ribosomal subunit protein bS6, non-modified isoform | RS6_ECOLI 1-131 H | 30S ribosomal protein S7 | RS7_ECOLI 1-156 I | 30S ribosomal protein S8 | RS8_ECOLI 1-130 J | 30S ribosomal protein S9 | RS9_ECOLI 1-130 K | 30S ribosomal protein S10 | RS10_ECOLI 1-103 L | 30S ribosomal protein S11 | RS11_ECOLI 1-129 M | 30S ribosomal protein S12 | RS12_ECOLI 1-124 N | 30S ribosomal protein S13 | RS13_ECOLI 1-118 O | 30S ribosomal protein S14 | RS14_ECOLI 1-101 P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89 Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82 R | 30S ribosomal protein S17 | RS17_ECOLI 1-84 S | 30S ribosomal protein S18 | RS18_ECOLI 1-75 T | 30S ribosomal protein S19 | RS19_ECOLI 1-92 U | 30S ribosomal protein S20 | RS20_ECOLI 1-87 V | 30S ribosomal protein S21 | RS21_ECOLI 1-71 W | tRNA(fmet) P-site | X | mRNA | Non-standard residues in 9guq #1 --- 2MG — 2N-methylguanosine-5'-monophosphate 4OC — 4N,O2'-methylcytidine-5'-monophosphate 4SU — 4-thiouridine-5'-monophosphate 5MC — 5-methylcytidine-5'-monophosphate 5MU — 5-methyluridine 5'-monophosphate D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid G7M — N7-methyl-guanosine-5'-monophosphate H2U — 5,6-dihydrouridine-5'-monophosphate MA6 — 6N-dimethyladenosine-5'-monophoshate MG — magnesium ion OMC — O2'-methylycytidine-5'-monophosphate UR3 — 3-methyluridine-5'-monophoshate > open 9guS 9gus title: 30S mRNA delivery complex TEC resolved (30S only) [more info...] Chain information for 9gus #2 --- Chain | Description | UniProt A | 16S ribosomal RNA | B | 30S ribosomal protein S1 | RS1_ECOLI 1-557 C | 30S ribosomal protein S2 | RS2_ECOLI 1-241 D | Small ribosomal subunit protein uS3 | C3SQX2_ECOLX 1-233 E | Small ribosomal subunit protein uS4 | RS4_ECOBW 1-206 F | 30S ribosomal protein S5 | RS5_ECOLI 10-165 G | Small ribosomal subunit protein bS6 | W8T6F0_ECOLX 1-131 H | 30S ribosomal protein S7 | RS7_ECOLI 1-156 I | 30S ribosomal protein S8 | RS8_ECOLI 1-130 J | 30S ribosomal protein S9 | RS9_ECOLI 1-130 K | 30S ribosomal protein S10 | RS10_ECOLI 1-103 L | 30S ribosomal protein S11 | RS11_ECOLI 1-129 M | 30S ribosomal protein S12 | RS12_ECOLI 1-124 N | 30S ribosomal protein S13 | RS13_ECOLI 1-118 O | 30S ribosomal protein S14 | RS14_ECOLI 1-101 P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89 Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82 R | 30S ribosomal protein S17 | RS17_ECOLI 1-84 S | 30S ribosomal protein S18 | RS18_ECOLI 1-75 T | 30S ribosomal protein S19 | RS19_ECOLI 1-92 U | 30S ribosomal protein S20 | RS20_ECOLI 1-87 V | 30S ribosomal protein S21 | RS21_ECOLI 1-71 W | tRNA(fmet) P-site | X | mRNA | Non-standard residues in 9gus #2 --- 2MG — 2N-methylguanosine-5'-monophosphate 4OC — 4N,O2'-methylcytidine-5'-monophosphate 4SU — 4-thiouridine-5'-monophosphate 5MC — 5-methylcytidine-5'-monophosphate 5MU — 5-methyluridine 5'-monophosphate D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid G7M — N7-methyl-guanosine-5'-monophosphate H2U — 5,6-dihydrouridine-5'-monophosphate MA6 — 6N-dimethyladenosine-5'-monophoshate MG — magnesium ion OMC — O2'-methylycytidine-5'-monophosphate UR3 — 3-methyluridine-5'-monophoshate > open 9gup Summary of feedback from opening 9gup fetched from pdb --- note | Fetching compressed mmCIF 9gup from http://files.rcsb.org/download/9gup.cif 9gup title: 30S mRNA delivery complex (open head) [more info...] Chain information for 9gup #3 --- Chain | Description | UniProt A | 16S ribosomal RNA | B | 30S ribosomal protein S1 | RS1_ECOLI 1-557 C | 30S ribosomal protein S2 | RS2_ECOLI 1-241 D | Small ribosomal subunit protein uS3 | C3SQX2_ECOLX 1-233 E | Small ribosomal subunit protein uS4 | RS4_ECOBW 1-206 F | 30S ribosomal protein S5 | RS5_ECOLI 10-165 G | Small ribosomal subunit protein bS6 | W8T6F0_ECOLX 1-131 H | 30S ribosomal protein S7 | RS7_ECOLI 1-156 I | 30S ribosomal protein S8 | RS8_ECOLI 1-130 J | 30S ribosomal protein S9 | RS9_ECOLI 1-130 K | 30S ribosomal protein S10 | RS10_ECOLI 1-103 L | 30S ribosomal protein S11 | RS11_ECOLI 1-129 M | 30S ribosomal protein S12 | RS12_ECOLI 1-124 N | 30S ribosomal protein S13 | RS13_ECOLI 1-118 O | 30S ribosomal protein S14 | RS14_ECOLI 1-101 P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89 Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82 R | 30S ribosomal protein S17 | RS17_ECOLI 1-84 S | 30S ribosomal protein S18 | RS18_ECOLI 1-75 T | 30S ribosomal protein S19 | RS19_ECOLI 1-92 U | 30S ribosomal protein S20 | RS20_ECOLI 1-87 V | 30S ribosomal protein S21 | RS21_ECOLI 1-71 X | mRNA | Non-standard residues in 9gup #3 --- 2MG — 2N-methylguanosine-5'-monophosphate 4OC — 4N,O2'-methylcytidine-5'-monophosphate 5MC — 5-methylcytidine-5'-monophosphate D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid G7M — N7-methyl-guanosine-5'-monophosphate MA6 — 6N-dimethyladenosine-5'-monophoshate MG — magnesium ion UR3 — 3-methyluridine-5'-monophoshate > open 9guw Summary of feedback from opening 9guw fetched from pdb --- warnings | Atom OP1 has no neighbors to form bonds with according to residue template for A /X:38 Atom OP2 has no neighbors to form bonds with according to residue template for A /X:38 9guw title: 30S-TEC (TEC in expressome position) Inactive state 2 [more info...] Chain information for 9guw #4 --- Chain | Description | UniProt 1 2 | DNA-directed RNA polymerase subunit alpha | RPOA_ECOLI 1-329 3 | DNA-directed RNA polymerase subunit beta | RPOB_ECOLI 1-1342 4 | DNA-directed RNA polymerase subunit beta' | RPOC_ECO57 1-1406 5 | DNA-directed RNA polymerase subunit omega | RPOZ_ECOLI 1-91 6 | Non-Template DNA strand | 7 | Template DNA strand | A | 16S ribosomal RNA | B | 30S ribosomal protein S1 | RS1_ECOLI 1-557 C | 30S ribosomal protein S2 | RS2_ECOLI 1-241 D | Small ribosomal subunit protein uS3 | C3SQX2_ECOLX 1-233 E | Small ribosomal subunit protein uS4 | RS4_ECOBW 1-206 F | 30S ribosomal protein S5 | RS5_ECOLI 10-166 G | Small ribosomal subunit protein bS6 | W8T6F0_ECOLX 1-131 H | 30S ribosomal protein S7 | RS7_ECOLI 1-156 I | 30S ribosomal protein S8 | RS8_ECOLI 1-130 J | 30S ribosomal protein S9 | RS9_ECOLI 1-130 K | 30S ribosomal protein S10 | RS10_ECOLI 1-103 L | 30S ribosomal protein S11 | RS11_ECOLI 1-129 M | 30S ribosomal protein S12 | RS12_ECOLI 1-124 N | 30S ribosomal protein S13 | RS13_ECOLI 1-118 O | 30S ribosomal protein S14 | RS14_ECOLI 1-101 P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89 Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82 R | 30S ribosomal protein S17 | RS17_ECOLI 1-84 S | 30S ribosomal protein S18 | RS18_ECOLI 1-75 T | 30S ribosomal protein S19 | RS19_ECOLI 1-92 U | 30S ribosomal protein S20 | RS20_ECOLI 1-87 X | mRNA | Z | Transcription termination/antitermination protein NusG | NUSG_ECOLI 1-181 Non-standard residues in 9guw #4 --- 2MG — 2N-methylguanosine-5'-monophosphate 5MC — 5-methylcytidine-5'-monophosphate D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid G7M — N7-methyl-guanosine-5'-monophosphate MA6 — 6N-dimethyladenosine-5'-monophoshate MG — magnesium ion ZN — zinc ion > open 9guv 9guv title: 30S mRNA delivery complex (closed-head) [more info...] Chain information for 9guv #5 --- Chain | Description | UniProt A | 16S ribosomal RNA | B | 30S ribosomal protein S1 | RS1_ECOLI 1-557 C | 30S ribosomal protein S2 | RS2_ECOLI 1-241 D | Small ribosomal subunit protein uS3 | C3SQX2_ECOLX 1-233 E | Small ribosomal subunit protein uS4 | RS4_ECOBW 1-206 F | Small ribosomal subunit protein uS5 | C3SR27_ECOLX 1-165 G | Small ribosomal subunit protein bS6 | W8T6F0_ECOLX 1-131 H | 30S ribosomal protein S7 | RS7_ECOLI 1-156 I | 30S ribosomal protein S8 | RS8_ECOLI 1-130 J | 30S ribosomal protein S9 | RS9_ECOLI 1-130 K | 30S ribosomal protein S10 | RS10_ECOLI 1-103 L | 30S ribosomal protein S11 | RS11_ECOLI 1-129 M | 30S ribosomal protein S12 | RS12_ECOLI 1-124 N | 30S ribosomal protein S13 | RS13_ECOLI 1-118 O | 30S ribosomal protein S14 | RS14_ECOLI 1-101 P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89 Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82 R | 30S ribosomal protein S17 | RS17_ECOLI 1-84 S | 30S ribosomal protein S18 | RS18_ECOLI 1-75 T | 30S ribosomal protein S19 | RS19_ECOLI 1-92 U | 30S ribosomal protein S20 | RS20_ECOLI 1-87 V | 30S ribosomal protein S21 | RS21_ECOLI 1-71 W | tRNA(fmet) P-site | X | mRNA | Non-standard residues in 9guv #5 --- 2MG — 2N-methylguanosine-5'-monophosphate 4OC — 4N,O2'-methylcytidine-5'-monophosphate 4SU — 4-thiouridine-5'-monophosphate 5MC — 5-methylcytidine-5'-monophosphate 5MU — 5-methyluridine 5'-monophosphate D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid G7M — N7-methyl-guanosine-5'-monophosphate H2U — 5,6-dihydrouridine-5'-monophosphate MA6 — 6N-dimethyladenosine-5'-monophoshate MG — magnesium ion OMC — O2'-methylycytidine-5'-monophosphate UR3 — 3-methyluridine-5'-monophoshate > hide #!4 models > hide #!1 models > hide #!2 models > hide #!3 models > show #!4 models > hide #!5 models > hide #!4 models > show #!5 models > close #5 > open 9gux 9gux title: 30S-TEC (TEC in expressome position) Inactive state 1 [more info...] Chain information for 9gux #5 --- Chain | Description | UniProt 1 2 | DNA-directed RNA polymerase subunit alpha | RPOA_ECOLI 1-329 3 | DNA-directed RNA polymerase subunit beta | RPOB_ECOLI 1-1342 4 | DNA-directed RNA polymerase subunit beta' | RPOC_ECO57 1-1406 5 | DNA-directed RNA polymerase subunit omega | RPOZ_ECOLI 1-91 6 | Non-Template DNA strand | 7 | Template DNA strand | A | 16S ribosomal RNA | B | 30S ribosomal protein S1 | RS1_ECOLI 1-557 C | 30S ribosomal protein S2 | RS2_ECOLI 1-241 D | Small ribosomal subunit protein uS3 | C3SQX2_ECOLX 1-233 E | Small ribosomal subunit protein uS4 | RS4_ECOBW 1-206 F | 30S ribosomal protein S5 | RS5_ECOLI 10-166 G | Small ribosomal subunit protein bS6 | W8T6F0_ECOLX 1-131 H | 30S ribosomal protein S7 | RS7_ECOLI 1-156 I | 30S ribosomal protein S8 | RS8_ECOLI 1-130 J | 30S ribosomal protein S9 | RS9_ECOLI 1-130 K | 30S ribosomal protein S10 | RS10_ECOLI 1-103 L | 30S ribosomal protein S11 | RS11_ECOLI 1-129 M | 30S ribosomal protein S12 | RS12_ECOLI 1-124 N | 30S ribosomal protein S13 | RS13_ECOLI 1-118 O | 30S ribosomal protein S14 | RS14_ECOLI 1-101 P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89 Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82 R | 30S ribosomal protein S17 | RS17_ECOLI 1-84 S | 30S ribosomal protein S18 | RS18_ECOLI 1-75 T | 30S ribosomal protein S19 | RS19_ECOLI 1-92 U | 30S ribosomal protein S20 | RS20_ECOLI 1-87 V | 30S ribosomal protein S21 | RS21_ECOLI 1-71 X | mRNA | Z | Transcription termination/antitermination protein NusG | NUSG_ECOLI 1-180 Non-standard residues in 9gux #5 --- 2MG — 2N-methylguanosine-5'-monophosphate 5MC — 5-methylcytidine-5'-monophosphate D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid G7M — N7-methyl-guanosine-5'-monophosphate MA6 — 6N-dimethyladenosine-5'-monophoshate MG — magnesium ion ZN — zinc ion > open ""/Volumes/LaCie/P147/Final MAps/cryosparc_P147_J438_008_volume_map.mrc"" Opened cryosparc_P147_J438_008_volume_map.mrc as #6, grid size 360,360,360, pixel 0.731, shown at level 0.0504, step 2, values float32 > close #1-4 > close #5 > surface dust #6 size 7.31 > volume #6 step 1 > volume #6 level 0.1029 > volume #6 level 0.06193 > volume #6 level 0.03989 > volume #6 level 0.09446 > volume #6 level 0.04724 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > view > ui tool show ""Side View"" > view > lighting simple > ui tool show ""Volume Viewer"" > volume #6 level 0.07788 > volume #6 level 0.05195 > volume #6 level 0.06373 > volume #6 level 0.04959 > volume #6 level 0.05431 > open 1iw7 Summary of feedback from opening 1iw7 fetched from pdb --- notes | Fetching compressed mmCIF 1iw7 from http://files.rcsb.org/download/1iw7.cif Fetching CCD PB from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/PB/PB.cif 1iw7 title: Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A resolution [more info...] Chain information for 1iw7 #1 --- Chain | Description | UniProt A B K L | RNA polymerase alpha subunit | RPOA_THETH 1-315 C M | RNA polymerase beta subunit | D N | RNA polymerase beta subunit | E O | RNA polymerase omega subunit | F P | RNA polymerase sigma-70 subunit | Non-standard residues in 1iw7 #1 --- MG — magnesium ion PB — lead (II) ion 1iw7 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > hide atoms > show cartoons > ui tool show ""Model Panel"" > close #1 > open 1907 Fetching url http://files.rcsb.org/download/1907.cif failed: HTTP Error 404: Not Found > open 1907 Fetching url http://files.rcsb.org/download/1907.cif failed: HTTP Error 404: Not Found > view > open /Volumes/LaCie/30S_IFs/Maps/cryosparc_P1_J470_008_volume_map.mrc Opened cryosparc_P1_J470_008_volume_map.mrc as #1, grid size 600,600,600, pixel 0.729, shown at level 0.0663, step 4, values float32 > open /Volumes/LaCie/30S_IFs/cryosparc_P1_J472_007_volume_map.mrc Opened cryosparc_P1_J472_007_volume_map.mrc as #2, grid size 600,600,600, pixel 0.729, shown at level 0.0503, step 4, values float32 > open /Volumes/LaCie/30S_IFs/cryosparc_P1_J476_008_volume_map.mrc Opened cryosparc_P1_J476_008_volume_map.mrc as #3, grid size 600,600,600, pixel 0.729, shown at level 0.0609, step 4, values float32 > surface dust #1 size 7.29 > surface dust #2 size 7.29 > surface dust #3 size 7.29 > open /Volumes/LaCie/30S_IFs/cryosparc_P1_J498_010_volume_map.mrc Opened cryosparc_P1_J498_010_volume_map.mrc as #4, grid size 600,600,600, pixel 0.729, shown at level 0.0583, step 4, values float32 > select add #4 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,3.8846,0,1,0,9.0861,0,0,1,-0.25038 > view matrix models > #4,-0.98939,0.10777,0.097446,391.6,-0.10521,-0.99396,0.031094,464.23,0.10021,0.020512,0.99475,-25.361 > view matrix models > #4,-0.98939,0.10777,0.097446,384.99,-0.10521,-0.99396,0.031094,452.43,0.10021,0.020512,0.99475,-18.659 > select subtract #4 Nothing selected > surface dust #1 size 7.29 > surface dust #2 size 7.29 > surface dust #3 size 7.29 > surface dust #4 size 7.29 > open /Volumes/LaCie/30S_IFs/cryosparc_P1_J499_008_volume_map.mrc Opened cryosparc_P1_J499_008_volume_map.mrc as #5, grid size 600,600,600, pixel 0.729, shown at level 0.0486, step 4, values float32 > open /Volumes/LaCie/30S_IFs/cryosparc_P1_J500_008_volume_map.mrc Opened cryosparc_P1_J500_008_volume_map.mrc as #7, grid size 600,600,600, pixel 0.729, shown at level 0.0511, step 4, values float32 > open /Volumes/LaCie/30S_IFs/cryosparc_P1_J501_004_volume_map.mrc Opened cryosparc_P1_J501_004_volume_map.mrc as #8, grid size 600,600,600, pixel 0.729, shown at level 0.0492, step 4, values float32 > surface dust #1 size 7.29 > surface dust #2 size 7.29 > surface dust #3 size 7.29 > surface dust #4 size 7.29 > surface dust #5 size 7.29 > surface dust #7 size 7.29 > surface dust #8 size 7.29 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,8 Model Number: Z1FE001RUFN/A Chip: Apple M4 Pro Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 48 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 4 days, 19 hours, 31 minutes Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: BE27A: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported 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: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.2.2 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-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX