id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9511 Crash saving session including maps bta4001@… Tom Goddard "{{{ 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. 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How to cite UCSF ChimeraX > open ""/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My > Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG- > reaction/Models/Model Building-NEW/State2-ssDNA-conf.1-CT/State2-Protein- > and-DNA-model-ssDNA-conf.1-coot-1.pdb"" Chain information for State2-Protein-and-DNA-model-ssDNA-conf.1-coot-1.pdb #1 --- Chain | Description 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available X | No description available Y | No description available > open ""/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My > Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG- > reaction/Models/Model Building-NEW/State3-ssDNA-conf.2-CT/Protein-and-DNA- > model-ssDNA-conf.2-coot-0.pdb"" Summary of feedback from opening /Users/ben/Library/CloudStorage/GoogleDrive- ballwein@gmail.com/My Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-reaction/Models/Model Building-NEW/State3-ssDNA- conf.2-CT/Protein-and-DNA-model-ssDNA-conf.2-coot-0.pdb --- warning | PDB SEQRES record for chain 6 is incomplete. Ignoring input sequence records as basis for sequence. Chain information for Protein-and-DNA-model-ssDNA-conf.2-coot-0.pdb #2 --- Chain | Description 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available X | No description available Y | No description available > open ""/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My > Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG- > reaction/Models/Model Building-NEW/State2-ssDNA-conf.1-CT/State2-composite- > map-ssDNA-conf.1.mrc"" Opened State2-composite-map-ssDNA-conf.1.mrc as #3, grid size 448,448,448, pixel 0.826, shown at level 0.396, step 2, values float32 > volume #3 step 1 > volume #3 level 1.235 > hide atoms > show cartoons > hide #!3 models > ui autostart false Log > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > ui mousemode right zoom > lighting soft > rename #2 State3-Protein-and-DNA-model-ssDNA-conf.2-coot-0.pdb > rename #2 id #4 > rename #4 id #2 > rename #2 id #4 > rename #3 id #2 > rename #4 id #3 > color #1 #a9f3a8ff > color #3 #f3b3dfff > hide #!3 models > show #!3 models > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > nucleotides slab > style nucleic stick Changed 2845 atom styles > select nucleic-acid 2845 atoms, 3192 bonds, 137 residues, 2 models selected > style sel stick Changed 2845 atom styles > style sel stick Changed 2845 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 2845 atom styles > show sel atoms > nucleotides sel fill > style nucleic & sel stick Changed 2845 atom styles > nucleotides sel tube/slab shape box > align #3 toAtoms #1 Unequal number of atoms to pair, 48514 and 48564 > show sel surfaces > select add #3 49947 atoms, 51100 bonds, 62 pseudobonds, 6033 residues, 9 models selected > select add #1 97078 atoms, 99038 bonds, 125 pseudobonds, 11933 residues, 12 models selected > show sel surfaces > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > hide #!3 models > select subtract #1 48514 atoms, 49492 bonds, 62 pseudobonds, 5964 residues, 33 models selected > select subtract #3 15 models selected > show #!1 models > show #!3 models > graphics silhouettes true > lighting soft > lighting flat > graphics silhouettes false > graphics silhouettes true > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > hide #!3 models > morph #3 #1 Computed 51 frame morph #4 > coordset #4 1,51 > view #4 clip false > color #!4 bychain > nucleotides #!4 tube/slab shape box > movie record > movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0 Movie saved to /Users/ben/Desktop/movie.mp4 > morph #1 #3 Computed 51 frame morph #5 > coordset #5 1,51 > hide #!4 models > nucleotides #!5 tube/slab shape box > color #!5 bychain > lighting soft > lighting flat > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting flat > lighting soft > view #5 clip false > morph #1 #3 #1 Computed 51 frame morph #6 > coordset #6 1,51 > hide #!5 models > show #!5 models > hide #!5 models > close #6 > show #!5 models > open ""/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My > Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG- > reaction/Models/Model Building-NEW/State2-ssDNA-conf.1-CT/State2-Protein- > and-DNA-model-ssDNA-conf.1-coot-1.pdb"" Chain information for State2-Protein-and-DNA-model-ssDNA-conf.1-coot-1.pdb #6 --- Chain | Description 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available X | No description available Y | No description available > show #!5-6 cartoons > hide #!5-6 atoms > morph #1 #3 #6 Computed 101 frame morph #7 > coordset #7 1,101 > hide #!5 models > nucleotides #!7 tube/slab shape box > color #!7 bychain > movie record > movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0 Error processing trigger ""new frame"": Movie encoding failed because no images were recorded. > movie record > movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0 Movie saved to /Users/ben/Desktop/movie.mp4 > movie record > movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0 Movie saved to /Users/ben/Desktop/movie.mp4 > movie record > movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0 Error processing trigger ""new frame"": Movie encoding failed because no images were recorded. > movie record > movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0 Movie saved to /Users/ben/Desktop/movie.mp4 > hide #!7 models > open ""/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My > Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG- > reaction/Density Modification/J1171_denmod_map.ccp4"" Opened J1171_denmod_map.ccp4 as #8, grid size 247,215,219, pixel 0.826, shown at level 4.35, step 1, values float32 > volume #8 level 1.2 > surface dust #8 size 8.26 > view #8 clip false > graphics silhouettes false > lighting soft > hide #!8 models > show #!8 models > color #8 #a2a7ffff models > color #8 #f8a4ffff models > set bgColor white > close #8 > show #!7 models > hide #!7 models > set bgColor black > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 surfaces > show #!3 models > hide #!1,3 surfaces > hide #!3 models > show #!3 models > hide #!1 models > hide #!3 models > show #!7 models > view #7 clip false > show #!6 models > hide #!6 models > show #!5 models > hide #!7 models > movie record > movie encode /Users/ben/Desktop/movie.mp4 framerate 25.0 Movie saved to /Users/ben/Desktop/movie.mp4 > show #!1 models > hide #!5 models > color #!1 bychain > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > hide #!1 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!1 models > hide #!1 models > show #!4 models > view #4 clip false > show #!5 models > hide #!4 models > hide #!5 models > show #!5 models > show #!4 models > hide #!5 models > hide #!4 models > show #!3 models > show #!2 models > show #!6 models > hide #!3 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > close #6 > rainbow #!1 > color #!1 bychain > show #!7 models > hide #!1 models > open ""/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My > Drive/Grad School/Thesis Work/EM Data > Processing/20230103-ssDNA-T15/Maps/cryosparc_P37_J1186_004_volume_map.mrc"" Opened cryosparc_P37_J1186_004_volume_map.mrc as #6, grid size 192,192,192, pixel 1.65, shown at level 0.88, step 1, values float32 > view #6 clip false Must specify one map, got 0 > fitmap #6 inMap #2 Fit map cryosparc_P37_J1186_004_volume_map.mrc in map State2-composite-map- ssDNA-conf.1.mrc using 70710 points correlation = 0.02191, correlation about mean = 0.0005065, overlap = 3623 steps = 60, shift = 2.41, angle = 1.05 degrees Position of cryosparc_P37_J1186_004_volume_map.mrc (#6) relative to State2-composite-map-ssDNA-conf.1.mrc (#2) coordinates: Matrix rotation and translation 0.99984352 0.00441790 0.01712935 -2.73168958 -0.00433589 0.99997897 -0.00482212 3.40130991 -0.01715029 0.00474709 0.99984165 3.17174316 Axis 0.26109025 0.93530015 -0.23884200 Axis point 207.02842200 0.00000000 187.43707829 Rotation angle (degrees) 1.05003132 Shift along axis 1.71048269 > show #!2 models > select add #6 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #6,0.99984,0.0044179,0.017129,2.4532,-0.0043359,0.99998,-0.0048221,36.099,-0.01715,0.0047471,0.99984,34.408 > view matrix models > #6,0.99984,0.0044179,0.017129,2.2068,-0.0043359,0.99998,-0.0048221,30.22,-0.01715,0.0047471,0.99984,31.847 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.99982,-0.015082,0.011457,6.0527,0.014078,0.99643,0.083193,13.838,-0.012671,-0.083017,0.99647,44.907 > fitmap #6 inMap #2 Fit map cryosparc_P37_J1186_004_volume_map.mrc in map State2-composite-map- ssDNA-conf.1.mrc using 70710 points correlation = 0.04464, correlation about mean = 0.01502, overlap = 1.029e+04 steps = 72, shift = 1.71, angle = 2.27 degrees Position of cryosparc_P37_J1186_004_volume_map.mrc (#6) relative to State2-composite-map-ssDNA-conf.1.mrc (#2) coordinates: Matrix rotation and translation 0.99936355 -0.02301927 -0.02725075 12.89966060 0.02527985 0.99599622 0.08574644 13.10365671 0.02516783 -0.08638076 0.99594424 40.54146978 Axis -0.92391693 -0.28136408 0.25925233 Axis point 0.00000000 489.94099490 -113.22443911 Rotation angle (degrees) 5.34489668 Shift along axis -5.09464238 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.99936,-0.023019,-0.027251,35.045,0.02528,0.996,0.085746,11.037,0.025168,-0.086381,0.99594,35.901 > fitmap #6 inMap #2 Fit map cryosparc_P37_J1186_004_volume_map.mrc in map State2-composite-map- ssDNA-conf.1.mrc using 70710 points correlation = 0.6082, correlation about mean = 0.4079, overlap = 2.413e+05 steps = 96, shift = 0.94, angle = 5.48 degrees Position of cryosparc_P37_J1186_004_volume_map.mrc (#6) relative to State2-composite-map-ssDNA-conf.1.mrc (#2) coordinates: Matrix rotation and translation 0.99993979 -0.01078503 -0.00202036 28.26595694 0.01077417 0.99992786 -0.00530861 26.83639602 0.00207747 0.00528652 0.99998386 23.80889650 Axis 0.43477884 -0.16815756 0.88469791 Axis point -2931.06092995 1474.56504051 0.00000000 Rotation angle (degrees) 0.69813758 Shift along axis 28.84037816 > select subtract #6 Nothing selected > ui mousemode right zoom > hide #!2 models > transparency #6.1 50 > hide #!7 models > show #!1 models > volume #6 level 0.5307 > close #1-7 > open ""/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My > Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-reaction/CMG- > EM-Data/State3/State3-Models/State3-Protein-model-ssDNA-conf.2-coot-12.pdb"" Summary of feedback from opening /Users/ben/Library/CloudStorage/GoogleDrive- ballwein@gmail.com/My Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-reaction/CMG-EM- Data/State3/State3-Models/State3-Protein-model-ssDNA-conf.2-coot-12.pdb --- warning | PDB SEQRES record for chain 6 is incomplete. Ignoring input sequence records as basis for sequence. Chain information for State3-Protein-model-ssDNA-conf.2-coot-12.pdb #1 --- Chain | Description 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available X | No description available Y | No description available > show cartoons > hide atoms > open emdb-10227 'emdb-10227' has no suffix > open emdb:10227 Opened emdb 10227 as #2, grid size 360,360,360, pixel 1.05, shown at level 0.0111, step 2, values float32 > volume #2 step 1 > open pdb:6skl 6skl title: Cryo-EM structure of the CMG Fork Protection Complex at a replication fork - Conformation 1 [more info...] Chain information for 6skl #3 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_YEAST 3 | DNA replication licensing factor MCM3 | MCM3_YEAST 4 | DNA replication licensing factor MCM4 | MCM4_YEAST 5 | Minichromosome maintenance protein 5 | MCM5_YEAST 6 | DNA replication licensing factor MCM6 | MCM6_YEAST 7 | DNA replication licensing factor MCM7 | MCM7_YEAST A | DNA replication complex GINS protein PSF1 | PSF1_YEAST B | DNA replication complex GINS protein PSF2 | PSF2_YEAST C | DNA replication complex GINS protein PSF3 | PSF3_YEAST D | DNA replication complex GINS protein SLD5 | SLD5_YEAST E | Cell division control protein 45 | CDC45_YEAST F G H | DNA polymerase alpha-binding protein | CTF4_YEAST I | DNA fork, leading-strand template | J | DNA fork, lagging-strand template | X | Topoisomerase 1-associated factor 1 | TOF1_YEAST Y | Chromosome segregation in meiosis protein 3 | CSM3_YEAST Non-standard residues in 6skl #3 --- ANP — phosphoaminophosphonic acid-adenylate ester MG — magnesium ion ZN — zinc ion > show cartoons > hide atoms > hide #!1 models > volume #2 level 0.01251 > transparency 50 > show #!1 models > view #1 clip false > hide #!3 models > show #!3 models > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > hide #!1 models > view #3 clip false > select #3/I:49 32 atoms, 33 bonds, 1 residue, 1 model selected > select up 1192 atoms, 1279 bonds, 37 residues, 1 model selected > select up 118220 atoms, 119405 bonds, 7321 residues, 1 model selected > select down 1192 atoms, 1279 bonds, 37 residues, 1 model selected > show sel atoms > nucleotides sel stubs > nucleotides sel tube/slab shape box > select clear > select #2 4 models selected > hide #!2 models > select #3/7:363 20 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 20 atom styles > select clear > show #!2 models > volume #2 level 0.02158 > volume #2 level 0.02363 > hide #!3 models > hide #!2 models > show #!1 models > open ""/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My > Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-reaction/CMG- > EM-Data/State3/State3-Maps/State3_denmod_map-(C-tier).mrc"" Opened State3_denmod_map-(C-tier).mrc as #4, grid size 448,448,448, pixel 0.826, shown at level 0.504, step 2, values float32 > volume #4 level 1.25 > volume #4 step 1 > hide #!1 models > view #4 clip false > surface dust #4 size 8.26 > ui tool show ""Segment Map"" Segmenting State3_denmod_map-(C-tier).mrc, density threshold 1.250051 Only showing 60 of 985 regions. Showing 60 of 985 region surfaces 6810 watershed regions, grouped to 985 regions Showing State3_denmod_map-(C-tier).seg - 985 regions, 60 surfaces > hide #!4 models > show #!1 models > hide #!5 models > show #!4 models > show #!5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!1 models > show #!1 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > show #!4 models > molmap #1 4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 4 as #6, grid size 155,135,141, pixel 1.33, shown at level 0.0965, step 1, values float32 > hide #!6 models > hide #!5 models > hide #!1 models > show #!6 models > molmap #1 4 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 4 as #6, grid size 448,448,448, pixel 0.826, shown at level 0.0966, step 1, values float32 > close #5 > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!4 models > show #!6 models > molmap #1 3 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #5, grid size 448,448,448, pixel 0.826, shown at level 0.111, step 1, values float32 > molmap #1 2 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 2 as #5, grid size 448,448,448, pixel 0.826, shown at level 0.19, step 1, values float32 > molmap #1 1 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 1 as #5, grid size 448,448,448, pixel 0.826, shown at level 0.773, step 1, values float32 > volume #5 step 2 > volume #5 step 4 > volume #5 step 16 > volume #5 step 1 > molmap #1 3 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #5, grid size 448,448,448, pixel 0.826, shown at level 0.111, step 1, values float32 > hide #!5 models > show #!5 models > show #!1 models > hide #!5 models > show #!5 models > hide #!1 models > hide #!5 models > show #!5 models > show #!1 models > select #1/2 5222 atoms, 5310 bonds, 6 pseudobonds, 657 residues, 3 models selected > hide #!5 models > molmap #1/2 3 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #6, grid size 448,448,448, pixel 0.826, shown at level 0.109, step 1, values float32 > hide #!6 models > molmap #1/2:469-865 3 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #7, grid size 448,448,448, pixel 0.826, shown at level 0.11, step 1, values float32 > close #6 > close #5 > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > molmap #1/3:338-739 3 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #5, grid size 448,448,448, pixel 0.826, shown at level 0.111, step 1, values float32 > molmap #1/4:501-836 3 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #6, grid size 448,448,448, pixel 0.826, shown at level 0.11, step 1, values float32 > molmap #1/4:340-694 3 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #8, grid size 448,448,448, pixel 0.826, shown at level 0.107, step 1, values float32 > molmap #1/5:500-835 3 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #9, grid size 448,448,448, pixel 0.826, shown at level 0.109, step 1, values float32 > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > close #8 > close #9 > molmap #1/5:340-694 3 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #8, grid size 448,448,448, pixel 0.826, shown at level 0.11, step 1, values float32 > molmap #1/6:500-835 3 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #9, grid size 448,448,448, pixel 0.826, shown at level 0.111, step 1, values float32 > molmap #1/7:409-730 3 onGrid #4 Opened State3-Protein-model-ssDNA-conf.2-coot-12.pdb map 3 as #10, grid size 448,448,448, pixel 0.826, shown at level 0.112, step 1, values float32 > hide #!1 models > select #5 2 models selected > select #8 2 models selected > select #5 2 models selected > select #8 2 models selected > select #7 2 models selected > select #8 2 models selected > select #10 2 models selected > show #!1 models No segmentation chosen > ui tool show ""DICOM Browser"" > vop add #5,8,10 Opened volume sum as #11, grid size 448,448,448, pixel 0.826, shown at step 1, values float32 > rename #11 Mcm7,3,5 > vop add #6,7,9 Opened volume sum as #12, grid size 448,448,448, pixel 0.826, shown at step 1, values float32 > rename #12 Mcm4,6,2 > save ""/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My > Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-reaction/CMG- > EM-Data/State3/State3-Masks/State3-Mcm7-3-5-mask.mrc"" models #11 > save ""/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My > Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG-reaction/CMG- > EM-Data/State3/State3-Masks/State3-Mcm4-6-2-mask.mrc"" models #12 > volume #11 level 0.05216 > lighting soft > show #!4 models > hide #!12 models > hide #!11 models > hide #!4 models > show #!11 models > show #!12 models > save ""/Users/ben/Library/CloudStorage/GoogleDrive-ballwein@gmail.com/My > Drive/Grad School/Thesis Work/EM Data Processing/20221108-CMG- > reaction/ChimeraX Sessions/20221108-reaction-session-4.cxs"" includeMaps true ===== Log before crash end ===== 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 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.6 (21G115) Kernel Version: Darwin 21.6.0 Time since boot: 50 days 14:25 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 ASUS PB287Q: Resolution: 6016 x 3384 UI Looks like: 3008 x 1692 @ 60.00Hz Mirror: Off Online: Yes 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-PhenixUI: 1.1.13 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 Sessions limitation all ChimeraX