id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8135 Crash in event loop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit 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. 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GUARD 44K 11 \nStack 153.6M 37 \nStack Guard 56.1M 26 \nVM_ALLOCATE 231.5M 274 \nVM_ALLOCATE (reserved) 96.1M 13 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 45.9M 736 \n__DATA_CONST 39.1M 380 \n__DATA_DIRTY 1829K 223 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 197.5M 148 \n__OBJC_RO 65.1M 1 \n__OBJC_RW 1980K 2 \n__TEXT 884.0M 737 \ndyld private memory 416K 3 \nmapped file 4.7G 1736 \nshared memory 3060K 30 \nunshared pmap 14.0M 10 \n=========== ======= ======= \nTOTAL 9.6G 5836 \nTOTAL, minus reserved VM space 8.6G 5836 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62699e1ec1ff2978b47f6c3b"", ""factorPackIds"" : { ""SIRI_FIND_MY_CONFIGURATION_FILES"" : ""631f72d1de559130376df1fb"" }, ""deploymentId"" : 240000023 }, { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""63605e98c8a2104545a56f10"" }, ""deploymentId"" : 240000045 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/kunwoong/Desktop/M393T/cholesterol.cxs Opened TMEM175_WT_2.77_P5_J329_zflip (1).mrc as #2, grid size 400,400,400, pixel 0.553, shown at level 0.0787, step 1, values float32 Log from Mon Dec 5 11:03:58 2022 Startup Messages --- note | available bundle cache has not been initialized yet 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 ""/Users/kunwoong/Desktop/hs/TMEM175_WT_2.77_P5_J329_zflip-coot-0 > (3).pdb"" Chain information for TMEM175_WT_2.77_P5_J329_zflip-coot-0 (3).pdb #1 --- Chain | Description A | No description available B | No description available > set bgColor white > open ""/Users/kunwoong/Desktop/hs/TMEM175_WT_2.77_P5_J329_zflip (1).mrc"" Opened TMEM175_WT_2.77_P5_J329_zflip (1).mrc as #2, grid size 400,400,400, pixel 0.553, shown at level 0.0394, step 2, values float32 > volume #2 step 1 > volume #2 level 0.06713 > transparency 50 > ui tool show ""Color Actions"" > color bychain > surface dust #2 size 5.53 Alignment identifier is 1/A Alignment identifier is 1/B > select > /A:35-47,50-57,67-100,107-132,137-162,165-168,172-175,181-201,258-274,277-280,288-291,293-295,299-331,339-362,373-395,416-438,442-457,459-469 2287 atoms, 2325 bonds, 294 residues, 1 model selected > select clear > select /A:93 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:93 5 atoms, 4 bonds, 1 residue, 1 model selected > style sel stick Changed 5 atom styles > style sel stick Changed 5 atom styles > show sel atoms > select clear > ui mousemode right zoom > select /A:93 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select clear > select /A:93,97 16 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > select clear > select /A:93,97,339 27 atoms, 24 bonds, 3 residues, 1 model selected > show sel atoms > select clear > lighting soft > graphics silhouettes true > select /A:92-93,97,339 41 atoms, 40 bonds, 4 residues, 1 model selected > show sel atoms > select /A:90,92-93,97,339 48 atoms, 46 bonds, 5 residues, 1 model selected > show sel atoms > select /A:86,90,92-93,97,339 56 atoms, 53 bonds, 6 residues, 1 model selected > show sel atoms > select /A:86,90,92-93,97,339,343 64 atoms, 60 bonds, 7 residues, 1 model selected > show sel atoms > select clear > ui tool show ""Side View"" > ui mousemode right ""contour level"" > volume #2 level 0.08146 > ui tool show ""Color Actions"" > color byelement target a > color byhetero target a > color bynucleotide target a > color bychain target a > color bypolymer target a > ui tool show ""Color Actions"" > color dodger blue target a > color turquoise target a > ui tool show ""Color Actions"" > color byelement target a > color light salmon target a > color byelement target a > color byhetero target a > color byelement target a > color bynucleotide target a > color bypolymer target a > color turquoise target a > save /Users/kunwoong/Desktop/image1.png supersample 3 > volume #2 level -0.05741 > volume #2 level -0.4989 > volume #2 level -0.7445 > volume #2 level -0.6764 > volume #2 level -0.6087 > volume #2 level -0.4212 > volume #2 level -0.2114 > volume #2 level -0.2222 > volume #2 level -0.279 > volume #2 level -0.3249 > ui mousemode right zoom > ui mousemode right ""contour level"" > volume #2 level -0.7142 > volume #2 level -0.6487 > volume #2 level -0.002813 > volume #2 level 0.02368 > volume #2 level 0.03998 > volume #2 level 0.06036 > volume #2 level 0.1011 > ui mousemode right zoom > volume #2 level 0.07872 > save /Users/kunwoong/Desktop/image2.png supersample 3 > open /Users/kunwoong/Downloads/rcsb_pdb_7P0K.fasta Summary of feedback from opening /Users/kunwoong/Downloads/rcsb_pdb_7P0K.fasta --- note | Alignment identifier is rcsb_pdb_7P0K.fasta Opened 1 sequences from rcsb_pdb_7P0K.fasta > save /Users/kunwoong/Desktop/hs/cholesterol.cxs includeMaps true ——— End of log from Mon Dec 5 11:03:58 2022 ——— opened ChimeraX session > ui mousemode right ""contour level"" > volume #2 level 0.08239 > ui mousemode right ""pick blobs"" > measure blob #!2.1 triangleNumber 356755 color #30cdb5ff Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob: volume = 43.23 area = 84.212 size = 8.7856 4.8655 3.171 > measure blob #!2.1 triangleNumber 215257 color #30cdb5ff Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob: volume = 21266 area = 33751 size = 68.575 67.308 59.659 > volume #2 level 0.08239 > measure blob #!2.1 triangleNumber 342734 color #30cdb5ff Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob: volume = 43.23 area = 84.212 size = 8.7856 4.8655 3.171 > ui mousemode right ""contour level"" > volume #2 level 0.1 > ui mousemode right ""pick blobs"" > measure blob #!2.1 triangleNumber 205434 color #30cdb5ff Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob: volume = 52.621 area = 105.67 size = 15.053 3.2253 3.067 > measure blob #!2.1 triangleNumber 287060 color #30cdb5ff Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob: volume = 35.094 area = 73.53 size = 8.419 4.532 2.8658 > volume #2 level 0.1061 > measure blob #!2.1 triangleNumber 289446 color #30cdb5ff Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob: volume = 32.545 area = 70.109 size = 8.3169 4.4226 2.7597 > measure blob #!2.1 triangleNumber 175039 color #30cdb5ff Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob: volume = 48.929 area = 100.54 size = 14.512 3.1301 2.992 > ui tool show ""Color Actions"" > color byelement target a > color cyan target a > color byelement target a > color byhetero target a > color cyan target a > color byhetero target a > select #2 4 models selected > select #2 4 models selected > select clear > measure blob #!2.1 triangleNumber 254567 color #0000ccff outline true Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob: volume = 1153.3 area = 2061.3 size = 48.656 23.736 14.389 > ui tool show ""Volume Viewer"" > measure blob #!2.1 triangleNumber 295216 color #26d2caff Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob: volume = 32.545 area = 70.109 size = 8.3169 4.4226 2.7597 > volume #2 level 0.1081 > measure blob #!2.1 triangleNumber 197688 color #26d2caff Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob: volume = 47.788 area = 99.029 size = 14.437 3.1389 2.9703 > measure blob #!2.1 triangleNumber 290902 color #26d2caff Surface TMEM175_WT_2.77_P5_J329_zflip (1).mrc #2.1 blob: volume = 31.741 area = 69.015 size = 8.2855 4.384 2.7255 > ui tool show ""Side View"" > movie record > turn y 2 180 > wait 180 > movie encode /Users/kunwoong/Desktop/movie3.mp4 Movie saved to /Users/kunwoong/Desktop/movie3.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/kunwoong/Desktop/movie4.mp4 Movie saved to /Users/kunwoong/Desktop/movie4.mp4 > close session > open > /Users/kunwoong/Desktop/enpp2_new/662/cryosparc_P11_J662_012_volume_map_sharp.mrc Opened cryosparc_P11_J662_012_volume_map_sharp.mrc as #1, grid size 224,224,224, pixel 0.901, shown at level 0.146, step 1, values float32 > volume #1 level 0.1894 > open > ""/Users/kunwoong/Desktop/enpp2_new/662/cryosparc_P11_J662_012_volume_map_sharp_cryonet > (1)-coot-0.pdb"" Summary of feedback from opening /Users/kunwoong/Desktop/enpp2_new/662/cryosparc_P11_J662_012_volume_map_sharp_cryonet (1)-coot-0.pdb --- warning | Ignored bad PDB record found on line 4 REMARK INFO: [occupancy]=sse [bfactor]=score Chain information for cryosparc_P11_J662_012_volume_map_sharp_cryonet (1)-coot-0.pdb #2 --- Chain | Description A | No description available > transparency 50 > set bgColor white > surface dust #1 size 9.01 > color zone #1 near #2 distance 5.41 > hide atoms > color zone #1 near #2 distance 5.41 > surface dust #1 size 9.01 > volume #1 color #bfbeba80 Alignment identifier is 2/A > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1894 atoms, 1906 bonds, 225 residues, 1 model selected > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1894 atoms, 1906 bonds, 225 residues, 1 model selected > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1894 atoms, 1906 bonds, 225 residues, 1 model selected > select clear > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1894 atoms, 1906 bonds, 225 residues, 1 model selected > select clear > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1894 atoms, 1906 bonds, 225 residues, 1 model selected > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1894 atoms, 1906 bonds, 225 residues, 1 model selected > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-254,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1894 atoms, 1906 bonds, 225 residues, 1 model selected > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1908 atoms, 1922 bonds, 226 residues, 1 model selected > select clear > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1908 atoms, 1922 bonds, 226 residues, 1 model selected > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1908 atoms, 1922 bonds, 226 residues, 1 model selected > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1908 atoms, 1922 bonds, 226 residues, 1 model selected > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1915 atoms, 1929 bonds, 227 residues, 1 model selected > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1915 atoms, 1929 bonds, 227 residues, 1 model selected > select clear > select > /A:81-83,90-94,105-107,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 1960 atoms, 1975 bonds, 233 residues, 1 model selected > select > /A:81-83,90-94,105-107,113-118,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2005 atoms, 2019 bonds, 239 residues, 1 model selected > select > /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,405-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2019 atoms, 2033 bonds, 241 residues, 1 model selected > select > /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2087 atoms, 2101 bonds, 249 residues, 1 model selected > select > /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2186 atoms, 2203 bonds, 261 residues, 1 model selected > select clear > select > /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2186 atoms, 2203 bonds, 261 residues, 1 model selected > select > /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2186 atoms, 2203 bonds, 261 residues, 1 model selected > select > /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2186 atoms, 2203 bonds, 261 residues, 1 model selected > select > /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2186 atoms, 2203 bonds, 261 residues, 1 model selected > select > /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2186 atoms, 2203 bonds, 261 residues, 1 model selected > select > /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2186 atoms, 2203 bonds, 261 residues, 1 model selected > select > /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2186 atoms, 2203 bonds, 261 residues, 1 model selected > select > /A:81-83,90-94,105-107,109-119,124-127,134-139,144-146,158-163,176-181,187-195,207,210-219,223-226,248-250,252-255,260-267,282-294,312-318,323-346,373-375,391-412,426-428,431-433,482-484,506-517,532-534,543-554,560-562,593-596,661-663,667-671,684-686,690-696,699-701,707-718,720-728,750-752,812-814,816-823,827-834,846-853 2186 atoms, 2203 bonds, 261 residues, 1 model selected > select /A:255 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:255 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:252,255 24 atoms, 25 bonds, 2 residues, 1 model selected > select /A:252,255,261 38 atoms, 40 bonds, 3 residues, 1 model selected > style sel stick Changed 38 atom styles > show sel atoms > select clear > ui tool show ""Color Actions"" > color byhetero target a > color byelement target a > color cyan target a > color byhetero target a > color hot pink target c > color light sea green target c > color purple target c > color salmon target c > ui mousemode right ""contour level"" > volume #1 level 0.2784 > volume #1 level 0.6169 > volume #1 level 0.6579 > volume #1 level 0.6438 > volume #1 level 0.6582 > ui mousemode right ""pick blobs"" > measure blob #!1.1 triangleNumber 85971 color #18cdbcff Surface cryosparc_P11_J662_012_volume_map_sharp.mrc #1.1 blob: volume = 8606.1 area = 19289 size = 63.452 50.169 38.552 > volume #1 level 0.6731 > measure blob #!1.1 triangleNumber 82371 color #18cdbcff Surface cryosparc_P11_J662_012_volume_map_sharp.mrc #1.1 blob: volume = 8167.3 area = 18452 size = 63.407 49.698 39.081 > volume #1 level 0.8215 > measure blob #!1.1 triangleNumber 62799 color #18cdbcff Surface cryosparc_P11_J662_012_volume_map_sharp.mrc #1.1 blob: volume = 3317.4 area = 7966 size = 52.89 40.4 34.138 > volume #1 level 1.267 > measure blob #!1.1 triangleNumber 25443 color #18cdbcff Surface cryosparc_P11_J662_012_volume_map_sharp.mrc #1.1 blob: volume = 37.55 area = 100.94 size = 9.4419 6.9629 3.1214 > volume #1 level 0.5841 > volume #1 level 0.7473 > ui mousemode right ""pick blobs"" > volume #1 level 0.3466 > measure blob #!1.1 triangleNumber 172292 color #18cdbcff Surface cryosparc_P11_J662_012_volume_map_sharp.mrc #1.1 blob: volume = 27253 area = 51149 size = 87.501 63.859 48.02 > volume #1 level 0.3763 > ui mousemode right zoom > volume #1 level 0.7324 > volume #1 level 0.6286 > volume #1 level 0.6582 > lighting soft > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > lighting simple > lighting soft > lighting flat > lighting full > lighting flat > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > volume #1 level 0.6731 > ui tool show ""Color Actions"" > color dodger blue target c > color dark turquoise target c > color medium spring green target c > color cornflower blue target c > ui tool show ""Side View"" > save /Users/kunwoong/Desktop/image1.png supersample 3 > save /Users/kunwoong/Desktop/image2.png supersample 3 > ui tool show ""Volume Viewer"" > volume #1 level 0.1543 > volume #1 level -0.06192 > volume #1 level -0.134 > volume #1 level -0.004273 > volume #1 level -0.2781 > volume #1 level -0.2637 > volume #1 level 0.356 > volume #1 level 0.1254 > surface dust #1 size 9.01 > ui tool show ""Volume Viewer"" > volume #1 level 0.2119 > volume #1 level 0.3128 > volume #1 level 0.1543 > view orient > turn y 90 > lighting soft > transparency 0 > transparency 50 > transparency 0 > transparency 50 > transparency 0 > transparency 50 > transparency 0 > transparency 50 > transparency 0 > open ""/Users/kunwoong/Desktop/enpp2_new/hs/P11_J330_zflip_ENPP2_Chem2.mrc 2"" Unrecognized file suffix '.mrc 2' > open /Users/kunwoong/Desktop/enpp2_new/hs/P11_J330_zflip_ENPP2_Chem2.mrc Opened P11_J330_zflip_ENPP2_Chem2.mrc as #3, grid size 224,224,224, pixel 0.901, shown at level 0.208, step 1, values float32 > surface dust #1 size 9.01 > surface dust #3 size 9.01 > open ""/Users/kunwoong/Desktop/enpp2_new/hs/Chem02_real_space_refined_004 > (3).pdb"" Chain information for Chem02_real_space_refined_004 (3).pdb #4 --- Chain | Description A | No description available > view orient > ui tool show ""Volume Viewer"" > view > ui tool show ""DICOM Browser"" > ui tool show ""Surface Zone"" > select add #3 2 models selected > select add #4 5720 atoms, 5887 bonds, 2 pseudobonds, 703 residues, 4 models selected > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #3,1,0,0,-36.586,0,1,0,84.165,0,0,1,-4.7299,#4,1,0,0,-36.586,0,1,0,84.165,0,0,1,-4.7299 ===== 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 - 83 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 Model Number: MKGR3KH/A Chip: Unknown Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0.1 (22A400) Kernel Version: Darwin 22.1.0 Time since boot: 8 days, 14 hours, 26 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 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 Core can't reproduce Tom Goddard all ChimeraX