id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8367 Crash destroying atomic structure chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. 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] } } Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/tina/PG/projects/minicell- > structure/periplasmic_scaffold/lafter/lafter_vs_raw.cxs Opened scaffold-new-postprocess_imasked as #4, grid size 800,800,800, pixel 2.2, shown at level 0.00631, step 1, values float32 Opened Refine3d_job975_scaffold_LAFTER_filtered_imasked as #3, grid size 800,800,800, pixel 2.2, shown at level 0.126, step 1, values float32 Log from Sun Jan 22 21:45:11 2023UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open Refine3d_job975_scaffold_LAFTER_filtered.mrc Opened Refine3d_job975_scaffold_LAFTER_filtered.mrc as #1, grid size 800,800,800, pixel 2.2, shown at step 1, values float32 > volume #1 region 0,0,0,799,799,799 step 4 [Repeated 1 time(s)] > set bgColor white > lighting soft > volume #1 change image level -0.007422,0 level 0.1291,0.8 level 1.139,1 > volume #1 level 0.07052 > volume #1 step 1 > volume #1 color #4f4f4f > volume #1 color #4d4d4d > volume #1 color #4d4d4d82 > volume #1 color #f4f4f482 > volume #1 color #f4f4f4 > color #1 silver models transparency 0 > color #1 #d6d6d6 models transparency 0 > color #1 silver models transparency 0 > color #1 darkgrey models transparency 0 > color #1 #a9a9a982 models > color #1 #a9a9a980 models > color #1 darkgrey models transparency 0 > volume #1 level 0.2472 > view > lighting soft > lighting simple > view orient > turn x -90 > clip > zoom 1.5 > volume #1 level 0.05312 > ~clip > zoom 0.6 > view orient > turn x -30 [Repeated 1 time(s)] > volume #1 level 0.04366 > volume #1 level 0.045 > volume #1 level 0.05 > volume #1 level 0.06 > volume #1 level 0.07 > lighting shadows true intensity 0.5 > lighting shadows false > lighting depthCue false > lighting soft [Repeated 1 time(s)] > lighting shadows true intensity 0.5 > lighting shadows false > camera ortho > save lafter_turn60.png format png transparentBackground true > save lafter_turn-60.png format png transparentBackground true > view orient > save lafter.png format png transparentBackground true > turn x -60 > volume #1 level 0.2736 > save lafter_low_turn-60.png format png transparentBackground true > view orient > turn x -60 > turn x -30 > volume #1 level 0.07947 > volume #1 level 0.2641 > volume #1 level 0.2546 > volume #1 level 0.2499 > volume #1 level 0.2452 > volume #1 level 0.2073 > volume #1 level 0.212 > volume #1 level 0.2168 > volume #1 level 0.2262 > volume #1 level 0.1079 > volume #1 level 0.05106 > open /Users/tina/PG/projects/minicell- > structure/periplasmic_scaffold/scaffold-new-postprocess.mrc Opened scaffold-new-postprocess.mrc as #2, grid size 800,800,800, pixel 2.2, shown at step 1, values float32 > volume #2 region 0,0,0,799,799,799 step 4 [Repeated 1 time(s)] > volume #2 step 1 > volume #2 change image level -0.0001261,0 level 0.006522,0.8 level 0.01695,1 > volume #2 level 0.002151 > volume #2 level 0.002823 > volume #2 color darkgrey > volume #2 level 0.007591 > view orient > volume #2 level 0.002285 > volume #2 level 0.002823 > view orient > turn x -30 [Repeated 1 time(s)] > volume #2 level 0.002688 > volume #2 level 0.002352 > volume #2 level 0.002151 > volume #2 level 0.001882 > ui tool show ""Hide Dust"" > surface dust #2 size 13.2 [Repeated 1 time(s)] > surface dust #2 size 13.96 > surface dust #2 size 27.61 > surface dust #2 size 28.22 > surface dust #2 size 55.85 > surface dust #2 size 57.06 > surface dust #2 size 160.48 > surface dust #2 size 156.97 > surface dust #2 size 74.34 > volume #2 level 0.001949 > volume #2 level 0.002017 > view orient > turn x -30 [Repeated 1 time(s)] > view orient > turn x -50 > ui tool show ""Segment Map"" Segmenting scaffold-new-postprocess.mrc, density threshold 0.002017 Only showing 60 of 552 regions. Showing 60 of 552 region surfaces 5661 watershed regions, grouped to 552 regions Showing scaffold-new-postprocess.seg - 552 regions, 60 surfaces > hide #!2 models Showing 552 region surfaces Opened scaffold-new-postprocess_imasked as #4, grid size 800,800,800, pixel 2.2, shown at step 1, values float32 > hide #!3 models > close #2 > show #!1 models > hide #!4 models > volume #1 level 0.008091 > volume #1 level 0.01239 > volume #1 level 0.01669 Segmenting Refine3d_job975_scaffold_LAFTER_filtered.mrc, density threshold 0.016685 Showing 593 region surfaces 8935 watershed regions, grouped to 593 regions Showing Refine3d_job975_scaffold_LAFTER_filtered.seg - 593 regions, 593 surfaces > hide #!1 models Ungrouped to 64 regions Ungrouped to 3 regions Ungrouped to 4 regions Ungrouped to 3 regions Ungrouped to 4 regions Ungrouped to 2 regions Ungrouped to 10 regions Ungrouped to 3 regions Ungrouped to 43 regions Ungrouped to 4 regions Ungrouped to 3 regions [Repeated 5 time(s)]Ungrouped to 4 regions Ungrouped to 3 regions [Repeated 2 time(s)]Ungrouped to 4 regions Ungrouped to 2 regions Ungrouped to 3 regions [Repeated 1 time(s)]Ungrouped to 2 regions Ungrouped to 20 regions > select clear Drag select of 13248, 13264, 13268, 13263, 13299, 13258, 13265, 13257, 13262, 13267, 12609, 12418, 12401, 12425, 12649, 12383, 12407, 13308, 13311, 13260, 13199, 13309, 13110, 13307, 12688, 12331, 12697, 12816, 12479, 12902, 12920, 12412, 12904, 12414, 12813, 12918, 12486, 12687, 13208, 13286, 13280, 13285, 13226, 13152, 13291, 13181, 13259, 12815, 13290, 12703, 13225, 13287, 13278, 13241, 13060, 13224, 13180, 12689, 13298, 13134, 13115, 13057, 13059, 13127, 13072, 13243, 13132, 13054, 13098, 13099, 13083, 13055, 13074, 13131, 13201, 13223, 12345, 12347, 12444, 12437, 12485, 12712, 12411, 12597, 12738, 12921, 12560, 13202, 12478, 12343, 12441, 12443, 12882, 12473, 12540, 12644, 12474, 12346, 13332, 12521, 12690, 12409, 12923, 12919, 12449, 12456, 12641, 12774, 12580, 12730, 12737, 12595, 13028, 12557, 12525, 12445, 13013, 12599, 12733, 12448, 13014, 12598, 12576, 12739, 12968, 12735, 12442, 13221, 12578, 13173, 12562, 12572, 12453, 12575, 12458, 12577, 13245, 13270, 13313, 13266, 13327, 13126, 13312, 13342, 13319, 13252, 13251, 13061, 13081, 13116, 13320, 13317, 13091, 13318, 13092, 13094, 13084, 13177, 13114, 13206, 13247, 13249, 13242, 13276, 13153, 13237, 13236, 13141, 13123, 13073, 13179, 13168, 13163, 13340, 13275, 13143, 13066, 13146, 13086, 13246, 13080, 13335, 13269, 13065, 13129, 13274, 13164, 13250, 13079, 13144, 13314, 13064, 13339, 13149, 13322, 13111, 13106, 13078, 13156, 13101, 13088, 13056, 13097, 13137, 13159, 12715, 13316, 12373, 12875, 12995, 12978, 12695, 12376, 12996, 13067, 12694, 12926, 12402, 12405, 13261, 12924, 13169, 13063, 13128, 13176, 13109, 13166, 13139, 13171, 13162, 13334, 13336, 13121, 13058, 13172, 13167, 13087, 13089, 13107, 13130, 13326, 12748, 12997, 12372, 13192, 12940, 13108, 12483, 12983, 12692, 12476, 12750, 12980, 12753, 12480, 12982, 12922, 12404, 12817, 12700, 12611, 12482, 12403, 12976, 13341, 12561, 13119, 13211, 13151, 12714, 13117, 13120, 13209, 13205, 13178, 12830, 12550, 13329, 13118, 13210, 12464, 12770, 12891, 12591, 12604, 13069, 12552, 12603, 13207, 13271, 13138, 13315, 13273, 13331, 12672, 13142, 12760, 12772, 12320, 13321, 13147, 13289, 13170, 13272, 13277, 13070, 13232, 12861, 13148, 13112, 13160, 12844, 13090, 12605, 12512, 13155, 13191, 13095, 13227, 12802, 13068, 13165, 12333, 13154, 13150, 12909, 13145, 12505, 12836, 12640, 12860, 12837, 12856, 12868, 13037, 13093, 13255, 12857, 13113, 13024, 12664, 13253, 12931, 12494, 13293, 12910, 12653, 12884, 12936, 12881, 12887, 12354, 12803, 12790, 12869, 12786, 12797, 12801, 12509, 12349, 12906, 12933, 12805, 12928, 12855, 12500, 12870, 12811, 12806, 12851, 12911, 13161, 12930, 13294, 12666, 12885, 12934, 12659, 12886, 12636, 13254, 13231, 12546, 13125, 12519, 13295, 13292, 12800, 12513, 12501, 12356, 12352, 13002, 12510, 12847, 12709, 12496, 12927, 12665, 12645, 12788, 12607, 10705, 12633, 13026, 12862, 12780, 13001, 12932, 12716, 12663, 13000, 12925, 12756, 12895, 13071, 12455, 12988, 13075, 12796, 13005, 12631, 12507, 12839, 12514, 12504, 12710, 13122, 12718, 13102, 12515, 12520, 12502, 12792, 12994, 12495, 12794, 12508, 10051, 10062, 10056, 11876, 10061, 10054, 10052, 9944, 9950, 9943, 10049, 10069, 10059, 10063, 9942, 10070, 11855, 12434, 868, 887, 899, 828, 835, 841, 894, 904, 843, 854, 859, 881, 909, 834, 906, 831, 871, 13193, 12524, 13196, 12431, 13195, 7872, 7882, 7824, 7880, 7865, 7838, 7812, 7806, 7883, 7816, 11251, 8472, 11763, 12958, 12682, 10642, 12211, 13045, 12547, 12907, 12523, 12543, 12318, 12545, 12742, 12551, 12614, 12522, 12544, 12746, 12554, 12616, 12717, 12582, 12548, 13011, 12602, 11493, 10621, 12859, 12542, 12680, 11762, 11233, 11497, 8955, 8468, 8731, 8723, 8465, 8545, 12194, 10637, 8712, 11508, 11239, 8699, 8453, 8695, 8522, 8708, 8540, 12555, 12617, 12766, 12359, 12549, 12357, 12619, 12773, 11766, 10643, 12620, 12588, 12618, 12671, 12587, 12899, 12556, 12769, 10967, 12228, 8924, 8467, 8728, 11498, 11857, 8471, 8733, 11499, 12197, 8476, 8738, 11510, 10679, 8583, 8748, 8603, 11757, 7442, 8774, 8601, 8772, 11260, 11765, 8753, 8586, 11496, 11787, 10641, 11741, 11201, 10638, 13044, 12553, 12615, 12771, 12765, 12484, 12754, 12757, 12763, 12764, 12858 > select clear Drag select of 13248, 13264, 13268, 13263, 13299, 13258, 13265, 13257, 13262, 13267, 12609, 12418, 12401, 12425, 12649, 12383, 12407, 13308, 13311, 13260, 13199, 13309, 13110, 13307, 12688, 12331, 12697, 12816, 12479, 12902, 12920, 12412, 12904, 12414, 12813, 12918, 12486, 12687, 13208, 13286, 13280, 13285, 13226, 13152, 13291, 13181, 13259, 12815, 13290, 12703, 13225, 13287, 13278, 13241, 13060, 13224, 13180, 12689, 13298, 13134, 13115, 13057, 13059, 13127, 13072, 13243, 13132, 13054, 13098, 13099, 13083, 13055, 13074, 13131, 13201, 13223, 12345, 12347, 12444, 12437, 12485, 12712, 12411, 12597, 12738, 12921, 12560, 13202, 12478, 12343, 12441, 12443, 12882, 12473, 12540, 12644, 12474, 12346, 13332, 12521, 12690, 12409, 12923, 12919, 12449, 12456, 12641, 12774, 12580, 12730, 12737, 12595, 13028, 12557, 12525, 12445, 13013, 12599, 12733, 12448, 13014, 12598, 12576, 12739, 12968, 12735, 12442, 13221, 12578, 13173, 12562, 12572, 12453, 12575, 12458, 12577, 13245, 13270, 13313, 13266, 13327, 13126, 13312, 13342, 13319, 13252, 13251, 13061, 13081, 13116, 13320, 13317, 13091, 13318, 13092, 13094, 13084, 13177, 13114, 13206, 13247, 13249, 13242, 13276, 13153, 13237, 13236, 13141, 13123, 13073, 13179, 13168, 13163, 13340, 13275, 13143, 13066, 13146, 13086, 13246, 13080, 13335, 13269, 13065, 13129, 13274, 13164, 13250, 13079, 13144, 13314, 13064, 13339, 13149, 13322, 13111, 13106, 13078, 13156, 13101, 13088, 13056, 13097, 13137, 13159, 12715, 13316, 12373, 12875, 12995, 12978, 12695, 12376, 12996, 13067, 12694, 12926, 12402, 12405, 13261, 12924, 13169, 13063, 13128, 13176, 13109, 13166, 13139, 13171, 13162, 13334, 13336, 13121, 13058, 13172, 13167, 13087, 13089, 13107, 13130, 13326, 12748, 12997, 12372, 13192, 12940, 13108, 12483, 12983, 12692, 12476, 12750, 12980, 12753, 12480, 12982, 12922, 12404, 12817, 12700, 12611, 12482, 12403, 12976, 13341, 12561, 13119, 13211, 13151, 12714, 13117, 13120, 13209, 13205, 13178, 12830, 12550, 13329, 13118, 13210, 12464, 12770, 12891, 12591, 12604, 13069, 12552, 12603, 13207, 13271, 13138, 13315, 13273, 13331, 12672, 13142, 12760, 12772, 12320, 13321, 13147, 13289, 13170, 13272, 13277, 13070, 13232, 12861, 13148, 13112, 13160, 12844, 13090, 12605, 12512, 13155, 13191, 13095, 13227, 12802, 13068, 13165, 12333, 13154, 13150, 12909, 13145, 12505, 12836, 12640, 12860, 12837, 12856, 12868, 13037, 13093, 13255, 12857, 13113, 13024, 12664, 13253, 12931, 12494, 13293, 12910, 12653, 12884, 12936, 12881, 12887, 12354, 12803, 12790, 12869, 12786, 12797, 12801, 12509, 12349, 12906, 12933, 12805, 12928, 12855, 12500, 12870, 12811, 12806, 12851, 12911, 13161, 12930, 13294, 12666, 12885, 12934, 12659, 12886, 12636, 13254, 13231, 12546, 13125, 12519, 13295, 13292, 12800, 12513, 12501, 12356, 12352, 13002, 12510, 12847, 12709, 12496, 12927, 12665, 12645, 12788, 12607, 10705, 12633, 13026, 12862, 12780, 13001, 12932, 12716, 12663, 13000, 12925, 12756, 12895, 13071, 12455, 12988, 13075, 12796, 13005, 12631, 12507, 12839, 12514, 12504, 12710, 13122, 12718, 13102, 12515, 12520, 12502, 12792, 12994, 12495, 12794, 12508, 10051, 10062, 10056, 11876, 10061, 10054, 10052, 9944, 9950, 9943, 10049, 10069, 10059, 10063, 9942, 10070, 11855, 12434, 868, 887, 899, 828, 835, 841, 894, 904, 843, 854, 859, 881, 909, 834, 906, 831, 871, 13193, 12524, 13196, 12431, 13195, 7872, 7882, 7824, 7880, 7865, 7838, 7812, 7806, 7883, 7816, 11251, 8472, 11763, 12958, 12682, 10642, 12211, 13045, 12547, 12907, 12523, 12543, 12318, 12545, 12742, 12551, 12614, 12522, 12544, 12746, 12554, 12616, 12717, 12582, 12548, 13011, 12602, 11493, 10621, 12859, 12542, 12680, 11762, 11233, 11497, 8955, 8468, 8731, 8723, 8465, 8545, 12194, 10637, 8712, 11508, 11239, 8699, 8453, 8695, 8522, 8708, 8540, 12555, 12617, 12766, 12359, 12549, 12357, 12619, 12773, 11766, 10643, 12620, 12588, 12618, 12671, 12587, 12899, 12556, 12769, 10967, 12228, 8924, 8467, 8728, 11498, 11857, 8471, 8733, 11499, 12197, 8476, 8738, 11510, 10679, 8583, 8748, 8603, 11757, 7442, 8774, 8601, 8772, 11260, 11765, 8753, 8586, 11496, 11787, 10641, 11741, 11201, 10638, 13044, 12553, 12615, 12771, 12765, 12484, 12754, 12757, 12763, 12764, 12858 Opened Refine3d_job975_scaffold_LAFTER_filtered_imasked as #3, grid size 800,800,800, pixel 2.2, shown at step 1, values float32 > hide #!2 models > surface dust #3 size 13.2 > surface dust #3 size 13.45 > surface dust #3 size 8.13 > view orient > turn x -60 > volume #3 level 0.02072 > save maps_postprocess1.png format png transparentBackground true > save maps_lafter1.png format png transparentBackground true > camera ortho > turn x -30 > turn x 90 > turn x -30 > volume #3 level 0.1216 > volume #3 level 0.1862 > volume #3 level 0.1781 > volume #4 level 0.005524 > volume #4 level 0.007338 > volume #4 level 0.007459 > surface dust #3 size 8.13 > surface dust #3 size 7.87 > surface dust #3 size 10.46 > surface dust #3 size 10.82 > surface dust #3 size 17.6 > surface dust #3 size 17.89 > surface dust #3 size 33.27 > surface dust #3 size 35.57 > surface dust #3 size 33.82 > surface dust #4 size 13.2 > surface undust #4 [Repeated 2 time(s)] > volume #3 level 0.166 > surface undust #3 > volume #3 level 0.1297 > volume #3 level 0.1256 > surface dust #3 size 4.68 > surface dust #3 size 4.84 > surface dust #3 size 6.01 > surface dust #3 size 6.22 > surface dust #3 size 10.12 > surface dust #3 size 10.46 > surface dust #3 size 11.57 > surface dust #3 size 11.76 > surface dust #3 size 11 > volume #4 level 0.00631 > volume #4 level 0.006008 > volume #4 level 0.00631 > volume #4 level 0.006855 > volume #4 level 0.006008 > volume #4 level 0.006734 > zoom 0.8 > volume #4 level 0.00631 > save maps_lafter2.png format png transparentBackground true > save maps_postprocess2.png format png transparentBackground true > zoom 0.9 [Repeated 1 time(s)] > save maps_postprocess3.png format png transparentBackground true > save maps_lafter3.png format png transparentBackground true > close #2 > close #1 > save /Users/tina/PG/projects/minicell- > structure/periplasmic_scaffold/lafter/lafter_vs_raw.cxs includeMaps true ——— End of log from Sun Jan 22 21:45:11 2023 ——— opened ChimeraX session OpenGL version: 4.1 INTEL-18.8.5 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 3.1 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 499.40.2.0.0 OS Loader Version: 540.120.3~22 SMC Version (system): 2.44f6 Software: System Software Overview: System Version: macOS 12.6.2 (21G320) Kernel Version: Darwin 21.6.0 Time since boot: 6 days 20:49 Graphics/Displays: Intel Iris Plus Graphics 650: Chipset Model: Intel Iris Plus Graphics 650 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5927 Revision ID: 0x0006 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal HP E272q: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: CNK7101NF8 Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 0.00 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX