id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19808 Crash on Mac waking from sleep chengtao.xu@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.7.1-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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(pooled)"",""threadState"":{""x"":[{""value"":260},{""value"":0},{""value"":60672},{""value"":0},{""value"":0},{""value"":160},{""value"":29},{""value"":999999000},{""value"":14071360840},{""value"":0},{""value"":0},{""value"":2},{""value"":2},{""value"":0},{""value"":0},{""value"":0},{""value"":305},{""value"":8733529344},{""value"":0},{""value"":105553151997696},{""value"":105553151997760},{""value"":14071361760},{""value"":999999000},{""value"":29},{""value"":60672},{""value"":60673},{""value"":60928},{""value"":18446744072709551616},{""value"":1}],""flavor"":""ARM_THREAD_STATE64"",""lr"":{""value"":6871580828},""cpsr"":{""value"":1610612736},""fp"":{""value"":14071360960},""sp"":{""value"":14071360816},""esr"":{""value"":1442840704,""description"":"" Address size fault""},""pc"":{""value"":6871323596},""far"":{""value"":0}},""frames"":[{""imageOffset"":17356,""symbol"":""__psynch_cvwait"",""symbolLocation"":8,""imageIndex"":239},{""imageOffset"":28828,""symbol"":""_pthread_cond_wait"",""symbolLocation"":984,""imageIndex"":240},{""imageOffset"":2251416,""imageIndex"":45},{""imageOffset"":2251024,""symbol"":""QWaitCondition::wait(QMutex*, QDeadlineTimer)"",""symbolLocation"":108,""imageIndex"":45},{""imageOffset"":2226388,""imageIndex"":45},{""imageOffset"":2192952,""imageIndex"":45},{""imageOffset"":27592,""symbol"":""_pthread_start"",""symbolLocation"":136,""imageIndex"":240},{""imageOffset"":7040,""symbol"":""thread_start"",""symbolLocation"":8,""imageIndex"":240}]}], ""usedImages"" : [ [deleted to fit within ticket limits] ], ""sharedCache"" : { ""base"" : 6866911232, ""size"" : 5039341568, ""uuid"" : ""e93019e7-f1c3-3ee2-9cac-6c6940bee5d1"" }, [deleted to fit within ticket limits] > color sel byhetero > select #2/A:70,93,94,146,147 48 atoms, 49 bonds, 5 residues, 1 model selected > color sel byhetero > show sel atoms > style sel stick Changed 48 atom styles > cofr sel > select #2/A:70,93,94,146,147,115 58 atoms, 59 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 58 atom styles > color sel byhetero > select #1/A:70,93,94,146,147,115 58 atoms, 59 bonds, 6 residues, 1 model selected > show sel atoms > color sel byhetero > mmaker #1/A:70,93,94,146,147,115 to #2/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker merged_real_space_refined_014.pdb, chain A (#2) with merged_ivc_apo_refine_007.pdb, chain A (#1), sequence alignment score = 40 RMSD between 6 pruned atom pairs is 0.637 angstroms; (across all 6 pairs: 0.637) > select #1/A:159 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > select #1/A:159, #2/A:159 Expected an objects specifier or a keyword > show sel atoms > select #2/A:159 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > color sel byhetero > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > color #1 #eceeedff > open ""/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC > apo/merged_ivc_apo_refine_008.pdb"" Summary of feedback from opening /Users/xuchengtao/Documents/Building models undergoing/20260114 IVC apo/merged_ivc_apo_refine_008.pdb --- warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15 Chain information for merged_ivc_apo_refine_008.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E F G H | No description available I | No description available J | No description available K L M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker merged_ivc_apo_refine_007.pdb, chain A (#1) with merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 2572.9 RMSD between 504 pruned atom pairs is 0.004 angstroms; (across all 504 pairs: 0.004) > style sel stick Changed 9 atom styles > hide sel atoms > undo > hide #!3 models > select add #2 30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected > select subtract #2 Nothing selected > select add #3 31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected > hide #3 > show #!3 models > select subtract #3 Nothing selected > show #3/A:70, 115,146,147,93,94,159 > style stick Changed 93851 atom styles > hide #!1 models > color #3 #e1e4eeff > color #3 #b2b5bdff > mmaker #3/A:70, 115,146,147,93,94,159 to #2/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker merged_real_space_refined_014.pdb, chain A (#2) with merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 45.3 RMSD between 7 pruned atom pairs is 0.851 angstroms; (across all 7 pairs: 0.851) > show #1/A:97 > show #!1 models > hide #!1 models > show #2/A:97 > show #3/A:97 > hide #!3 models > show #!3 models > open ""/Users/xuchengtao/Documents/Building models > undergoing/20251003IVC/20251222 Xiaomeng AI > IVC/cryosparc_P6_J91_004_volume_map.mrc"" Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 1.07, shown at level 0.0524, step 2, values float32 > volume #4 step 1 > volume #4 level 0.1661 > ui tool show ""Hide Dust"" > surface dust #4 size 11.38 > surface dust #4 size 12.58 > surface dust #4 size 10.12 > volume #4 color #b2b2b2ab > ui tool show ""Color Actions"" > color light sky blue > hide #!4 models > hide #!3 models > show #!3 models > select #2 30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected > color sel byhetero > select #3 31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected > ui tool show ""Color Actions"" > color sel pink > color sel byhetero > select subtract #3 Nothing selected > open ""/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC > apo/cryosparc_P38_J47_006_volume_map.mrc"" Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512, pixel 1.07, shown at level 0.0338, step 2, values float32 > volume #5 step 1 > surface dust #5 size 9.46 > mmaker #5 to #4 No 'to' model specified > mmaker #5 to #3 No molecules/chains to match specified > surface dust #5 size 9.3 > surface dust #5 size 11.38 > surface dust #5 size 9.62 > surface dust #5 size 10.29 > surface dust #5 size 13.23 > volume #5 level 0.09228 > ui tool show ""Fit in Map"" > ui mousemode right ""translate selected models"" > select add #5 2 models selected > view matrix models > #5,-0.97381,-0.031588,0.22517,490.36,-0.071884,0.98228,-0.17308,73.711,-0.21571,-0.18473,-0.95882,664.68 > view matrix models > #5,-0.97381,-0.031588,0.22517,436.09,-0.071884,0.98228,-0.17308,0.20124,-0.21571,-0.18473,-0.95882,557.69 > volume #5 level 0.1173 > view matrix models > #5,-0.93478,0.30346,0.18464,345.57,0.2887,0.95188,-0.10282,-106.34,-0.20696,-0.042808,-0.97741,523.25 > fitmap #5 inMap #4 Fit map cryosparc_P38_J47_006_volume_map.mrc in map cryosparc_P6_J91_004_volume_map.mrc using 310271 points correlation = 0.9347, correlation about mean = 0.7922, overlap = 1.556e+04 steps = 220, shift = 18.3, angle = 17.3 degrees Position of cryosparc_P38_J47_006_volume_map.mrc (#5) relative to cryosparc_P6_J91_004_volume_map.mrc (#4) coordinates: Matrix rotation and translation -0.97760466 0.20023007 -0.06478454 435.09526992 0.19862444 0.97960384 0.03040797 -118.87262867 0.06955178 0.01685918 -0.99743587 434.81572276 Axis -0.10034105 -0.99488204 -0.01189115 Axis point 216.14301063 0.00000000 225.62653040 Rotation angle (degrees) 176.12880575 Shift along axis 69.43586944 > view matrix models > #5,-0.99043,0.12889,-0.049357,453.43,0.1291,0.99163,-0.0012337,-93.971,0.048785,-0.0075941,-0.99878,447.49 > volume #5 level 0.1674 > view matrix models > #5,-0.98693,0.15429,-0.046578,444.85,0.15422,0.98802,0.0051166,-101.57,0.04681,-0.0021338,-0.9989,446.59 > view matrix models > #5,-0.99436,0.088993,0.057707,435.97,0.099112,0.97336,0.20674,-137.79,-0.037772,0.21129,-0.97669,405.88 > view matrix models > #5,-0.99438,0.087718,0.059321,435.88,0.098341,0.97272,0.21009,-138.33,-0.039274,0.21474,-0.97588,405.13 > undo > view matrix models > #5,-0.98265,0.16324,-0.088032,452.62,0.16414,0.98643,-0.0029871,-101.62,0.08635,-0.017385,-0.99611,439.18 > volume #5 level 0.2085 > color sel pink > volume #5 color #ffc0cbad > volume #4 level 0.12 > show #2/B > select #2/B 2 atoms, 2 residues, 1 model selected > style sel sphere Changed 2 atom styles > ui tool show ""Color Actions"" > color sel slate gray > hide #!3 models > volume #4 level 0.13 > volume #4 level 0.14 > matchmaker #4 to #2 No molecules/chains to match specified > select add #2 30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected > select subtract #2 Nothing selected > hide #!2 models > close #2 > open ""/Users/xuchengtao/Documents/Building models > undergoing/20251003IVC/20251222 Xiaomeng AI > IVC/merged_real_space_refined_015.pdb"" Chain information for merged_real_space_refined_015.pdb #2 --- Chain | Description A | No description available C H I J K L | No description available D | No description available E | No description available F | No description available G | No description available M | No description available N O P Q R | No description available S | No description available > hide #2 > combine #2 > color #2 lightskyblue > color #6 lightskyblue > select #2/A:70,93,94,97,115,146,159 66 atoms, 64 bonds, 7 residues, 1 model selected > show (sel-residues & sidechain) target ab > style sel stick Changed 66 atom styles > color sel byhetero > select #2/B 2 atoms, 2 residues, 1 model selected > style sel sphere Changed 2 atom styles > show sel atoms > color sel gray > ui tool show ""Color Actions"" > color sel slate gray > volume #4 color #87cefa27 > volume #4 color #87cefa26 > lighting full > lighting soft > lighting full > hide #2/A:94 > select #5/A:94,147 Nothing selected > show #5/A:94,147 & ~@N,C,O > show #!5 models > hide #!5 models > show #6/A:94,147 & ~@N,C,O > select #6/A 4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected > style sel stick Changed 4478 atom styles > color sel byhetero > select add #6 30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected > select subtract #6 Nothing selected > combine #3 > hide #3 > hide #7 > show #!5 models > volume #5 level 0.1566 > volume #5 color #ffc0cb2b > select #3/A:70,93,97,115,146,159 58 atoms, 56 bonds, 6 residues, 1 model selected > show (#2,4,6-7 & sidechain) target ab > select #3/A:70,93,97,115,146,159 58 atoms, 56 bonds, 6 residues, 1 model selected > show #3/A:70,93,97,115,146,159& ~@N,,C,O Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #3/A:70,93,97,115,146,159& ~@N,C,O > show #!3 models > hide #2/A:97 > hide #3/A:97 > mmaker #3/A:70,93,94,115 to #2/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker merged_real_space_refined_015.pdb, chain A (#2) with merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 26.4 RMSD between 4 pruned atom pairs is 0.646 angstroms; (across all 4 pairs: 0.646) > mmaker #3/A:70,93,94,115,146 to #2/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker merged_real_space_refined_015.pdb, chain A (#2) with merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 33.2 RMSD between 5 pruned atom pairs is 0.680 angstroms; (across all 5 pairs: 0.680) > close #7 > combine #3 > hide #7 > show #7/A:94,147 & ~@N,CA,C,O > show #7/A:94,147 & ~@N,,C,O Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #7/A:94,147 & ~@N,C,O > select add #3 31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected > select subtract #3 Nothing selected > hide #!2 models > show #!2 models > hide #!4 models > show #!5 models > show #!4 models > select add #5 2 models selected > view matrix models > #5,-0.97841,0.20197,-0.043758,428.89,0.20245,0.97927,-0.0068224,-109.08,0.041473,-0.015534,-0.99902,451.71 > undo > select subtract #5 Nothing selected > select add #4 2 models selected > select subtract #4 Nothing selected > hide #!4 models > hide #!2 models > hide #!6 models > select add #5 2 models selected > view matrix models > #5,-0.95877,0.093992,-0.2682,514.11,0.090359,0.99557,0.025885,-91.881,0.26944,0.00058378,-0.96302,375.36 > volume #5 level 0.1727 > view matrix models > #5,-0.97116,0.2003,-0.12934,450.76,0.20327,0.97907,-0.010053,-108.32,0.12462,-0.036052,-0.99155,432.49 > cofr @3/A > cofr #3/A > view matrix models > #5,-0.96897,0.21997,-0.11274,440.16,0.22373,0.97441,-0.021689,-109.42,0.10508,-0.046238,-0.99339,440.91 > view matrix models > #5,-0.98673,0.16214,0.0085692,427.41,0.16178,0.98627,-0.033106,-92.633,-0.013819,-0.03128,-0.99942,470.88 > view matrix models > #5,-0.99996,-0.0010926,-0.0093869,480.02,-0.0013883,0.9995,0.031557,-69.497,0.0093478,0.031569,-0.99946,447.61 > view matrix models > #5,-0.99994,-0.010838,0.0021348,479.5,-0.010849,0.99993,-0.0051597,-56.987,-0.0020787,-0.0051825,-0.99998,460.79 > view matrix models > #5,-0.99926,-0.0041216,0.038311,467.59,-0.0039274,0.99998,0.0051435,-61.705,-0.038331,0.0049892,-0.99925,467.71 > view matrix models > #5,-0.99926,-0.0041216,0.038311,467.58,-0.0039274,0.99998,0.0051435,-61.937,-0.038331,0.0049892,-0.99925,467.37 > volume #5 level 0.16 > volume #5 color #ffc0cbd6 > volume #5 level 0.17 > view matrix models > #5,-0.9987,-0.049666,0.011361,487.1,-0.049572,0.99873,0.0084327,-50.07,-0.011765,0.0078586,-0.9999,459.55 > view matrix models > #5,-0.9987,-0.049666,0.011361,486.96,-0.049572,0.99873,0.0084327,-49.824,-0.011765,0.0078586,-0.9999,459.82 > volume #5 level 0.15 > volume #5 level 0.175 > view matrix models > #5,-0.9987,-0.049666,0.011361,487.47,-0.049572,0.99873,0.0084327,-50.955,-0.011765,0.0078586,-0.9999,458.34 > view matrix models > #5,-0.99639,-0.068145,-0.0506,508.8,-0.077294,0.97481,0.20922,-91.913,0.035067,0.21238,-0.97656,383.96 > undo > view matrix models > #5,-0.90445,-0.37278,0.20738,495.44,-0.36083,0.92786,0.094206,29.42,-0.22754,0.010378,-0.97371,509.22 > view matrix models > #5,-0.90445,-0.37278,0.20738,496,-0.36083,0.92786,0.094206,27.507,-0.22754,0.010378,-0.97371,509.24 > view matrix models > #5,-0.90445,-0.37278,0.20738,506.69,-0.36083,0.92786,0.094206,29.176,-0.22754,0.010378,-0.97371,509.83 > view matrix models > #5,-0.90435,-0.36259,0.22513,499.05,-0.35913,0.93151,0.05762,37.745,-0.2306,-0.028742,-0.97262,520.93 > view matrix models > #5,-0.90435,-0.36259,0.22513,500.51,-0.35913,0.93151,0.05762,36.126,-0.2306,-0.028742,-0.97262,518.8 > view matrix models > #5,-0.90384,-0.33625,0.2646,482.45,-0.35563,0.93422,-0.027601,57.769,-0.23792,-0.11905,-0.96396,542.81 > view matrix models > #5,-0.90384,-0.33625,0.2646,487.46,-0.35563,0.93422,-0.027601,49.35,-0.23792,-0.11905,-0.96396,540.04 > view matrix models > #5,-0.9033,-0.31727,0.28876,475.58,-0.3537,0.93169,-0.082759,64.605,-0.24278,-0.17689,-0.95382,554.21 > view matrix models > #5,-0.9033,-0.31727,0.28876,479.2,-0.3537,0.93169,-0.082759,57.847,-0.24278,-0.17689,-0.95382,553.3 > volume #5 level 0.1947 > volume #5 level 0.175 > show #!2 models > hide #!2 models > show #!4 models > view matrix models > #5,-0.90789,-0.32005,0.27076,486.12,-0.35802,0.92795,-0.1036,65.738,-0.21809,-0.19099,-0.95706,551.27 > fitmap #5 inMap #4 Fit map cryosparc_P38_J47_006_volume_map.mrc in map cryosparc_P6_J91_004_volume_map.mrc using 186216 points correlation = 0.9452, correlation about mean = 0.7716, overlap = 1.379e+04 steps = 380, shift = 27.5, angle = 38 degrees Position of cryosparc_P38_J47_006_volume_map.mrc (#5) relative to cryosparc_P6_J91_004_volume_map.mrc (#4) coordinates: Matrix rotation and translation -0.97747656 0.20090883 -0.06461583 434.82603912 0.19929299 0.97946158 0.03061556 -119.07093066 0.06943966 0.01704851 -0.99744046 434.80014734 Axis -0.10068315 -0.99484628 -0.01199138 Axis point 216.05419591 0.00000000 225.60664569 Rotation angle (degrees) 176.13677177 Shift along axis 69.46376469 > hide #!4 models > volume #5 level 0.1589 > volume #5 level 0.15 > view matrix models > #5,-0.97451,0.21473,-0.064928,430.36,0.21213,0.97622,0.044705,-125.65,0.072984,0.029792,-0.99689,430.23 > undo > view matrix models > #5,-0.97748,0.20091,-0.064616,436.21,0.19929,0.97946,0.030616,-119.26,0.06944,0.017049,-0.99744,436.08 > view matrix models > #5,-0.97239,0.22414,-0.065027,428.65,0.22083,0.9738,0.054308,-130.26,0.075496,0.038448,-0.9964,428.35 > view matrix models > #5,-0.97239,0.22414,-0.065027,428.82,0.22083,0.9738,0.054308,-127.24,0.075496,0.038448,-0.9964,428.69 > undo > hide #!4 models > volume #5 level 0.1661 > view matrix models > #5,-0.96662,0.25053,-0.05365,415.47,0.24919,0.96798,0.030408,-129.49,0.05955,0.016024,-0.9981,437.95 > view matrix models > #5,-0.96653,0.25013,-0.056982,416.46,0.2497,0.96821,0.01465,-125.38,0.058835,-6.834e-05,-0.99827,442.54 > view matrix models > #5,-0.96653,0.25013,-0.056982,416.26,0.2497,0.96821,0.01465,-126.49,0.058835,-6.834e-05,-0.99827,443.79 > undo > view matrix models > #5,-0.97268,0.22126,-0.070311,429.58,0.21796,0.97459,0.051693,-128.6,0.079962,0.034956,-0.99618,426.75 > view matrix models > #5,-0.97268,0.22126,-0.070311,430.14,0.21796,0.97459,0.051693,-126.95,0.079962,0.034956,-0.99618,427.81 > view matrix models > #5,-0.97268,0.22126,-0.070311,430.12,0.21796,0.97459,0.051693,-127.05,0.079962,0.034956,-0.99618,427.18 > volume #5 level 0.1589 > view matrix models > #5,-0.97111,0.22523,-0.078833,430.95,0.22249,0.97403,0.042032,-125.48,0.086252,0.023278,-0.996,428.57 > undo > view matrix models > #5,-0.96202,0.25857,-0.087537,421.85,0.25149,0.96419,0.084256,-142.27,0.10619,0.059042,-0.99259,412.55 > view matrix models > #5,-0.96202,0.25857,-0.087537,422.58,0.25149,0.96419,0.084256,-138.97,0.10619,0.059042,-0.99259,414.88 > volume #5 level 0.1446 > undo > volume #5 level 0.1607 > volume #5 level 0.1446 > view matrix models > #5,-0.9737,0.21948,-0.061119,428.33,0.21816,0.97552,0.027604,-120.53,0.065681,0.013544,-0.99775,437.95 > view matrix models > #5,-0.9737,0.21948,-0.061119,429.45,0.21816,0.97552,0.027604,-123.69,0.065681,0.013544,-0.99775,436.46 > view matrix models > #5,-0.9737,0.21948,-0.061119,430.1,0.21816,0.97552,0.027604,-123.83,0.065681,0.013544,-0.99775,436.76 > view matrix models > #5,-0.96936,0.23489,-0.071894,427.76,0.23263,0.9718,0.038497,-129.84,0.07891,0.020593,-0.99667,430.93 > view matrix models > #5,-0.96936,0.23489,-0.071894,427.42,0.23263,0.9718,0.038497,-128.58,0.07891,0.020593,-0.99667,431.63 > view matrix models > #5,-0.96792,0.23643,-0.085073,430.29,0.23421,0.97154,0.035438,-128.09,0.091031,0.014376,-0.99574,429.72 > view matrix models > #5,-0.96792,0.23643,-0.085073,430.23,0.23421,0.97154,0.035438,-127.81,0.091031,0.014376,-0.99574,429.7 > view matrix models > #5,-0.96792,0.23643,-0.085073,430.59,0.23421,0.97154,0.035438,-127.05,0.091031,0.014376,-0.99574,429.19 > view matrix models > #5,-0.96792,0.23643,-0.085073,430.19,0.23421,0.97154,0.035438,-128.03,0.091031,0.014376,-0.99574,428.89 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.53,0.23421,0.97154,0.035438,-128.27,0.091031,0.014376,-0.99574,428.38 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.63,0.23421,0.97154,0.035438,-128.15,0.091031,0.014376,-0.99574,429.1 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.59,0.23421,0.97154,0.035438,-128.12,0.091031,0.014376,-0.99574,428.9 > view matrix models > #5,-0.96958,0.23531,-0.067362,425.42,0.23325,0.97171,0.037075,-128.3,0.074181,0.020235,-0.99704,432.33 > view matrix models > #5,-0.9663,0.24851,-0.0672,420.91,0.24554,0.96813,0.049372,-134.15,0.077327,0.031207,-0.99652,428.36 > view matrix models > #5,-0.9663,0.24851,-0.0672,422.24,0.24554,0.96813,0.049372,-132.3,0.077327,0.031207,-0.99652,429.54 > view matrix models > #5,-0.9663,0.24851,-0.0672,422.17,0.24554,0.96813,0.049372,-132.3,0.077327,0.031207,-0.99652,429.18 > view matrix models > #5,-0.9663,0.24851,-0.0672,422.48,0.24554,0.96813,0.049372,-132.23,0.077327,0.031207,-0.99652,429.48 > view matrix models > #5,-0.96297,0.26101,-0.067585,418.3,0.25702,0.96439,0.062399,-138.01,0.081465,0.042718,-0.99576,425.02 > view matrix models > #5,-0.96297,0.26101,-0.067585,418.54,0.25702,0.96439,0.062399,-136.93,0.081465,0.042718,-0.99576,425.35 > undo > volume #5 level 0.1339 > volume #5 color #ffc0cb29 > volume #5 color #ffc0cb61 > show #!4 models > view matrix models > #5,-0.96792,0.23643,-0.085073,429.64,0.23421,0.97154,0.035438,-128.16,0.091031,0.014376,-0.99574,429.11 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.59,0.23421,0.97154,0.035438,-128.26,0.091031,0.014376,-0.99574,429.29 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.69,0.23421,0.97154,0.035438,-128.37,0.091031,0.014376,-0.99574,429.46 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.4,0.23421,0.97154,0.035438,-128.44,0.091031,0.014376,-0.99574,429.31 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.37,0.23421,0.97154,0.035438,-128.43,0.091031,0.014376,-0.99574,429.16 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.43,0.23421,0.97154,0.035438,-128.61,0.091031,0.014376,-0.99574,429.7 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.22,0.23421,0.97154,0.035438,-128.65,0.091031,0.014376,-0.99574,429.53 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.16,0.23421,0.97154,0.035438,-128.43,0.091031,0.014376,-0.99574,429.54 > hide #!3 models > show #!3 models > hide #!4 models > view matrix models > #5,-0.96792,0.23643,-0.085073,429.36,0.23421,0.97154,0.035438,-128.09,0.091031,0.014376,-0.99574,429.64 > view matrix models > #5,-0.96792,0.23643,-0.085073,429.21,0.23421,0.97154,0.035438,-127.78,0.091031,0.014376,-0.99574,429.58 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.37,0.23421,0.97154,0.035438,-127.04,0.091031,0.014376,-0.99574,429.41 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.35,0.23421,0.97154,0.035438,-126.11,0.091031,0.014376,-0.99574,429.73 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.3,0.23421,0.97154,0.035438,-126,0.091031,0.014376,-0.99574,429.7 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.24,0.23421,0.97154,0.035438,-126.37,0.091031,0.014376,-0.99574,429.57 > volume #5 level 0.1464 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.2,0.23421,0.97154,0.035438,-126.21,0.091031,0.014376,-0.99574,429.4 > view matrix models > #5,-0.96792,0.23643,-0.085073,428.13,0.23421,0.97154,0.035438,-125.77,0.091031,0.014376,-0.99574,429.31 > show #3/T > select #3/T 2 atoms, 2 residues, 1 model selected > style sel sphere Changed 2 atom styles > ui tool show ""Color Actions"" > color sel slate gray > select add #3 31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected > select subtract #3 Nothing selected > ui tool show ""Side View"" > hide #!3 models > hide #!5 models > hide #!7 models > show #!4 models > show #!6 models > show #!2 models > volume #4 level 0.12 > volume #4 level 0.125 > lighting full > lighting soft > lighting simple > lighting full > lighting flat > lighting full > lighting simple > lighting full > volume #4 level 0.13 > save /Users/xuchengtao/Desktop/image275.png supersample 3 > hide #!4 models > hide #!2 models > show #!3 models > show #!5 models > hide #!6 models > show #!7 models > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"" > save /Users/xuchengtao/Desktop/image276.png supersample 3 > hide #!3 models > hide #!5 models > hide #!7 models > show #!3 models > show #!7 models > hide #!7 models > show #!7 models > hide #3/T > show #!4 models > hide #!4 models > show #!2 models > show #!6 models > show #2/A:86-96 cartoons > cartoon style #2-3,6-7 modeHelix tube sides 20 > cartoon style (#2-3,6-7 & coil) xsection oval > cartoon style #2-3,6-7 xsection barbell modeHelix default > cartoon style #2-3,6-7 modeHelix tube sides 20 > show #2/A:136-160 cartoons > combine #7 > color #8 white > color #8 #ffffffb4 > color #8 #ffffff82 > color #8 #ffffff80 > color #8 #f5f4f680 > show #8/A:136-160 cartoons > show #8/A:86-96 cartoons > show #8/A:136-180 cartoons > show #2/A:136-180 cartoons > show #2/A:136-160 cartoons > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"" > hide #2/A:161-180 cartoons > hide #8/A:161-180 cartoons > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > hide #8/A:147 > hide #8/A:94] > hide #8/A:94 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > lighting full > lighting soft > hide #!2 models > hide #!6 models > show #!2 models > show #!6 models > lighting shadows true intensity 0.5 > lighting full > lighting shadows false > save /Users/xuchengtao/Desktop/image277.png supersample 3 > ui tool show Distances > select #2/A:159 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:159 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:159, #2/A:159 Expected an objects specifier or a keyword Exactly two atoms must be selected! > select #2,3/A:159@CA 2 atoms, 2 residues, 2 models selected > distance #3/A:159@CA #2/A:159@CA Distance between merged_ivc_apo_refine_008.pdb #3/A GLU 159 CA and merged_real_space_refined_015.pdb #2/A GLU 159 CA: 2.124Å > undo > ~distance #3/A:159@CA #2/A:159@CA > lighting shadows true > lighting full > lighting soft > depthCue true Unknown command: depthCue true > depthCue true Unknown command: depthCue true > depthCue true Unknown command: depthCue true > depthCue Unknown command: depthCue > lighting depthCue true > lighting depthCueStart 0.4 depthCueEnd 0.9 > lighting depthCueStart 0.4 depthCueEnd 0.8 > lighting depthCueStart 0.2 depthCueEnd 0.8 > lighting depthCueStart 0.1 depthCueEnd 0.8 > lighting depthCueStart 0.1 depthCueEnd 0.4 > lighting depthCueStart 0.2 depthCueEnd 0.4 > lighting depthCueStart 0.3 depthCueEnd 0.4 > lighting simple > lighting flat > lighting full > lighting soft > lighting depthCueStart 0.3 depthCueEnd 0.4 > lighting depthCueStart 0.4 depthCueEnd 0.9 > lighting depthCueStart 0.4 depthCueEnd 0.5 > lighting depthCueStart 0.3 depthCueEnd 0.5 > lighting depthCueStart 0.3 depthCueEnd 0.4 > lighting depthCueStart 0.4 > lighting depthCueStart 0.9 > lighting depthCueStart 0. > lighting depthCueStart 0.5 > lighting depthCueStart 0.4 > show #!2 models > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM6.cxs"" Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 1.07, shown at level 0.227, step 1, values float32 Opened cryosparc_P6_J91_004_volume_map.mrc copy as #1, grid size 384,384,384, pixel 1.07, shown at level 0.266, step 1, values float32 Opened cryosparc_P6_J91_004_volume_map.mrc as #3, grid size 384,384,384, pixel 1.07, shown at level 0.153, step 1, values float32 > view name session-start opened ChimeraX session > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"" Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 1.07, shown at level 0.13, step 1, values float32 Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512, pixel 1.07, shown at level 0.146, step 1, values float32 > view name session-start opened ChimeraX session > open ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel 1.07, shown at level 0.13, step 1, values float32 Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512, pixel 1.07, shown at level 0.146, step 1, values float32 > view name session-start opened ChimeraX session > lighting depthCueStart 0.4 depthCueStart 0.9 Repeated keyword argument ""depthCueStart"" > lighting depthCueStart 0.4 depthCueEnd 0.9 > lighting depthCueStart 0.4 depthCueEnd 0.6 > lighting depthCueStart 0.1 depthCueEnd 0.6 > lighting depthCueStart 0.2 depthCueEnd 0.6 > lighting depthCueStart 0.2 depthCueEnd 0.3 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > lighting depthCueStart 0.2 depthCueEnd 0.25 > lighting depthCueStart 0.2 depthCueEnd 0.5 > lighting depthCueStart 0.2 depthCueEnd 0.25 > lighting depthCueStart 0.2 depthCueEnd 0.28 > lighting depthCueStart 0.2 depthCueEnd 0.3 > lighting depthCueStart 0.2 depthCueEnd 0.34 > save /Users/xuchengtao/Desktop/image278.png supersample 3 > save /Users/xuchengtao/Desktop/image279.png supersample 3 > lighting depthCueStart 0.2 depthCueEnd 0.33 > lighting depthCueStart 0.2 depthCueEnd 0.3 > save /Users/xuchengtao/Desktop/image280.png supersample 3 > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > lighting depthCue false > save ""/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV > with Terns/20260111 IVC > manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"" > close session > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_00_00162_volume.mrc Opened J31_class_00_00162_volume.mrc as #1, grid size 128,128,128, pixel 3.01, shown at level 0.108, step 1, values float32 > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_01_00162_volume.mrc Opened J31_class_01_00162_volume.mrc as #2, grid size 128,128,128, pixel 3.01, shown at level 0.126, step 1, values float32 > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_02_00162_volume.mrc Opened J31_class_02_00162_volume.mrc as #3, grid size 128,128,128, pixel 3.01, shown at level 0.0868, step 1, values float32 > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_03_00162_volume.mrc Opened J31_class_03_00162_volume.mrc as #4, grid size 128,128,128, pixel 3.01, shown at level 0.241, step 1, values float32 > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_04_00162_volume.mrc Opened J31_class_04_00162_volume.mrc as #5, grid size 128,128,128, pixel 3.01, shown at level 0.105, step 1, values float32 > open > /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_05_00162_volume.mrc Opened J31_class_05_00162_volume.mrc as #6, grid size 128,128,128, pixel 3.01, shown at level 0.27, step 1, values float32 > color #1-6 lightgrey > ui tool show ""Hide Dust"" > surface dust #1 size 18.06 > surface dust #1 size 30.1 > surface dust #2 size 30.1 > surface dust #3 size 30.1 > surface dust #4 size 30.1 > surface dust #5 size 30.1 > surface dust #6 size 30.1 > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!1 models > show #!2 models > show #!3 models > show #!4 models > hide #!3 models > hide #!2 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > hide #!5 models > hide #!6 models > hide #!4 models > hide #!3 models > hide #!2 models > save /Users/xuchengtao/Desktop/image281.png supersample 3 > lighting full > lighting soft > save /Users/xuchengtao/Desktop/image282.png supersample 3 > hide #!1 models > show #!2 models > save /Users/xuchengtao/Desktop/image283.png supersample 3 > hide #!2 models > show #!3 models > save /Users/xuchengtao/Desktop/image284.png supersample 3 > hide #!3 models > show #!4 models > save /Users/xuchengtao/Desktop/image285.png supersample 3 > hide #!4 models > show #!5 models > save /Users/xuchengtao/Desktop/image286.png supersample 3 > hide #!5 models > show #!6 models > save /Users/xuchengtao/Desktop/image287.png supersample 3 > hide #!6 models > open /Users/xuchengtao/Downloads/cryosparc_P9_J32_007_volume_map.mrc Opened cryosparc_P9_J32_007_volume_map.mrc as #7, grid size 360,360,360, pixel 1.07, shown at level 0.0564, step 2, values float32 > color #7 #f4f6fcff models > volume #7 step 1 > volume #7 level 0.07916 > surface dust #7 size 10.7 > volume #7 level 0.11 > lighting full > volume #7 color #cecfd4 > lighting simple > volume #7 color #a3a4a7 > color #7 lightgrey > color #7 grey > volume #7 color #b6b6b6 > save /Users/xuchengtao/Desktop/image288.png supersample 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 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 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,8 Model Number: Z1FF000ENLL/A Chip: Apple M4 Pro Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 48 GB System Firmware Version: 13822.1.2 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.7.1 (24G231) Kernel Version: Darwin 24.6.0 Time since boot: 26 days, 11 hours, 19 minutes Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 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 HP 23f: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.25.2 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.10.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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-MutationScores: 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit duplicate all ChimeraX