id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18080 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-14.5-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff846ff0fc0 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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""factorPackIds"" : { }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/dongju/Desktop/Research projects- > Monash/Modelling_GPR3_OEA/cryosparc_P161_J67_004_volume_map.mrc"" Opened cryosparc_P161_J67_004_volume_map.mrc as #1, grid size 288,288,288, pixel 0.75, shown at level 0.0482, step 2, values float32 > volume #1 step 1 > volume #1 level 0.04046 > volume #1 level 0.0763 > open 8ww2 8ww2 title: GPR3/Gs complex [more info...] Chain information for 8ww2 #2 --- Chain | Description | UniProt A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 N | Nb35 | R | G-protein coupled receptor 3 | GPR3_HUMAN 1-330 Non-standard residues in 8ww2 #2 --- OLA — oleic acid PLM — palmitic acid Y01 — cholesterol hemisuccinate > hide atoms > show cartoons > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > select add #2 7792 atoms, 7943 bonds, 3 pseudobonds, 1025 residues, 2 models selected > view matrix models > #2,0.87528,0.48295,0.025505,-53.678,0.48227,-0.87556,0.028443,191.41,0.036068,-0.012595,-0.99927,268.69 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.87528,0.48295,0.025505,-43.924,0.48227,-0.87556,0.028443,155.38,0.036068,-0.012595,-0.99927,239.44 > view matrix models > #2,0.87528,0.48295,0.025505,-83.849,0.48227,-0.87556,0.028443,149.43,0.036068,-0.012595,-0.99927,240.47 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule 8ww2 (#2) to map cryosparc_P161_J67_004_volume_map.mrc (#1) using 7792 atoms average map value = 0.1191, steps = 300 shifted from previous position = 9.18 rotated from previous position = 43.5 degrees atoms outside contour = 2740, contour level = 0.076296 Position of 8ww2 (#2) relative to cryosparc_P161_J67_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.96878402 -0.24789375 0.00249685 3.35268084 -0.24710133 -0.96640024 -0.07079219 286.54509380 0.01996190 0.06796537 -0.99748798 229.46459950 Axis 0.99215567 -0.12488001 0.00566603 Axis point 0.00000000 139.43229763 119.70920918 Rotation angle (degrees) 175.99018772 Shift along axis -31.15722066 > fitmap #2 inMap #1 Fit molecule 8ww2 (#2) to map cryosparc_P161_J67_004_volume_map.mrc (#1) using 7792 atoms average map value = 0.1191, steps = 28 shifted from previous position = 0.0144 rotated from previous position = 0.00891 degrees atoms outside contour = 2748, contour level = 0.076296 Position of 8ww2 (#2) relative to cryosparc_P161_J67_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.96879775 -0.24784059 0.00244760 3.34754125 -0.24705438 -0.96642225 -0.07065541 286.52369625 0.01987669 0.06784611 -0.99749780 229.48026603 Axis 0.99215917 -0.12485375 0.00563206 Axis point 0.00000000 139.42849517 119.70748752 Rotation angle (degrees) 175.99761294 Shift along axis -31.15981858 > select subtract #2 Nothing selected > addh Summary of feedback from adding hydrogens to 8ww2 #2 --- warnings | Not adding hydrogens to /A LYS 17 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 24 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ARG 31 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLU 50 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 58 CB because it is missing heavy-atom bond partners 39 messages similar to the above omitted notes | Termini for 8ww2 (#2) chain A determined from SEQRES records Termini for 8ww2 (#2) chain B determined from SEQRES records Termini for 8ww2 (#2) chain G determined from SEQRES records Termini for 8ww2 (#2) chain N determined from SEQRES records Termini for 8ww2 (#2) chain R determined from SEQRES records Chain-initial residues that are actual N termini: /N GLN 1 Chain-initial residues that are not actual N termini: /A SER 13, /A THR 204, /A THR 263, /B GLU 3, /G SER 8, /R LEU 37, /R THR 242 Chain-final residues that are actual C termini: /A LEU 394, /B SER 342 Chain-final residues that are not actual C termini: /A ARG 61, /A SER 251, /G ARG 62, /N SER 128, /R HIS 232, /R CYS 313 Missing OXT added to C-terminal residue /B SER 342 777 hydrogen bonds Adding 'H' to /A SER 13 Adding 'H' to /A THR 204 Adding 'H' to /A THR 263 Adding 'H' to /B GLU 3 Adding 'H' to /G SER 8 2 messages similar to the above omitted /G ARG 62 is not terminus, removing H atom from 'C' /N SER 128 is not terminus, removing H atom from 'C' /R CYS 313 is not terminus, removing H atom from 'C' 7631 hydrogens added > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 59 residues in model #2 to IUPAC-IUB standards. 8ww2 title: GPR3/Gs complex [more info...] Chain information for 8ww2 --- Chain | Description | UniProt 2.2/A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | 2.2/B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 2.2/G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 2.2/N | Nb35 | 2.2/R | G-protein coupled receptor 3 | GPR3_HUMAN 1-330 Non-standard residues in 8ww2 #2.2 --- OLA — oleic acid PLM — palmitic acid Y01 — cholesterol hemisuccinate > clipper associate #1 toModel #2 Opened cryosparc_P161_J67_004_volume_map.mrc as #2.1.1.1, grid size 288,288,288, pixel 0.75, shown at step 1, values float32 > isolde sim start /A-R Loading residue template for OLA from internal database Loading residue template for PLM from internal database Loading residue template for Y01 from internal database ISOLDE: started sim > ui tool show ""Ramachandran Plot"" > isolde sim pause > volume #2.1.1.1 level 0.1096 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 23 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > volume #2.1.1.1 level 0.0201 > save ""/Users/dongju/Desktop/Research projects- > Monash/Modelling_GPR3_OEA/GPR3_8ww2_after_ISOLDE_004.pdb"" relModel #2.1.1.1 > save ""/Users/dongju/Desktop/Research projects- > Monash/Modelling_GPR3_OEA/J67_after_ISOLDE.mrc"" models #2.1.1.1 > select add #2 15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 22 models selected > select add #2 15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 22 models selected > open 8ww2 8ww2 title: GPR3/Gs complex [more info...] Chain information for 8ww2 #1 --- Chain | Description | UniProt A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 N | Nb35 | R | G-protein coupled receptor 3 | GPR3_HUMAN 1-330 Non-standard residues in 8ww2 #1 --- OLA — oleic acid PLM — palmitic acid Y01 — cholesterol hemisuccinate > hide sel atoms > show sel cartoons > select add #1 23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 24 models selected > hide sel atoms > show sel cartoons > select add #2 23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 24 models selected > select add #2 23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 24 models selected > select add #2 23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 24 models selected > select subtract #2.1 23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 19 models selected > select add #2.2 23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 19 models selected > select subtract #2.3 23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 18 models selected > select subtract #1 15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 16 models selected > select add #1 23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 18 models selected > hide #!2 models > hide #!2.1 models > hide #!2.2 models > hide #2.3 models > select subtract #1 15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 16 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/R Alignment identifier is 1/R > select #1/R:169 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/R:169 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/R:175 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/R:175 5 atoms, 4 bonds, 1 residue, 1 model selected > open /Users/dongju/Downloads/cryosparc_P161_J68_005_volume_map.mrc Opened cryosparc_P161_J68_005_volume_map.mrc as #3, grid size 288,288,288, pixel 0.75, shown at level 0.0511, step 2, values float32 > open /Users/dongju/Downloads/cryosparc_P161_J69_004_volume_map.mrc Opened cryosparc_P161_J69_004_volume_map.mrc as #4, grid size 288,288,288, pixel 0.75, shown at level 0.0544, step 2, values float32 > open /Users/dongju/Downloads/cryosparc_P161_J70_003_volume_map.mrc Opened cryosparc_P161_J70_003_volume_map.mrc as #5, grid size 288,288,288, pixel 0.75, shown at level 0.054, step 2, values float32 > hide #!1 models > tile #3 #4 #5 columns 3 3 models tiled The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #3 step 1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #4 step 1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #5 step 1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #4 level 0.08238 > volume #5 level 0.09146 > volume #3 level 0.07913 > tile #3 #4 #5 columns 3 spacingFactor 1.3 3 models tiled > tile #3 #4 #5 columns 3 spacingFactor 1.1 3 models tiled > tile #3 #4 #5 columns 3 spacingFactor 0.8 3 models tiled > show #!1 models > select #1/R:41-67,73-92,106-144,146-167,192-230,243-270,275-298,301-313 1568 atoms, 1591 bonds, 212 residues, 1 model selected > select #1/R:218 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/R:218 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/R:270 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/R:270 4 atoms, 3 bonds, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/dongju/Downloads/cryosparc_P161_J65_003_volume_map.mrc Opened cryosparc_P161_J65_003_volume_map.mrc as #6, grid size 288,288,288, pixel 0.75, shown at level 0.0485, step 2, values float32 > hide #!3 models > hide #!4 models > hide #!5 models > hide #!1 models > volume #6 step 1 > volume #6 level 0.0771 > volume #6 level 0.04849 > volume #6 level 0.0771 > show #!5 models > show #!4 models > hide #!6 models > show #!3 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/dongju/Downloads/cryosparc_P161_J72_022_volume_map.mrc Opened cryosparc_P161_J72_022_volume_map.mrc as #7, grid size 288,288,288, pixel 0.75, shown at level 0.054, step 2, values float32 > hide #!3 models > hide #!4 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #7 step 1 > volume #7 level 0.08411 > volume #7 level 0.06233 > open /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series.cs Unrecognized file suffix '.cs' The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open > /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_00_00239_volume.mrc Opened J74_class_00_00239_volume.mrc as #8, grid size 80,80,80, pixel 2.7, shown at level 0.371, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_01_00239_volume.mrc Opened J74_class_01_00239_volume.mrc as #9, grid size 80,80,80, pixel 2.7, shown at level 0.367, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_02_00239_volume.mrc Opened J74_class_02_00239_volume.mrc as #10, grid size 80,80,80, pixel 2.7, shown at level 0.373, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_03_00239_volume.mrc Opened J74_class_03_00239_volume.mrc as #11, grid size 80,80,80, pixel 2.7, shown at level 0.35, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_04_00239_volume.mrc Opened J74_class_04_00239_volume.mrc as #12, grid size 80,80,80, pixel 2.7, shown at level 0.383, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_05_00239_volume.mrc Opened J74_class_05_00239_volume.mrc as #13, grid size 80,80,80, pixel 2.7, shown at level 0.364, step 1, values float32 > hide #!5 models > hide #!7 models > show #!7 models > hide #!7 models > tile #8 #9 #10 #11 #12 #13 columns 3 spacingFactor 0.8 6 models tiled > tile #8 #9 #10 #11 #12 #13 columns 3 spacingFactor 1 6 models tiled > tile #8 #9 #10 #11 #12 #13 columns 3 spacingFactor 1.2 6 models tiled > set bgColor white > set bgColor black > set bgColor white > set bgColor black > volume #8-13 level 0.4 > volume #8-13 level 0.45 > volume #8-13 level 0.48 > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > open > /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_00_00145_volume.mrc Opened J73_class_00_00145_volume.mrc as #14, grid size 80,80,80, pixel 2.7, shown at level 0.38, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_01_00145_volume.mrc Opened J73_class_01_00145_volume.mrc as #15, grid size 80,80,80, pixel 2.7, shown at level 0.349, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_02_00145_volume.mrc Opened J73_class_02_00145_volume.mrc as #16, grid size 80,80,80, pixel 2.7, shown at level 0.365, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_03_00145_volume.mrc Opened J73_class_03_00145_volume.mrc as #17, grid size 80,80,80, pixel 2.7, shown at level 0.381, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_04_00145_volume.mrc Opened J73_class_04_00145_volume.mrc as #18, grid size 80,80,80, pixel 2.7, shown at level 0.377, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_05_00145_volume.mrc Opened J73_class_05_00145_volume.mrc as #19, grid size 80,80,80, pixel 2.7, shown at level 0.378, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_06_00145_volume.mrc Opened J73_class_06_00145_volume.mrc as #20, grid size 80,80,80, pixel 2.7, shown at level 0.362, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_07_00145_volume.mrc Opened J73_class_07_00145_volume.mrc as #21, grid size 80,80,80, pixel 2.7, shown at level 0.384, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_08_00145_volume.mrc Opened J73_class_08_00145_volume.mrc as #22, grid size 80,80,80, pixel 2.7, shown at level 0.36, step 1, values float32 > open > /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_09_00145_volume.mrc Opened J73_class_09_00145_volume.mrc as #23, grid size 80,80,80, pixel 2.7, shown at level 0.368, step 1, values float32 > volume #14-23 level 0.48 > tile #14-23 columns 5 10 models tiled > tile #14-23 columns 5 spacingFactor 1.2 10 models tiled > tile #14-23 columns 4 spacingFactor 1.2 10 models tiled > volume #14-23 level 0.5.2 Invalid ""level"" argument: Expected a number > volume #14-23 level 0.52 > volume #14-23 level 0.55 > volume #14-23 level 0.6 > open /Users/dongju/Downloads/cryosparc_P161_J77_006_volume_map.mrc Opened cryosparc_P161_J77_006_volume_map.mrc as #24, grid size 288,288,288, pixel 0.75, shown at level 0.0487, step 2, values float32 > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > hide #!19 models > hide #!20 models > hide #!21 models > hide #!22 models > hide #!23 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #24 step 1 > volume #24 color #ff8ffc > volume #24 level 0.07336 > volume #24 level 0.0947 > volume #24 level 0.08485 > show #!7 models > hide #!7 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > open /Users/dongju/Downloads/cryosparc_P161_J75_004_volume_map.mrc Opened cryosparc_P161_J75_004_volume_map.mrc as #25, grid size 288,288,288, pixel 0.75, shown at level 0.0514, step 2, values float32 > hide #!24 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #25 step 1 > volume #25 level 0.07913 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #25 level 0.1017 > open /Users/dongju/Downloads/cryosparc_P161_J78_004_volume_map.mrc Opened cryosparc_P161_J78_004_volume_map.mrc as #26, grid size 288,288,288, pixel 0.75, shown at level 0.0522, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #26 step 1 > hide #!25 models > volume #26 level 0.08951 > show #!25 models > show #!24 models > tile #24-26 columns 3 spacingFactor 1 3 models tiled > volume #26 color #ff959d > open /Users/dongju/Downloads/cryosparc_P161_J80_006_volume_map.mrc Opened cryosparc_P161_J80_006_volume_map.mrc as #27, grid size 288,288,288, pixel 0.75, shown at level 0.0485, step 2, values float32 > hide #!24 models > hide #!25 models > hide #!26 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #27 step 1 > volume #27 level 0.09433 > show #!26 models > show #!5 models > hide #!26 models > volume #27 level 0.07906 > open > /Users/dongju/Downloads/cryosparc_P161_8ww2_receptor_only_mask_12A_mask_th0.0051_ns4_ngs15.mrc Opened cryosparc_P161_8ww2_receptor_only_mask_12A_mask_th0.0051_ns4_ngs15.mrc as #28, grid size 288,288,288, pixel 0.75, shown at level 0.998, step 2, values float32 > hide #!27 models Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 84, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 150, in status r.draw_background() File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1220, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 84, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 150, in status r.draw_background() File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1220, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/dongju/Downloads/cryosparc_P161_J80_004_volume_map.mrc Opened cryosparc_P161_J80_004_volume_map.mrc as #29, grid size 288,288,288, pixel 0.75, shown at level 0.0514, step 2, values float32 > hide #!28 models > show #!26 models > select add #27 4 atoms, 3 bonds, 1 residue, 3 models selected > show #!28 models > hide #!26 models > show #!26 models > hide #!5 models > volume #24 level 0.1013 > volume #26 level 0.03793 > volume #26 level 0.06106 > volume #26 level 0.07351 > open /Users/dongju/Downloads/cryosparc_P161_J81_004_volume_map.mrc Opened cryosparc_P161_J81_004_volume_map.mrc as #30, grid size 288,288,288, pixel 0.75, shown at level 0.0499, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #30 step 1 > volume #30 level 0.09329 > volume #30 level 0.07421 > volume #24 level 0.121 > volume #24 level 0.1013 > volume #24 level 0.06516 > volume #24 level 0.04382 > volume #30 level 0.06033 > volume #30 level 0.04645 > volume #30 level 0.04299 > volume #30 level 0.05339 > volume #30 level 0.07074 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #30 level 0.06554 > volume #30 level 0.0638 > volume #30 level 0.05686 > volume #30 level 0.04992 > volume #24 level 0.08157 > volume #26 level 0.1215 > volume #26 level 0.08596 > volume #26 level 0.05928 > volume #25 level 0.07047 > volume #25 level 0.06354 > volume #25 level 0.04969 > volume #25 level 0.06701 > volume #25 level 0.0774 > volume #26 level 0.08062 > volume #26 level 0.07173 > volume #26 level 0.06283 > open 8X2K 8x2k title: a lipid receptor complex structure [more info...] Chain information for 8x2k #31 --- Chain | Description | UniProt A | Soluble cytochrome b562,G-protein coupled receptor 3 | C562_ECOLX -105--1, GPR3_HUMAN 1-330 B | Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 26-394 C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340 D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71 E | scfv16 | Non-standard residues in 8x2k #31 --- 5YM — (Z)-N-(2-hydroxyethyl)octadec-9-enamide > show #!31 cartoons > hide #!31 atoms > select ::name=""OLA"" 73 atoms, 71 bonds, 2 residues, 2 models selected > show #!31 atoms > hide #!31 atoms > show #!31 cartoons > select ::name=""OLA"" 73 atoms, 71 bonds, 2 residues, 2 models selected > show #!31 atoms > hide #!31 atoms > show #!31 cartoons > select OLA Expected an objects specifier or a keyword > ui tool show ""File History"" > select #31 ligand Expected a keyword > select #31 lipid Expected a keyword > select #31 ligands Expected a keyword > select #31 ligand Expected a keyword > select #31 lipid Expected a keyword > select ::name=""OLA"" 73 atoms, 71 bonds, 2 residues, 2 models selected > show #!31 atoms > hide #!31 atoms > select ::name=""OLA Nothing selected > select ::name=""OLA"" 73 atoms, 71 bonds, 2 residues, 2 models selected > style #!31 stick Changed 8570 atom styles > select ::name=""OLA"" 73 atoms, 71 bonds, 2 residues, 2 models selected > show #31 target ab > select ::name=""OLA"" 73 atoms, 71 bonds, 2 residues, 2 models selected > select ::name=""Y01"" 119 atoms, 125 bonds, 2 residues, 2 models selected > select ::name=""5YM"" 23 atoms, 22 bonds, 1 residue, 1 model selected > select ~sel & ##selected 8547 atoms, 8715 bonds, 6 pseudobonds, 1113 residues, 2 models selected > hide sel atoms > select add #31 8570 atoms, 8737 bonds, 6 pseudobonds, 1114 residues, 2 models selected > select subtract #31 Nothing selected > hide #!31 models > open /Users/dongju/Downloads/cryosparc_P161_J84_007_volume_map.mrc Opened cryosparc_P161_J84_007_volume_map.mrc as #32, grid size 288,288,288, pixel 0.75, shown at level 0.0495, step 2, values float32 > open /Users/dongju/Downloads/cryosparc_P161_J85_005_volume_map.mrc Opened cryosparc_P161_J85_005_volume_map.mrc as #33, grid size 288,288,288, pixel 0.75, shown at level 0.0487, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #32 step 1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #33 step 1 > tile #32 #33 2 models tiled > tile #32 #33 spacingFactor 1 2 models tiled > tile #32 #33 spacingFactor 0.8 2 models tiled > volume #32 level 0.06332 > volume #33 level 0.06644 > volume #32 level 0.04605 > volume #33 level 0.05353 > volume #33 level 0.04546 > volume #33 level 0.04062 > volume #33 level 0.0503 > open /Users/dongju/Downloads/cryosparc_P161_J86_class_02_00294_volume.mrc Opened cryosparc_P161_J86_class_02_00294_volume.mrc as #34, grid size 80,80,80, pixel 2.7, shown at level 0.377, step 1, values float32 > open /Users/dongju/Downloads/cryosparc_P161_J86_class_01_00294_volume.mrc Opened cryosparc_P161_J86_class_01_00294_volume.mrc as #35, grid size 80,80,80, pixel 2.7, shown at level 0.37, step 1, values float32 > open /Users/dongju/Downloads/cryosparc_P161_J86_class_00_00294_volume.mrc Opened cryosparc_P161_J86_class_00_00294_volume.mrc as #36, grid size 80,80,80, pixel 2.7, shown at level 0.367, step 1, values float32 > tile #34-46 spacingFactor 0.8 3 models tiled > tile #34-46 spacingFactor 1 3 models tiled > tile #34-46 columns 3 spacingFactor 1 3 models tiled > volume #34 level 0.3461 > volume #34 level 0.3717 > volume #34 level 0.3288 > volume #35 level 0.2813 > volume #36 level 0.2577 > open /Users/dongju/Downloads/cryosparc_P161_J87_class_02_00412_volume.mrc Opened cryosparc_P161_J87_class_02_00412_volume.mrc as #37, grid size 80,80,80, pixel 2.7, shown at level 0.372, step 1, values float32 > open /Users/dongju/Downloads/cryosparc_P161_J87_class_01_00412_volume.mrc Opened cryosparc_P161_J87_class_01_00412_volume.mrc as #38, grid size 80,80,80, pixel 2.7, shown at level 0.348, step 1, values float32 > open /Users/dongju/Downloads/cryosparc_P161_J87_class_00_00412_volume.mrc Opened cryosparc_P161_J87_class_00_00412_volume.mrc as #39, grid size 80,80,80, pixel 2.7, shown at level 0.366, step 1, values float32 > tile #37-39 columns 3 spacingFactor 1 3 models tiled > volume #37 level 0.2957 > volume #37 level 0.2578 > volume #38 level 0.2979 > volume #38 level 0.2567 > volume #39 level 0.2668 > volume #39 level 0.2095 > volume #39 level 0.2512 > open /Users/dongju/Downloads/cryosparc_P161_J88_003_volume_map.mrc Opened cryosparc_P161_J88_003_volume_map.mrc as #40, grid size 288,288,288, pixel 0.75, shown at level 0.051, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #40 step 1 > volume #40 level 0.06686 > volume #40 level 0.07392 > open /Users/dongju/Downloads/cryosparc_P161_J89_002_volume_map.mrc Opened cryosparc_P161_J89_002_volume_map.mrc as #41, grid size 288,288,288, pixel 0.75, shown at level 0.0506, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #41 step 1 > volume #41 level 0.09116 > volume #41 level 0.049 > open /Users/dongju/Downloads/cryosparc_P161_J90_003_volume_map.mrc Opened cryosparc_P161_J90_003_volume_map.mrc as #42, grid size 288,288,288, pixel 0.75, shown at level 0.0507, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #42 step 1 > volume #42 level 0.04716 > open /Users/dongju/Downloads/cryosparc_P161_J91_002_volume_map.mrc Opened cryosparc_P161_J91_002_volume_map.mrc as #43, grid size 288,288,288, pixel 0.75, shown at level 0.0509, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #43 step 1 > volume #43 level 0.06735 > volume #43 level 0.05584 > volume #42 level 0.05968 > volume #43 level 0.04762 > volume #43 level 0.04597 > tile #40-43 columns 2 spacingFactor 1 4 models tiled > volume #40 level 0.06686 > volume #41 level 0.05711 > volume #41 level 0.05387 > volume #42 level 0.05615 > volume #43 level 0.05255 > volume #43 level 0.04104 > volume #43 level 0.02953 > volume #43 level 0.04762 > volume #43 level 0.03939 > volume #43 level 0.06899 > volume #43 level 0.05748 > volume #42 level 0.05436 > volume #40 level 0.06156 > open ""/Users/dongju/Downloads/emd_38015 (2).map"" Opened emd_38015 (2).map as #44, grid size 320,320,320, pixel 0.85, shown at level 0.177, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #44 step 1 > volume #44 level 0.5649 > volume #44 level 0.493 > volume #44 level 0.4354 > volume #44 level 0.2485 > volume #44 level 0.723 > volume #44 level 0.5073 > volume #43 level 0.05584 > volume #44 level 0.5649 > open /Users/dongju/Downloads/cryosparc_P161_J92_003_volume_map.mrc Opened cryosparc_P161_J92_003_volume_map.mrc as #45, grid size 288,288,288, pixel 0.75, shown at level 0.0499, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #45 step 1 > volume #45 color #ff928c > volume #45 level 0.05159 > volume #45 level 0.04644 > volume #45 level 0.04816 > volume #45 level 0.0825 > volume #45 level 0.06704 > volume #45 level 0.05846 > volume #45 level 0.08078 > volume #45 level 0.06704 > volume #45 level 0.05502 > volume #42 level 0.07939 > volume #42 level 0.07403 > volume #42 level 0.133 > volume #42 level 0.07761 > volume #42 level 0.06151 > volume #42 level 0.05436 > volume #42 level 0.06509 > volume #44 level 0.4786 > volume #44 level 0.493 > open /Users/dongju/Downloads/cryosparc_P161_J93_004_volume_map.mrc Opened cryosparc_P161_J93_004_volume_map.mrc as #46, grid size 288,288,288, pixel 0.75, shown at level 0.0469, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #46 step 1 > volume #46 level 0.06435 > volume #46 level 0.0494 > volume #46 level 0.07929 > volume #46 level 0.05189 > volume #46 level 0.0768 > volume #46 level 0.05687 > volume #45 level 0.04301 > volume #45 level 0.09795 > volume #46 level 0.07929 > volume #46 level 0.05687 > tile #45-46 columns 2 spacingFactor 1 2 models tiled > tile #45-46 columns 2 spacingFactor 0.8 2 models tiled The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #45 level 0.06361 > volume #45 level 0.04301 > volume #46 level 0.08407 > volume #46 level 0.07414 > volume #46 level 0.05677 > volume #46 level 0.05429 > volume #46 level 0.04935 > volume #33 level 0.07289 > volume #33 level 0.06644 > volume #33 level 0.0503 > volume #33 level 0.04707 > volume #33 level 0.03739 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #44 level 0.4211 > view matrix models #44-46 Invalid ""models"" argument: Expected model id and 12 comma-separated numbers > view initial #44 > lighting simple > lighting soft > lighting full > lighting simple > view > ui mousemode right ""rotate selected models"" > ui mousemode right select > select #46 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #46,0.95507,-0.005669,-0.29632,34.061,0.0087808,-0.99884,0.04741,94.834,-0.29625,-0.047882,-0.95391,218.55 > view matrix models > #46,0.96129,0.027545,-0.27417,27.619,0.041247,-0.99816,0.044335,91.619,-0.27245,-0.053927,-0.96066,217.35 > view matrix models > #46,0.96268,0.011121,-0.27041,28.792,0.044789,-0.99192,0.11866,82.831,-0.26691,-0.12634,-0.9554,223.77 > ui mousemode right select > ui mousemode right ""rotate selected models"" > view matrix models > #46,0.18365,-0.1684,0.96846,1.3672,-0.10944,-0.98259,-0.1501,126.38,0.97688,-0.07842,-0.19888,7.0163 > view matrix models > #46,0.14922,-0.18429,0.97148,6.3867,-0.10719,-0.9797,-0.16939,127.85,0.98298,-0.078857,-0.16594,2.9727 > view matrix models > #46,0.14339,-0.20306,0.96861,9.2664,-0.19365,-0.96556,-0.17376,136.06,0.97054,-0.16265,-0.17778,14.281 > view matrix models > #46,0.22128,-0.17314,0.95972,-1.2419,-0.19739,-0.9717,-0.12979,132.51,0.95503,-0.16072,-0.24919,23.189 > view matrix models > #46,0.21533,-0.18803,0.95827,1.0979,-0.26654,-0.95534,-0.12756,137.95,0.93946,-0.22795,-0.25583,32.56 > ui mousemode right select > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #7 level 0.09557 > volume #7 level 0.05358 > volume #7 level 0.07633 > volume #24 level 0.049 > view > volume #24 level 0.04386 > volume #33 level 0.0635 > volume #33 level 0.03581 > volume #42 level 0.03708 > volume #42 level 0.04268 > view > volume #42 level 0.07069 > volume #42 level 0.05949 > volume #45 level 0.06811 > volume #45 level 0.04301 > volume #45 level 0.03942 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #45 level 0.05018 > volume #45 level 0.05556 > volume #45 level 0.04839 > open ""/Users/dongju/Downloads/cryosparc_P161_J44_010_volume_map (2).mrc"" Opened cryosparc_P161_J44_010_volume_map (2).mrc as #47, grid size 288,288,288, pixel 0.75, shown at level 0.0507, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #47 step 1 > volume #47 level 0.09491 > volume #47 level 0.05955 Drag select of 47 cryosparc_P161_J44_010_volume_map (2).mrc > select clear Drag select of 47 cryosparc_P161_J44_010_volume_map (2).mrc > select clear > volume #47 level 0.05365 > volume #47 level 0.05513 > set bgColor white > set bgColor #ffffff00 > view > volume #47 level 0.05807 > volume #47 level 0.05955 > volume #47 level 0.07428 > volume #47 level 0.06544 > open ""/Users/dongju/Downloads/cryosparc_P161_J51_008_volume_map (1).mrc"" Opened cryosparc_P161_J51_008_volume_map (1).mrc as #48, grid size 288,288,288, pixel 0.75, shown at level 0.0521, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #48 step 1 > volume #48 level 0.04671 > volume #48 level 0.0615 > volume #48 level 0.05209 > volume #48 level 0.07361 > volume #48 level 0.05209 > volume #48 level 0.09244 > volume #48 level 0.0494 > open /Users/dongju/Downloads/cryosparc_P161_J54_class_02_00142_volume.mrc Opened cryosparc_P161_J54_class_02_00142_volume.mrc as #49, grid size 128,128,128, pixel 1.69, shown at level 0.179, step 1, values float32 > open /Users/dongju/Downloads/cryosparc_P161_J54_class_01_00142_volume.mrc Opened cryosparc_P161_J54_class_01_00142_volume.mrc as #50, grid size 128,128,128, pixel 1.69, shown at level 0.188, step 1, values float32 > open /Users/dongju/Downloads/cryosparc_P161_J54_class_00_00142_volume.mrc Opened cryosparc_P161_J54_class_00_00142_volume.mrc as #51, grid size 128,128,128, pixel 1.69, shown at level 0.198, step 1, values float32 > volume #49 level 0.2314 > view > volume #49 level 0.2431 Drag select of 50 cryosparc_P161_J54_class_01_00142_volume.mrc > select clear > volume #50 level 0.1882 > volume #50 level 0.1684 > volume #50 level 0.218 Drag select of 51 cryosparc_P161_J54_class_00_00142_volume.mrc > select clear > volume #51 level 0.2199 > volume #51 level 0.2557 > volume #51 level 0.2447 > open /Users/dongju/Downloads/cryosparc_P161_J56_007_volume_map.mrc Opened cryosparc_P161_J56_007_volume_map.mrc as #52, grid size 288,288,288, pixel 0.75, shown at level 0.0563, step 2, values float32 > open /Users/dongju/Downloads/cryosparc_P161_J55_004_volume_map.mrc Opened cryosparc_P161_J55_004_volume_map.mrc as #53, grid size 288,288,288, pixel 0.75, shown at level 0.0495, step 2, values float32 > volume #52 level 0.06859 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #52 step 1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #53 step 1 > volume #53 level 0.04477 > volume #53 level 0.05585 > volume #52 level 0.06412 > open /Users/dongju/Downloads/cryosparc_P161_J62_003_volume_map.mrc Opened cryosparc_P161_J62_003_volume_map.mrc as #54, grid size 288,288,288, pixel 0.75, shown at level 0.0493, step 2, values float32 > view > volume #54 color #ffad92 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #54 step 1 > volume #54 level 0.04316 > volume #54 level 0.06148 > volume #54 level 0.04927 > volume #54 level 0.04622 > volume #54 level 0.05385 > volume #54 level 0.05843 > volume #54 level 0.04927 > volume #54 level 0.05079 > open > /Users/dongju/Downloads/cryosparc_P138_J63_molmap_mask_th0.0064_ns8_ngs10.mrc Opened cryosparc_P138_J63_molmap_mask_th0.0064_ns8_ngs10.mrc as #55, grid size 288,288,288, pixel 0.75, shown at level 1, step 2, values float32 > volume #55 level 0.9884 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #55 step 1 > view > lighting simple > lighting soft > lighting simple > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting simple > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting simple > graphics silhouettes false > lighting simple > volume #55 color #83a2ff > volume #55 color #83a2ff80 > select #54 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #54,0.044887,0.99862,0.027264,0.51408,0.92813,-0.051783,0.36864,-25.226,0.36954,0.0087578,-0.92917,179.74 > view matrix models > #54,0.044887,0.99862,0.027264,0.56339,0.92813,-0.051783,0.36864,-25.348,0.36954,0.0087578,-0.92917,179.97 > ui mousemode right ""rotate selected models"" > view matrix models > #54,0.031293,-0.92551,-0.37744,247.28,-0.94743,-0.14778,0.28381,196.47,-0.31844,0.34871,-0.88147,213.53 > view matrix models > #54,0.089047,-0.92584,-0.36727,239.98,-0.94005,-0.2,0.27625,201.97,-0.32922,0.32065,-0.88814,218.36 > view matrix models > #54,0.4429,-0.78218,-0.43822,194.26,-0.80449,-0.56246,0.19085,234.5,-0.39577,0.26802,-0.87837,230.03 > view matrix models > #54,0.51821,-0.78489,-0.33971,175.87,-0.78232,-0.59553,0.18257,236.46,-0.3456,0.17115,-0.92264,239.51 > view matrix models > #54,0.12681,-0.90345,-0.40951,238.07,-0.93186,-0.24999,0.26296,207.75,-0.33994,0.34826,-0.87359,215.06 > view matrix models > #54,0.3627,-0.864,-0.34922,201.99,-0.92188,-0.27783,-0.2701,266.64,0.13634,0.4199,-0.89727,158.61 > view matrix models > #54,0.34857,-0.86918,-0.35076,204.23,-0.93414,-0.29154,-0.20587,262.53,0.076673,0.39942,-0.91356,168.95 > view matrix models > #54,0.32551,-0.8868,-0.32808,206.14,-0.94048,-0.2678,-0.20925,261.09,0.097701,0.37667,-0.92118,169.88 > view matrix models > #54,0.95477,0.061799,-0.29087,34.608,0.061071,-0.99807,-0.011589,208.35,-0.29102,-0.0066992,-0.95669,255.92 > view matrix models > #54,0.97768,-0.00084969,-0.21011,30.065,-0.0039945,-0.99989,-0.014543,215.89,-0.21008,0.015058,-0.97757,247.12 > view matrix models > #54,0.97883,-0.045487,-0.19957,33.497,-0.0074596,-0.98227,0.1873,192.81,-0.20455,-0.18184,-0.96182,265.51 > view matrix models > #54,0.97496,-0.061475,-0.21372,37.106,-0.020733,-0.98197,0.18788,194.15,-0.22141,-0.17874,-0.95866,266.66 > view matrix models > #54,0.9749,-0.057148,-0.21517,36.814,-0.020685,-0.98556,0.16804,196.65,-0.22166,-0.15937,-0.96201,265.02 > ui mousemode right zoom > ui mousemode right select > select clear > select #54 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #54,-0.16569,0.9642,-0.20704,52.006,0.98524,0.17099,0.0078431,-16.285,0.042963,-0.20268,-0.9783,242.71 > volume #55 level 0.9981 > view matrix models > #54,0.94256,-0.10668,-0.31656,56.359,-0.034997,-0.97395,0.22403,190.98,-0.33221,-0.20008,-0.92174,276.93 > view matrix models > #54,0.94237,-0.088029,-0.32279,55.089,-0.044773,-0.98927,0.13907,202.74,-0.33157,-0.1166,-0.9362,269.64 > ui mousemode right ""translate selected models"" > view matrix models > #54,0.94237,-0.088029,-0.32279,54.081,-0.044773,-0.98927,0.13907,202.74,-0.33157,-0.1166,-0.9362,265.26 > ui mousemode right ""rotate selected models"" > view matrix models > #54,0.13436,0.98091,-0.14059,9.7097,0.98359,-0.11478,0.13916,-0.173,0.12037,-0.15698,-0.98024,225.37 > ui mousemode right select > select clear > volume #6 level 0.06216 > volume #6 color #9489ff > volume #6 level 0.04572 > volume #6 level 0.06664 > volume #6 level 0.05618 > volume #6 level 0.04871 > volume #24 level 0.06271 > volume #24 level 0.049 > volume #24 level 0.06957 Drag select of 24 cryosparc_P161_J77_006_volume_map.mrc > select clear > volume #24 level 0.06443 > volume #24 level 0.05414 > volume #24 level 0.05072 > volume #24 level 0.05243 > volume #24 level 0.06957 > ui mousemode right ""translate selected models"" > ui mousemode right select > volume #26 level 0.04983 > volume #26 level 0.07212 > volume #26 level 0.06283 > volume #26 level 0.08141 > ui mousemode right ""translate selected models"" > ui mousemode right select > select #25 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #25,0.75969,0.38221,-0.52611,34.791,0.45013,-0.89296,0.0012527,-45.751,-0.46931,-0.23777,-0.85042,272.03 > ui mousemode right select > select clear > volume #25 level 0.1009 > volume #25 level 0.08102 > volume #25 color #63bfff > volume #25 level 0.07017 > volume #25 level 0.06112 > volume #25 level 0.05208 > volume #25 level 0.06112 > volume #25 level 0.05931 > select #30 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #30,-0.68895,0.66493,-0.28847,168.69,0.60337,0.74666,0.28007,-377.71,0.40162,0.018903,-0.91561,310.54 > view matrix models > #30,-0.68895,0.66493,-0.28847,192.73,0.60337,0.74666,0.28007,-503.61,0.40162,0.018903,-0.91561,433.97 > ui mousemode right select > select #30 2 models selected > select #30 2 models selected > select #30 2 models selected > select #30 2 models selected > select #30 2 models selected > select #30 2 models selected > select #30 2 models selected > select #30 2 models selected > select #30 2 models selected > hide #!30 models > show #!30 models > select subtract #30 Nothing selected > volume #30 level 0.03543 > volume #30 level 0.04449 > volume #30 level 0.09159 > volume #30 level 0.06985 > volume #30 level 0.05536 > ui mousemode right ""translate selected models"" > ui mousemode right select > volume #42 color #d5876c > volume #42 level 0.07443 > volume #42 level 0.07069 > volume #42 level 0.06696 > volume #42 level 0.06322 > volume #42 level 0.06135 Drag select of 42 cryosparc_P161_J90_003_volume_map.mrc > select clear > open /Users/dongju/Downloads/cryosparc_P161_J71_map.mrc Opened cryosparc_P161_J71_map.mrc as #56, grid size 288,288,288, pixel 0.75, shown at level 0.0493, step 2, values float32 > volume #41 level 0.04878 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #56 step 1 > volume #56 level 0.04189 > volume #56 level 0.0387 > volume #56 level 0.07802 > open ""/Users/dongju/Downloads/cryosparc_P163_J35_008_volume_map (1).mrc"" Opened cryosparc_P163_J35_008_volume_map (1).mrc as #57, grid size 288,288,288, pixel 0.75, shown at level 0.112, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #57 step 1 > volume #57 color #ff75c0 > volume #57 level 0.1523 Drag select of 57 cryosparc_P163_J35_008_volume_map (1).mrc > select clear > volume #57 level 0.1174 > open ""/Users/dongju/Downloads/cryosparc_P163_J46_009_volume_map (1).mrc"" Opened cryosparc_P163_J46_009_volume_map (1).mrc as #58, grid size 288,288,288, pixel 0.75, shown at level 0.117, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #58 step 1 > volume #58 level 0.1174 > volume #58 level 0.1302 > volume #58 level 0.1195 > open ""/Users/dongju/Downloads/cryosparc_P163_J51_008_volume_map (2).mrc"" Opened cryosparc_P163_J51_008_volume_map (2).mrc as #59, grid size 288,288,288, pixel 0.75, shown at level 0.119, step 2, values float32 > volume #59 color #85fc5f The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #59 step 1 > volume #59 level 0.1554 > volume #59 level 0.1486 > volume #59 level 0.1349 > tile #58-59 columns 2 2 models tiled > tile #58-59 columns 2 spacingFactor 1 2 models tiled > tile #58-59 columns 2 spacingFactor 0.5 2 models tiled > tile #58-59 columns 2 spacingFactor 0.7 2 models tiled > volume #59 level 0.1235 > volume #59 color #4ba5f8 > volume #58 color #ff8681 > volume #58 level 0.1131 > volume #59 level 0.1099 > volume #59 level 0.1395 > volume #59 level 0.1144 > open /Users/dongju/Downloads/cryosparc_P161_run_class001.mrc Opened cryosparc_P161_run_class001.mrc as #60, grid size 288,288,288, pixel 0.75, shown at level 0.00175, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #60 step 1 > volume #60 level 0.002935 Drag select of 60 cryosparc_P161_run_class001.mrc > select clear > volume #60 level 0.001967 > volume #60 color #7092eb Drag select of 60 cryosparc_P161_run_class001.mrc > select clear Drag select of 60 cryosparc_P161_run_class001.mrc > select clear > volume #60 level 0.002397 Drag select of 60 cryosparc_P161_run_class001.mrc > select clear Drag select of 60 cryosparc_P161_run_class001.mrc > select clear > select #47 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #47,-0.84423,-0.18459,-0.5032,270.72,-0.16257,0.98278,-0.087778,28.952,0.51074,0.0077016,-0.8597,163.45 > ui mousemode right ""translate selected models"" > view matrix models > #47,-0.84423,-0.18459,-0.5032,276.69,-0.16257,0.98278,-0.087778,98.496,0.51074,0.0077016,-0.8597,179.05 > ui mousemode right select > select clear > select #30 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #30,-0.84114,0.50506,-0.19338,159.96,0.43533,0.84448,0.31199,-153.77,0.32088,0.17825,-0.9302,133.11 > view matrix models > #30,-0.84114,0.50506,-0.19338,162.05,0.43533,0.84448,0.31199,-140.73,0.32088,0.17825,-0.9302,140.27 > ui mousemode right select > select #47 2 models selected Drag select of 47 cryosparc_P161_J44_010_volume_map (2).mrc > ui mousemode right ""translate selected models"" > view matrix models > #47,-0.20523,0.86583,-0.45631,86.524,0.86746,0.37682,0.32483,34.352,0.4532,-0.32917,-0.82841,224.88 > ui mousemode right ""rotate selected models"" > view matrix models > #47,-0.3803,0.7969,-0.46938,114.84,0.79726,0.53971,0.27035,30.172,0.46877,-0.2714,-0.84059,218.15 > view matrix models > #47,-0.39197,0.82691,-0.40321,105.06,0.81143,0.51728,0.27204,30.933,0.43352,-0.22055,-0.87374,220.17 > view matrix models > #47,-0.496,0.83248,-0.24689,97.588,0.79377,0.54997,0.25975,30.642,0.35201,-0.067136,-0.93358,218.91 > view matrix models > #47,-0.53984,0.73625,-0.40806,131.88,0.70939,0.65887,0.25029,28.791,0.45314,-0.15436,-0.87797,211.14 > view matrix models > #47,-0.24383,0.86729,-0.43401,87.975,0.85659,0.40244,0.32295,32.897,0.45475,-0.29302,-0.84103,222.14 > ui mousemode right select > select clear > volume #30 level 0.08072 > volume #30 level 0.09884 > select #30 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #30,0.28817,-0.88836,-0.35746,203.42,-0.87201,-0.3977,0.28538,134.79,-0.39568,0.22947,-0.88926,208.39 > view matrix models > #30,0.78674,0.56073,-0.25812,-13.648,0.57098,-0.81995,-0.040874,57.449,-0.23456,-0.11522,-0.96525,235.26 > ui mousemode right select > select clear > volume #30 level 0.07348 > volume #60 level 0.002504 > open /Users/dongju/Downloads/cryosparc_P161_J97_005_volume_map.mrc Opened cryosparc_P161_J97_005_volume_map.mrc as #61, grid size 288,288,288, pixel 0.75, shown at level 0.0477, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #61 step 1 > select #61 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #61,-0.94615,0.13199,-0.29559,234.33,-0.014714,0.89462,0.44658,-38.832,0.32338,0.42689,-0.84451,132.37 > view matrix models > #61,-0.4934,0.49563,-0.71478,193.37,0.047505,0.8359,0.54682,-50.917,0.86851,0.23584,-0.43598,45.706 > view matrix models > #61,-0.50616,0.39283,-0.76778,212.23,0.40972,0.89289,0.18674,-55.13,0.75891,-0.22005,-0.61289,128.42 > view matrix models > #61,-0.70179,0.39954,-0.58979,212.32,0.41459,0.90233,0.11794,-48.689,0.57931,-0.16175,-0.7989,163.47 > ui mousemode right ""translate selected models"" > view matrix models > #61,0.99398,-0.06137,0.090732,6.3966,-0.1026,-0.81174,0.57494,243.61,0.038367,-0.58079,-0.81315,297.34 > ui mousemode right ""rotate selected models"" > view matrix models > #61,0.99188,-0.073784,0.10362,6.49,-0.12305,-0.76308,0.63449,233.58,0.032253,-0.64208,-0.76596,299.25 > view matrix models > #61,0.99565,-0.048721,0.079446,6.1397,-0.082855,-0.85303,0.51524,252.92,0.042667,-0.51958,-0.85336,294.84 > view matrix models > #61,0.99557,-0.049404,0.080013,6.1572,-0.083896,-0.85099,0.51844,252.44,0.042478,-0.52285,-0.85136,294.98 > view matrix models > #61,0.99735,-0.030738,0.065954,5.5504,-0.056294,-0.90026,0.43169,264.91,0.046106,-0.43426,-0.89961,290.48 > view matrix models > #61,0.90682,0.42016,-0.033726,-22.348,0.37909,-0.77795,0.50109,195.44,0.1843,-0.46719,-0.86474,274.81 > view matrix models > #61,0.91057,0.41251,-0.026589,-22.752,0.35981,-0.7593,0.54222,190.73,0.20348,-0.50329,-0.83982,273.76 > view matrix models > #61,0.9254,0.35716,-0.12681,-6.6388,0.36524,-0.75107,0.55,188.32,0.1012,-0.55528,-0.82548,289.06 > ui mousemode right select > select clear > volume #61 color #ea7348 > volume #61 level 0.06096 > select clear Drag select of 61 cryosparc_P161_J97_005_volume_map.mrc > select clear > volume #61 level 0.05436 > volume #61 level 0.04114 > volume #61 level 0.04246 Drag select of 61 cryosparc_P161_J97_005_volume_map.mrc > select clear Drag select of 61 cryosparc_P161_J97_005_volume_map.mrc > select clear > volume #60 level 0.001913 > volume #60 level 0.001537 > volume #60 level 0.001806 > volume #61 level 0.0475 > volume #61 level 0.04251 > volume #61 level 0.06277 > volume #61 level 0.04286 > volume #61 level 0.0582 > volume #61 level 0.05445 > volume #61 level 0.03787 > volume #61 level 0.04772 > volume #61 level 0.0539 > volume #61 level 0.03921 > volume #61 level 0.04462 > volume #61 level 0.03668 > open ""/Users/dongju/Downloads/emd_38015 (3).map"" Opened emd_38015 (3).map as #62, grid size 320,320,320, pixel 0.85, shown at level 0.177, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #62 step 1 > volume #62 level 0.5198 > select #62 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #62,0.99158,0.051256,0.11889,-15.104,-0.052578,0.99858,0.0080081,136.81,-0.11832,-0.014192,0.99287,27.751 > ui mousemode right ""rotate selected models"" > view matrix models > #62,0.75026,-0.65967,0.044023,124.05,0.62245,0.72724,0.28928,45.254,-0.22285,-0.18964,0.95623,70.572 > view matrix models > #62,0.72365,-0.6893,0.03451,132.93,0.60299,0.65578,0.45426,35.362,-0.33575,-0.30792,0.8902,110.7 > ui mousemode right ""translate selected models"" > view matrix models > #62,0.71972,-0.69351,0.032493,123.88,0.59831,0.6433,0.47769,-111.81,-0.35219,-0.32436,0.87793,93.288 > ui mousemode right select > select clear > volume #62 color #aad543 > volume #61 level 0.0684 > volume #62 level 0.5649 > volume #62 level 0.4447 > volume #61 level 0.03932 > volume #62 level 0.4748 > volume #62 level 0.5048 > volume #61 level 0.05518 > open /Users/dongju/Downloads/cryosparc_P161_J100_map_half_A.mrc Opened cryosparc_P161_J100_map_half_A.mrc as #63, grid size 288,288,288, pixel 0.75, shown at level 0.0515, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #63 step 1 > select #63 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #63,0.99801,-0.060914,0.016539,26.528,0.060397,0.99772,0.030138,227.28,-0.018337,-0.029079,0.99941,63.56 > ui mousemode right ""rotate selected models"" > view matrix models > #63,-0.62778,0.39342,-0.67165,226.67,0.15178,0.90818,0.3901,188.34,0.76345,0.14295,-0.62984,136.25 > view matrix models > #63,-0.63571,-0.47405,-0.60922,314.17,-0.58042,0.81385,-0.02761,322.25,0.5089,0.33605,-0.79252,160.37 > view matrix models > #63,-0.83153,-0.49385,-0.2543,299.18,-0.51146,0.8593,0.0036653,306.57,0.21671,0.13311,-0.96712,232.45 > view matrix models > #63,-0.86286,-0.37857,-0.33489,298.81,-0.40708,0.91324,0.01651,288.15,0.29959,0.15058,-0.94211,218.96 > ui mousemode right select > select clear > volume #63 level 0.07522 > open /Users/dongju/Downloads/cryosparc_P161_J100_map_locres.mrc Opened cryosparc_P161_J100_map_locres.mrc as #64, grid size 288,288,288, pixel 0.75, shown at level 5.35, step 2, values float32 > select #64 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #64,0.98064,0.086853,0.17549,0.41923,-0.090425,0.99583,0.012443,342.46,-0.17368,-0.028071,0.9844,96.506 > ui mousemode right ""rotate selected models"" > view matrix models > #64,-0.9163,0.14974,-0.37144,262.75,0.027421,0.94875,0.31484,299.93,0.39955,0.2783,-0.87345,214.97 > view matrix models > #64,-0.78378,-0.34145,-0.51876,319.51,-0.48645,0.8568,0.17102,382.5,0.38608,0.3864,-0.83764,200.38 > view matrix models > #64,-0.72934,-0.11997,-0.67356,307.05,-0.36782,0.89888,0.23818,357.22,0.57687,0.42146,-0.69971,159.86 > view matrix models > #64,-0.69238,-0.52474,-0.49523,327.07,-0.61599,0.78729,0.027021,420.87,0.37571,0.32377,-0.86834,211.95 > view matrix models > #64,-0.82974,-0.17149,-0.53115,307.2,-0.28107,0.95054,0.13217,354.34,0.48221,0.25896,-0.8369,203.9 > ui mousemode right select > select #64 2 models selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #64 step 1 > volume #64 level 6.342 > close #64 > ui tool show ""Surface Color"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/dongju/Downloads/cryosparc_P161_J100_map_locres.mrc Opened cryosparc_P161_J100_map_locres.mrc as #64, grid size 288,288,288, pixel 0.75, shown at level 5.35, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color sample #63.1 map #64 palette > 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff Map values for surface ""surface"": minimum 0, mean 0, maximum 0 > color sample #61.1 map #64 palette > 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff Map values for surface ""surface"": minimum 0, mean 0, maximum 0 > color single #61.1 > color sample #61.1 map #64 palette #ff0000:#ffff00:#00ff00:#00ffff:#0000ff Map values for surface ""surface"": minimum 0, mean 0, maximum 0 > color sample #61.1 map #64 palette #ff0000:#ffff00:#00ff00:#00ffff:#0000ff Map values for surface ""surface"": minimum 0, mean 0, maximum 0 > color sample #61.1 map #64 palette > 0,#ff0000:0,#ffff00:0,#00ff00:0,#00ffff:0,#0000ff Map values for surface ""surface"": minimum 0, mean 0, maximum 0 > color single #61.1 > color sample #63.1 map #64 palette > 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff Map values for surface ""surface"": minimum 0, mean 0, maximum 0 > color sample #63.1 map #64 palette > 2,#ff0000:2.5,#ffff00:3,#00ff00:4.5,#00ffff:5.5,#0000ff Map values for surface ""surface"": minimum 0, mean 0, maximum 0 > color sample #63.1 map #63 palette > 2,#ff0000:2.5,#ffff00:3,#00ff00:4.5,#00ffff:5.5,#0000ff Map values for surface ""surface"": minimum 0.07522, mean 0.07522, maximum 0.07523 > color sample #63.1 map #63 palette > 2.5,#ff0000:3,#ffff00:3.5,#00ff00:4.5,#00ffff:5.5,#0000ff Map values for surface ""surface"": minimum 0.07522, mean 0.07522, maximum 0.07523 > color sample #63.1 map #63 palette > 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff Map values for surface ""surface"": minimum 0.07522, mean 0.07522, maximum 0.07523 > color sample #63.1 map #64 palette > 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff Map values for surface ""surface"": minimum 0, mean 0, maximum 0 > color sample #61.1 map #64 palette > 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff Map values for surface ""surface"": minimum 0, mean 0, maximum 0 > color single #61.1 > close #64 > close #63 > volume #61 level 0.05397 > volume #60 color #5a86ef > volume #60 level 0.002396 > select clear Drag select of 60 cryosparc_P161_run_class001.mrc > select clear > volume #60 level 0.002298 Drag select of 61 cryosparc_P161_J97_005_volume_map.mrc > select clear > volume #61 level 0.06486 > volume #61 level 0.05518 > volume #61 level 0.0576 > volume #61 level 0.06365 > tile #60-61 2 models tiled > select #61 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #61,-0.20992,-0.97379,-0.087548,238.7,-0.96548,0.22058,-0.13855,65.31,0.15423,0.055443,-0.98648,145.45 > view matrix models > #61,-0.90591,-0.10548,-0.41011,256.41,-0.12197,0.99243,0.014168,-128.99,0.40552,0.062855,-0.91192,108.65 > view matrix models > #61,-0.84196,-0.13266,-0.52298,265.57,-0.1603,0.98704,0.0076999,-123.48,0.51518,0.090317,-0.85231,86.783 > view matrix models > #61,-0.84255,-0.13305,-0.52193,265.56,-0.16055,0.987,0.0075702,-123.43,0.51413,0.090176,-0.85296,86.987 > ui mousemode right select > select clear > tile #60-61 columns 2 spaingFactor 1 Expected a keyword > tile #60-61 columns 2 spacingFactor 1 2 models tiled > tile #60-61 columns 2 spacingFactor 0.8 2 models tiled > tile #60-61 columns 2 spacingFactor 0.9 2 models tiled > volume #61 level 0.06607 > volume #60 level 0.002445 > tile #60-61 columns 2 spacingFactor 0.6 2 models tiled > volume #61 level 0.03825 > volume #60 level 0.002002 > volume #60 level 0.001658 > volume #60 level 0.00215 > volume #61 level 0.05035 > volume #60 level 0.002396 > volume #61 level 0.05397 > volume #44 color #6ce6ff > select #44 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #44,0.7259,-0.65031,0.22397,66.641,0.55466,0.74603,0.36849,-282.48,-0.40672,-0.14326,0.90225,-8.3567 > view matrix models > #44,0.7259,-0.65031,0.22397,66.637,0.55466,0.74603,0.36849,-282.44,-0.40672,-0.14326,0.90225,-8.3806 > ui mousemode right select > select clear > open ""/Users/dongju/Downloads/emd_42023 (2).map"" Opened emd_42023 (2).map as #63, grid size 256,256,256, pixel 0.86, shown at level 0.167, step 1, values float32 > select #63 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #63,1,0,0,-20.61,0,1,0,-156.64,0,0,1,-66.319 > ui mousemode right ""rotate selected models"" > view matrix models > #63,-0.97631,0.20061,0.081134,168.14,0.21204,0.812,0.54377,-224.96,0.043204,0.54809,-0.8353,89.084 > view matrix models > #63,0.89146,-0.035537,-0.4517,47.972,-0.10357,-0.98651,-0.12678,69.705,-0.4411,0.1598,-0.88311,187.33 > view matrix models > #63,0.891,-0.051501,-0.45107,49.557,-0.087143,-0.99447,-0.05859,60.689,-0.44556,0.091512,-0.89056,195.57 > view matrix models > #63,0.89091,-0.053244,-0.45104,49.738,-0.088873,-0.99434,-0.058166,60.818,-0.44539,0.091907,-0.89061,195.52 > ui mousemode right select > select clear > volume #63 level 0.2612 > open /Users/dongju/Downloads/emd_37881.map Opened emd_37881.map as #64, grid size 256,256,256, pixel 1.1, shown at level 0.322, step 1, values float32 > volume #64 level 0.6891 > select #64 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #64,1,0,0,-32.534,0,1,0,-18.188,0,0,1,-138.88 > ui mousemode right select > select clear > volume #64 level 1.03 > open > /Users/dongju/Downloads/cryosparc_P161_J101_component_000/J101_component_000_frame_000.mrc Opened J101_component_000_frame_000.mrc as #65, grid size 288,288,288, pixel 0.75, shown at level 0.0514, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #65 step 1 > volume #65 color #ff7f8d > Incomplete command: vseries The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #65 style image > volume #65 style surface > hide #!65 models > show #!65 models > volume #65 change image level -0.006732,0 level 0.05131,0.8 level 0.2737,1 > volume #65 style image colorMode opaque8 showOutlineBox true imageMode ""box > faces"" > volume #65 style mesh > volume #65 style surface > volume #65 style image colorMode auto8 imageMode ""full region"" > volume #65 style surface > ui mousemode right ""crop volume"" > ui mousemode right select > select clear > set bgColor white > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > ui mousemode right ""move planes"" > volume #65 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 108 tiltedSlabSpacing 0.75 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #!65 region all imageMode ""full region"" > volume unzone #!65 > mousemode rightMode ""crop volume"" > volume #!65 planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #!65 showOutlineBox false > volume #!65 region all imageMode ""full region"" > volume unzone #!65 > mousemode rightMode ""crop volume"" > volume #!65 region all imageMode ""full region"" > volume unzone #!65 > mousemode rightMode ""crop volume"" > volume #65 orthoplanes xyz positionPlanes 144,144,144 style image region all > mousemode rightMode ""move planes"" > volume #65 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 108 tiltedSlabSpacing 0.75 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #!65 planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > ui mousemode right ""crop volume"" > volume #65 region 0,0,143,287,287,257 > volume #65 region 0,0,143,287,287,287 > volume #65 style surface > close #65 > volume #64 color #7c50ff > volume #64 region 0,0,0,255,255,255 > volume #64 region 11,0,0,255,255,255 > volume #63 level 0.3177 > volume #63 color #ffdb44 > volume #63 level 0.28 > volume #63 region 0,0,0,255,255,255 > volume #62 region 96,0,0,319,319,319 > volume #62 region 92,0,0,319,319,319 > volume #62 level 0.656 > volume #62 level 0.5735 > volume #62 level 0.491 > volume #62 level 0.5185 > volume #61 region 0,0,0,287,287,287 > ui mousemode right select > select #61 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #61,-0.91049,-0.30014,0.28447,208.27,-0.012093,0.70694,0.70717,-159.24,-0.41335,0.64043,-0.64729,134.11 > ui mousemode right ""rotate selected models"" > view matrix models > #61,-0.862,-0.47334,0.18142,233.97,-0.4897,0.87004,-0.056726,-35.845,-0.13099,-0.13774,-0.98177,227.54 > view matrix models > #61,0.78289,-0.61232,-0.11024,102.81,-0.4373,-0.6676,0.60257,50.512,-0.44256,-0.42353,-0.79042,270.82 > view matrix models > #61,0.97076,0.23918,-0.0203,-21.77,0.20457,-0.78014,0.59121,-6.1939,0.12557,-0.57808,-0.80626,227.33 > view matrix models > #61,0.13752,0.37645,0.91617,-54.5,-0.26925,-0.87592,0.40033,78.508,0.9532,-0.30173,-0.019098,14.58 > view matrix models > #61,-0.37962,0.31395,0.87024,14.42,-0.17868,-0.94783,0.264,92.345,0.90772,-0.055278,0.41591,-58.143 > ui mousemode right select > select clear > select #61 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #61,0.94414,0.078156,0.32014,-37.975,-0.11776,-0.82732,0.54925,61.513,0.30779,-0.55627,-0.7719,209.94 > ui mousemode right select > select #61 2 models selected > select clear > volume #61 level 0.06849 > volume #61 level 0.04793 > volume #61 level 0.05276 > open /Users/dongju/Downloads/cryosparc_P163_J46_009_volume_map.mrc Opened cryosparc_P163_J46_009_volume_map.mrc as #65, grid size 288,288,288, pixel 0.75, shown at level 0.117, step 2, values float32 > volume #65 color #fc65ed > volume #65 level 0.1391 > volume #65 level 0.1083 > volume #65 level 0.1155 > volume #65 level 0.1337 > volume #63 level 0.2894 > volume #63 level 0.28 > volume #63 color #ff835e > volume #63 level 0.3083 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #65 step 1 > volume #63 level 0.2612 > select #65 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #65,0.93557,-0.34281,-0.084758,27.627,-0.25377,-0.81958,0.5137,-75.094,-0.24557,-0.45909,-0.85377,210.93 > ui mousemode right select > select clear > volume #65 level 0.1042 > volume #65 level 0.1258 > volume #65 level 0.118 > open /Users/dongju/Downloads/cryosparc_P161_J97_005_volume_map_sharp.mrc Opened cryosparc_P161_J97_005_volume_map_sharp.mrc as #66, grid size 288,288,288, pixel 0.75, shown at level 0.0993, step 2, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #66 step 1 > select #66 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #66,1,-0.00010955,1.6327e-05,-1.3257,0.00010955,1,0.00047679,53.573,-1.6379e-05,-0.00047679,1,-13.767 > ui mousemode right ""rotate selected models"" > view matrix models > #66,-0.90835,-0.27533,0.31478,200.97,-0.089159,0.86289,0.49746,23.877,-0.40859,0.4238,-0.80836,181.85 > view matrix models > #66,-0.5662,0.57279,-0.59274,171.2,0.20296,0.79384,0.57325,-8.595,0.79889,0.20427,-0.56573,48.212 > view matrix models > #66,-0.13312,0.7085,-0.69304,120.53,0.071561,0.70431,0.70628,0.81845,0.98851,0.044423,-0.14446,-1.006 > view matrix models > #66,-0.19566,0.56408,-0.8022,154.81,0.76572,0.59894,0.2344,-11.604,0.61269,-0.5684,-0.54912,150.05 > view matrix models > #66,-0.8811,-0.4681,-0.067514,260.51,-0.38784,0.79685,-0.46326,168.13,0.27065,-0.38199,-0.88365,203.47 > view matrix models > #66,-0.97152,-0.23503,-0.030291,241.08,-0.18806,0.84246,-0.50486,146.08,0.14417,-0.48478,-0.86267,226 > view matrix models > #66,-0.96966,-0.16566,0.17979,210.48,-0.23481,0.83585,-0.49621,150.92,-0.068074,-0.52336,-0.84939,251.72 > view matrix models > #66,-0.94169,0.0060802,0.33642,171.82,-0.18433,0.82713,-0.53092,150.18,-0.28149,-0.56198,-0.77778,271.23 > view matrix models > #66,-0.88594,-0.074842,-0.45772,261.1,-0.095359,0.9952,0.021845,62.11,0.45389,0.063001,-0.88883,136.1 > ui mousemode right ""translate selected models"" > view matrix models > #66,-0.88594,-0.074842,-0.45772,265.76,-0.095359,0.9952,0.021845,76.726,0.45389,0.063001,-0.88883,154.19 > ui mousemode right select > select clear > volume #66 level 0.1919 > volume #66 level 0.175 > volume #66 level 0.1498 > volume #66 level 0.2172 > volume #66 level 0.2003 > volume #66 level 0.1414 > volume #66 level 0.1245 > volume #66 level 0.1666 > open /Users/dongju/Downloads/cryosparc_P161_J104_007_volume_map.mrc Opened cryosparc_P161_J104_007_volume_map.mrc as #67, grid size 288,288,288, pixel 0.75, shown at level 0.0404, step 2, values float32 > select #67 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #67,0.99937,-0.034572,-0.0083988,16.21,0.034508,0.99937,-0.0076891,122.19,0.0086593,0.0073944,0.99994,29.575 > ui mousemode right ""rotate selected models"" > view matrix models > #67,0.42712,-0.89905,0.096289,160.95,0.86718,0.37715,-0.32521,133.05,0.25606,0.2224,0.94073,-14.302 > view matrix models > #67,-0.81863,-0.10581,-0.56448,283.34,-0.032081,0.98977,-0.139,144.82,0.57342,-0.095685,-0.81366,176.55 > ui mousemode right select > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #67 step 1 > volume #67 level 0.08403 > volume #67 level 0.04837 > volume #67 level 0.0563 > volume #67 level 0.04441 > volume #67 level 0.08007 > volume #67 level 0.06818 > volume #67 level 0.06026 > volume #66 level 0.1329 > volume #67 level 0.08403 Drag select of 66 cryosparc_P161_J97_005_volume_map_sharp.mrc , 67 cryosparc_P161_J104_007_volume_map.mrc > select clear > volume #67 level 0.05233 > ui tool show ""Side View"" > view > tile 2 models tiled > select clear Drag select of 67 cryosparc_P161_J104_007_volume_map.mrc > select #67 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #67,0.14302,0.96877,0.20258,-41.634,-0.80965,0.23224,-0.53901,71.212,-0.56922,-0.086927,0.81758,32.97 > view matrix models > #67,-0.18784,0.4962,0.84765,-24.395,-0.75902,0.4744,-0.44591,30.02,-0.62338,-0.72714,0.28752,163.56 > view matrix models > #67,-0.26629,0.20525,0.94179,4.9279,-0.76516,0.54919,-0.33604,10.993,-0.58619,-0.8101,0.010801,197.93 > view matrix models > #67,-0.81719,-0.49463,-0.29587,272.59,-0.41894,0.8623,-0.28447,-65.86,0.39584,-0.10851,-0.91189,114.43 > view matrix models > #67,-0.86081,-0.41723,-0.29142,268.74,-0.46244,0.88034,0.1056,-104.84,0.21249,0.22566,-0.95075,103.48 > view matrix models > #67,0.64917,-0.75581,-0.085669,115.86,-0.74345,-0.65426,0.13864,84.924,-0.16083,-0.026309,-0.98663,175.18 > view matrix models > #67,0.95992,0.27878,0.028833,-40.141,0.25782,-0.9187,0.29919,-14.82,0.1099,-0.27977,-0.95376,168.58 > view matrix models > #67,0.99596,0.087471,0.020457,-22.985,0.079628,-0.96505,0.24968,15.058,0.041582,-0.24704,-0.96811,174.2 > ui mousemode right ""translate selected models"" > view matrix models > #67,0.99596,0.087471,0.020457,-14.345,0.079628,-0.96505,0.24968,103.68,0.041582,-0.24704,-0.96811,198.57 > ui mousemode right select > select clear > volume #67 level 0.09196 > select clear > select #67 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #67,0.97906,0.18186,0.091535,-28.73,0.15103,-0.95024,0.27246,92.23,0.13653,-0.25293,-0.9578,187.82 > view matrix models > #67,0.63356,0.75521,-0.16812,-25.132,0.74413,-0.53531,0.39963,-26.818,0.21181,-0.37829,-0.90113,187.07 > view matrix models > #67,0.54931,0.82573,-0.12819,-26.811,0.7898,-0.46295,0.40236,-39.445,0.27289,-0.32226,-0.90646,175.17 > view matrix models > #67,0.60895,0.7909,-0.060501,-36.096,0.55401,-0.36949,0.74602,-55.156,0.56767,-0.48781,-0.66316,137.1 > view matrix models > #67,0.69509,0.70932,-0.11708,-31.947,0.53167,-0.39756,0.74785,-50.02,0.48392,-0.58207,-0.65347,154.97 > view matrix models > #67,0.65686,0.75376,0.019625,-45.02,0.49817,-0.45337,0.73911,-39.853,0.56601,-0.47571,-0.6733,137 > ui mousemode right ""translate selected models"" > view matrix models > #67,0.65686,0.75376,0.019625,-43.299,0.49817,-0.45337,0.73911,-40.065,0.56601,-0.47571,-0.6733,144.52 > ui mousemode right select > select clear > open /Users/dongju/Downloads/cryosparc_P161_J104_007_volume_map_sharp.mrc Opened cryosparc_P161_J104_007_volume_map_sharp.mrc as #68, grid size 288,288,288, pixel 0.75, shown at level 0.0986, step 2, values float32 > select #68 2 models selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #68,1,-6.1047e-05,0.00027243,-12.352,6.1053e-05,1,-2.3363e-05,-135.18,-0.00027243,2.3379e-05,1,-33.458 > view matrix models > #68,1,-6.1047e-05,0.00027243,-13.342,6.1053e-05,1,-2.3363e-05,-145.75,-0.00027243,2.3379e-05,1,-36.19 > ui mousemode right ""rotate selected models"" > view matrix models > #68,0.89939,-0.0071355,-0.43708,44.669,-0.12095,-0.9649,-0.23312,103.37,-0.42007,0.26253,-0.86868,179.11 > view matrix models > #68,0.89831,-0.030642,-0.4383,47.444,-0.09885,-0.98609,-0.13366,92.714,-0.42811,0.16339,-0.88884,192.77 > view matrix models > #68,0.89802,-0.040174,-0.43811,48.48,-0.089691,-0.99163,-0.092914,87.999,-0.43071,0.12273,-0.8941,197.99 > view matrix models > #68,0.89787,-0.047179,-0.43773,49.209,-0.082886,-0.99458,-0.062818,84.39,-0.43239,0.092684,-0.89691,201.7 > view matrix models > #68,0.89893,-0.015739,-0.43781,45.721,-0.11294,-0.9739,-0.19689,99.631,-0.42328,0.22643,-0.87725,184.24 > view matrix models > #68,0.89856,-0.023864,-0.43819,46.676,-0.10529,-0.98108,-0.16248,95.928,-0.42603,0.19214,-0.88407,188.95 > view matrix models > #68,0.89861,-0.022647,-0.43815,46.535,-0.10644,-0.98008,-0.16765,96.493,-0.42563,0.19729,-0.88313,188.25 > view matrix models > #68,0.065555,0.97384,0.21756,-39.434,0.98867,-0.033879,-0.14626,-126.62,-0.13506,0.22468,-0.96503,162.38 > view matrix models > #68,-0.15873,0.86279,0.48,-30.888,-0.39568,0.38983,-0.83155,50.949,-0.90457,-0.32192,0.27951,173.07 > view matrix models > #68,-0.080275,0.80672,0.58545,-44.558,-0.86641,0.23394,-0.44115,77.572,-0.49285,-0.54265,0.68017,109.6 > volume #68 level 0.2481 > view matrix models > #68,-0.012401,0.78705,0.61677,-52.73,-0.9836,0.1014,-0.14918,77.623,-0.17995,-0.6085,0.77288,74.024 > view matrix models > #68,0.20256,0.94412,0.25999,-60.087,0.8527,-0.3006,0.42725,-132.47,0.48153,0.13515,-0.86595,73.364 > view matrix models > #68,0.15154,0.96062,0.23291,-53.8,0.95793,-0.20083,0.20505,-134.14,0.24375,0.19204,-0.95064,100.98 > volume #68 level 0.4615 > view matrix models > #68,0.18588,0.95044,0.24922,-58.008,0.89641,-0.2679,0.35311,-134.41,0.40238,0.15776,-0.90178,82.702 > view matrix models > #68,0.17227,0.95489,0.2419,-56.303,0.92492,-0.24129,0.29378,-134.7,0.33889,0.17313,-0.92476,90.167 > view matrix models > #68,0.24131,0.92427,0.29578,-65.695,0.69908,-0.37696,0.60761,-125.58,0.6731,0.060151,-0.7371,47.93 > view matrix models > #68,0.22858,0.93182,0.2819,-63.789,0.75981,-0.35179,0.54674,-129.07,0.60863,0.089218,-0.78842,56.744 > ui mousemode right ""translate selected models"" > view matrix models > #68,0.22858,0.93182,0.2819,-57.943,0.75981,-0.35179,0.54674,-130.33,0.60863,0.089218,-0.78842,82.377 > ui mousemode right ""rotate selected models"" > view matrix models > #68,0.0068193,0.99995,-0.0075008,-13.927,0.71445,0.00037614,0.69969,-175.24,0.69965,-0.01013,-0.71441,75.69 > ui mousemode right select > select clear > volume #68 level 0.3334 > volume #68 level 0.2907 > volume #68 level 0.2694 > volume #68 level 0.2054 > volume #67 level 0.0563 > select #62 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #62,-0.38567,0.87373,0.29641,33.576,-0.51028,0.065659,-0.8575,214.92,-0.76868,-0.48196,0.42052,267.74 > ui mousemode right rotate > ui mousemode right select > select clear > volume #62 level 0.6697 > volume #62 level 0.546 > volume #62 level 0.4361 > volume #62 level 0.3536 > volume #67 level 0.04837 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #68 step 1 Drag select of 68 cryosparc_P161_J104_007_volume_map_sharp.mrc > select clear > volume #68 level 0.2784 > volume #68 level 0.5708 > volume #68 level 0.4977 > volume #68 level 0.4246 > volume #68 level 0.2541 > volume #68 level 0.3515 > volume #68 level 0.3028 ===== Log before crash end ===== Log: Startup Messages --- warning | Could not find virtual screen for QCocoaScreen(0x6000023f1290, ""DELL P2422H"", QRect(1536,61 1920x1080), dpr=1, displayId=4128833, ) with displayId 4128833 note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Could not find virtual screen for QCocoaScreen(0x6000023f1290, ""DELL P2422H"", QRect(1536,61 1920x1080), dpr=1, displayId=4128833, ) with displayId 4128833 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. OpenGL version: 4.1 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0) OS Loader Version: 580~2215 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 19 days, 23 hours, 32 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect new normal Unassigned