id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16324 Crash on Mac waking from sleep michelle.moritz@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.6.9-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. 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""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""65a855f5f087695cfac03d1f"" }, ""deploymentId"" : 240000155 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet > volume step 1 Error running startup command 'volume step 1': No volumes specified 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/moritz/Library/Mobile > Documents/com~apple~CloudDocs/EMData/230701TuSC110+Hrr25/csparc/Local > Refinement/Fit Hrr25 in J106 map.cxs"" format session Opened cryosparc_P49_J106_007_volume_map.mrc as #1, grid size 256,256,256, pixel 1.73, shown at level 0.101, step 1, values float32 opened ChimeraX session > open ""/Users/moritz/Library/Mobile > Documents/com~apple~CloudDocs/EMData/230701TuSC110+Hrr25/csparc/Homo > Refinement/J93/cryosparc_P49_J93_004_volume_map.mrc"" format mrc Opened cryosparc_P49_J93_004_volume_map.mrc as #6, grid size 256,256,256, pixel 1.73, shown at level 0.263, step 1, values float32 > color #1 #bf80ae8e models > close session > open ""/Users/moritz/Library/Mobile > Documents/com~apple~CloudDocs/EMData/230701TuSC110+Hrr25/csparc/Local > Refinement/J106/cryosparc_P49_J106_007_volume_map.mrc"" Opened cryosparc_P49_J106_007_volume_map.mrc as #1, grid size 256,256,256, pixel 1.73, shown at level 0.0215, step 1, values float32 > open ""/Users/moritz/Library/Mobile > Documents/com~apple~CloudDocs/EMData/230701TuSC110+Hrr25/csparc/Homo > Refinement/J93/cryosparc_P49_J93_004_volume_map.mrc"" Opened cryosparc_P49_J93_004_volume_map.mrc as #2, grid size 256,256,256, pixel 1.73, shown at level 0.263, step 1, values float32 > surface dust #1 size 17.3 > surface dust #2 size 17.3 > volume #1 level 0.09852 > open ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF > yeast fits /col_best_001.pdb"" ""/Users/moritz/Library/Mobile > Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_002.pdb"" > ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast > fits /col_best_003.pdb"" ""/Users/moritz/Library/Mobile > Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_004.pdb"" > ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast > fits /col_best_005.pdb"" ""/Users/moritz/Library/Mobile > Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_006.pdb"" > ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast > fits /col_best_007.pdb"" ""/Users/moritz/Library/Mobile > Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_008.pdb"" > ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast > fits /col_best_009.pdb"" ""/Users/moritz/Library/Mobile > Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_010.pdb"" Summary of feedback from opening /Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_001.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK File name col_best_001.pdb Ignored bad PDB record found on line 3 REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into map ../cryosparc_P49_J106_007_volume_map.mrc Ignored bad PDB record found on line 5 REMARK Resolution anisotropy factor (Z vs. XY): 1.000000 Ignored bad PDB record found on line 6 REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000 Ignored bad PDB record found on line 7 REMARK Angular step 15.000000 degrees, 4416 Euler angles 33 messages similar to the above omitted Summary of feedback from opening /Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_002.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK File name col_best_002.pdb Ignored bad PDB record found on line 3 REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into map ../cryosparc_P49_J106_007_volume_map.mrc Ignored bad PDB record found on line 5 REMARK Resolution anisotropy factor (Z vs. XY): 1.000000 Ignored bad PDB record found on line 6 REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000 Ignored bad PDB record found on line 7 REMARK Angular step 15.000000 degrees, 4416 Euler angles 33 messages similar to the above omitted Summary of feedback from opening /Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_003.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK File name col_best_003.pdb Ignored bad PDB record found on line 3 REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into map ../cryosparc_P49_J106_007_volume_map.mrc Ignored bad PDB record found on line 5 REMARK Resolution anisotropy factor (Z vs. XY): 1.000000 Ignored bad PDB record found on line 6 REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000 Ignored bad PDB record found on line 7 REMARK Angular step 15.000000 degrees, 4416 Euler angles 33 messages similar to the above omitted Summary of feedback from opening /Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_004.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK File name col_best_004.pdb Ignored bad PDB record found on line 3 REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into map ../cryosparc_P49_J106_007_volume_map.mrc Ignored bad PDB record found on line 5 REMARK Resolution anisotropy factor (Z vs. XY): 1.000000 Ignored bad PDB record found on line 6 REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000 Ignored bad PDB record found on line 7 REMARK Angular step 15.000000 degrees, 4416 Euler angles 33 messages similar to the above omitted Summary of feedback from opening /Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_005.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK File name col_best_005.pdb Ignored bad PDB record found on line 3 REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into map ../cryosparc_P49_J106_007_volume_map.mrc Ignored bad PDB record found on line 5 REMARK Resolution anisotropy factor (Z vs. XY): 1.000000 Ignored bad PDB record found on line 6 REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000 Ignored bad PDB record found on line 7 REMARK Angular step 15.000000 degrees, 4416 Euler angles 33 messages similar to the above omitted Summary of feedback from opening /Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_006.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK File name col_best_006.pdb Ignored bad PDB record found on line 3 REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into map ../cryosparc_P49_J106_007_volume_map.mrc Ignored bad PDB record found on line 5 REMARK Resolution anisotropy factor (Z vs. XY): 1.000000 Ignored bad PDB record found on line 6 REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000 Ignored bad PDB record found on line 7 REMARK Angular step 15.000000 degrees, 4416 Euler angles 33 messages similar to the above omitted Summary of feedback from opening /Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_007.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK File name col_best_007.pdb Ignored bad PDB record found on line 3 REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into map ../cryosparc_P49_J106_007_volume_map.mrc Ignored bad PDB record found on line 5 REMARK Resolution anisotropy factor (Z vs. XY): 1.000000 Ignored bad PDB record found on line 6 REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000 Ignored bad PDB record found on line 7 REMARK Angular step 15.000000 degrees, 4416 Euler angles 33 messages similar to the above omitted Summary of feedback from opening /Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_008.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK File name col_best_008.pdb Ignored bad PDB record found on line 3 REMARK Low-resolution fit of structure dir_001/AF-O13565-F1-model_v4.pdb into map ../cryosparc_P49_J106_007_volume_map.mrc Ignored bad PDB record found on line 5 REMARK Resolution anisotropy factor (Z vs. XY): 1.000000 Ignored bad PDB record found on line 6 REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000 Ignored bad PDB record found on line 7 REMARK Angular step 15.000000 degrees, 4416 Euler angles 33 messages similar to the above omitted Summary of feedback from opening /Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_009.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK File name col_best_009.pdb Ignored bad PDB record found on line 3 REMARK Low-resolution fit of structure dir_001/AF-O13565-F1-model_v4.pdb into map ../cryosparc_P49_J106_007_volume_map.mrc Ignored bad PDB record found on line 5 REMARK Resolution anisotropy factor (Z vs. XY): 1.000000 Ignored bad PDB record found on line 6 REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000 Ignored bad PDB record found on line 7 REMARK Angular step 15.000000 degrees, 4416 Euler angles 33 messages similar to the above omitted Summary of feedback from opening /Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_010.pdb --- warnings | Ignored bad PDB record found on line 2 REMARK File name col_best_010.pdb Ignored bad PDB record found on line 3 REMARK Low-resolution fit of structure dir_001/AF-O13565-F1-model_v4.pdb into map ../cryosparc_P49_J106_007_volume_map.mrc Ignored bad PDB record found on line 5 REMARK Resolution anisotropy factor (Z vs. XY): 1.000000 Ignored bad PDB record found on line 6 REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000 Ignored bad PDB record found on line 7 REMARK Angular step 15.000000 degrees, 4416 Euler angles 33 messages similar to the above omitted Chain information for col_best_001.pdb #3 --- Chain | Description A | No description available Chain information for col_best_002.pdb #4 --- Chain | Description A | No description available Chain information for col_best_003.pdb #5 --- Chain | Description A | No description available Chain information for col_best_004.pdb #6 --- Chain | Description A | No description available Chain information for col_best_005.pdb #7 --- Chain | Description A | No description available Chain information for col_best_006.pdb #8 --- Chain | Description A | No description available Chain information for col_best_007.pdb #9 --- Chain | Description A | No description available Chain information for col_best_008.pdb #10 --- Chain | Description A | No description available Chain information for col_best_009.pdb #11 --- Chain | Description A | No description available Chain information for col_best_010.pdb #12 --- Chain | Description A | No description available > volume #1 color #b2b2b280 > volume #2 color #ffffb2c2 > hide #12 models > hide #11 models > hide #10 models > hide #9 models > hide #8 models > hide #7 models > hide #6 models > hide #5 models > hide #4 models > show #4 models > hide #3 models > show #3 models > show #5 models > show #6 models > show #7 models > show #8 models > show #9 models > show #10 models > show #11 models > show #12 models > close #3-12 > open ""/Users/moritz/Library/Mobile > Documents/com~apple~CloudDocs/Colores/4xhl_C_lobe_core.pdb"" Chain information for 4xhl_C_lobe_core.pdb #3 --- Chain | Description A | No description available > select add #3 1604 atoms, 1641 bonds, 193 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,153,0,1,0,186.69,0,0,1,264.04 > view matrix models #3,1,0,0,256.5,0,1,0,209.06,0,0,1,202.74 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.17033,-0.24666,0.95402,318.72,-0.13446,0.96493,0.22547,216.99,-0.97617,-0.089877,-0.19752,241.3 > view matrix models > #3,-0.1567,-0.084719,0.98401,314.33,-0.15219,0.98649,0.060697,216.37,-0.97585,-0.14025,-0.16747,242.67 > view matrix models > #3,-0.15265,-0.027389,0.9879,312.78,-0.15884,0.9873,0.0028284,216.33,-0.97543,-0.15649,-0.15506,243.11 > view matrix models > #3,-0.20074,-0.51202,0.83519,325.89,-0.10929,0.85893,0.5003,219.92,-0.97353,0.0091509,-0.22838,238.6 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.20074,-0.51202,0.83519,322.52,-0.10929,0.85893,0.5003,218.34,-0.97353,0.0091509,-0.22838,239.91 > view matrix models > #3,-0.20074,-0.51202,0.83519,316.16,-0.10929,0.85893,0.5003,216.76,-0.97353,0.0091509,-0.22838,230.25 > view matrix models > #3,-0.20074,-0.51202,0.83519,316.19,-0.10929,0.85893,0.5003,216.77,-0.97353,0.0091509,-0.22838,230.32 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.035583,-0.83093,0.55523,312.15,0.37105,0.52686,0.76469,205.26,-0.92793,0.17881,0.32707,227.12 > ui tool show ""Fit in Map"" > fitmap #3 inMap #1 Fit molecule 4xhl_C_lobe_core.pdb (#3) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using 1604 atoms average map value = 0.2343, steps = 124 shifted from previous position = 7.4 rotated from previous position = 25.9 degrees atoms outside contour = 696, contour level = 0.098515 Position of 4xhl_C_lobe_core.pdb (#3) relative to cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.15832689 -0.95151169 0.26373871 306.60858615 0.64353911 0.30202317 0.70330606 203.77006596 -0.74885914 0.05837392 0.66015337 218.21785171 Axis -0.32305299 0.50722044 0.79897697 Axis point 122.20713563 274.78975330 0.00000000 Rotation angle (degrees) 86.54573873 Shift along axis 178.65655861 > select subtract #3 Nothing selected > hide #!2 models > open ""/Users/moritz/Library/Mobile > Documents/com~apple~CloudDocs/Colores/4xhl_C_lobe_end.pdb"" Chain information for 4xhl_C_lobe_end.pdb #4 --- Chain | Description A | No description available > select add #4 449 atoms, 462 bonds, 1 pseudobond, 52 residues, 2 models selected > view matrix models > #4,0.94695,0.31789,-0.047162,-10.826,-0.27895,0.74018,-0.61182,25.035,-0.15958,0.59252,0.78959,-17.131 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.94695,0.31789,-0.047162,96.668,-0.27895,0.74018,-0.61182,203.05,-0.15958,0.59252,0.78959,233.31 > view matrix models > #4,0.94695,0.31789,-0.047162,98.637,-0.27895,0.74018,-0.61182,200,-0.15958,0.59252,0.78959,236.83 > view matrix models > #4,0.94695,0.31789,-0.047162,220.49,-0.27895,0.74018,-0.61182,212.83,-0.15958,0.59252,0.78959,151.07 > view matrix models > #4,0.94695,0.31789,-0.047162,231.31,-0.27895,0.74018,-0.61182,216.36,-0.15958,0.59252,0.78959,163.48 > view matrix models > #4,0.94695,0.31789,-0.047162,233.48,-0.27895,0.74018,-0.61182,217.87,-0.15958,0.59252,0.78959,168.62 > fitmap #4 inMap #1 Fit molecule 4xhl_C_lobe_end.pdb (#4) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using 449 atoms average map value = 0.4371, steps = 208 shifted from previous position = 12 rotated from previous position = 32.1 degrees atoms outside contour = 132, contour level = 0.098515 Position of 4xhl_C_lobe_end.pdb (#4) relative to cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.69113669 0.59179546 -0.41485926 227.72588040 -0.72128378 0.60102393 -0.34426724 255.14537826 0.04560455 0.53716698 0.84224216 154.55474733 Axis 0.53512419 -0.27955044 -0.79717856 Axis point 446.01395496 -217.73931155 0.00000000 Rotation angle (degrees) 55.44469983 Shift along axis -72.67210643 > select subtract #4 Nothing selected > open ""/Users/moritz/Library/Mobile > Documents/com~apple~CloudDocs/Colores/4xhl_N_lobe.pdb"" Chain information for 4xhl_N_lobe.pdb #5 --- Chain | Description A | No description available > select add #5 564 atoms, 575 bonds, 1 pseudobond, 69 residues, 2 models selected > view matrix models #5,1,0,0,133.97,0,1,0,166.21,0,0,1,264.94 > view matrix models #5,1,0,0,223.03,0,1,0,203.75,0,0,1,136.68 > view matrix models #5,1,0,0,254.46,0,1,0,194.77,0,0,1,193.19 > fitmap #5 inMap #1 Fit molecule 4xhl_N_lobe.pdb (#5) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using 564 atoms average map value = 0.3198, steps = 156 shifted from previous position = 16 rotated from previous position = 67.4 degrees atoms outside contour = 162, contour level = 0.098515 Position of 4xhl_N_lobe.pdb (#5) relative to cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.40061129 0.27104603 -0.87523976 276.66835012 -0.07300854 0.96164891 0.26438821 192.97051132 0.91333474 -0.04201692 0.40503608 176.80750028 Axis -0.16589712 -0.96838901 -0.18628168 Axis point 23.31635982 0.00000000 249.77508989 Rotation angle (degrees) 67.44015931 Shift along axis -265.70500535 > select subtract #5 Nothing selected > hide #!4 models > hide #3 models > open 4xhl Summary of feedback from opening 4xhl fetched from pdb --- note | Fetching compressed mmCIF 4xhl from http://files.rcsb.org/download/4xhl.cif 4xhl title: Structure of S. cerevisiae Hrr25 1-394 (K38R mutant) [more info...] Chain information for 4xhl #6 --- Chain | Description | UniProt A | Casein kinase I homolog HRR25 | HRR25_YEAST 1-394 Non-standard residues in 4xhl #6 --- CKI — N-(2-aminoethyl)-5-chloroisoquinoline-8-sulfonamide SO4 — sulfate ion > color #6 #9eacdbff > color #6 #928bdbff > select add #6 2811 atoms, 2866 bonds, 2 pseudobonds, 345 residues, 2 models selected > view matrix models #6,1,0,0,116.76,0,1,0,162.78,0,0,1,272.63 > view matrix models #6,1,0,0,214.31,0,1,0,208.11,0,0,1,153.1 > view matrix models #6,1,0,0,245.54,0,1,0,202.68,0,0,1,194.57 > hide #!5 models > fitmap #6 inMap #1 Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using 2811 atoms average map value = 0.1375, steps = 100 shifted from previous position = 8.7 rotated from previous position = 12 degrees atoms outside contour = 1628, contour level = 0.098515 Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.97987496 -0.17254456 -0.10036655 255.03434362 0.17794314 0.98289282 0.04751793 192.68596538 0.09045060 -0.06442117 0.99381517 185.88345765 Axis -0.27007944 -0.46039129 0.84563406 Axis point -929.35267507 1585.84701948 0.00000000 Rotation angle (degrees) 11.96028733 Shift along axis -0.40108880 > select subtract #6 Nothing selected > ui tool show ""Side View"" > show #!2 models > save ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera > sessions/cs_P49_J93_J106_kinase_fits.cxs"" > volume #2 level 0.06284 > volume #2 level 0.05372 > volume #2 level 0.01725 > view > volume #1 level 0.06772 > select add #6 2811 atoms, 2866 bonds, 2 pseudobonds, 345 residues, 2 models selected > view matrix models > #6,0.97987,-0.17254,-0.10037,255.14,0.17794,0.98289,0.047518,193.17,0.090451,-0.064421,0.99382,186.26 > fitmap #6 inMap #1 Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using 2811 atoms average map value = 0.1375, steps = 48 shifted from previous position = 0.601 rotated from previous position = 0.119 degrees atoms outside contour = 1545, contour level = 0.067718 Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.97995844 -0.17189236 -0.10067012 254.98725932 0.17749046 0.98287625 0.04951178 192.71670937 0.09043557 -0.06638747 0.99368713 185.97000251 Axis -0.27943973 -0.46076679 0.84238198 Axis point -924.00066790 1585.62876830 0.00000000 Rotation angle (degrees) 11.96873457 Shift along axis -3.39325106 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.88076,-0.22234,-0.41812,258.77,0.23468,0.97181,-0.022419,190.66,0.41132,-0.078381,0.90811,174.26 > fitmap #6 inMap #1 Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using 2811 atoms average map value = 0.1432, steps = 120 shifted from previous position = 5.83 rotated from previous position = 8.71 degrees atoms outside contour = 1544, contour level = 0.067718 Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.88312303 -0.31472882 -0.34790730 265.26051186 0.27947381 0.94856941 -0.14869585 193.78932549 0.37681310 0.03408575 0.92566195 171.24445361 Axis 0.19142788 -0.75900247 0.62231071 Axis point -270.29554587 0.00000000 847.60505810 Rotation angle (degrees) 28.51679626 Shift along axis 10.25893752 > surface dust #1 size 17.3 > surface dust #2 size 17.3 > surface dust #1 size 17.3 > surface dust #2 size 17.3 > save ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera > sessions/cs_P49_J93_J106_kinase_fits.cxs"" > select subtract #6 Nothing selected > fitmap #6 inMap #1 Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using 2811 atoms average map value = 0.1432, steps = 96 shifted from previous position = 0.0209 rotated from previous position = 0.0335 degrees atoms outside contour = 1545, contour level = 0.067718 Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.88318799 -0.31424338 -0.34818110 265.25060865 0.27907714 0.94873832 -0.14836292 193.78691359 0.37695482 0.03386297 0.92561243 171.26051218 Axis 0.19091373 -0.75970764 0.62160779 Axis point -270.84303671 0.00000000 847.26876748 Rotation angle (degrees) 28.50573286 Shift along axis 9.87545241 > volume #1 level 0.05186 > ui tool show ""Fit in Map"" > open https://www.rbvi.ucsf.edu/chimerax/tutorials.html Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html > volume #1 style mesh > fitmap #6 inMap #1 Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using 2811 atoms average map value = 0.1432, steps = 104 shifted from previous position = 0.0173 rotated from previous position = 0.0351 degrees atoms outside contour = 1499, contour level = 0.051864 Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.88326811 -0.31410041 -0.34810685 265.24443124 0.27916762 0.94880415 -0.14777049 193.79589028 0.37670000 0.03334080 0.92573512 171.29489506 Axis 0.18984440 -0.75975676 0.62187520 Axis point -271.66725279 0.00000000 847.80372240 Rotation angle (degrees) 28.48960246 Shift along axis 9.64147963 > volume #2 color #ffffb283 > volume #2 color #ffffb280 > volume #1 style surface > open ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera > sessions/centerTuSC_110.pdb"" Chain information for centerTuSC_110.pdb #7 --- Chain | Description A B | No description available C | No description available D | No description available E | No description available Q | No description available R | No description available > hide #7 models > open ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera > sessions/TuSCmodels_new_&_old.cxs"" opened ChimeraX session > hide #!1 models > show #!1 models > hide #!4 models > show #!4 models > hide #!1 models > show #!3 models > hide #!3 models > show #!1 models > open ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera > sessions/cs_P49_J93_J106_kinase_fits.cxs"" format session Opened cryosparc_P49_J106_007_volume_map.mrc as #1, grid size 256,256,256, pixel 1.73, shown at level 0.0677, step 1, values float32 Opened cryosparc_P49_J93_004_volume_map.mrc as #2, grid size 256,256,256, pixel 1.73, shown at level 0.0172, step 1, values float32 opened ChimeraX session > volume #1 color #b2b2b258 > volume #1 color #b2b2b259 > volume #2 color #ffffb280 > ui mousemode right ""map eraser"" > select add #7 2811 atoms, 2866 bonds, 2 pseudobonds, 345 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #6,0.88312,-0.31473,-0.34791,261.83,0.27947,0.94857,-0.1487,192.81,0.37681,0.034086,0.92566,172.11,#7,1,0,0,217.03,0,1,0,216.32,0,0,1,224.26 > undo > select subtract #6 1 model selected > view matrix models #7,1,0,0,367.58,0,1,0,274.78,0,0,1,184.44 > view matrix models #7,1,0,0,383.13,0,1,0,271.66,0,0,1,181.34 > view matrix models #7,1,0,0,368.52,0,1,0,258.24,0,0,1,138.84 > view matrix models #7,1,0,0,373.65,0,1,0,264.87,0,0,1,135.93 Can only have one displayed volume when erasing > view matrix models #7,1,0,0,381.89,0,1,0,263.08,0,0,1,78.051 > view matrix models #7,1,0,0,371.86,0,1,0,265.22,0,0,1,137.93 Can only have one displayed volume when erasing > open ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera > sessions/centerTuSC_110.pdb"" Chain information for centerTuSC_110.pdb #7 --- Chain | Description A B | No description available C | No description available D | No description available E | No description available Q | No description available R | No description available > select add #7 38207 atoms, 38598 bonds, 2397 residues, 1 model selected > cartoon sel > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > cartoon sel > view matrix models #7,1,0,0,-43.187,0,1,0,-19.93,0,0,1,-76.836 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.84847,0.45734,0.26634,-197.81,-0.12109,-0.32214,0.93892,38.957,0.5152,-0.8289,-0.21795,370.39 > hide #!2 models > hide #!1 models > hide #!6 models > view matrix models > #7,-0.78452,-0.08856,-0.61375,634.28,-0.49994,-0.49523,0.7105,250.83,-0.36687,0.86424,0.34425,13.851 > view matrix models > #7,-0.7383,-0.062768,-0.67154,634.05,-0.5342,-0.5534,0.63904,296.17,-0.41174,0.83055,0.37505,24.078 > select subtract #7 Nothing selected > select #7/C:47 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 20 atoms, 19 bonds, 2 residues, 1 model selected > select up 492 atoms, 494 bonds, 30 residues, 1 model selected > color sel lime > select clear > select #7/Q:170 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 259 atoms, 260 bonds, 30 residues, 1 model selected > select add #7/R:203 267 atoms, 267 bonds, 31 residues, 1 model selected > select up 548 atoms, 550 bonds, 64 residues, 1 model selected > color sel lime > select #7/D 12189 atoms, 12307 bonds, 729 residues, 1 model selected > ui tool show ""Color Actions"" > color sel dodger blue > select clear > select #7/E 11160 atoms, 11279 bonds, 674 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light sky blue > select clear > select #7/A 6909 atoms, 6984 bonds, 450 residues, 1 model selected > select #7/B 6909 atoms, 6984 bonds, 450 residues, 1 model selected > select #7/AB Nothing selected > select #7/AB Nothing selected > select #7/A,B 13818 atoms, 13968 bonds, 900 residues, 1 model selected > color sel yellow > ui tool show ""Color Actions"" > color sel pale goldenrod > color sel khaki > color sel gold > color sel khaki > select clear > show #!2 models > select add #7 38207 atoms, 38598 bonds, 2397 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.7383,-0.062768,-0.67154,671.05,-0.5342,-0.5534,0.63904,281.76,-0.41174,0.83055,0.37505,0.68948 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.80414,-0.26184,-0.53366,693.39,-0.54215,-0.045121,0.83907,98.127,-0.24378,0.96406,-0.10567,74.723 > volume #2 level 0.4793 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.80414,-0.26184,-0.53366,682.28,-0.54215,-0.045121,0.83907,101.56,-0.24378,0.96406,-0.10567,79.555 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.68978,-0.25355,-0.67817,695.64,-0.64875,-0.19941,0.73441,199.39,-0.32144,0.94655,-0.026945,79.427 > view matrix models > #7,-0.68372,-0.31618,-0.65769,702.85,-0.56856,-0.33418,0.75171,205.8,-0.45746,0.88789,0.048715,105.42 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.68372,-0.31618,-0.65769,701.16,-0.56856,-0.33418,0.75171,205.13,-0.45746,0.88789,0.048715,102.48 > ui tool show ""Fit in Map"" > fitmap #7 inMap #2 Fit molecule centerTuSC_110.pdb (#7) to map cryosparc_P49_J93_004_volume_map.mrc (#2) using 38207 atoms average map value = 0.5293, steps = 64 shifted from previous position = 3.53 rotated from previous position = 5.17 degrees atoms outside contour = 15375, contour level = 0.47926 Position of centerTuSC_110.pdb (#7) relative to cryosparc_P49_J93_004_volume_map.mrc (#2) coordinates: Matrix rotation and translation -0.72376092 -0.25058743 -0.64294328 691.96452944 -0.57765717 -0.28965214 0.76316042 192.25393123 -0.37746831 0.92374649 0.06488528 63.83963619 Axis 0.35620814 -0.58887019 -0.72549821 Axis point 380.81144853 18.20709652 0.00000000 Rotation angle (degrees) 166.97298544 Shift along axis 86.95524693 > volume #2 level 0.0172 > select clear > show #!6 models > select add #6 2811 atoms, 2866 bonds, 2 pseudobonds, 345 residues, 2 models selected > fitmap #6 inMap #1 Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using 2811 atoms average map value = 0.1432, steps = 96 shifted from previous position = 0.0104 rotated from previous position = 0.0266 degrees atoms outside contour = 1543, contour level = 0.067718 Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.88326448 -0.31429314 -0.34794206 265.25037566 0.27909242 0.94871554 -0.14847978 193.79339019 0.37676422 0.03403892 0.92568357 171.24941094 Axis 0.19126658 -0.75944048 0.62182574 Axis point -270.74685697 0.00000000 847.65443656 Rotation angle (degrees) 28.49823674 Shift along axis 10.04627679 > select clear > save ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera > sessions/cs_P49_J93_J106_kinase_fits.cxs"" > ui mousemode right ""map eraser"" > hide #!1 models > select add #8 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,363.71,0,1,0,217.51,0,0,1,220.3 > view matrix models #8,1,0,0,371.59,0,1,0,205.49,0,0,1,218.22 > volume erase #2 center 371.59,205.49,218.22 radius 40.302 Opened cryosparc_P49_J93_004_volume_map.mrc copy as #9, grid size 256,256,256, pixel 1.73, shown at step 1, values float32 > surface dust #9 size 17.3 > view matrix models #8,1,0,0,370.19,0,1,0,205.79,0,0,1,214.36 > view matrix models #8,1,0,0,392.95,0,1,0,147.21,0,0,1,231.4 > view matrix models #8,1,0,0,373.51,0,1,0,136.99,0,0,1,231.23 > view matrix models #8,1,0,0,359.25,0,1,0,134.43,0,0,1,230.66 > view matrix models #8,1,0,0,372.13,0,1,0,132.68,0,0,1,234.35 > view matrix models #8,1,0,0,373.37,0,1,0,131.75,0,0,1,231.07 > view matrix models #8,1,0,0,374.44,0,1,0,133.85,0,0,1,231.35 > volume erase #9 center 374.44,133.85,231.35 radius 75.29 > view matrix models #8,1,0,0,385.19,0,1,0,280.65,0,0,1,100.54 > view matrix models #8,1,0,0,369.08,0,1,0,289,0,0,1,126.87 > view matrix models #8,1,0,0,386.31,0,1,0,316.5,0,0,1,111.88 > view matrix models #8,1,0,0,325.52,0,1,0,365.28,0,0,1,141.79 > volume erase #9 center 325.52,365.28,141.79 radius 75.29 > view matrix models #8,1,0,0,249.96,0,1,0,319.39,0,0,1,71.606 > view matrix models #8,1,0,0,326.31,0,1,0,225.05,0,0,1,86.547 > view matrix models #8,1,0,0,351.22,0,1,0,206.49,0,0,1,125.15 > view matrix models #8,1,0,0,313.56,0,1,0,162.42,0,0,1,66.373 > view matrix models #8,1,0,0,406.96,0,1,0,194.11,0,0,1,70.874 > view matrix models #8,1,0,0,398.4,0,1,0,240.91,0,0,1,116.42 > volume erase #9 center 398.4,240.91,116.42 radius 75.29 > view matrix models #8,1,0,0,372.27,0,1,0,351.16,0,0,1,35.303 > ui mousemode right ""map eraser"" > select add #8 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #8,1,0,0,306.08,0,1,0,349.2,0,0,1,211.87 > view matrix models #8,1,0,0,295.86,0,1,0,377.11,0,0,1,205.67 > view matrix models #8,1,0,0,297.89,0,1,0,378.44,0,0,1,210.3 > volume erase #2 center 297.89,378.44,210.3 radius 68.757 Opened cryosparc_P49_J93_004_volume_map.mrc copy as #10, grid size 256,256,256, pixel 1.73, shown at step 1, values float32 > surface dust #10 size 17.3 > view matrix models #8,1,0,0,281.35,0,1,0,363.72,0,0,1,178.33 > view matrix models #8,1,0,0,237.54,0,1,0,398.02,0,0,1,193.89 > volume erase #10 center 237.54,398.02,193.89 radius 68.646 > view matrix models #8,1,0,0,249.43,0,1,0,414.16,0,0,1,164.72 > volume erase #10 center 249.43,414.16,164.72 radius 68.646 > view matrix models #8,1,0,0,301.26,0,1,0,358.72,0,0,1,95.652 > view matrix models #8,1,0,0,291.96,0,1,0,269.15,0,0,1,72.692 > volume erase #10 center 291.96,269.15,72.692 radius 68.646 > view matrix models #8,1,0,0,298.7,0,1,0,353.65,0,0,1,100.52 > volume erase #10 center 298.7,353.65,100.52 radius 68.646 > view matrix models #8,1,0,0,209.77,0,1,0,341.8,0,0,1,107.53 > volume erase #10 center 209.77,341.8,107.53 radius 68.646 > view matrix models #8,1,0,0,225.86,0,1,0,274.62,0,0,1,38.108 > volume erase #10 center 225.86,274.62,38.108 radius 68.646 > view matrix models #8,1,0,0,229.32,0,1,0,238.59,0,0,1,27.323 > view matrix models #8,1,0,0,341.4,0,1,0,342.4,0,0,1,118.74 > volume erase #10 center 341.4,342.4,118.74 radius 68.646 > view matrix models #8,1,0,0,389.63,0,1,0,278.17,0,0,1,147.8 > volume erase #10 center 389.63,278.17,147.8 radius 68.646 > view matrix models #8,1,0,0,373.84,0,1,0,165.4,0,0,1,199.95 > volume erase #10 center 373.84,165.4,199.95 radius 68.646 > view matrix models #8,1,0,0,387.14,0,1,0,169.4,0,0,1,242.25 > view matrix models #8,1,0,0,411.91,0,1,0,247.77,0,0,1,280.33 > volume erase #10 center 411.91,247.77,280.33 radius 68.646 > view matrix models #8,1,0,0,364.19,0,1,0,100.95,0,0,1,209.21 > volume erase #10 center 364.19,100.95,209.21 radius 68.646 > view matrix models #8,1,0,0,223.34,0,1,0,50.114,0,0,1,2.1595 > view matrix models #8,1,0,0,253.04,0,1,0,72.112,0,0,1,40.565 > view matrix models #8,1,0,0,232.15,0,1,0,183.15,0,0,1,61.671 > view matrix models #8,1,0,0,235.43,0,1,0,182.39,0,0,1,51.39 > volume erase #10 center 235.43,182.39,51.39 radius 68.646 > view matrix models #8,1,0,0,195.65,0,1,0,232.08,0,0,1,39.419 > view matrix models #8,1,0,0,144.97,0,1,0,223.78,0,0,1,-14.378 > view matrix models #8,1,0,0,74.122,0,1,0,200.05,0,0,1,49.758 > volume erase #10 center 74.122,200.05,49.758 radius 68.646 > view matrix models #8,1,0,0,100.62,0,1,0,204.65,0,0,1,37.983 > view matrix models #8,1,0,0,115.35,0,1,0,214.35,0,0,1,39.987 > volume erase #10 center 115.35,214.35,39.987 radius 68.646 > view matrix models #8,1,0,0,168.54,0,1,0,30.519,0,0,1,84.812 > view matrix models #8,1,0,0,291.9,0,1,0,59.451,0,0,1,123.68 > view matrix models #8,1,0,0,293.43,0,1,0,83.011,0,0,1,92.626 > volume erase #10 center 293.43,83.011,92.626 radius 68.646 > view matrix models #8,1,0,0,374.23,0,1,0,80.14,0,0,1,208.56 > toolshed show Downloading bundle ChimeraX_PhenixUI-1.3.7-py3-none-any.whl Installed ChimeraX-PhenixUI (1.3.7) > ui tool show ""Local EM Fitting"" > save ""/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera > sessions/cs_P49_J93_J106_kinase_fits.cxs"" ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet > volume step 1 Error running startup command 'volume step 1': No volumes specified UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.14.1 OpenGL renderer: AMD Radeon Pro 560 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: iMac Model Identifier: iMac18,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 3.4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 16 GB System Firmware Version: 529.140.2.0.0 OS Loader Version: 577.140.2~22 SMC Version (system): 2.40f1 Software: System Software Overview: System Version: macOS 13.6.9 (22G830) Kernel Version: Darwin 22.6.0 Time since boot: 81 days, 18 hours, 25 minutes Graphics/Displays: Radeon Pro 560: Chipset Model: Radeon Pro 560 Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00c0 ROM Revision: 113-C980AA-921 VBIOS Version: 113-C9810A1X-017 EFI Driver Version: 01.00.921 Metal Support: Metal 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: 4096 x 2304 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) 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-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-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-PhenixUI: 1.3.7 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 closed normal Window Toolkit duplicate all ChimeraX