id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16537 Crash in python_instances_of_class chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.1-arm64-arm-64bit ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 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 0x00000001dd3b5ec0 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 44 in python_instances_of_class File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 176 in _copy_custom_attrs File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 162 in copy File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py"", line 65 in combine_cmd File 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""rollouts"" : [ { ""rolloutId"" : ""64628732bf2f5257dedc8988"", ""factorPackIds"" : { }, ""deploymentId"" : 240000001 }, { ""rolloutId"" : ""632c763c58740028737bfdd2"", ""factorPackIds"" : { ""SIRI_DIALOG_ASSETS"" : ""64a57d23fa6fd41b2353e2ae"" }, ""deploymentId"" : 240000034 } ], ""experiments"" : [ { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Connector/Corndog_34_portal/fold_corndog_34_portal_1_model_0.cif"" format > mmcif Chain information for fold_corndog_34_portal_1_model_0.cif #1 --- Chain | Description A | . > close > close # Expected a models specifier or a keyword > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/Adaptor_43_12mer-coot-1.pdb"" format pdb Chain information for Adaptor_43_12mer-coot-1.pdb #1 --- Chain | Description C | No description available > rainbow > lighting soft > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/cryosparc_P2_J176_014_volume_map_sharp Connector.mrc"" format mrc Opened cryosparc_P2_J176_014_volume_map_sharp Connector.mrc as #2, grid size 512,512,512, pixel 1.06, shown at level 0.281, step 2, values float32 > volume #2 step 1 > volume #2 level 0.3 > surface dust #2 size 10.6 > ui mousemode right ""map eraser"" Already setting window visible! > view #1 clip false > volume erase #2 center 272.63,236.53,233.88 radius 60.29 Opened cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy as #4, grid size 512,512,512, pixel 1.06, shown at step 1, values float32 > surface dust #4 size 10.6 > close #4 > show #!2 models > volume erase #2 center 274.5,216.62,232.18 radius 60.027 Opened cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy as #4, grid size 512,512,512, pixel 1.06, shown at step 1, values float32 > volume erase #4 center 276.41,226.09,232.08 radius 60.027 > volume erase #4 center 276.89,235.64,231.66 radius 60.027 > undo > close #4 > show #!2 models > volume erase #2 center 279.36,223.16,232.56 radius 60.027 Opened cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy as #4, grid size 512,512,512, pixel 1.06, shown at step 1, values float32 > surface dust #4 size 10.6 > hide #3 models > transparency #4.1 50 > ui mousemode right ""translate selected models"" > close #3 > set bgColor white > set bgColor black > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule Adaptor_43_12mer-coot-1.pdb (#1) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 1567 atoms average map value = 0.5955, steps = 40 shifted from previous position = 0.0104 rotated from previous position = 0.0247 degrees atoms outside contour = 647, contour level = 0.3 Position of Adaptor_43_12mer-coot-1.pdb (#1) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates: Matrix rotation and translation 0.99999992 -0.00033049 -0.00020902 0.15752939 0.00033045 0.99999993 -0.00017957 -0.05875495 0.00020908 0.00017950 0.99999996 -0.12340587 Axis 0.41725084 -0.48583640 0.76802651 Axis point 178.64624203 477.25218445 0.00000000 Rotation angle (degrees) 0.02465345 Shift along axis -0.00050441 > fitmap #1 inMap #2 Fit molecule Adaptor_43_12mer-coot-1.pdb (#1) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 1567 atoms average map value = 0.5956, steps = 28 shifted from previous position = 0.0187 rotated from previous position = 0.00688 degrees atoms outside contour = 643, contour level = 0.3 Position of Adaptor_43_12mer-coot-1.pdb (#1) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates: Matrix rotation and translation 0.99999993 -0.00024857 -0.00029318 0.16521746 0.00024852 0.99999996 -0.00015458 -0.04607092 0.00029322 0.00015450 0.99999995 -0.15299874 Axis 0.37303676 -0.70774694 0.59994820 Axis point 526.89971304 0.00000000 560.28495790 Rotation angle (degrees) 0.02373617 Shift along axis 0.00244742 > fitmap #1 inMap #4 Fit molecule Adaptor_43_12mer-coot-1.pdb (#1) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#4) using 1567 atoms average map value = 0.5955, steps = 40 shifted from previous position = 0.021 rotated from previous position = 0.0198 degrees atoms outside contour = 647, contour level = 0.3 Position of Adaptor_43_12mer-coot-1.pdb (#1) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#4) coordinates: Matrix rotation and translation 0.99999999 0.00001674 -0.00015462 0.03313623 -0.00001679 0.99999995 -0.00032672 0.08058353 0.00015461 0.00032672 0.99999993 -0.15762887 Axis 0.90292304 -0.42729761 -0.04633287 Axis point 0.00000000 482.11485866 250.21649370 Rotation angle (degrees) 0.02073214 Shift along axis 0.00278971 > fitmap #1 inMap #4 Fit molecule Adaptor_43_12mer-coot-1.pdb (#1) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#4) using 1567 atoms average map value = 0.5955, steps = 28 shifted from previous position = 0.0212 rotated from previous position = 0.0253 degrees atoms outside contour = 643, contour level = 0.3 Position of Adaptor_43_12mer-coot-1.pdb (#1) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#4) coordinates: Matrix rotation and translation 0.99999985 -0.00028505 -0.00046315 0.21673683 0.00028494 0.99999993 -0.00023018 -0.04011459 0.00046321 0.00023005 0.99999987 -0.22444309 Axis 0.38968716 -0.78435988 0.48262149 Axis point 492.59215065 0.00000000 461.41299305 Rotation angle (degrees) 0.03383415 Shift along axis 0.00760277 > close #1 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/Adaptor_2-coot-1.pdb"" Chain information for Adaptor_2-coot-1.pdb #1 --- Chain | Description C | No description available > fitmap #1 inMap #2 Fit molecule Adaptor_2-coot-1.pdb (#1) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 1567 atoms average map value = 0.6217, steps = 40 shifted from previous position = 0.0457 rotated from previous position = 0.075 degrees atoms outside contour = 614, contour level = 0.3 Position of Adaptor_2-coot-1.pdb (#1) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates: Matrix rotation and translation 0.99999951 -0.00098248 0.00013979 0.30152291 0.00098260 0.99999915 -0.00085292 -0.07189625 -0.00013895 0.00085306 0.99999963 -0.24322525 Axis 0.65184200 0.10650403 0.75083879 Axis point 74.10947823 302.70658502 0.00000000 Rotation angle (degrees) 0.07497650 Shift along axis 0.00626510 > fitmap #1 inMap #2 Fit molecule Adaptor_2-coot-1.pdb (#1) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 1567 atoms average map value = 0.6218, steps = 44 shifted from previous position = 0.00793 rotated from previous position = 0.00907 degrees atoms outside contour = 614, contour level = 0.3 Position of Adaptor_2-coot-1.pdb (#1) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates: Matrix rotation and translation 0.99999948 -0.00102080 0.00006461 0.33301576 0.00102085 0.99999922 -0.00071901 -0.12180944 -0.00006388 0.00071907 0.99999974 -0.22755992 Axis 0.57509686 0.05138190 0.81647015 Axis point 119.54389250 326.47128569 0.00000000 Rotation angle (degrees) 0.07163647 Shift along axis -0.00053837 > close #1 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/Adaptor_2-coot-2.pdb"" Chain information for Adaptor_2-coot-2.pdb #1 --- Chain | Description C | No description available > fitmap #1 inMap #2 Fit molecule Adaptor_2-coot-2.pdb (#1) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 1567 atoms average map value = 0.6578, steps = 40 shifted from previous position = 0.055 rotated from previous position = 0.127 degrees atoms outside contour = 582, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#1) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates: Matrix rotation and translation 0.99999761 0.00173928 -0.00132610 -0.18860977 -0.00173975 0.99999842 -0.00035268 0.59975565 0.00132548 0.00035499 0.99999906 -0.54745669 Axis 0.15970351 -0.59839258 -0.78512490 Axis point 358.67246685 112.68204194 0.00000000 Rotation angle (degrees) 0.12694382 Shift along axis 0.04081090 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/Adaptor_43_12mer.pdb"" Chain information for Adaptor_43_12mer.pdb #3 --- Chain | Description A B C D E F G H I J K L | No description available > hide atoms > show cartoons > ui tool show Matchmaker > matchmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Adaptor_2-coot-2.pdb, chain C (#1) with Adaptor_43_12mer.pdb, chain A (#3), sequence alignment score = 726 RMSD between 72 pruned atom pairs is 1.441 angstroms; (across all 201 pairs: 4.565) > fitmap #3 inMap #2 Fit molecule Adaptor_43_12mer.pdb (#3) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 18804 atoms average map value = 0.2915, steps = 92 shifted from previous position = 3.91 rotated from previous position = 5.09 degrees atoms outside contour = 12050, contour level = 0.3 Position of Adaptor_43_12mer.pdb (#3) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates: Matrix rotation and translation 0.49992944 -0.86597188 0.01277702 367.74881585 0.86585474 0.50007896 0.01471764 -103.56155269 -0.01913458 0.00370526 0.99981005 4.27642792 Axis -0.00635761 0.01842306 0.99981007 Axis point 273.58159553 266.68175583 0.00000000 Rotation angle (degrees) 60.00600542 Shift along axis 0.02969137 > fitmap #3 inMap #2 Fit molecule Adaptor_43_12mer.pdb (#3) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 18804 atoms average map value = 0.2915, steps = 28 shifted from previous position = 0.012 rotated from previous position = 0.00736 degrees atoms outside contour = 12052, contour level = 0.3 Position of Adaptor_43_12mer.pdb (#3) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates: Matrix rotation and translation 0.50001522 -0.86592204 0.01279857 367.71065865 0.86580648 0.50016484 0.01463780 -103.55550122 -0.01907658 0.00376196 0.99981095 4.25608290 Axis -0.00627915 0.01840307 0.99981093 Axis point 273.56745779 266.68838155 0.00000000 Rotation angle (degrees) 60.00029757 Shift along axis 0.04062990 > fitmap #3 inMap #2 Fit molecule Adaptor_43_12mer.pdb (#3) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) using 18804 atoms average map value = 0.2916, steps = 44 shifted from previous position = 0.00871 rotated from previous position = 0.0182 degrees atoms outside contour = 12041, contour level = 0.3 Position of Adaptor_43_12mer.pdb (#3) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#2) coordinates: Matrix rotation and translation 0.49979023 -0.86605447 0.01262479 367.85635166 0.86593726 0.49993678 0.01469291 -103.54394916 -0.01903646 0.00358890 0.99981235 4.29548029 Axis -0.00640992 0.01827683 0.99981242 Axis point 273.60362640 266.72390586 0.00000000 Rotation angle (degrees) 60.01523661 Shift along axis 0.04429002 > close #3 > combine #1 > rename #1 id #6 > rename #2 id #1 > rename #4 id #2 > 6 Unknown command: 6 > combine #6 > rename #3 id #15 > rename #6 id #3 > rename #15 id #6 > turn z 30 models #4-14 > undo > turn z 30 models #4-14 > turn z 30 models #5-14 > turn z 30 models #6-14 > turn z 30 models #7-14 > turn z 30 models #8-14 > turn z 30 models #9-14 > turn z 30 models #10-14 > turn z 30 models #11-14 > turn z 30 models #12-14 > turn z 30 models #13-14 > turn z 30 models #14 > combine #3-14 Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #4 to 'D' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #5 to 'E' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #6 to 'F' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #7 to 'G' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #8 to 'H' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #9 to 'I' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #10 to 'J' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #11 to 'K' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #12 to 'L' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #13 to 'M' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #14 to 'N' > fitmap #15 inMap #1 Fit molecule combination (#15) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 18804 atoms average map value = 0.2283, steps = 104 shifted from previous position = 0.897 rotated from previous position = 2.27 degrees atoms outside contour = 13280, contour level = 0.3 Position of combination (#15) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates: Matrix rotation and translation 0.99942096 -0.02826281 0.01894608 4.24802800 0.02856999 0.99946142 -0.01614373 -4.52134455 -0.01847961 0.01667567 0.99969016 0.24582676 Axis 0.43440789 0.49537815 0.75225679 Axis point 157.45622219 150.29827764 0.00000000 Rotation angle (degrees) 2.16485567 Shift along axis -0.20947355 > close #4-15 > combine #3 > view orient > turn x 90 > turn y 30 models #4-14 > turn y 30 models #5-14 > turn y 30 models #6-14 > turn y 30 models #7-14 > turn y 30 models #8-14 > turn y 30 models #9-14 > turn y 30 models #10-14 > turn y 30 models #11-14 > turn y 30 models #12-14 > turn y 30 models #13-14 > turn y 30 models #14 > combine #3-14 Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #4 to 'D' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #5 to 'E' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #6 to 'F' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #7 to 'G' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #8 to 'H' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #9 to 'I' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #10 to 'J' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #11 to 'K' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #12 to 'L' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #13 to 'M' Remapping chain ID 'C' in copy of Adaptor_2-coot-2.pdb #14 to 'N' > fitmap #15 inMap #1 Fit molecule combination (#15) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 18804 atoms average map value = 0.4918, steps = 80 shifted from previous position = 3.29 rotated from previous position = 4.12 degrees atoms outside contour = 9084, contour level = 0.3 Position of combination (#15) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates: Matrix rotation and translation 0.99999628 -0.00000665 -0.00272739 0.63908524 -0.00019030 0.99738981 -0.07220479 18.50702535 0.00272075 0.07220504 0.99738610 -23.02952725 Axis 0.99928829 -0.03770014 -0.00127083 Axis point 0.00000000 327.79605354 244.44764766 Rotation angle (degrees) 4.14359431 Shift along axis -0.02982039 > close #4-14 > select add #15 18804 atoms, 19188 bonds, 2412 residues, 1 model selected > save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/Adaptor_43_12mer_1.pdb"" models #15 selectedOnly true relModel #1 > select subtract #15 Nothing selected > hide #15 models > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/Adaptor_43_12mer_1.pdb"" Chain information for Adaptor_43_12mer_1.pdb #4 --- Chain | Description C D E F G H I J K L M N | No description available > close #4 > ui tool show ""Volume Viewer"" > volume #2 level 0.4 > hide #!2 models > ui mousemode right ""translate selected atoms"" > select #3/C:124 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 58 atoms, 58 bonds, 7 residues, 1 model selected > select up 1567 atoms, 1599 bonds, 201 residues, 1 model selected > select down 58 atoms, 58 bonds, 7 residues, 1 model selected > select #3/C:36 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #3/C:124 18 atoms, 16 bonds, 2 residues, 1 model selected > select up 198 atoms, 198 bonds, 25 residues, 1 model selected > select add #3/C:50 206 atoms, 205 bonds, 26 residues, 1 model selected > select add #3/C:51 213 atoms, 211 bonds, 27 residues, 1 model selected > select add #3/C:52 221 atoms, 218 bonds, 28 residues, 1 model selected > select add #3/C:53 228 atoms, 224 bonds, 29 residues, 1 model selected > select subtract #3/C:53 221 atoms, 218 bonds, 28 residues, 1 model selected > select add #3/C:54 229 atoms, 225 bonds, 29 residues, 1 model selected > select add #3/C:53 236 atoms, 231 bonds, 30 residues, 1 model selected > show #!2 models > hide #!2 models Drag select of 15 residues > select add #3/C:124 133 atoms, 6 bonds, 16 residues, 1 model selected > select add #3/C:125 143 atoms, 16 bonds, 17 residues, 1 model selected > show #!2 models > undo > show #!2 models > select add #3 1567 atoms, 1599 bonds, 201 residues, 1 model selected > select subtract #3 Nothing selected > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 1567 atoms average map value = 0.6571, steps = 44 shifted from previous position = 0.0337 rotated from previous position = 0.0451 degrees atoms outside contour = 579, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates: Matrix rotation and translation 0.99999881 0.00099716 -0.00117907 -0.00451165 -0.00099783 0.99999934 -0.00056808 0.43091602 0.00117850 0.00056926 0.99999914 -0.53651150 Axis 0.34557567 -0.71633837 -0.60616565 Axis point 447.53964939 0.00000000 -8.66775769 Rotation angle (degrees) 0.09428448 Shift along axis 0.01497404 > hide #3 models > show #15 models > hide #15 models > show #3 models > volume #2 level 0.3 > volume #2 level 0.2 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/Adaptor_43_12mer_1.pdb"" Chain information for Adaptor_43_12mer_1.pdb #4 --- Chain | Description C D E F G H I J K L M N | No description available > surface dust #2 size 10.6 > hide #!2 models > show #!1 models > fitmap #4 inMap #1 Fit molecule Adaptor_43_12mer_1.pdb (#4) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 18804 atoms average map value = 0.4918, steps = 44 shifted from previous position = 0.00145 rotated from previous position = 0.00179 degrees atoms outside contour = 9078, contour level = 0.3 Position of Adaptor_43_12mer_1.pdb (#4) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 -0.00002927 -0.00000893 0.01078239 0.00002927 1.00000000 -0.00000594 -0.00654465 0.00000893 0.00000594 1.00000000 -0.00279115 Axis 0.19048351 -0.28657387 0.93893102 Axis point 210.78197138 359.84566614 0.00000000 Rotation angle (degrees) 0.00178618 Shift along axis 0.00130870 > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 1567 atoms average map value = 0.6571, steps = 40 shifted from previous position = 0.0136 rotated from previous position = 0.0284 degrees atoms outside contour = 582, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates: Matrix rotation and translation 0.99999899 0.00120479 -0.00075772 -0.16889046 -0.00120534 0.99999901 -0.00072836 0.53821529 0.00075684 0.00072928 0.99999945 -0.44949892 Axis 0.45579559 -0.47359205 -0.75363184 Axis point 449.11248303 143.16421170 -0.00000000 Rotation angle (degrees) 0.09161645 Shift along axis 0.00688269 > close #4 > show #!2 models > hide #!1 models > surface dust #2 size 10.6 > volume #2 level 0.3 > hide #3 models > show #3 models > hide #3 models > ui tool show ""Color Zone"" > show #3 models > volume zone #2 nearAtoms #3 range 6.37 > ui tool show ""Volume Viewer"" > fitmap #3 inMap #2 Fit molecule Adaptor_2-coot-2.pdb (#3) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#2) using 1567 atoms average map value = 0.657, steps = 40 shifted from previous position = 0.00469 rotated from previous position = 0.0147 degrees atoms outside contour = 580, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc copy (#2) coordinates: Matrix rotation and translation 0.99999884 0.00127969 -0.00082816 -0.17761096 -0.00128049 0.99999872 -0.00096330 0.61908370 0.00082692 0.00096436 0.99999919 -0.54443324 Axis 0.53443905 -0.45886642 -0.70980033 Axis point 485.99931216 142.34080285 0.00000000 Rotation angle (degrees) 0.10332988 Shift along axis 0.00743994 > surface dust #2 size 10.6 > volume zone #2 nearAtoms #3 range 6.37 > hide #3 models > show #3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #3/C Alignment identifier is 3/C > select add #3/C:29 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/C:22 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/C:22-41 158 atoms, 160 bonds, 20 residues, 1 model selected > hide #3 models > show #3 models > select #3/C:20 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/C:20-22 20 atoms, 19 bonds, 3 residues, 1 model selected > select #3/C:23 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/C:23-24 16 atoms, 15 bonds, 2 residues, 1 model selected > select #3/C:22 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/C:22 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/C:23 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/C:23-24 16 atoms, 15 bonds, 2 residues, 1 model selected > select #3/C:24 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/C:24 7 atoms, 6 bonds, 1 residue, 1 model selected > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 1567 atoms average map value = 0.5971, steps = 40 shifted from previous position = 0.0457 rotated from previous position = 0.187 degrees atoms outside contour = 642, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates: Matrix rotation and translation 0.99999873 -0.00144948 0.00066657 0.31259248 0.00144945 0.99999895 0.00004585 -0.46826383 -0.00066664 -0.00004489 0.99999978 0.22477488 Axis -0.02842665 0.41765944 0.90815886 Axis point 323.12392904 215.36783362 0.00000000 Rotation angle (degrees) 0.09144699 Shift along axis -0.00032946 > select #3/C:23 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/C:23 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/C:24 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/C:24 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/C:25-26 18 atoms, 17 bonds, 2 residues, 1 model selected > select #3/C:25-26 18 atoms, 17 bonds, 2 residues, 1 model selected > select #3/C:25 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/C:25 9 atoms, 8 bonds, 1 residue, 1 model selected > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 1567 atoms average map value = 0.597, steps = 44 shifted from previous position = 0.00485 rotated from previous position = 0.046 degrees atoms outside contour = 644, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates: Matrix rotation and translation 0.99999747 -0.00195521 0.00111388 0.36205722 0.00195564 0.99999801 -0.00038824 -0.51847459 -0.00111312 0.00039041 0.99999930 0.22785124 Axis 0.17048196 0.48759232 0.85626493 Axis point 266.30709557 184.48011974 0.00000000 Rotation angle (degrees) 0.13084482 Shift along axis 0.00402102 > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) using 1567 atoms average map value = 0.597, steps = 40 shifted from previous position = 0.0163 rotated from previous position = 0.0273 degrees atoms outside contour = 644, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to cryosparc_P2_J176_014_volume_map_sharp Connector.mrc (#1) coordinates: Matrix rotation and translation 0.99999741 -0.00174590 0.00145701 0.20811390 0.00174684 0.99999827 -0.00064418 -0.38482860 -0.00145588 0.00064673 0.99999873 0.25808610 Axis 0.27305586 0.61614105 0.73879003 Axis point 224.08093269 117.24487028 0.00000000 Rotation angle (degrees) 0.13543717 Shift along axis 0.01038947 > select #3/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/C:26-27 17 atoms, 16 bonds, 2 residues, 1 model selected > select #3/C:28 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/C:28 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/C:27 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/C:27-28 16 atoms, 15 bonds, 2 residues, 1 model selected > select #3/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/C:26-27 17 atoms, 16 bonds, 2 residues, 1 model selected > undo > redo > undo > redo > undo > close #3 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/Adaptor_2-coot-2.pdb"" Chain information for Adaptor_2-coot-2.pdb #3 --- Chain | Description C | No description available > color #3 #e1984eff > hide #3 models > show #3 models > hide #!2 models > select add #3/C:21 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #3/C:22 12 atoms, 10 bonds, 2 residues, 1 model selected > save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/123.pdb"" models #3 selectedOnly true relModel #1 > select add #3 1567 atoms, 1599 bonds, 201 residues, 1 model selected > select subtract #3 Nothing selected > show #!2 models > hide #3 models > show #3 models > hide #!2 models > rainbow #3 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #3 models > show #3 models > hide #!2 models > show #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #3/C Alignment identifier is 3/C > close #15 > volume #!2 style mesh > volume #!2 style surface > volume #!2 style mesh > color #2 #b2b2b2b3 models > color #2 #b2b2b2ff models > volume #!2 style surface > color #2 #b2b2b280 models > color #2 #b2b2b24d models > open /Users/melvinshen/Downloads/00-Portal-12mers-Adaptor-12mers.pdb Chain information for 00-Portal-12mers-Adaptor-12mers.pdb #4 --- Chain | Description A B C D E F G H I J K L | No description available M N O P Q R S T U V W X | No description available > close #1-2 > hide atoms > show cartoons > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/P2_J332_011_C12_volume_map_sharp.mrc"" Opened P2_J332_011_C12_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.06, shown at level 0.285, step 2, values float32 > volume #1 step 1 > volume #1 level 0.3 > surface dust #1 size 10.6 > hide #3 models > hide #4 models > close #4 > show #3 models > color #3 #bcbf184d > transparency 50 > select add #3 1567 atoms, 1599 bonds, 201 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,-18.95,0,1,0,-13.091,0,0,1,70.632 > view matrix models #3,1,0,0,-11.871,0,1,0,-9.273,0,0,1,71.453 > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms average map value = 0.2166, steps = 80 shifted from previous position = 1.55 rotated from previous position = 4.52 degrees atoms outside contour = 1121, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99760716 -0.00575805 -0.06889699 5.97424029 0.00837524 0.99925179 0.03775856 -19.50381451 0.06862803 -0.03824524 0.99690897 62.58862401 Axis -0.48175651 -0.87171393 0.08958507 Axis point -874.75432638 0.00000000 255.05820010 Rotation angle (degrees) 4.52430396 Shift along axis 19.73062421 > view matrix models > #3,0.99761,-0.0057581,-0.068897,12.266,0.0083752,0.99925,0.037759,-13.4,0.068628,-0.038245,0.99691,59.807 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.87578,0.10978,-0.47006,105.94,-0.23544,0.94726,-0.21742,133.43,0.42139,0.30109,0.85544,-114.74 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.87578,0.10978,-0.47006,112.58,-0.23544,0.94726,-0.21742,136.98,0.42139,0.30109,0.85544,-110.78 > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms average map value = 0.242, steps = 104 shifted from previous position = 1.84 rotated from previous position = 4.5 degrees atoms outside contour = 1103, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.86674560 0.12284752 -0.48338448 115.70681546 -0.21724618 0.96540840 -0.14418985 109.54084581 0.44895008 0.22998935 0.86345164 -98.05323479 Axis 0.35279184 -0.87904411 -0.32065459 Axis point 289.43839471 0.00000000 177.11640020 Rotation angle (degrees) 32.02651011 Shift along axis -24.02959503 > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms average map value = 0.2419, steps = 48 shifted from previous position = 0.0173 rotated from previous position = 0.0212 degrees atoms outside contour = 1102, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.86663964 0.12260116 -0.48363695 115.85755879 -0.21711022 0.96542073 -0.14431201 109.52546092 0.44922031 0.23006903 0.86328984 -98.11157730 Axis 0.35284633 -0.87919853 -0.32017091 Axis point 289.45347606 0.00000000 177.25080832 Rotation angle (degrees) 32.04030564 Shift along axis -24.00223726 > view matrix models > #3,0.86664,0.1226,-0.48364,118.63,-0.21711,0.96542,-0.14431,109.52,0.44922,0.23007,0.86329,-101.58 > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms average map value = 0.2405, steps = 76 shifted from previous position = 2.81 rotated from previous position = 2.25 degrees atoms outside contour = 1080, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.85444584 0.09816424 -0.51018240 133.79208191 -0.20709205 0.96495486 -0.16116762 112.26995028 0.47648210 0.24336372 0.84483070 -110.15790860 Axis 0.36470413 -0.88952471 -0.27520298 Axis point 305.06812248 0.00000000 190.04606926 Rotation angle (degrees) 33.68331092 Shift along axis -20.75658552 > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms average map value = 0.2408, steps = 44 shifted from previous position = 0.0208 rotated from previous position = 0.0174 degrees atoms outside contour = 1081, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.85452828 0.09825733 -0.51002639 133.70788669 -0.20702362 0.96500590 -0.16094978 112.19049997 0.47636398 0.24312365 0.84496642 -110.09999940 Axis 0.36442404 -0.88960159 -0.27532550 Axis point 304.96722692 0.00000000 190.01192680 Rotation angle (degrees) 33.66940294 Shift along axis -20.76514188 > select subtract #3 Nothing selected > hide #3 models > hide #!1 models > show #!1 models > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/00-Portal-12mers-Adaptor-12mers.pdb"" Chain information for 00-Portal-12mers-Adaptor-12mers.pdb #2 --- Chain | Description A B C D E F G H I J K L | No description available M N O P Q R S T U V W X | No description available > hide #2 atoms > show #2 cartoons > fitmap #2 inMap #1 Fit molecule 00-Portal-12mers-Adaptor-12mers.pdb (#2) to map P2_J332_011_C12_volume_map_sharp.mrc (#1) using 49956 atoms average map value = 1.039, steps = 28 shifted from previous position = 0.00906 rotated from previous position = 0.00469 degrees atoms outside contour = 4456, contour level = 0.3 Position of 00-Portal-12mers-Adaptor-12mers.pdb (#2) relative to P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 0.00003549 -0.00006197 0.00701912 -0.00003548 1.00000000 0.00004018 0.00781922 0.00006197 -0.00004018 1.00000000 -0.00498758 Axis -0.49039345 -0.75627130 -0.43309119 Axis point 130.78051680 0.00000000 56.32430662 Rotation angle (degrees) 0.00469460 Shift along axis -0.00719551 > ui tool show Matchmaker > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 00-Portal-12mers-Adaptor-12mers.pdb, chain M (#2) with Adaptor_2-coot-2.pdb, chain C (#3), sequence alignment score = 775.9 RMSD between 60 pruned atom pairs is 1.400 angstroms; (across all 200 pairs: 5.942) > hide #2 models > show #3 models > hide #!1 models > show #2 models > color #3 #c8c7494d > color #3 #c8c749ff > show #!1 models > hide #3 models > hide #2 models > show #3 models > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms average map value = 0.3518, steps = 80 shifted from previous position = 0.612 rotated from previous position = 3.16 degrees atoms outside contour = 909, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.83332690 0.53356068 0.14449666 324.59128234 0.53760965 0.84309777 -0.01272857 -100.20625812 -0.12861628 0.06707574 -0.98942342 558.74796488 Axis 0.28044566 0.95976444 0.01422876 Axis point 197.74833283 0.00000000 268.05474333 Rotation angle (degrees) 171.82012698 Shift along axis 2.80610688 > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms average map value = 0.3518, steps = 60 shifted from previous position = 0.000463 rotated from previous position = 0.00808 degrees atoms outside contour = 909, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.83335245 0.53350123 0.14456876 324.60043449 0.53754247 0.84313921 -0.01282068 -100.17742127 -0.12873144 0.06702771 -0.98941170 558.79379278 Axis 0.28041137 0.95977500 0.01419201 Axis point 197.76241472 0.00000000 268.06706478 Rotation angle (degrees) 171.81457045 Shift along axis 2.80427569 > fitmap #3 inMap #1 Fit molecule Adaptor_2-coot-2.pdb (#3) to map P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms average map value = 0.3519, steps = 80 shifted from previous position = 0.00255 rotated from previous position = 0.00247 degrees atoms outside contour = 909, contour level = 0.3 Position of Adaptor_2-coot-2.pdb (#3) relative to P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.83334836 0.53350474 0.14457944 324.59388486 0.53754133 0.84313930 -0.01286233 -100.16808263 -0.12876272 0.06699862 -0.98940960 558.81313734 Axis 0.28041244 0.95977496 0.01417352 Axis point 197.76178843 0.00000000 268.07404732 Rotation angle (degrees) 171.81330513 Shift along axis 2.80169296 > select add #3 1567 atoms, 1599 bonds, 201 residues, 1 model selected > save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/Adaptor_2-coot-3.pdb"" models #3 selectedOnly true relModel #1 > select subtract #3 Nothing selected > hide #3 models > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/Adaptor_2-coot-3.pdb"" Chain information for Adaptor_2-coot-3.pdb #4 --- Chain | Description C | No description available > close #4 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Connector/Fitted > Models/Adaptor_2-coot-4.pdb"" Chain information for Adaptor_2-coot-4.pdb #4 --- Chain | Description C | No description available > fitmap #4 inMap #1 Fit molecule Adaptor_2-coot-4.pdb (#4) to map P2_J332_011_C12_volume_map_sharp.mrc (#1) using 1567 atoms average map value = 0.8939, steps = 60 shifted from previous position = 0.0283 rotated from previous position = 0.0647 degrees atoms outside contour = 366, contour level = 0.3 Position of Adaptor_2-coot-4.pdb (#4) relative to P2_J332_011_C12_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999952 0.00097204 0.00012724 -0.36581334 -0.00097211 0.99999937 0.00056184 0.08623047 -0.00012669 -0.00056196 0.99999983 0.22814539 Axis -0.49728066 0.11236319 -0.86028278 Axis point 88.99826283 378.76771246 0.00000000 Rotation angle (degrees) 0.06474138 Shift along axis -0.00466852 > combine #4 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16U0000PTA/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.41.12 OS Loader Version: 10151.41.12 Software: System Software Overview: System Version: macOS 14.1 (23B74) Kernel Version: Darwin 23.1.0 Time since boot: 20 hours, 46 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina 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: 2.14.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.1.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.16 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.5 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.56 ChimeraX-AtomicLibrary: 14.0.2 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 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: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8.dev202403220040 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 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: 1.1.9 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 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: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.3 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: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.3 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: 1.0 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: 1.16.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2 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: 1.37.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.9 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.1 fonttools: 4.50.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.10.0 html2text: 2024.2.26 idna: 3.6 ihm: 0.43 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.1.0 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.3 matplotlib-inline: 0.1.6 MolecularDynamicsViewer: 1.6 msgpack: 1.0.8 ndindex: 1.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.9.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.3 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.2.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.0 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3302 pyparsing: 3.1.2 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.12.0 setuptools: 69.2.0 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: 2.0.0 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: 0.6.1 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.1 typing-extensions: 4.10.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX