id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7144 Crash in garbage collection after tool destruction chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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All rights reserved. How to cite UCSF ChimeraX > open > ""/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Core > Phosphatase module > AlphaFold/prediction_Corepho_noDis2_4e8f1/rank_1_model_5_ptm_seed_0_unrelaxed.pdb"" Chain information for rank_1_model_5_ptm_seed_0_unrelaxed.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > open > /Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/cryosparc_P8_J39__localfilter.mrc > format mrc Opened cryosparc_P8_J39__localfilter.mrc as #2, grid size 128,128,128, pixel 1.96, shown at level 0.694, step 1, values float32 > select #1 7606 atoms, 7772 bonds, 951 residues, 1 model selected > ui tool show ""Color Actions"" > color sel bychain > set bgColor white > lighting flat > transparency 50 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.37758,0.46543,-0.8005,4.119,-0.85721,0.15123,0.49225,11.277,0.35017,0.87207,0.34188,-8.6283 > view matrix models > #1,-0.82232,0.56199,0.089191,31.29,0.40101,0.68356,-0.60987,-22.91,-0.40371,-0.46574,-0.78747,-42.133 > view matrix models > #1,-0.72483,0.58723,0.36024,36.672,0.6423,0.76512,0.045122,-9.7184,-0.24913,0.26409,-0.93177,-38.278 > view matrix models > #1,0.082465,-0.25804,0.96261,30.218,0.64483,-0.72265,-0.24896,-35.035,0.75987,0.64125,0.1068,-21.927 > view matrix models > #1,-0.020652,0.99118,-0.13087,21.759,0.99862,0.014117,-0.050661,-25.616,-0.048367,-0.13174,-0.9901,-46.997 > view matrix models > #1,-0.42256,0.73376,-0.53202,14.203,0.70843,0.63353,0.31107,-6.0212,0.5653,-0.24545,-0.78752,-51.224 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.42256,0.73376,-0.53202,124.38,0.70843,0.63353,0.31107,110.22,0.5653,-0.24545,-0.78752,137.16 > view matrix models > #1,-0.42256,0.73376,-0.53202,129.29,0.70843,0.63353,0.31107,130.9,0.5653,-0.24545,-0.78752,115.59 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.50313,0.75493,-0.42065,133.1,0.39525,0.63387,0.66482,142.89,0.76853,0.16823,-0.6173,122.18 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.50313,0.75493,-0.42065,128.94,0.39525,0.63387,0.66482,128.05,0.76853,0.16823,-0.6173,125.04 > ui tool show ""Fit in Map"" Fit molecule rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) to map cryosparc_P8_J39__localfilter.mrc (#2) using 7606 atoms average map value = 0.7995, steps = 168 shifted from previous position = 4.91 rotated from previous position = 35.5 degrees atoms outside contour = 2942, contour level = 0.69429 Position of rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) relative to cryosparc_P8_J39__localfilter.mrc (#2) coordinates: Matrix rotation and translation -0.45678741 0.31007802 -0.83378468 122.16260201 0.11907689 0.95016139 0.28812156 127.79428353 0.88157017 0.03232581 -0.47094488 120.83486993 Axis -0.14660394 -0.98311951 -0.10946828 Axis point 20.65596258 0.00000000 82.86017704 Rotation angle (degrees) 119.26078393 Shift along axis -156.77415828 > ~select #1 Nothing selected > ui tool show XMAS Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1).csv Unique peptide pairs: 199 out of 199 Unique peptide pairs with pseudobonds: 29 Pseudobonds are stored in /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1)_1.pb Mapping information is stored in /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1)_1.tsv Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/reports 2/uniprot-Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides.csv Unique peptide pairs: 82 out of 82 Unique peptide pairs with pseudobonds: 23 Pseudobonds are stored in /Users/alexau/Downloads/reports 2/uniprot- Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides_1.pb Mapping information is stored in /Users/alexau/Downloads/reports 2/uniprot- Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides_1.tsv > hide #!2 models > open > ""/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Core > Phosphatase module > AlphaFold/prediction_Corepho_noDis2_4e8f1/rank_2_model_4_ptm_seed_0_unrelaxed.pdb"" Chain information for rank_2_model_4_ptm_seed_0_unrelaxed.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > open > ""/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Core > Phosphatase module > AlphaFold/prediction_Corepho_noDis2_4e8f1/rank_3_model_1_ptm_seed_0_unrelaxed.pdb"" Chain information for rank_3_model_1_ptm_seed_0_unrelaxed.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > select #5 7606 atoms, 7772 bonds, 951 residues, 1 model selected > view matrix models #5,1,0,0,71.167,0,1,0,47.419,0,0,1,45.429 > view matrix models #5,1,0,0,70.208,0,1,0,41.442,0,0,1,41.021 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.44006,0.89781,-0.016977,42.505,-0.08176,-0.021232,0.99643,34.153,0.89424,0.43987,0.082748,63.541 > view matrix models > #5,-0.34896,-0.16145,0.92312,38.86,0.87933,0.28421,0.38211,55.73,-0.32405,0.94507,0.042791,40.856 > select #6 7606 atoms, 7772 bonds, 951 residues, 1 model selected > view matrix models > #6,0.37493,-0.54152,-0.75245,-1.0825,-0.50119,0.56441,-0.65593,-1.2934,0.77989,0.62305,-0.059795,-14.815 > view matrix models > #6,-0.60334,-0.19311,-0.77375,0.029629,0.79748,-0.14163,-0.58649,-1.0629,0.0036656,-0.9709,0.23945,-0.82265 > view matrix models > #6,0.51444,0.024965,-0.85716,-5.5897,0.74871,-0.5004,0.43478,9.5256,-0.41806,-0.86544,-0.27612,-4.2627 > show #!2 models > select #2 2 models selected > view matrix models > #2,0.99775,0.054774,0.038582,-11.466,-0.054425,0.99847,-0.010043,8.2415,-0.039073,0.0079208,0.9992,3.9746 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.99775,0.054774,0.038582,-171.73,-0.054425,0.99847,-0.010043,-75.754,-0.039073,0.0079208,0.9992,-82.121 > view matrix models > #2,0.99775,0.054774,0.038582,-148.26,-0.054425,0.99847,-0.010043,-81.649,-0.039073,0.0079208,0.9992,-82.453 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.62928,-0.22646,0.74346,-159.83,0.51183,0.84062,-0.17717,-110.71,-0.58484,0.49201,0.64489,-28.09 > view matrix models > #2,0.76388,-0.082181,0.64011,-180.77,-0.10647,0.96222,0.25059,-104.68,-0.63652,-0.25957,0.72627,59.955 > view matrix models > #2,0.15848,-0.89213,0.42306,21.921,0.79621,0.36886,0.47958,-173.56,-0.5839,0.26084,0.76878,-15.965 > view matrix models > #2,0.30176,-0.90058,0.31287,19.542,0.78959,0.41999,0.44738,-174.82,-0.53431,0.11204,0.83783,-12.84 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.30176,-0.90058,0.31287,58.072,0.78959,0.41999,0.44738,-166.69,-0.53431,0.11204,0.83783,20.73 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.36653,-0.82692,0.42645,117.08,0.83752,-0.093608,0.53833,-121.44,-0.40524,0.55447,0.72687,-35.119 > view matrix models > #2,-0.12308,-0.6628,0.73861,26.13,0.98558,0.0054789,0.16915,-103.9,-0.11616,0.74878,0.65256,-85.124 > view matrix models > #2,0.32552,-0.6707,0.66648,-19.115,0.83717,0.5321,0.12658,-144.59,-0.43953,0.51676,0.7347,-27.259 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.32552,-0.6707,0.66648,-11.332,0.83717,0.5321,0.12658,-151.28,-0.43953,0.51676,0.7347,-27.116 > view matrix models > #2,0.32552,-0.6707,0.66648,-9.4136,0.83717,0.5321,0.12658,-137.85,-0.43953,0.51676,0.7347,-51.884 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.089513,-0.31791,0.94389,-37.373,0.78269,0.56362,0.26406,-152.87,-0.61594,0.76241,0.19838,9.6486 > view matrix models > #2,0.41365,-0.76093,0.49987,12.423,0.84267,0.52786,0.10621,-135.36,-0.34468,0.37729,0.85956,-62.78 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.41365,-0.76093,0.49987,24.148,0.84267,0.52786,0.10621,-130.34,-0.34468,0.37729,0.85956,-68.072 Fit molecule rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#5) to map cryosparc_P8_J39__localfilter.mrc (#2) using 7606 atoms average map value = 0.8322, steps = 100 shifted from previous position = 1.89 rotated from previous position = 15.5 degrees atoms outside contour = 2748, contour level = 0.69429 Position of rank_2_model_4_ptm_seed_0_unrelaxed.pdb (#5) relative to cryosparc_P8_J39__localfilter.mrc (#2) coordinates: Matrix rotation and translation 0.82201767 -0.20147306 0.53263080 125.63556203 0.46769559 0.77246050 -0.42961100 126.13520323 -0.32488121 0.60225691 0.72920424 119.56900014 Axis 0.68823856 0.57194611 0.44632425 Axis point 0.00000000 -29.33241355 26.93239860 Rotation angle (degrees) 48.55955516 Shift along axis 211.97632088 Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1).csv Unique peptide pairs: 199 out of 199 Unique peptide pairs with pseudobonds: 29 Pseudobonds are stored in /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1)_5.pb Mapping information is stored in /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1)_5.tsv Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/reports 2/uniprot-Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides.csv Unique peptide pairs: 82 out of 82 Unique peptide pairs with pseudobonds: 23 Pseudobonds are stored in /Users/alexau/Downloads/reports 2/uniprot- Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides_5.pb Mapping information is stored in /Users/alexau/Downloads/reports 2/uniprot- Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides_5.tsv > close #5 > close #8 > close #3 > ~select #7 2 models selected > select #7 Nothing selected > close #7 > close #4 > select #6 7606 atoms, 7772 bonds, 951 residues, 1 model selected > ui tool show ""Color Actions"" > color sel bychain > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #6,0.51444,0.024965,-0.85716,26.579,0.74871,-0.5004,0.43478,19.42,-0.41806,-0.86544,-0.27612,43.459 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.87076,-0.089912,-0.48342,29.121,0.13913,-0.89791,0.41762,23.533,-0.47161,-0.43091,-0.76935,37.133 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.87076,-0.089912,-0.48342,31.095,0.13913,-0.89791,0.41762,27.975,-0.47161,-0.43091,-0.76935,50.135 > view matrix models > #6,0.87076,-0.089912,-0.48342,31.608,0.13913,-0.89791,0.41762,45.423,-0.47161,-0.43091,-0.76935,30.883 > view matrix models > #6,0.87076,-0.089912,-0.48342,34.829,0.13913,-0.89791,0.41762,48.51,-0.47161,-0.43091,-0.76935,40.021 Fit molecule rank_3_model_1_ptm_seed_0_unrelaxed.pdb (#6) to map cryosparc_P8_J39__localfilter.mrc (#2) using 7606 atoms average map value = 0.8079, steps = 84 shifted from previous position = 6.24 rotated from previous position = 9.83 degrees atoms outside contour = 2895, contour level = 0.69429 Position of rank_3_model_1_ptm_seed_0_unrelaxed.pdb (#6) relative to cryosparc_P8_J39__localfilter.mrc (#2) coordinates: Matrix rotation and translation 0.73818032 -0.51605516 0.43448463 123.70794997 -0.67169057 -0.62203891 0.40236722 126.53414362 0.06262267 -0.58885879 -0.80580626 120.07375117 Axis -0.92632576 0.34751441 -0.14544523 Axis point 0.00000000 103.26273783 25.72532531 Rotation angle (degrees) 147.65398602 Shift along axis -88.08557767 > open > /Users/alexau/Downloads/prediction_168S_a5f72/rank_1_model_4_ptm_seed_0_unrelaxed.pdb Chain information for rank_1_model_4_ptm_seed_0_unrelaxed.pdb #3 --- Chain | Description A | No description available B | No description available > select #3 2944 atoms, 3024 bonds, 368 residues, 1 model selected > ui tool show ""Color Actions"" > color sel bychain > ~select #3 Nothing selected > ui tool show Matchmaker > hide #3 models > show #3 models > hide #6 models > show #6 models > select #6/A:1-197 1587 atoms, 1619 bonds, 197 residues, 1 model selected > select #6/B:1-322 2563 atoms, 2608 bonds, 322 residues, 1 model selected > select #6/C:1-91 741 atoms, 758 bonds, 91 residues, 1 model selected > select #6/D:1-341 2715 atoms, 2787 bonds, 341 residues, 1 model selected > ui tool show Matchmaker > select #5/D:1-341 Nothing selected > select #5/D:1-341 Nothing selected > select #5/D:1-341 Nothing selected > select #5/D:1-341 Nothing selected > select #5/D:1-341 Nothing selected > select #5/C:1-91 Nothing selected > select #3 2944 atoms, 3024 bonds, 368 residues, 1 model selected > ~select #3 Nothing selected > select #6 7606 atoms, 7772 bonds, 951 residues, 1 model selected > select #6/D:1-341 2715 atoms, 2787 bonds, 341 residues, 1 model selected > select #6/D:1-341 2715 atoms, 2787 bonds, 341 residues, 1 model selected > select #6/C:1-91 741 atoms, 758 bonds, 91 residues, 1 model selected > select #6/D:1-341 2715 atoms, 2787 bonds, 341 residues, 1 model selected > ui tool show Matchmaker > matchmaker #6 to #1/D pairing bs Parameters --- Chain pairing | bs 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 rank_1_model_5_ptm_seed_0_unrelaxed.pdb, chain D (#1) with rank_3_model_1_ptm_seed_0_unrelaxed.pdb, chain D (#6), sequence alignment score = 1720.7 RMSD between 328 pruned atom pairs is 0.552 angstroms; (across all 341 pairs: 1.063) > select #3 2944 atoms, 3024 bonds, 368 residues, 1 model selected > select #6 7606 atoms, 7772 bonds, 951 residues, 1 model selected > view matrix models > #6,0.85616,0.50727,0.09826,92.404,0.20426,-0.50695,0.83742,121.13,0.47462,-0.6969,-0.53765,39.803 > view matrix models > #6,0.85616,0.50727,0.09826,93.248,0.20426,-0.50695,0.83742,100.98,0.47462,-0.6969,-0.53765,45.059 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.6912,0.49542,-0.52612,88.719,0.72164,-0.43435,0.53905,96.399,0.03854,-0.75226,-0.65774,45.827 > view matrix models > #6,0.79839,0.4352,-0.41615,89.607,0.6016,-0.6061,0.52032,97.608,-0.025783,-0.66577,-0.74571,44.83 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.79839,0.4352,-0.41615,71.768,0.6016,-0.6061,0.52032,52.554,-0.025783,-0.66577,-0.74571,14.566 > view matrix models > #6,0.79839,0.4352,-0.41615,31.472,0.6016,-0.6061,0.52032,64.803,-0.025783,-0.66577,-0.74571,26.842 > view matrix models > #6,0.79839,0.4352,-0.41615,35.177,0.6016,-0.6061,0.52032,54.367,-0.025783,-0.66577,-0.74571,42.539 > view matrix models > #6,0.79839,0.4352,-0.41615,35.588,0.6016,-0.6061,0.52032,57.327,-0.025783,-0.66577,-0.74571,40.914 > close #6 > select #1 7606 atoms, 7772 bonds, 951 residues, 1 model selected > view matrix models > #1,-0.45679,0.31008,-0.83378,27.6,0.11908,0.95016,0.28812,60.243,0.88157,0.032326,-0.47094,37.636 > view matrix models > #1,-0.45679,0.31008,-0.83378,38.377,0.11908,0.95016,0.28812,57.079,0.88157,0.032326,-0.47094,48.839 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.045432,0.046119,-0.9979,25.175,-0.20687,0.97771,0.035768,55.574,0.97731,0.20481,0.05396,61.934 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.045432,0.046119,-0.9979,30.697,-0.20687,0.97771,0.035768,45.854,0.97731,0.20481,0.05396,51.462 > view matrix models > #1,0.045432,0.046119,-0.9979,26.235,-0.20687,0.97771,0.035768,49.314,0.97731,0.20481,0.05396,51.127 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.17175,0.33372,-0.92689,34.1,-0.16651,0.9175,0.36119,55.586,0.97097,0.21637,-0.10201,47.747 Fit molecule rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) to map cryosparc_P8_J39__localfilter.mrc (#2) using 7606 atoms average map value = 0.7995, steps = 236 shifted from previous position = 10.6 rotated from previous position = 58.7 degrees atoms outside contour = 2943, contour level = 0.69429 Position of rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) relative to cryosparc_P8_J39__localfilter.mrc (#2) coordinates: Matrix rotation and translation -0.45683527 0.31006471 -0.83376341 122.16744111 0.11906275 0.95016487 0.28811595 127.78866813 0.88154728 0.03235136 -0.47098597 120.83841766 Axis -0.14659011 -0.98312119 -0.10947176 Axis point 20.66043040 0.00000000 82.86266713 Rotation angle (degrees) 119.26359055 Shift along axis -156.76868015 > select #3 2944 atoms, 3024 bonds, 368 residues, 1 model selected > matchmaker #3 to #1/D pairing bs Parameters --- Chain pairing | bs 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 rank_1_model_5_ptm_seed_0_unrelaxed.pdb, chain D (#1) with rank_1_model_4_ptm_seed_0_unrelaxed.pdb, chain B (#3), sequence alignment score = 1748.3 RMSD between 324 pruned atom pairs is 0.419 angstroms; (across all 341 pairs: 2.281) > ~select #3 Nothing selected > ui tool show XMAS Traceback (most recent call last): File ""/Users/alexau/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/xmas/tool.py"", line 285, in function = lambda _, s=selector, t=key: self.map_button_clicked(s, File ""/Users/alexau/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/xmas/tool.py"", line 443, in map_button_clicked self.map_crosslinks(self.checked_models, checked_files) File ""/Users/alexau/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/xmas/tool.py"", line 456, in map_crosslinks evidence = Evidence(evidence_file) File ""/Users/alexau/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/xmas/read_evidence.py"", line 38, in __init__ self.peptide_pairs = evidence.peptide_pairs AttributeError: 'Tabular' object has no attribute 'peptide_pairs' AttributeError: 'Tabular' object has no attribute 'peptide_pairs' File ""/Users/alexau/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/xmas/read_evidence.py"", line 38, in __init__ self.peptide_pairs = evidence.peptide_pairs See log for complete Python traceback. Traceback (most recent call last): File ""/Users/alexau/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/xmas/tool.py"", line 285, in function = lambda _, s=selector, t=key: self.map_button_clicked(s, File ""/Users/alexau/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/xmas/tool.py"", line 443, in map_button_clicked self.map_crosslinks(self.checked_models, checked_files) File ""/Users/alexau/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/xmas/tool.py"", line 456, in map_crosslinks evidence = Evidence(evidence_file) File ""/Users/alexau/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/xmas/read_evidence.py"", line 38, in __init__ self.peptide_pairs = evidence.peptide_pairs AttributeError: 'Tabular' object has no attribute 'peptide_pairs' AttributeError: 'Tabular' object has no attribute 'peptide_pairs' File ""/Users/alexau/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/xmas/read_evidence.py"", line 38, in __init__ self.peptide_pairs = evidence.peptide_pairs See log for complete Python traceback. Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/reports 2/uniprot-Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides.csv Unique peptide pairs: 82 out of 82 Unique peptide pairs with pseudobonds: 23 Pseudobonds are stored in /Users/alexau/Downloads/reports 2/uniprot- Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides_1,3.pb Mapping information is stored in /Users/alexau/Downloads/reports 2/uniprot- Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides_1,3.tsv Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1).csv Unique peptide pairs: 199 out of 199 Unique peptide pairs with pseudobonds: 29 Pseudobonds are stored in /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1)_1,3.pb Mapping information is stored in /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1)_1,3.tsv > hide #3 models > hide #!2 models > show #!2 models > hide #1 models > close #1 > close #3 > close #4 > close #5 > open > /Users/alexau/Downloads/prediction_CorePho_noDis2_534_591_ba56f/rank_1_model_5_ptm_seed_0_unrelaxed.pdb Chain information for rank_1_model_5_ptm_seed_0_unrelaxed.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > select #1 7232 atoms, 7393 bonds, 903 residues, 1 model selected > view matrix models > #1,-0.05011,-0.20274,0.97795,24.294,0.92547,0.35872,0.12179,-7.3458,-0.3755,0.91116,0.16966,-8.1856 > view matrix models > #1,-0.85842,-0.27988,0.42987,20.449,0.24265,-0.9599,-0.14042,-11.985,0.45194,-0.016235,0.8919,-5.3662 > view matrix models > #1,-0.76636,-0.35685,0.53419,21.287,0.5516,-0.79175,0.26244,-6.5736,0.32929,0.49578,0.8036,-3.9849 > view matrix models > #1,-0.53048,0.84178,0.099935,16.584,0.37137,0.12481,0.92006,9.934,0.76202,0.52519,-0.37882,-27.903 > view matrix models > #1,-0.37804,-0.11556,-0.91855,-6.2144,0.32181,0.91391,-0.24742,-7.1082,0.86806,-0.38913,-0.30831,-31.05 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.37804,-0.11556,-0.91855,24.752,0.32181,0.91391,-0.24742,31.051,0.86806,-0.38913,-0.30831,52.773 > view matrix models > #1,-0.37804,-0.11556,-0.91855,37.423,0.32181,0.91391,-0.24742,58.451,0.86806,-0.38913,-0.30831,45.128 Fit molecule rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) to map cryosparc_P8_J39__localfilter.mrc (#2) using 7232 atoms average map value = 0.8516, steps = 124 shifted from previous position = 6.62 rotated from previous position = 27 degrees atoms outside contour = 2502, contour level = 0.69429 Position of rank_1_model_5_ptm_seed_0_unrelaxed.pdb (#1) relative to cryosparc_P8_J39__localfilter.mrc (#2) coordinates: Matrix rotation and translation -0.04175649 0.93328165 -0.35670965 124.64432532 0.49389743 0.32963059 0.80461731 128.65548557 0.86851697 -0.14257999 -0.47470962 122.03972416 Axis -0.58839832 -0.76110995 -0.27294518 Axis point -9.37721050 0.00000000 39.36952496 Rotation angle (degrees) 126.39991928 Shift along axis -204.57163495 > ~select #1 Nothing selected > select #1 7232 atoms, 7393 bonds, 903 residues, 1 model selected > ui tool show ""Color Actions"" > color sel bychain > ~select #1 Nothing selected Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/reports 2/uniprot-Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides.csv Unique peptide pairs: 82 out of 82 Unique peptide pairs with pseudobonds: 22 Pseudobonds are stored in /Users/alexau/Downloads/reports 2/uniprot- Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides_1.pb Mapping information is stored in /Users/alexau/Downloads/reports 2/uniprot- Spodopterafrugiperda+HA-XL-Spombe+CON_2021.02.26.filtered_cross- linked_peptides_1.tsv Peptide pair mapping of pLink evidence file: /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1).csv Unique peptide pairs: 199 out of 199 Unique peptide pairs with pseudobonds: 24 Pseudobonds are stored in /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1)_1.pb Mapping information is stored in /Users/alexau/Downloads/uniprot- Spodopterafrugiperda+Alex-XL+CON_2021.11.30.filtered_cross-linked_peptides (1)_1.tsv > open > /Users/alexau/Downloads/prediction_CorePhoDis273_5477c/rank_1_model_4_ptm_seed_0_unrelaxed.pdb Chain information for rank_1_model_4_ptm_seed_0_unrelaxed.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > hide atoms > show cartoons > select #5 10132 atoms, 10361 bonds, 1262 residues, 1 model selected > view matrix models #5,1,0,0,-14.923,0,1,0,-5.8194,0,0,1,-33.546 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.6273,-0.52263,-0.57737,-22.974,0.76261,0.26193,0.59146,-6.6003,-0.15789,-0.81133,0.56287,-42.588 > view matrix models > #5,0.42451,-0.40902,-0.80777,-23.651,0.25601,-0.80152,0.5404,-19.148,-0.86847,-0.4362,-0.23554,-45.147 > view matrix models > #5,-0.12668,-0.84696,-0.51635,-30.205,-0.98617,0.051451,0.15754,-19.765,-0.10687,0.52917,-0.84176,-33.321 > view matrix models > #5,-0.14285,-0.76392,-0.6293,-29.799,-0.9887,0.080905,0.12622,-19.584,-0.045512,0.64022,-0.76684,-31.815 > view matrix models > #5,-0.040568,0.017318,-0.99903,-23.033,-0.94318,0.32935,0.04401,-17.281,0.32979,0.94405,0.0029733,-25.289 > view matrix models > #5,0.15561,0.49048,-0.85745,-17.377,-0.87908,0.46469,0.10627,-15.57,0.45057,0.73722,0.50348,-25.364 > view matrix models > #5,0.53123,0.83822,-0.12321,-10.533,-0.76895,0.53807,0.34524,-13.768,0.35568,-0.088661,0.93039,-32.363 > ~select #5 Nothing selected > select #5 10132 atoms, 10361 bonds, 1262 residues, 1 model selected > view matrix models > #5,-0.078884,0.91689,0.39127,-12.392,0.41789,-0.32593,0.84802,-13.328,0.90507,0.2304,-0.35745,-28.947 > view matrix models > #5,-0.073012,0.75796,0.6482,-13.232,0.89878,-0.23169,0.37216,-10.624,0.43227,0.60977,-0.66433,-29.032 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.073012,0.75796,0.6482,44.058,0.89878,-0.23169,0.37216,9.228,0.43227,0.60977,-0.66433,35.452 > hide #1 models > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.0049357,0.59634,-0.80271,40.07,-0.2598,0.77593,0.57484,11.698,0.96565,0.20571,0.15876,36.752 > view matrix models > #5,-0.48781,0.37102,-0.79018,35.169,-0.11081,0.87154,0.47764,13.229,0.86589,0.32056,-0.38404,36.048 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.48781,0.37102,-0.79018,43.508,-0.11081,0.87154,0.47764,52.296,0.86589,0.32056,-0.38404,42.362 > view matrix models > #5,-0.48781,0.37102,-0.79018,49.92,-0.11081,0.87154,0.47764,50.091,0.86589,0.32056,-0.38404,38.328 Fit molecule rank_1_model_4_ptm_seed_0_unrelaxed.pdb (#5) to map cryosparc_P8_J39__localfilter.mrc (#2) using 10132 atoms average map value = 0.582, steps = 196 shifted from previous position = 13.5 rotated from previous position = 34.6 degrees atoms outside contour = 5524, contour level = 0.69429 Position of rank_1_model_4_ptm_seed_0_unrelaxed.pdb (#5) relative to cryosparc_P8_J39__localfilter.mrc (#2) coordinates: Matrix rotation and translation -0.18847903 0.97826567 0.08644046 114.93170075 0.44182459 0.00585777 0.89708235 121.16459042 0.87707851 0.20727272 -0.43332589 124.29387326 Axis -0.58535955 -0.67092066 -0.45521387 Axis point -2.89716252 0.00000000 19.79061174 Rotation angle (degrees) 143.89841341 Shift along axis -205.14849042 > ~select #5 Nothing selected > show #1 models > hide #5 models Please select pseudobonds > ~select #4 21 pseudobonds, 1 model selected > ~select #3 Nothing selected /Users/alexau/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/xmas/tool.py:1100: UserWarning: Tight layout not applied. The left and right margins cannot be made large enough to accommodate all axes decorations. plt.tight_layout() > close #5 > select /A 2452 atoms, 2496 bonds, 16 pseudobonds, 307 residues, 3 models selected > color (#1 & sel) lime > select /B 1587 atoms, 1619 bonds, 11 pseudobonds, 197 residues, 3 models selected > color (#1 & sel) blue > select /C 2715 atoms, 2787 bonds, 341 residues, 1 model selected > color sel magenta > select /D 478 atoms, 491 bonds, 58 residues, 1 model selected > color sel cyan > select #1 7232 atoms, 7393 bonds, 43 pseudobonds, 903 residues, 3 models selected > ~select #1 Nothing selected > ui tool show ""Side View"" > hide #!2 models > show #!2 models > ui tool show XMAS > ~select #3 22 pseudobonds, 1 model selected > ~select #4 Nothing selected > lighting flat > lighting full > lighting soft > lighting simple > lighting shadows true > graphics silhouettes false > lighting flat > lighting soft > lighting flat > lighting soft > lighting flat > save /Users/alexau/Desktop/image2.png supersample 3 > hide #!2 models > show #!2 models > hide #!2 models > select /A 2452 atoms, 2496 bonds, 16 pseudobonds, 307 residues, 3 models selected > color (#1 & sel) lime > select /B 1587 atoms, 1619 bonds, 11 pseudobonds, 197 residues, 3 models selected > color (#1 & sel) blue > select clear > show #!2 models > save /Users/alexau/Desktop/image3.png supersample 3 > hide #!2 models > save /Users/alexau/Desktop/image4.png supersample 3 > show #!2 models > hide #!2 models > show #!2 models > save /Users/alexau/Desktop/image5.png supersample 3 > hide #!2 models > save /Users/alexau/Desktop/image6.png supersample 3 > open /Users/alexau/Downloads/AF-P23193-F1-model_v2.pdb AF-P23193-F1-model_v2.pdb title: Alphafold monomer V2.0 prediction for transcription elongation factor A protein 1 (P23193) [more info...] Chain information for AF-P23193-F1-model_v2.pdb #5 --- Chain | Description | UniProt A | transcription elongation factor A protein 1 | TCEA1_HUMAN > hide #4 models > hide #3 models > hide #1 models > ui tool show ""Side View"" > view #5 clip false > open > ""/Users/alexau/Documents/Oxford_DPhil_Structural_Biology/Data/Model/AlphaFold/Ppn1 > AlphaFold/ppn1_ffb23_unrelaxed_rank_1_model_3.pdb"" Chain information for ppn1_ffb23_unrelaxed_rank_1_model_3.pdb #6 --- Chain | Description A | No description available > hide #5 models > color #6 #a6a6a6 transparency 0 > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A Alignment identifier is 6/A ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: AppleHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 16 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 11:47 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-XMAS: 1.1.1 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 et-xmlfile: 1.1.0 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openpyxl: 3.0.10 openvr: 1.16.801 packaging: 21.0 pandas: 1.4.2 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 QtRangeSlider: 0.1.5 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 seaborn: 0.11.2 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal UI can't reproduce Tom Goddard all ChimeraX