id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16599 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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: [ { ""rolloutId"" : ""64628732bf2f5257dedc8988"", ""factorPackIds"" : { }, ""deploymentId"" : 240000001 }, { ""rolloutId"" : ""632c763c58740028737bfdd2"", ""factorPackIds"" : { ""SIRI_DIALOG_ASSETS"" : ""64a57d23fa6fd41b2353e2ae"" }, ""deploymentId"" : 240000034 } ], ""experiments"" : [ ] } } ===== 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 /Baseplate/CornDog-Baseplate- > GP49-GP58-GP59-GP60-GP61-2_74A/Baseplate-coot-1-ACEG.pdb"" Summary of feedback from opening /Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate-GP49-GP58-GP59-GP60-GP61-2_74A/Baseplate- coot-1-ACEG.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 SER M 20 PHE M 22 1 3 Start residue of secondary structure not found: HELIX 2 2 GLY M 38 THR M 41 1 4 Start residue of secondary structure not found: HELIX 3 3 PRO M 142 ARG M 148 1 7 Start residue of secondary structure not found: HELIX 4 4 GLU M 262 ILE M 267 1 6 Start residue of secondary structure not found: HELIX 5 5 SER N 20 PHE N 22 1 3 381 messages similar to the above omitted End residue of secondary structure not found: HELIX 3 3 PRO M 142 ARG M 148 1 7 Start residue of secondary structure not found: HELIX 4 4 GLU M 262 ILE M 267 1 6 Start residue of secondary structure not found: HELIX 5 5 SER N 20 PHE N 22 1 3 Start residue of secondary structure not found: HELIX 6 6 GLY N 38 THR N 41 1 4 End residue of secondary structure not found: HELIX 7 7 PRO N 142 ARG N 148 1 7 Start residue of secondary structure not found: HELIX 8 8 GLU N 262 ILE N 267 1 6 Start residue of secondary structure not found: HELIX 9 9 SER O 20 PHE O 22 1 3 Start residue of secondary structure not found: HELIX 10 10 GLY O 38 THR O 41 1 4 End residue of secondary structure not found: HELIX 11 11 PRO O 142 ARG O 148 1 7 Start residue of secondary structure not found: HELIX 12 12 GLU O 262 ILE O 267 1 6 Start residue of secondary structure not found: HELIX 13 13 SER P 20 PHE P 22 1 3 Start residue of secondary structure not found: HELIX 14 14 GLY P 38 THR P 41 1 4 End residue of secondary structure not found: HELIX 15 15 PRO P 142 ARG P 148 1 7 Start residue of secondary structure not found: HELIX 16 16 GLU P 262 ILE P 267 1 6 Start residue of secondary structure not found: HELIX 17 17 SER Q 20 PHE Q 22 1 3 Start residue of secondary structure not found: HELIX 18 18 GLY Q 38 THR Q 41 1 4 End residue of secondary structure not found: HELIX 19 19 PRO Q 142 ARG Q 148 1 7 Start residue of secondary structure not found: HELIX 20 20 GLU Q 262 ILE Q 267 1 6 Start residue of secondary structure not found: HELIX 21 21 SER R 20 PHE R 22 1 3 Start residue of secondary structure not found: HELIX 22 22 GLY R 38 THR R 41 1 4 End residue of secondary structure not found: HELIX 23 23 PRO R 142 ARG R 148 1 7 Start residue of secondary structure not found: HELIX 24 24 GLU R 262 ILE R 267 1 6 Start residue of secondary structure not found: HELIX 25 25 SER A 20 PHE A 22 1 3 Start residue of secondary structure not found: HELIX 26 26 GLY A 38 THR A 41 1 4 End residue of secondary structure not found: HELIX 27 27 PRO A 142 ARG A 148 1 7 Start residue of secondary structure not found: HELIX 28 28 GLU A 262 ILE A 267 1 6 Start residue of secondary structure not found: HELIX 29 29 SER C 20 PHE C 22 1 3 Start residue of secondary structure not found: HELIX 30 30 GLY C 38 THR C 41 1 4 End residue of secondary structure not found: HELIX 31 31 PRO C 142 ARG C 148 1 7 Start residue of secondary structure not found: HELIX 32 32 GLU C 262 ILE C 267 1 6 Start residue of secondary structure not found: HELIX 33 33 SER E 20 PHE E 22 1 3 Start residue of secondary structure not found: HELIX 34 34 GLY E 38 THR E 41 1 4 End residue of secondary structure not found: HELIX 35 35 PRO E 142 ARG E 148 1 7 Start residue of secondary structure not found: HELIX 36 36 GLU E 262 ILE E 267 1 6 Start residue of secondary structure not found: HELIX 37 37 SER G 20 PHE G 22 1 3 Start residue of secondary structure not found: HELIX 38 38 GLY G 38 THR G 41 1 4 End residue of secondary structure not found: HELIX 39 39 PRO G 142 ARG G 148 1 7 Start residue of secondary structure not found: HELIX 40 40 GLU G 262 ILE G 267 1 6 Start residue of secondary structure not found: HELIX 41 41 SER I 20 PHE I 22 1 3 Start residue of secondary structure not found: HELIX 42 42 GLY I 38 THR I 41 1 4 End residue of secondary structure not found: HELIX 43 43 PRO I 142 ARG I 148 1 7 Start residue of secondary structure not found: HELIX 44 44 GLU I 262 ILE I 267 1 6 Start residue of secondary structure not found: HELIX 45 45 SER K 20 PHE K 22 1 3 Start residue of secondary structure not found: HELIX 46 46 GLY K 38 THR K 41 1 4 End residue of secondary structure not found: HELIX 47 47 PRO K 142 ARG K 148 1 7 Start residue of secondary structure not found: HELIX 48 48 GLU K 262 ILE K 267 1 6 Start residue of secondary structure not found: SHEET 1 1 1 ALA M 29 ASP M 35 0 Start residue of secondary structure not found: SHEET 2 2 2 HIS M 72 VAL M 75 0 Start residue of secondary structure not found: SHEET 3 3 3 ASP M 78 THR M 81 0 Start residue of secondary structure not found: SHEET 4 4 4 GLU M 102 GLN M 112 0 263 messages similar to the above omitted End residue of secondary structure not found: SHEET 76 7676 GLU A 102 GLN A 112 0 Start residue of secondary structure not found: SHEET 77 7777 ASP A 122 PHE A 134 0 Start residue of secondary structure not found: SHEET 78 7878 GLY A 171 PRO A 175 0 Start residue of secondary structure not found: SHEET 79 7979 TYR A 183 LYS A 193 0 Start residue of secondary structure not found: SHEET 80 8080 LYS A 196 TYR A 204 0 Start residue of secondary structure not found: SHEET 81 8181 CYS A 207 ILE A 212 0 6 messages similar to the above omitted End residue of secondary structure not found: SHEET 88 8888 GLU C 102 GLN C 112 0 Start residue of secondary structure not found: SHEET 89 8989 ASP C 122 PHE C 134 0 Start residue of secondary structure not found: SHEET 90 9090 GLY C 171 PRO C 175 0 Start residue of secondary structure not found: SHEET 91 9191 TYR C 183 LYS C 193 0 Start residue of secondary structure not found: SHEET 92 9292 LYS C 196 TYR C 204 0 Start residue of secondary structure not found: SHEET 93 9393 CYS C 207 ILE C 212 0 51 messages similar to the above omitted Chain information for Baseplate-coot-1-ACEG.pdb --- Chain | Description 1.1/A 1.1/C 1.1/E 1.1/G 1.1/I 1.1/K 1.1/M 1.1/N 1.1/O 1.1/P 1.1/Q 1.1/R | No description available 1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F | No description available 1.3/A 1.3/B 1.3/C | No description available 1.4/A 1.4/B 1.4/D 1.4/E 1.4/F 1.4/G 1.4/H 1.4/I 1.4/J 1.4/K 1.4/L 1.4/M | No description available 1.5/A 1.5/B 1.5/C | No description available 1.4/C 1.4/N 1.4/O 1.4/P 1.4/Q 1.4/R | No description available Already setting window visible! > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/ChimeraX/Cluster > O/Corndog_61/Corndog_61_Trimer/Corndog_61_Trimer_1cf1e_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" Chain information for Corndog_61_Trimer_1cf1e_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #2 --- Chain | Description A B C | No description available > select add #2 18573 atoms, 18993 bonds, 2508 residues, 1 model selected > ui tool show Matchmaker > matchmaker #2 to #1.5 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 Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with Corndog_61_Trimer_1cf1e_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#2), sequence alignment score = 495.4 RMSD between 59 pruned atom pairs is 1.307 angstroms; (across all 101 pairs: 18.071) > select subtract #2 Nothing selected > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/ChimeraX/Cluster > O/Corndog_61/Corndog_61_Trimer/Corndog_61_Trimer_1cf1e_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb"" > ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/ChimeraX/Cluster > O/Corndog_61/Corndog_61_Trimer/Corndog_61_Trimer_1cf1e_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb"" > ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/ChimeraX/Cluster > O/Corndog_61/Corndog_61_Trimer/Corndog_61_Trimer_1cf1e_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb"" > ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/ChimeraX/Cluster > O/Corndog_61/Corndog_61_Trimer/Corndog_61_Trimer_1cf1e_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb"" Chain information for Corndog_61_Trimer_1cf1e_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb #3 --- Chain | Description A B C | No description available Chain information for Corndog_61_Trimer_1cf1e_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb #4 --- Chain | Description A B C | No description available Chain information for Corndog_61_Trimer_1cf1e_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb #5 --- Chain | Description A B C | No description available Chain information for Corndog_61_Trimer_1cf1e_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb #6 --- Chain | Description A B C | No description available > ui tool show Matchmaker > matchmaker #2-6 to #1.5 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 Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with Corndog_61_Trimer_1cf1e_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#2), sequence alignment score = 495.4 RMSD between 59 pruned atom pairs is 1.307 angstroms; (across all 101 pairs: 18.071) Matchmaker Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with Corndog_61_Trimer_1cf1e_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb, chain A (#3), sequence alignment score = 490.6 RMSD between 61 pruned atom pairs is 1.305 angstroms; (across all 101 pairs: 26.184) Matchmaker Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with Corndog_61_Trimer_1cf1e_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb, chain C (#4), sequence alignment score = 503.8 RMSD between 35 pruned atom pairs is 0.895 angstroms; (across all 101 pairs: 31.569) Matchmaker Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with Corndog_61_Trimer_1cf1e_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb, chain A (#5), sequence alignment score = 505 RMSD between 40 pruned atom pairs is 0.977 angstroms; (across all 101 pairs: 23.986) Matchmaker Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with Corndog_61_Trimer_1cf1e_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb, chain A (#6), sequence alignment score = 496.6 RMSD between 59 pruned atom pairs is 1.224 angstroms; (across all 101 pairs: 14.362) > hide #3 models > hide #4 models > hide #5 models > hide #6 models > hide #2 models > show #3 models > hide #3 models > show #4 models > hide #4 models > show #5 models > hide #5 models > show #6 models > close #5-6 > show #4 models > show #3 models > show #2 models > close #2-3 > rename #4 Corndog_61 > select add #4 18573 atoms, 18993 bonds, 2508 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.67349,0.26764,-0.68905,276.61,-0.72435,-0.42485,0.54298,277.3,-0.14742,0.8648,0.47999,79.851 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate- > GP49-GP58-GP59-GP60-GP61-2_74A/cryosparc_P2_J280_008_volume_map_sharp.mrc"" Opened cryosparc_P2_J280_008_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.06, shown at level 0.227, step 2, values float32 > surface dust #2 size 10.6 > volume #2 level 0.3 > volume #2 step 1 > transparency 50 > save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate- > GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer.pdb"" models #4 selectedOnly > true relModel #2 > ui tool show ""Fit in Map"" > fitmap #4 inMap #2 Fit molecule Corndog_61 (#4) to map cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) using 18573 atoms average map value = 0.08724, steps = 2000 shifted from previous position = 1.69 rotated from previous position = 4.84 degrees atoms outside contour = 17484, contour level = 0.3 Position of Corndog_61 (#4) relative to cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.61456329 0.31006657 -0.72537624 276.06442658 -0.77933139 -0.38117747 0.49733924 275.04870896 -0.12228881 0.87095491 0.47590229 79.79110445 Axis 0.28738893 -0.46390091 -0.83797586 Axis point 200.56043122 47.30830227 0.00000000 Rotation angle (degrees) 139.45707837 Shift along axis -115.12050621 > hide #1.5 models > hide #1.4 models > hide #1.3 models > hide #1.2 models > hide #1.1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1.5/A #1.5/B #1.5/C Alignment identifier is 1 > ui tool show ""Show Sequence Viewer"" > sequence chain #4/A #4/B #4/C Alignment identifier is 2 Already setting window visible! > select #1.5/A-C:6 12 atoms, 9 bonds, 3 residues, 1 model selected > select #1.5/A-C:6-11 150 atoms, 156 bonds, 18 residues, 1 model selected > select #4/A-C:5-6 39 atoms, 36 bonds, 6 residues, 1 model selected > select #4/A-C:1-6 132 atoms, 132 bonds, 18 residues, 1 model selected > select #4/A-C:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select #4/A-C:1-5 120 atoms, 120 bonds, 15 residues, 1 model selected > delete sel > select #1.5/A-C:106 24 atoms, 21 bonds, 3 residues, 1 model selected > select #1.5/A-C 2376 atoms, 2427 bonds, 303 residues, 1 model selected > select sequence > GEIPDWVRNVPRQVRKLPPNNQWEGISEEMMQQLRGQLLESILSAVVQAIRGLFVPGPFGSAAEQLEQWAQGLGAEIIAKIYELTGIDLSSWDAFLESLSD 4752 atoms, 4854 bonds, 606 residues, 2 models selected > select clear > select add #4 18453 atoms, 18870 bonds, 2493 residues, 1 model selected > view matrix models > #4,-0.65768,0.28234,-0.69838,276.79,-0.74308,-0.39535,0.53994,274.81,-0.12366,0.87406,0.46981,79.774 > view matrix models > #4,-0.65768,0.28234,-0.69838,276.99,-0.74308,-0.39535,0.53994,274.67,-0.12366,0.87406,0.46981,81.796 > fitmap #4 inMap #2 Fit molecule Corndog_61 (#4) to map cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) using 18453 atoms average map value = 0.08765, steps = 2000 shifted from previous position = 4.36 rotated from previous position = 2.85 degrees atoms outside contour = 17356, contour level = 0.3 Position of Corndog_61 (#4) relative to cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.62528913 0.29253997 -0.72348729 278.24689192 -0.76616580 -0.40634170 0.49787186 279.27516578 -0.14833564 0.86562509 0.47821517 80.13241653 Axis 0.29193203 -0.45657027 -0.84042804 Axis point 201.00137478 52.18998333 -0.00000000 Rotation angle (degrees) 140.96012791 Shift along axis -113.62508686 > fitmap #4 inMap #2 Fit molecule Corndog_61 (#4) to map cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) using 18453 atoms average map value = 0.08681, steps = 2000 shifted from previous position = 5.1 rotated from previous position = 1.98 degrees atoms outside contour = 17365, contour level = 0.3 Position of Corndog_61 (#4) relative to cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.62899903 0.32224368 -0.70747383 272.37984974 -0.76611149 -0.41150227 0.49369937 280.61671488 -0.13203559 0.85254026 0.50570912 79.99967427 Axis 0.27983143 -0.44873845 -0.84872150 Axis point 198.07337970 53.91316297 0.00000000 Rotation angle (degrees) 140.12063271 Shift along axis -117.60051061 > view matrix models > #4,-0.629,0.32224,-0.70747,272.84,-0.76611,-0.4115,0.4937,279.79,-0.13204,0.85254,0.50571,80.672 > fitmap #4 inMap #2 Fit molecule Corndog_61 (#4) to map cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) using 18453 atoms average map value = 0.08713, steps = 2000 shifted from previous position = 6.06 rotated from previous position = 2.58 degrees atoms outside contour = 17392, contour level = 0.3 Position of Corndog_61 (#4) relative to cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.62461800 0.30414044 -0.71927112 276.08488128 -0.77233484 -0.37686456 0.51134333 273.37549885 -0.11554761 0.87491239 0.47029465 79.74838108 Axis 0.28257069 -0.46922190 -0.83665083 Axis point 199.08540406 47.00859691 0.00000000 Rotation angle (degrees) 139.95986232 Shift along axis -116.98182556 > fitmap #4 inMap #2 Fit molecule Corndog_61 (#4) to map cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) using 18453 atoms average map value = 0.08799, steps = 2000 shifted from previous position = 5.9 rotated from previous position = 2.24 degrees atoms outside contour = 17350, contour level = 0.3 Position of Corndog_61 (#4) relative to cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.62636364 0.30559819 -0.71713202 275.76138126 -0.76611507 -0.41126712 0.49388972 280.30588585 -0.14400102 0.85876021 0.49172615 79.96047476 Axis 0.28754225 -0.45166541 -0.84458144 Axis point 199.88715672 53.35489490 0.00000000 Rotation angle (degrees) 140.61974856 Shift along axis -114.84455684 > select subtract #4 Nothing selected > hide #4 models > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate- > GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer-coot-0.pdb"" Chain information for Corndog_61_Trimer-coot-0.pdb #3 --- Chain | Description A B C | No description available > select #4/A-C:6 12 atoms, 9 bonds, 3 residues, 1 model selected > select #4/A-C:6-9 84 atoms, 84 bonds, 12 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #4/A Alignment identifier is 4/A > select #4/A:6 4 atoms, 3 bonds, 1 residue, 1 model selected > select #4/A:6-11 50 atoms, 52 bonds, 6 residues, 1 model selected > view clip false > select #4/A:12-13 18 atoms, 17 bonds, 2 residues, 1 model selected > select #4/A:12-18 60 atoms, 60 bonds, 7 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > select #3/A:6 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:6-13 68 atoms, 70 bonds, 8 residues, 1 model selected > view clip false > select #3/A:61 7 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:61-68 49 atoms, 51 bonds, 8 residues, 1 model selected > hide #3 models > show #1.5 models > select #1.5/A-C:6 12 atoms, 9 bonds, 3 residues, 1 model selected > select #1.5/A-C:6-12 171 atoms, 177 bonds, 21 residues, 1 model selected > show #3 models > select #3/A:56 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:56-60 41 atoms, 41 bonds, 5 residues, 1 model selected > select #3/A:48 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:48-52 33 atoms, 32 bonds, 5 residues, 1 model selected > select #3/A:41-42 13 atoms, 12 bonds, 2 residues, 1 model selected > select #3/A:41-44 29 atoms, 28 bonds, 4 residues, 1 model selected > select #3/A:35 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:35-37 25 atoms, 24 bonds, 3 residues, 1 model selected > select #3/A:30-31 12 atoms, 11 bonds, 2 residues, 1 model selected > select #3/A:30-32 18 atoms, 17 bonds, 3 residues, 1 model selected > view matrix models #3,1,0,0,0.68894,0,1,0,-0.99432,0,0,1,-1.7586 > undo > close #3 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate- > GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer-coot-1.pdb"" Summary of feedback from opening /Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate-GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer- coot-1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 10 ARG A 13 1 4 Start residue of secondary structure not found: HELIX 2 2 GLN A 27 GLU A 29 1 3 Chain information for Corndog_61_Trimer-coot-1.pdb #3 --- Chain | Description A B C | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > select #3/A:777-836 435 atoms, 441 bonds, 60 residues, 1 model selected > select #3/A 5944 atoms, 6075 bonds, 807 residues, 1 model selected > save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate- > GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer-coot-2.pdb"" models #3 > selectedOnly true relModel #2 > select #3/A:30 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:30 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:33 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:33 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1.5/A-C:10-13,33-55,66-89,97-104 1416 atoms, 1428 bonds, 177 residues, 1 model selected > view matrix models #1.5,1,0,0,0.5085,0,1,0,-1.2452,0,0,1,-1.608 > undo > select clear > close #3 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate- > GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer-coot-3.pdb"" Summary of feedback from opening /Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate-GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer- coot-3.pdb --- warnings | Start residue of secondary structure not found: HELIX 24 24 GLU B 33 ARG B 56 1 24 Start residue of secondary structure not found: HELIX 25 25 ALA B 67 GLN B 76 1 10 Start residue of secondary structure not found: HELIX 26 26 LEU B 78 THR B 90 1 13 Start residue of secondary structure not found: HELIX 27 27 TRP B 97 LEU B 101 1 5 Start residue of secondary structure not found: HELIX 28 28 GLU B 102 SER B 105 1 4 121 messages similar to the above omitted Chain information for Corndog_61_Trimer-coot-3.pdb #3 --- Chain | Description A | No description available > view orient > ui mousemode right ""map eraser"" > volume erase #2 center 299.53,293.01,461.09 radius 107.6 Opened cryosparc_P2_J280_008_volume_map_sharp.mrc copy as #6, grid size 512,512,512, pixel 1.06, shown at step 1, values float32 > surface dust #6 size 10.6 > volume erase #6 center 294.08,290.18,421.18 radius 107.56 > set bgColor white > set bgColor black > close #5 Cell requested for row 3 is out of bounds for table with 10 rows! Resizing table model. > close #4 > combine #3 ===== 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: 14 days, 21 hours, 48 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 all ChimeraX