id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14484 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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. > open ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 1-43 versus Bora 18-120 binding to > AURKA.cxs"" Log from Sun Oct 1 16:53:59 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"" Log from Sun Oct 1 15:28:21 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1ol5 Summary of feedback from opening 1ol5 fetched from pdb --- notes | Fetching compressed mmCIF 1ol5 from http://files.rcsb.org/download/1ol5.cif Fetching CCD ADP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ADP/ADP.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif Fetching CCD SO4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif 1ol5 title: Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and bound to TPX2 1-43 [more info...] Chain information for 1ol5 #1 --- Chain | Description | UniProt A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403 B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN 1-43 Non-standard residues in 1ol5 #1 --- ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion > open ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Alphafold File Bora 1-120 - Aurora A/best_model.pdb"" Chain information for best_model.pdb #2 --- Chain | Description B | No description available C | No description available > MatchMaker #2 to #1 Unknown command: MatchMaker #2 to #1 > matchmaker #2 to #1 align true Expected a keyword > matchmaker #2 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 1ol5, chain A (#1) with best_model.pdb, chain B (#2), sequence alignment score = 1379.7 RMSD between 260 pruned atom pairs is 0.622 angstroms; (across all 265 pairs: 0.926) > matchmaker #2 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 1ol5, chain A (#1) with best_model.pdb, chain B (#2), sequence alignment score = 1379.7 RMSD between 260 pruned atom pairs is 0.622 angstroms; (across all 265 pairs: 0.926) > color bychain [Repeated 1 time(s)] > select add #1 2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected > select subtract #1 Nothing selected > select add #1 2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected > select subtract #1 Nothing selected > hide atoms > hide #1.2 models > show #1.2 models > select add #1.2 1 pseudobond, 1 model selected > select subtract #1.2 Nothing selected > select add #1.1 13 pseudobonds, 1 model selected > select subtract #1.1 Nothing selected > color bychain [Repeated 1 time(s)] > hide #2 models > show #2 models > hide #2 models > select add #1 2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected > select subtract #1 Nothing selected > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > select #2/C:1-120 966 atoms, 992 bonds, 120 residues, 1 model selected > color #1 #1a28ebff > color #!1 bychain > select add #1 3573 atoms, 3511 bonds, 14 pseudobonds, 567 residues, 4 models selected > select subtract #1 966 atoms, 992 bonds, 120 residues, 1 model selected > select add #2 3180 atoms, 3262 bonds, 391 residues, 1 model selected > select subtract #2 Nothing selected > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > color #2 #28e816ff > show #2 models > hide #2 models > show #2 models > color byhetero [Repeated 1 time(s)] > color bychain > show #!1 target m > view #1 clip false > log metadata #1 Metadata for 1ol5 #1 --- Title | Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and bound to TPX2 1-43 Citation | Bayliss, R., Sardon, T., Vernos, I., Conti, E. (2003). Structural Basis of Aurora-A Activation by Tpx2 at the Mitotic Spindle. Mol.Cell, 12, 851. PMID: 14580337. DOI: 10.1016/S1097-2765(03)00392-7 Non-standard residues | ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion Gene source | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 2.500Å > log chains #1 Chain information for 1ol5 #1 --- Chain | Description | UniProt A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403 B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN 1-43 > log metadata #1 Metadata for 1ol5 #1 --- Title | Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and bound to TPX2 1-43 Citation | Bayliss, R., Sardon, T., Vernos, I., Conti, E. (2003). Structural Basis of Aurora-A Activation by Tpx2 at the Mitotic Spindle. Mol.Cell, 12, 851. PMID: 14580337. DOI: 10.1016/S1097-2765(03)00392-7 Non-standard residues | ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion Gene source | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 2.500Å > log chains #1 Chain information for 1ol5 #1 --- Chain | Description | UniProt A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403 B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN 1-43 > view #1 clip false > show #!1 target m > show sequence Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/B Alignment identifier is 1/B > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/C Alignment identifier is 2/C > select #1/B:43 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:7-43 238 atoms, 244 bonds, 1 pseudobond, 30 residues, 2 models selected > color (#!1 & sel) red > select #2/C:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C 966 atoms, 992 bonds, 120 residues, 1 model selected > color sel yellow > select #2/B:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/B 2214 atoms, 2270 bonds, 271 residues, 1 model selected > color sel blue > select #1/A:377-388 90 atoms, 93 bonds, 12 residues, 1 model selected > select #1/A:123-388 2180 atoms, 2234 bonds, 266 residues, 1 model selected > color sel magenta > select #2/C:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:1 8 atoms, 7 bonds, 1 residue, 1 model selected > save ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"" ——— End of log from Sun Oct 1 15:28:21 2023 ——— opened ChimeraX session > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/B Alignment identifier is 1/B > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/C Alignment identifier is 2/C > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > select #1/B:8 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:8 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:45 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:45 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > select #2/B:228-271 358 atoms, 368 bonds, 44 residues, 1 model selected > select #2/B 2214 atoms, 2270 bonds, 271 residues, 1 model selected > select #1/A:123-388 2180 atoms, 2234 bonds, 266 residues, 1 model selected > select #1/B:16 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:16 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > select #1/B:19 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:19 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > select #1/B:19 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:19 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:8 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:8 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:10 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:10 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel target ab > select #1/A:123-388 2180 atoms, 2234 bonds, 266 residues, 1 model selected > color sel blue > select #1/B:33 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/B:33-35 31 atoms, 33 bonds, 3 residues, 1 model selected > select #1/B:35 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:34-35 25 atoms, 27 bonds, 2 residues, 1 model selected > show sel target ab > select #2/C:103 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:103-104 22 atoms, 23 bonds, 2 residues, 1 model selected > show sel target ab > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:31 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/C:31 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:31 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/C:31 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:11 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:11 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:15 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:15 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:25-26 20 atoms, 20 bonds, 2 residues, 1 model selected > select #2/C:25-26 20 atoms, 20 bonds, 2 residues, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:28 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:28-30 21 atoms, 21 bonds, 3 residues, 1 model selected > select #1/B:13 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:13-15 21 atoms, 21 bonds, 3 residues, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/B:70 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/B:70 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel target ab > select #2/B:76 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/B:76 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:112 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/C:112 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel target ab > color sel lime > select #2/C:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:101 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > select > #2/B:11-13,47-53,56-68,99-106,111-131,140-142,174-176,179-182,189-205,215-223,235-244,249-251,255-260,262-267 944 atoms, 949 bonds, 113 residues, 1 model selected > select #2/B:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/B:131 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/B:1-45 359 atoms, 366 bonds, 45 residues, 1 model selected > select #2/B:1-45 359 atoms, 366 bonds, 45 residues, 1 model selected > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:39 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:39 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:41 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/C:41-42 13 atoms, 13 bonds, 2 residues, 1 model selected > select #2/C:41 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/C:41 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:25-26 20 atoms, 20 bonds, 2 residues, 1 model selected > select #2/C:34 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:34 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #1/B:42 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:42 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:79 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:79 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:32-35,42-45,60-66,73-85,90-105 366 atoms, 370 bonds, 44 residues, 1 model selected > select #2/C:74 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:27 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/C:27 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #2/C:34 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:34 8 atoms, 7 bonds, 1 residue, 1 model selected > save ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"" > select #2/C:73-74 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2/C:73-74 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2/C:74 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:74 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:75 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:75 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:22 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:22 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel target a > select #2/C:60 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:60-65 45 atoms, 44 bonds, 6 residues, 1 model selected > show sel target ab > hide sel target a > select #2/C:60 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:60 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:62 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:62 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:61 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:61 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #2/C:66 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:66 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:72 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:72 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:59 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/C:59 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel target ab > save ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"" > select #2/C:102 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:102 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:34 14 atoms, 15 bonds, 1 residue, 1 model selected > select #1/B:34-35 25 atoms, 27 bonds, 2 residues, 1 model selected > select #1/B:34 14 atoms, 15 bonds, 1 residue, 1 model selected > select #1/B:34 14 atoms, 15 bonds, 1 residue, 1 model selected > save ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"" [Repeated 1 time(s)] ——— End of log from Sun Oct 1 16:53:59 2023 ——— opened ChimeraX session > select #1/A:357-388 255 atoms, 261 bonds, 32 residues, 1 model selected > select #1/A:123-388 2180 atoms, 2234 bonds, 266 residues, 1 model selected > show sel surfaces > mlp sel Map values for surface ""1ol5_A SES surface"": minimum -25.48, mean 2.446e+28, maximum 2.596e+30 To also show corresponding color key, enter the above mlp command and add key true > select #2/C:61 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:61 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > hbonds sel reveal true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 1ol5 #1/A SER 388 N; 1ol5 #1/B LEU 22 N 5 hydrogen bonds found > select #2/C:88 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:88 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:76 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:76 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:75 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:75 8 atoms, 7 bonds, 1 residue, 1 model selected Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 1-43 versus Bora 18-120 binding to > AURKA.cxs"" Log from Sun Oct 1 16:53:59 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"" Log from Sun Oct 1 15:28:21 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1ol5 Summary of feedback from opening 1ol5 fetched from pdb --- notes | Fetching compressed mmCIF 1ol5 from http://files.rcsb.org/download/1ol5.cif Fetching CCD ADP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ADP/ADP.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif Fetching CCD SO4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif 1ol5 title: Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and bound to TPX2 1-43 [more info...] Chain information for 1ol5 #1 --- Chain | Description | UniProt A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403 B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN 1-43 Non-standard residues in 1ol5 #1 --- ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion > open ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Alphafold File Bora 1-120 - Aurora A/best_model.pdb"" Chain information for best_model.pdb #2 --- Chain | Description B | No description available C | No description available > MatchMaker #2 to #1 Unknown command: MatchMaker #2 to #1 > matchmaker #2 to #1 align true Expected a keyword > matchmaker #2 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 1ol5, chain A (#1) with best_model.pdb, chain B (#2), sequence alignment score = 1379.7 RMSD between 260 pruned atom pairs is 0.622 angstroms; (across all 265 pairs: 0.926) > matchmaker #2 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 1ol5, chain A (#1) with best_model.pdb, chain B (#2), sequence alignment score = 1379.7 RMSD between 260 pruned atom pairs is 0.622 angstroms; (across all 265 pairs: 0.926) > color bychain [Repeated 1 time(s)] > select add #1 2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected > select subtract #1 Nothing selected > select add #1 2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected > select subtract #1 Nothing selected > hide atoms > hide #1.2 models > show #1.2 models > select add #1.2 1 pseudobond, 1 model selected > select subtract #1.2 Nothing selected > select add #1.1 13 pseudobonds, 1 model selected > select subtract #1.1 Nothing selected > color bychain [Repeated 1 time(s)] > hide #2 models > show #2 models > hide #2 models > select add #1 2607 atoms, 2519 bonds, 14 pseudobonds, 447 residues, 3 models selected > select subtract #1 Nothing selected > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > select #2/C:1-120 966 atoms, 992 bonds, 120 residues, 1 model selected > color #1 #1a28ebff > color #!1 bychain > select add #1 3573 atoms, 3511 bonds, 14 pseudobonds, 567 residues, 4 models selected > select subtract #1 966 atoms, 992 bonds, 120 residues, 1 model selected > select add #2 3180 atoms, 3262 bonds, 391 residues, 1 model selected > select subtract #2 Nothing selected > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > color #2 #28e816ff > show #2 models > hide #2 models > show #2 models > color byhetero [Repeated 1 time(s)] > color bychain > show #!1 target m > view #1 clip false > log metadata #1 Metadata for 1ol5 #1 --- Title | Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and bound to TPX2 1-43 Citation | Bayliss, R., Sardon, T., Vernos, I., Conti, E. (2003). Structural Basis of Aurora-A Activation by Tpx2 at the Mitotic Spindle. Mol.Cell, 12, 851. PMID: 14580337. DOI: 10.1016/S1097-2765(03)00392-7 Non-standard residues | ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion Gene source | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 2.500Å > log chains #1 Chain information for 1ol5 #1 --- Chain | Description | UniProt A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403 B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN 1-43 > log metadata #1 Metadata for 1ol5 #1 --- Title | Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and bound to TPX2 1-43 Citation | Bayliss, R., Sardon, T., Vernos, I., Conti, E. (2003). Structural Basis of Aurora-A Activation by Tpx2 at the Mitotic Spindle. Mol.Cell, 12, 851. PMID: 14580337. DOI: 10.1016/S1097-2765(03)00392-7 Non-standard residues | ADP — adenosine-5'-diphosphate MG — magnesium ion SO4 — sulfate ion Gene source | Homo sapiens (human) Experimental method | X-ray diffraction Resolution | 2.500Å > log chains #1 Chain information for 1ol5 #1 --- Chain | Description | UniProt A | SERINE/THREONINE KINASE 6 | STK6_HUMAN 122-403 B | RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 | DIL2_HUMAN 1-43 > view #1 clip false > show #!1 target m > show sequence Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/B Alignment identifier is 1/B > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/C Alignment identifier is 2/C > select #1/B:43 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:7-43 238 atoms, 244 bonds, 1 pseudobond, 30 residues, 2 models selected > color (#!1 & sel) red > select #2/C:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C 966 atoms, 992 bonds, 120 residues, 1 model selected > color sel yellow > select #2/B:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/B 2214 atoms, 2270 bonds, 271 residues, 1 model selected > color sel blue > select #1/A:377-388 90 atoms, 93 bonds, 12 residues, 1 model selected > select #1/A:123-388 2180 atoms, 2234 bonds, 266 residues, 1 model selected > color sel magenta > select #2/C:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:1 8 atoms, 7 bonds, 1 residue, 1 model selected > save ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"" ——— End of log from Sun Oct 1 15:28:21 2023 ——— opened ChimeraX session > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/B Alignment identifier is 1/B > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/C Alignment identifier is 2/C > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > select #1/B:8 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:8 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:45 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:45 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > select #2/B:228-271 358 atoms, 368 bonds, 44 residues, 1 model selected > select #2/B 2214 atoms, 2270 bonds, 271 residues, 1 model selected > select #1/A:123-388 2180 atoms, 2234 bonds, 266 residues, 1 model selected > select #1/B:16 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:16 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > select #1/B:19 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:19 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > select #1/B:19 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:19 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:8 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:8 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:10 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:10 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel target ab > select #1/A:123-388 2180 atoms, 2234 bonds, 266 residues, 1 model selected > color sel blue > select #1/B:33 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/B:33-35 31 atoms, 33 bonds, 3 residues, 1 model selected > select #1/B:35 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/B:34-35 25 atoms, 27 bonds, 2 residues, 1 model selected > show sel target ab > select #2/C:103 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:103-104 22 atoms, 23 bonds, 2 residues, 1 model selected > show sel target ab > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:31 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/C:31 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:31 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/C:31 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/B:11 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:11 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:15 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:15 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:25-26 20 atoms, 20 bonds, 2 residues, 1 model selected > select #2/C:25-26 20 atoms, 20 bonds, 2 residues, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:28 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:28-30 21 atoms, 21 bonds, 3 residues, 1 model selected > select #1/B:13 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/B:13-15 21 atoms, 21 bonds, 3 residues, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/B:70 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/B:70 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel target ab > select #2/B:76 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/B:76 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:112 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/C:112 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel target ab > color sel lime > select #2/C:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:101 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > select > #2/B:11-13,47-53,56-68,99-106,111-131,140-142,174-176,179-182,189-205,215-223,235-244,249-251,255-260,262-267 944 atoms, 949 bonds, 113 residues, 1 model selected > select #2/B:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/B:131 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/B:1-45 359 atoms, 366 bonds, 45 residues, 1 model selected > select #2/B:1-45 359 atoms, 366 bonds, 45 residues, 1 model selected > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:39 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:39 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/C:44 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:41 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/C:41-42 13 atoms, 13 bonds, 2 residues, 1 model selected > select #2/C:41 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/C:41 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #2/C:25 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:25-26 20 atoms, 20 bonds, 2 residues, 1 model selected > select #2/C:34 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:34 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #1/B:42 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:42 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:79 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:79 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:32-35,42-45,60-66,73-85,90-105 366 atoms, 370 bonds, 44 residues, 1 model selected > select #2/C:74 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:26 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:27 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/C:27 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #2/C:34 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:34 8 atoms, 7 bonds, 1 residue, 1 model selected > save ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"" > select #2/C:73-74 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2/C:73-74 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2/C:74 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:74 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:75 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:75 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:22 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:22 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:36 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:37 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel target a > select #2/C:60 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:60-65 45 atoms, 44 bonds, 6 residues, 1 model selected > show sel target ab > hide sel target a > select #2/C:60 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:60 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/C:56 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/C:58 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel target ab > select #2/C:62 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:62 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:61 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:61 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > hide sel target a > select #2/C:66 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:66 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:72 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:72 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:59 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/C:59 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel target ab > save ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"" > select #2/C:102 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:102 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/C:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/B:34 14 atoms, 15 bonds, 1 residue, 1 model selected > select #1/B:34-35 25 atoms, 27 bonds, 2 residues, 1 model selected > select #1/B:34 14 atoms, 15 bonds, 1 residue, 1 model selected > select #1/B:34 14 atoms, 15 bonds, 1 residue, 1 model selected > save ""/Users/lionelpintard/Desktop/10-Structures/Alphafold Prediction/2- > Bora 18-120 - Aurora A/Superposition Tpx2 versus Bora binding to AURKA.cxs"" [Repeated 1 time(s)] ——— End of log from Sun Oct 1 16:53:59 2023 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Model Number: Z160000YLFN/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 2 jours, 18 heures et 57 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: PL2792H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: On Mirror Status: Master Mirror Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Mirror: On Mirror Status: Hardware Mirror Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 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 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate Tom Goddard all ChimeraX