id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10407 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-14.0-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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""rollouts"" : [ { ""rolloutId"" : ""632e3f9c01482c74ed76392d"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""657b9a2c741fc111f6da926c"" }, ""deploymentId"" : 240000350 }, { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF 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 /Users/jacobposner/Downloads/AF-A0A3Q2D0W7-F1-model_v4.pdb format pdb Summary of feedback from opening /Users/jacobposner/Downloads/AF-A0A3Q2D0W7-F1-model_v4.pdb --- warning | Ignored bad PDB record found on line 38 DBREF XXXX A 1 284 UNP A0A3Q2D0W7 A0A3Q2D0W7_CYPVA 1 284 AF-A0A3Q2D0W7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for methionine adenosyltransferase 2 subunit β (A0A3Q2D0W7) [more info...] Chain information for AF-A0A3Q2D0W7-F1-model_v4.pdb #1 --- Chain | Description A | methionine adenosyltransferase 2 subunit β > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > open 4NDN 4ndn title: Structural insights of MAT enzymes: MATa2b complexed with SAM and PPNP [more info...] Chain information for 4ndn #2 --- Chain | Description | UniProt A B C D | S-adenosylmethionine synthase isoform type-2 | METK2_HUMAN 1-395 E F | Methionine adenosyltransferase 2 subunit beta | MAT2B_HUMAN 1-323 Non-standard residues in 4ndn #2 --- EDO — 1,2-ethanediol (ethylene glycol) MG — magnesium ion PPK — (diphosphono)aminophosphonic acid SAM — S-adenosylmethionine > hide surfaces > hide cartoons > show cartoons > hide atoms > ui tool show Matchmaker > 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 AF-A0A3Q2D0W7-F1-model_v4.pdb, chain A (#1) with 4ndn, chain F (#2), sequence alignment score = 697.8 RMSD between 188 pruned atom pairs is 0.792 angstroms; (across all 252 pairs: 6.055) > select #1/A 2277 atoms, 2329 bonds, 284 residues, 1 model selected > color sel blue > select #2/E#2/F 4945 atoms, 4975 bonds, 1 pseudobond, 699 residues, 2 models selected > color (#!2 & sel) red > color (#!2 & sel) magenta > select clear > select #1/A 2277 atoms, 2329 bonds, 284 residues, 1 model selected > color sel purple > color sel #1cee30ff > color sel #1af020ff > color sel #1af215ff > color sel #1df214ff > color sel #1ff313ff > color sel #20f312ff > color sel #20f512ff > color sel #1ff311ff > color sel #20f510ff > color sel #1ff610ff > color sel #22f70fff > color sel #22f70eff > color sel #26f80bff > color sel #27f906ff > color sel #29fb04ff > color sel #2cfc02ff > color sel #2dfe02ff > color sel #2eff01ff > color sel #30ff01ff > color sel #33fe01ff > color sel #32fe01ff > color sel #2ffe01ff > color sel #2dfe02ff > color sel #2cfe02ff > color sel #28fe02ff > color sel #25fd02ff > color sel #1ffc02ff > color sel #1bfc02ff > color sel #13fc02ff > color sel #0bfd02ff > color sel #02fc02ff > color sel #01fd09ff > color sel #01fd12ff > color sel #01fc18ff > color sel #01fd23ff > color sel #01fd2bff > color sel #01fe34ff > color sel #01fd3eff > color sel #00fd48ff > color sel #00fe55ff > color sel #00fe5fff > color sel #00fe68ff > color sel #00fd70ff > color sel #00fd7aff > color sel #00fd81ff > color sel #00fe8dff > color sel #00feb4ff > color sel #00fec9ff > color sel #00fed8ff > color sel #00fee6ff > color sel #00fdf3ff > color sel #00fdf9ff > color sel #00fcfcff > color sel #00f4feff > color sel #00f1feff > color sel #00ecfeff > color sel #00ebfeff > color sel #00eafeff > color sel #00e9feff > color sel #01e2feff > color sel #04ddfdff > color sel #06d8faff > color sel #0bd1f8ff > color sel #0fcff6ff > color sel #12ccf4ff > color sel #16cbf0ff > color sel #18ceefff > color sel #19d2f0ff > color sel #1ad7efff > color sel #1adcefff > color sel #1ae5efff > color sel #1aeeefff > color sel #19f0e8ff > color sel #18f0dcff > color sel #16f0cbff > color sel #14f2b9ff > color sel #11f5a6ff > color sel #0ff591ff > color sel #0cf782ff > color sel #0af974ff > color sel #07fa68ff > color sel #06fa63ff > color sel #02fc5aff > color sel #01fd58ff > color sel #01ff57ff > color sel #00fe58ff > color sel #00fe5bff > color sel #00fe65ff > color sel #00ff6fff > color sel #00ff86ff > color sel #00ff9bff > color sel #00ffbcff > color sel #00fedcff > color sel #01fefaff > color sel #01e0fdff > color sel #02bbfeff > color sel #02a0fcff > color sel #0492fdff > color sel #0486fdff > color sel #0484fdff > color sel #0482fdff > color sel #0482fcff > color sel #0483fcff > color sel #0484fcff > color sel #0485fcff > color sel #0487fcff > color sel #0491fcff > color sel #049dfcff > color sel #04abfdff > color sel #02cafcff > color sel #02d5fcff > color sel #02e1feff > color sel #02e7feff > color sel #02e9feff > color sel #02eafeff > color sel #01ecfdff > color sel #01f1fdff > color sel #01f2feff > color sel #01f4ffff > color sel #01f5ffff > color sel #00f3feff > color sel #00f2feff > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #2/E #2/F Alignment identifier is 1 > open /Users/jacobposner/Downloads/AF-G7HV35-F1-model_v4.cif Chain information for AF-G7HV35-F1-model_v4.cif #3 --- Chain | Description | UniProt A | S-adenosylmethionine synthase | G7HV35_9CORY 1-407 > ui mousemode right zoom > close session > open /Users/jacobposner/Downloads/AF-G7HV35-F1-model_v4.cif format mmcif Chain information for AF-G7HV35-F1-model_v4.cif #1 --- Chain | Description | UniProt A | S-adenosylmethionine synthase | G7HV35_9CORY 1-407 > open 4NDN 4ndn title: Structural insights of MAT enzymes: MATa2b complexed with SAM and PPNP [more info...] Chain information for 4ndn #2 --- Chain | Description | UniProt A B C D | S-adenosylmethionine synthase isoform type-2 | METK2_HUMAN 1-395 E F | Methionine adenosyltransferase 2 subunit beta | MAT2B_HUMAN 1-323 Non-standard residues in 4ndn #2 --- EDO — 1,2-ethanediol (ethylene glycol) MG — magnesium ion PPK — (diphosphono)aminophosphonic acid SAM — S-adenosylmethionine > select add #2 17089 atoms, 16919 bonds, 20 pseudobonds, 2623 residues, 3 models selected > hide sel atoms > show sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #2/A #2/B #2/C #2/D Alignment identifier is 1 > sequence chain #2/E #2/F Alignment identifier is 2 > undo > redo > select #1/A:364-407 357 atoms, 364 bonds, 44 residues, 1 model selected > select #1/A 3074 atoms, 3130 bonds, 407 residues, 1 model selected > select #2/A-D:395 52 atoms, 52 bonds, 4 residues, 1 model selected > select #2/A,C:15-395/B:13-395/D:14-395 11583 atoms, 11814 bonds, 2 pseudobonds, 1487 residues, 2 models selected > select #2/E-F:281-323 722 atoms, 740 bonds, 86 residues, 1 model selected > select #2/E-F:15-323 4856 atoms, 4972 bonds, 1 pseudobond, 613 residues, 2 models selected > select #1/A:363-407 365 atoms, 372 bonds, 45 residues, 1 model selected > select #1/A 3074 atoms, 3130 bonds, 407 residues, 1 model selected > ui tool show Matchmaker > matchmaker #1 to #2/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 4ndn, chain D (#2) with AF-G7HV35-F1-model_v4.cif, chain A (#1), sequence alignment score = 1176.7 RMSD between 348 pruned atom pairs is 0.652 angstroms; (across all 375 pairs: 2.261) > color sel cornflower blue > color sel #97e67aff > color sel #abe57aff > color sel #d2e67aff > color sel #dfe57aff > color sel #e6df7aff > color sel #e6d97aff > color sel #e6d67aff > color sel #e6d37cff > color sel #e7d17fff > color sel #e7d081ff > color sel #e7d285ff > color sel #e8d38aff > color sel #e8d38eff > color sel #e8d490ff > color sel #e9d591ff > color sel #e9d592ff > color sel #e9d894ff > color sel #e9e39cff > color sel #eae89fff > color sel #e9e9a2ff > color sel #eaeaa3ff > color sel #e9eaa6ff > color sel #e9eaa9ff > color sel #e9ebafff > color sel #e8edb2ff > color sel #e8eeb6ff > color sel #e8edb7ff > color sel #e8edb8ff > color sel #e7edb8ff > color sel #e7eeb9ff > color sel #e6eebcff > color sel #e3efc4ff > color sel #e1f1caff > color sel #dff2ceff > color sel #dbf2cfff > color sel #d9f2d1ff > color sel #d9f2d2ff > color sel #d8f2d1ff > color sel #d7f2d2ff > color sel #d6f1d2ff > color sel #d4f2d2ff > color sel #d2f1d5ff > color sel #d3f2d7ff > color sel #d2f2dcff > color sel #d3f1deff > color sel #d2f2e0ff > color sel #d3f2e0ff > color sel #d3f1e2ff > color sel #d2f2e5ff > color sel #d2f1e7ff > color sel #d2f2e8ff > color sel #d1f2e8ff > color sel #d0f2e7ff > color sel #d0f1e9ff > color sel #d0f2e9ff > color sel #cff2e8ff > color sel #cdf1e8ff > color sel #c5efe7ff > color sel #b9ede6ff > color sel #93e8e0ff > color sel #7ee5dfff > color sel #66e4deff > color sel #39e7d6ff > color sel #27eac3ff > color sel #16f19aff > color sel #0ff56aff > color sel #07fa40ff > color sel #01fe15ff > color sel #00ff0dff > color sel #00ff0aff > color sel #00fe06ff > color sel #00fe05ff > color sel #01fd06ff > color sel #02fc09ff > color sel #05f81eff > color sel #06f637ff > color sel #07f570ff > color sel #09f3b4ff > color sel #09cdf3ff > color sel #098bf3ff > color sel #0950f3ff > color sel #0914f3ff > color sel #0a0af2ff > color sel #120af3ff > color sel #1709f3ff > color sel #210af2ff > color sel #280af2ff > color sel #2f0af1ff > color sel #3b0af0ff > color sel #450befff > color sel #630fe8ff > color sel #750fe2ff > color sel #8210deff > color sel #8d11daff > color sel #9611d4ff > color sel #9d13d1ff > color sel #a514c9ff > color sel #a314c4ff > color sel #a314c1ff > color sel #a015bcff > color sel #9616aeff > color sel #8f16a8ff > color sel #8a16a0ff > color sel #811794ff > color sel #7c178fff > color sel #79178bff > color sel #761688ff > color sel #741785ff > color sel #711681ff > color sel #6a167aff > color sel #661676ff > color sel #631673ff > color sel #5d166cff > color sel #51165fff > color sel #4b1458ff > color sel #461452ff > color sel #41134cff > color sel #3b1345ff > color sel #3a1243ff > color sel #391243ff > color sel #3a1243ff > color sel #3b1344ff > color sel #3e1346ff > color sel #401348ff > color sel #421449ff > color sel #44144bff > color sel #46144cff > color sel #481450ff > color sel #4c1452ff > color sel #551459ff > color sel #5b145eff > color sel #611563ff > color sel #671567ff > color sel #6d166bff > color sel #6f156dff > color sel #751671ff > color sel #781674ff > color sel #7b1676ff > color sel #811679ff > color sel #851779ff > color sel #8a167dff > color sel #91167fff > color sel #931680ff > color sel #97177fff > color sel #991681ff > color sel #a01685ff > color sel #a21685ff > color sel #a11684ff > color sel #9b1680ff > color sel #901779ff > color sel #8a1675ff > color sel #841672ff > color sel #7b1670ff > color sel #75166eff > color sel #70166bff > color sel #6b1569ff > color sel #57155eff > color sel #4b1458ff > color sel #3b1455ff > color sel #271453ff > color sel #1a1452ff > color sel #152952ff > color sel #153752ff > color sel #154152ff > color sel #154a54ff > color sel #165358ff > color sel #165e5aff > color sel #166056ff > color sel #166356ff > color sel #166453ff > color sel #166452ff > color sel #176b54ff > color sel #166d52ff > color sel #177252ff > color sel #177551ff > color sel #17784cff > color sel #177c3fff > color sel #177e36ff > color sel #177e2bff > color sel #177e1fff > color sel #177e1cff > color sel #177e17ff > color sel #177e16ff > color sel #1a7c16ff > color sel #1a7b16ff > color sel #1a7916ff > color sel #1b7116ff > color sel #1a6c16ff > color sel #1d6115ff > color sel #1d5b14ff > color sel #1f5614ff > color sel #215114ff > color sel #204d13ff > color sel #214b13ff > color sel #214a14ff > color sel #224a13ff > color sel #224913ff > color sel #224813ff > color sel #224913ff > color sel #224a13ff > color sel #224913ff > color sel #214914ff > color sel #214a14ff > color sel #214b14ff > color sel #224b14ff > color sel #224c14ff > color sel #234e14ff > color sel #235014ff > color sel #245214ff > color sel #265914ff > color sel #265f15ff > color sel #276416ff > color sel #296c16ff > color sel #2b7916ff > color sel #2b7f16ff > color sel #2a8216ff > color sel #2a8516ff > color sel #2a8616ff > color sel #2a8816ff > color sel #2b8b17ff > color sel #2b8f16ff > color sel #2c9616ff > color sel #2c9816ff > color sel #2c9916ff > color sel #2d9b16ff > color sel #2e9f16ff > color sel #2fa416ff > color sel #36b915ff > color sel #3cc614ff > color sel #3fd511ff > color sel #44f308ff > color sel #3ffc01ff > color sel #3bff00ff > color sel #1df610ff > color sel #1af01aff > color sel #25eb33ff > color sel #34e857ff > color sel #4ee598ff > color sel #58e3abff > color sel #5fe5bbff > color sel #64e5c6ff > color sel #68e4d0ff > color sel #6ae5d6ff > color sel #6ae5d7ff > color sel #6ae4d6ff > color sel #6ae3d5ff > color sel #6ae3d7ff > color sel #6ae4dcff > color sel #6de4e2ff > color sel #73d6e5ff > color sel #839ce7ff > color sel #8a8ce6ff > color sel #9d92e7ff > color sel #b196e7ff > color sel #cb9ae8ff > color 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#ff0155ff > color sel #fc0562ff > color sel #fa096dff > color sel #f80b70ff > color sel #f70f74ff > color sel #f5107bff > color sel #f31380ff > color sel #f2147fff > color sel #f21483ff > color sel #f21684ff > color sel #f11683ff > color sel #f01a8dff > color sel #f01a90ff > color sel #ed22a7ff > color sel #ea28b8ff > color sel #e831ceff > color sel #e642e4ff > color sel #c06be3ff > color sel #b37fe5ff > color sel #ac8fe8ff > color sel #ad99e8ff > color sel #ada0eaff > color sel #aea3eaff > color sel #ada3eaff > color sel #aea4eaff > color sel #aea5eaff > color sel #afa6ebff > color sel #afa5ebff > color sel #b0a6ebff > color sel #b2a7eaff > color sel #b6a9ebff > color sel #baabebff > color sel #c1adedff > color sel #c6afebff > color sel #d2b0ebff > color sel #d4b0ebff > color sel #d5b0ebff > color sel #d8b0edff > color sel #d8b1edff > color sel #d8b3ecff > color sel #d8b6eeff > color sel #d8baedff > color sel #d7c2f0ff > color sel #d9c7f0ff > color sel #ddcff1ff > color sel #dfd6f3ff > color sel #e6e0f6ff > color sel #e6e2f6ff > color sel #e8e3f6ff > color sel #e9e4f7ff > color sel #eae7f6ff > color sel #ebe8f7ff > color sel #ede9f8ff > color sel #edeaf8ff > color sel #eeedf9ff > color sel #f0eef9ff > color sel #f1f0faff > color sel #f2f1faff > color sel #f1f1faff > color sel #f2f1f9ff > color sel #f1f1faff > color sel #f1f0faff > color sel #f1effaff > color sel #f0eef9ff > color sel #eeedf9ff > color sel #ecebf8ff > color sel #ebeaf7ff > color sel #eae9f8ff > color sel #e9e7f7ff > color sel #e8e6f6ff > color sel #e5e2f7ff > color sel #e1def6ff > color sel #dcd8f4ff > color sel #ccc9f0ff > color sel #c1bfeeff > color sel #b4b7ebff > color sel #a7b5ebff > color sel #9bb7e9ff > color sel #93bce9ff > color sel #88c2e6ff > color sel #86c5e6ff > color sel #83c5e7ff > color sel #80c3e6ff > color sel #7ac0e6ff > color sel #73bce5ff > color sel #5fa0e5ff > color sel #5492e3ff > color sel #4a7ee5ff > color sel #4171e5ff > color sel #335ce7ff > color sel #2e58e9ff > color sel #2a54e9ff > color sel #2850eaff > color sel #254debff > color sel #2347eaff > color sel #2043edff > color sel #1d41eeff > color sel #1c3feeff > color sel #1a38efff > color sel #1936f0ff > color sel #1834efff > color sel #1734f0ff > color sel #1630f1ff > color sel #162df1ff > color sel #162cf1ff > color sel #162bf1ff > color sel #162af1ff > color sel #1629f1ff > color sel #1627f1ff > select #2/D 3113 atoms, 3049 bonds, 505 residues, 1 model selected > color sel #1a1deeff > color sel #1a1eeeff > color sel #1a20efff > color sel #1921f0ff > color sel #142bf2ff > color sel #1433f3ff > color sel #1148f3ff > color sel #1050f5ff > color sel #0f5df7ff > color sel #0c65f7ff > color sel #0c6ff7ff > color sel #0a7af7ff > color sel #0a84f9ff > color sel #0988f8ff > color sel #0790f9ff > color sel #0792f9ff > color sel #0793f9ff > color sel #0796f9ff > color sel #06a3faff > color sel #04d0fdff > color sel #02e9feff > color sel #01fcfcff > color sel #01fef0ff > color sel #01ffdcff > color sel #01ffd6ff > color sel #01ffd5ff > color sel #01ffd4ff > color sel #01ffd5ff > color sel #02fdd7ff > color sel #03fddaff > color sel #05fad9ff > color sel #07f8e0ff > color sel #0af9e1ff > color sel #0bf7e6ff > color sel #0cf7e7ff > color sel #0ff5edff > color sel #10f4efff > color sel #12f2f0ff > color sel #14f1f1ff > color sel #14f0f2ff > color sel #14eff2ff > color sel #14eef2ff > color sel #14edf2ff > color sel #14ebf2ff > color sel #14e8f2ff > color sel #14c2f3ff > color sel #1283f4ff > color sel #116df5ff > color sel #1161f4ff > color sel #1158f3ff > color sel #1157f3ff > color sel #1155f3ff > color sel #1154f3ff > color sel #114ff3ff > color sel #114cf4ff > color sel #1142f5ff > color sel #1431f2ff > color sel #152af1ff > color sel #1625f1ff > color sel #1722f0ff > color sel #1820efff > color sel #1920f0ff > color sel #191ff0ff > color sel #191cf0ff > color sel #1d19efff > color sel #521befff > color sel #7a1eeeff > color sel #a022edff > color sel #b425eaff > color sel #cd2de8ff > color sel #d32fe9ff > color sel #d430e8ff > color sel #d630e7ff > color sel #d631e7ff > color sel #d630e7ff > color sel #d830e7ff > color sel #d931e7ff > color sel #da33e7ff > color sel #e034e8ff > color sel #e335e8ff > color sel #e336e7ff > color sel #e735e7ff > color sel #e736e7ff > color sel #e735e8ff > color sel #e636e7ff > color sel #e735e8ff > color sel #e535e8ff > color sel #e435e8ff > color sel #e338e7ff > color sel #e13ee5ff > color sel #dd4be5ff > color sel #d978e5ff > color sel #db8ae7ff > color sel #df99e9ff > color sel #e1a2e9ff > color sel #e3a9ebff > color sel #e2aaebff > color sel #e1abebff > color sel #dbaaeaff > color sel #ceaaeaff > color sel #b4a8ebff > color sel #9fcdeaff > color sel #9be5e9ff > color sel #99e9e0ff > color sel #99e9d6ff > color sel #9be8c7ff > color sel #a0e9c3ff > color sel #a6eac1ff > color sel #aceabdff > color sel #b0edbdff > color sel #b6edbdff > color sel #bdefbdff > color sel #c3efc1ff > color sel #c6efc1ff > color sel #cdf0c2ff > color 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#9b5b16ff > color sel #995b16ff > color sel #955916ff > color sel #935817ff > color sel #8c5516ff > color sel #8a5316ff > color sel #865117ff > color sel #825016ff > color sel #7a4b16ff > color sel #6f4616ff > color sel #6c4515ff > color sel #684415ff > color sel #674116ff > color sel #654216ff > color sel #634115ff > color sel #624115ff > color sel #624015ff > color sel #614015ff > color sel #5f3d15ff > color sel #5c3a15ff > color sel #5a3515ff > color sel #563214ff > color sel #552f14ff > color sel #512914ff > color sel #512814ff > color sel #4f2914ff > color sel #4f2b14ff > color sel #4d2d13ff > color sel #4c2f13ff > color sel #4c3113ff > color sel #4c3514ff > color sel #4b3614ff > color sel #4b3a14ff > color sel #4b3b14ff > color sel #4b3c14ff > color sel #4a3b13ff > color sel #493a12ff > color sel #463913ff > color sel #433511ff > color sel #3d3011ff > color sel #372d11ff > color sel #2e250fff > color sel #2e220fff > color sel #2d220fff > color sel #2f240fff > color sel #34270fff > color sel #3d2d11ff > color sel #463313ff > color sel #523a14ff > color sel #5d4014ff > color sel #744f16ff > color sel #7c5316ff > color sel #825816ff > color sel #875b17ff > color sel #8c5e16ff > color sel #906016ff > color sel #9c6017ff > color sel #a06216ff > color sel #a45f16ff > color sel #a95f16ff > color sel #ab5c16ff > color sel #ad5a16ff > color sel #b05915ff > color sel #ba4d14ff > color sel #c14914ff > color sel #ca4313ff > color sel #d14212ff > color sel #dd3b11ff > color sel #e03c10ff > color sel #e33b0fff > color sel #e53b0fff > color sel #e73c0fff > color sel #e83b0eff > color sel #ea3b0eff > color sel #ee3b0cff > color sel #f33b09ff > color sel #f73a07ff > color sel #f93a05ff > color sel #fd3904ff > color sel #fe3902ff > color sel #fe3800ff > color sel #ff3701ff > color sel #ff3301ff > color sel #ff3101ff > color sel #ff2f01ff > color sel #ff3301ff > color sel #ff3b01ff > color sel #ff4201ff > color sel #ff4b01ff > color sel #ff5b01ff > color sel #ff6701ff > color sel #ff7701ff > color sel #ff8e01ff > color sel #ffb102ff > color sel #fed602ff > color sel #cbfc04ff > color sel #84f906ff > color sel #48f909ff > color sel #1ef70eff > color sel #0ff70fff > color sel #0ff618ff > color sel #10f533ff > color sel #11f445ff > color sel #12f356ff > color sel #12f36aff > color sel #13f27eff > color sel #14f2a7ff > color sel #14f2b0ff > color sel #14f1bfff > color sel #14f1cbff > color sel #14f1d7ff > color sel #14f1e2ff > color sel #14f2e9ff > color sel #14f0f2ff > color sel #14e8f3ff > color sel #13e0f2ff > color sel #12d7f3ff > color sel #12cff4ff > color sel #11c5f5ff > color sel #10b7f5ff > color sel #10aef5ff > color sel #10a3f5ff > color sel #0f96f6ff > color sel #0f85f6ff > color sel #0f73f6ff > color sel #0f49f6ff > color sel #0f34f6ff > color sel #0f1ff6ff > color sel #0f11f6ff > color sel #1c0ff5ff > color sel #2810f5ff > color sel #3711f5ff > color sel #4b12f2ff > color sel #7616f0ff > color sel #8e1aefff > color sel #b221ebff > color sel #bd26ebff > color sel #cf2de8ff > color sel #d42fe8ff > color sel #d530e7ff > color sel #d831e7ff > color sel #d931e7ff > color sel #de31e8ff > color sel #e232e8ff > color sel #e832e6ff > color sel #e834e0ff > color sel #e834d9ff > color sel #e735cdff > color sel #e737c6ff > color sel #e739c0ff > color sel #e73abeff > color sel #e73cb7ff > color sel #e73cb5ff > color sel #e641b3ff > color sel #e642b1ff > color sel #e64ab1ff > color sel #e550b1ff > color sel #e656b3ff > color sel #e66abaff > color sel #e672bdff > color sel #e67ac0ff > color sel #e77ec4ff > color sel #e782c5ff > color sel #e784c6ff > color sel #e785c6ff > color sel #e785c7ff > color sel #e887c9ff > color sel #e889caff > color sel #e88bcaff > color sel #e88ecbff > color sel #e88dccff > color sel #e88ccdff > color sel #e78aceff > color sel #e889cfff > color sel #e784d2ff > color sel #e781d1ff > color sel #e77cd2ff > color sel #e679d4ff > color sel #e674d2ff > color sel #e568d4ff > color sel #e561d3ff > color sel #e55ad2ff > color sel #e552d2ff > color sel #e642d1ff > color sel #e73bd2ff > color sel #e835d3ff > color sel #e92fd7ff > color sel #ea2bdaff > color sel #eb25e0ff > color sel #ed22e6ff > color sel #ee20e9ff > color sel #ee1deeff > color sel #ee1defff > color sel #ee1befff > color sel #ed1befff > color sel #eb1aefff > color sel #e81af0ff > color sel #e018f1ff > color sel #bc14f3ff > color sel #9d11f4ff > color sel #7e11f5ff > color sel #690ff6ff > color sel #530ff6ff > color sel #3f0ff7ff > color sel #3b0ef7ff > color sel #370ef7ff > color sel #360ef7ff > color sel #340ef7ff > color sel #2f0ef6ff > color sel #280ff6ff > color sel #1e0ff5ff > color sel #1810f5ff > color sel #141af2ff > color sel #161ff0ff > color sel #1a28efff > color sel #1a2beeff > color sel #1c2deeff > color sel #1d2feeff > color sel #1d30eeff > color sel #1d2feeff > color sel #1d2eeeff > color sel #1d2beeff > color sel #1d25eeff > color sel #201dedff > color sel #261eedff > color sel #291deeff > color sel #321deeff > color sel #391deeff > color sel #421cefff > color sel #4b1ceeff > color sel #5b1beeff > color sel #691aefff > color sel #841aeeff > color sel #911aefff > color sel #9e1aefff > color sel #a91aefff > color sel #ba1ceeff > color sel #be1ceeff > color sel #c61deeff > color sel #ce1eeeff > color sel #d220eeff > color sel #d521ebff > color sel #da24eaff > color sel #de25eaff > color sel #e025e9ff > color sel #e026e9ff > color sel #e027e9ff > color sel #e025e9ff > color sel #e126eaff > color sel #e125eaff > color sel #e123eaff > color sel #e222ecff > color sel #e223ebff > color sel #e222ecff > color sel #e322ebff > color sel #e322ecff > color sel #e322ebff > color sel #e622ebff > color sel #e722ebff > color sel #e922ecff > color sel #ec23ecff > color sel #eb24e8ff > color sel #eb26e0ff > color sel #ea28deff > color sel #ea29daff > color sel #ea2ad7ff > color sel #e92cd4ff > color sel #e92dd1ff > color sel #e92fd0ff > color sel #e930cfff > color sel #e833ceff > color sel #e836ceff > color sel #e73bcfff > color sel #e63ed0ff > color sel #e63fcfff > color sel #e640cfff > color sel #e641cfff > color sel #e641d0ff > color sel #e641cfff > color sel #e644d0ff > color sel #e644cfff > color sel #e646d1ff > color sel #e649d2ff > color sel #e64bd4ff > color sel #e64dd7ff > color sel #e550d7ff > color sel #e657deff > color sel #e55be2ff > color sel #e561e5ff > color sel #e264e5ff > color sel #e068e4ff > color sel #df6ae3ff > color sel #dc6ee5ff > color sel #db6fe4ff > color sel #d972e5ff > color sel #d773e5ff > color sel #d479e5ff > color sel #d37ae5ff > color sel #d37be5ff > color sel #d37ce6ff > color sel #d080e7ff > color sel #ce85e6ff > color sel #cc8ae6ff > color sel #c894e8ff > color sel #c4a5eaff > color sel #c4abeaff > color sel #c5b0ebff > color sel #c5b2ebff > color sel #c5b5edff > color sel #c5b6eeff > color sel #c6b6eeff > color sel #c8b6eeff > color sel #cab6edff > color sel #cdb6edff > color sel #cdb5edff > color sel #cfb5edff > color sel #ceaeebff > color sel #cea8ebff > color sel #cba3eaff > color sel #cb9feaff > color sel #c794e9ff > color sel #c78de8ff > color sel #c688e7ff > color sel #c483e6ff > color sel #c27ee6ff > color sel #c279e6ff > color sel #c379e6ff > color sel #c378e6ff > color sel #c377e6ff > color sel #c376e5ff > color sel #c373e4ff > color sel #c46ae3ff > color sel #c764e5ff > color sel #c760e5ff > color sel #c75be4ff > color sel #ca58e3ff > color sel #cb55e3ff > color sel #cb50e5ff > color sel #cd4ee4ff > color sel #ce4ce5ff > color sel #ce4ae5ff > color sel #ce48e5ff > color sel #d046e5ff > color sel #d045e5ff > color sel #d145e6ff > color sel #d143e5ff > color sel #d342e6ff > color sel #d341e5ff > color sel #d43de5ff > color sel #d73ae7ff > color sel #d935e7ff > color sel #da30e8ff > color sel #df29e9ff > color sel #e123eaff > color sel #e21eeeff > color sel #e51af0ff > color sel #e912f3ff > color sel #ea11f5ff > color sel #eb0ff5ff > color sel #eb0ff6ff > color sel #eb0ef6ff > color sel #eb0cf6ff > color sel #eb0df7ff > color sel #eb0df8ff > color sel #eb0af9ff > color sel #e707faff > color sel #da05fcff > color sel #b404fdff > color sel #6a01ffff > color sel #059bf9ff > color sel #0bed82ff > color sel #46da10ff > color sel #c27114ff > color sel #bc3115ff > color sel #b71915ff > color sel #ba1614ff > color sel #cf1812ff > color sel #dd1d11ff > color sel #ea2f0eff > color sel #fc7503ff > color sel #fea600ff > color sel #ffcd01ff > color sel #f9f707ff > color sel #e6f50fff > color sel #c9f115ff > color sel #abee1bff > color sel #7fe926ff > color sel #74e92aff > color sel #6ee92cff > color sel #6ce82dff > color sel #6be82dff > color sel #66e82dff > color sel #62e82dff > color sel #4fe92dff > color sel #48e92cff > color sel #44e92cff > color sel #3de929ff > color sel #37ea28ff > color sel #35ea26ff > color sel #31eb24ff > color sel #2ced20ff > color sel #26ef1bff > color sel #1ff117ff > color sel #19f311ff > color sel #12f80cff > color sel #0bfc07ff > color sel #08fb06ff > color sel #07fc05ff > color sel #05fc05ff > color sel #04fd04ff > color sel #03fe02ff > color sel #06ff02ff > color sel #0bfe01ff > color sel #39ff01ff > color sel #84fe01ff > color sel #ebfd03ff > color sel #f86f06ff > color sel #f63c07ff > color sel #f52707ff > color sel #f41f08ff > color sel #f41c08ff > color sel #f51c07ff > color sel #f61c09ff > color sel #f71b07ff > color sel #f81b06ff > color sel #fb1d05ff > color sel #fd2003ff > color sel #ff2e01ff > color sel #ff3801ff > color sel #fe4202ff > color sel #fc4a05ff > color sel #f9520aff > color sel #f56011ff > color sel #f26915ff > color sel #f16b18ff > color sel #f06c1aff > color sel #ef6e1bff > color sel #ef6d1bff > color sel #ef671bff > color sel #ef671cff > color sel #ef661bff > color sel #ef651bff > color sel #ef641bff > color sel #f0641aff > color sel #f0631aff > color sel #f0621aff > color sel #f15a18ff > color sel #f15616ff > color sel #f25014ff > color sel #f34d14ff > color sel #f54810ff > color sel #f7430fff > color sel #f83f0eff > color sel #f93c0aff > color sel #fa3906ff > color sel #fc3505ff > color sel #fd3004ff > color sel #fe2e03ff > color sel #fe2c02ff > color sel #ff2c01ff > color sel #ff2701ff > color sel #ff2601ff > color sel #ff2501ff > color sel #ff2401ff > set bgColor white > set bgColor #ffffff00 > select #2/A#2/B#2/C#2/D 12144 atoms, 11944 bonds, 19 pseudobonds, 1924 residues, 3 models selected > hide sel cartoons > select #2/D 3113 atoms, 3049 bonds, 505 residues, 1 model selected > show sel cartoons > open ""/Users/jacobposner/Downloads/AF-G7HV35-F1-model_v4 copy.cif"" Chain information for AF-G7HV35-F1-model_v4 copy.cif #3 --- Chain | Description | UniProt A | S-adenosylmethionine synthase | G7HV35_9CORY 1-407 > ui tool show Matchmaker > select #2/C 2949 atoms, 2912 bonds, 7 pseudobonds, 456 residues, 3 models selected > show sel cartoons > hide sel cartoons > matchmaker #3/A to #2/C pairing ss Parameters --- Chain pairing | ss 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 4ndn, chain C (#2) with AF-G7HV35-F1-model_v4 copy.cif, chain A (#3), sequence alignment score = 1145.2 RMSD between 324 pruned atom pairs is 0.793 angstroms; (across all 353 pairs: 1.714) > select ::name=""SAM"" 54 atoms, 58 bonds, 2 residues, 1 model selected > show sel atoms > select ::name=""EDO""::name=""HOH""::name=""MG""::name=""PPK""::name=""SAM"" 650 atoms, 133 bonds, 15 pseudobonds, 523 residues, 2 models selected > show sel atoms > ui mousemode right select > select clear Drag select of 1 atoms, 2 residues, 1 pseudobonds Drag select of 1 atoms, 5 residues > select clear Drag select of 3 atoms, 7 residues, 1 pseudobonds > select clear > select ::name=""MG"" 4 atoms, 4 residues, 1 model selected > color sel magenta > select clear Drag select of 9 residues, 3 atoms > select clear QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX 2023-12-27 12:24:45,531 WARNING Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 60] Operation timed out')': /cxservices/api/v1/chimerax/updates?uuid=26b2c1b5-d13b-5c92-862d-f16b76534655&OS=macosx&OSVersion=14.0&ChimeraXVersion=1.6.1 2023-12-27 12:26:00,537 WARNING Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 60] Operation timed out')': /cxservices/api/v1/chimerax/updates?uuid=26b2c1b5-d13b-5c92-862d-f16b76534655&OS=macosx&OSVersion=14.0&ChimeraXVersion=1.6.1 2023-12-27 12:27:15,541 WARNING Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno 60] Operation timed out')': /cxservices/api/v1/chimerax/updates?uuid=26b2c1b5-d13b-5c92-862d-f16b76534655&OS=macosx&OSVersion=14.0&ChimeraXVersion=1.6.1 OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M1 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 Pro Model Identifier: MacBookPro17,1 Model Number: Z11B000EMLL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 16 days, 42 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: XG2700 SERIES: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: No 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 MolecularDynamicsViewer: 1.4 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