id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15322 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.5-x86_64-i386-64bit ChimeraX Version: 1.8.dev202404150449 (2024-04-15 04:49:30 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000070001eb4c000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000070001b6a5000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff848657fc0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in __iter__ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 907 in atomspec_atoms File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 627 in _add_model_parts File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 476 in _check File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 490 in _check File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 470 in find_matches File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 612 in find_matches File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 455 in find_matches File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1011 in find_matches File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1008 in evaluate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1098 in evaluate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 36 in parse File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 71 in parse File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2495 in _parse_arg File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2791 in _process_keyword_arguments File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2865 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py"", line 303 in run_matchmaker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py"", line 171 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 283 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1006 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1169 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, 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Bytes before following region: 4405505879\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10696b000-10696f000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":77155}, ""vmregioninfo"" : ""0xa9 is not in any region. 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], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8.dev202404150449 (2024-04-15) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/juliendumont/Downloads/fold_2024_05_27_13_34/fold_2024_05_27_13_34_model_0.cif Chain information for fold_2024_05_27_13_34_model_0.cif #1 --- Chain | Description A | . B C | . D | . > select /A 7856 atoms, 8003 bonds, 987 residues, 1 model selected > color sel forest green > select clear > select /B 11657 atoms, 11738 bonds, 1475 residues, 1 model selected > color sel dark gray > select /C 11657 atoms, 11738 bonds, 1475 residues, 1 model selected > color sel dim gray > select clear > select /D 7855 atoms, 7969 bonds, 1020 residues, 1 model selected > rainbow sel > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain /D Alignment identifier is 1/D > select /D:1020 8 atoms, 7 bonds, 1 residue, 1 model selected > select /D:998-1020 175 atoms, 177 bonds, 23 residues, 1 model selected > select /D:969 7 atoms, 6 bonds, 1 residue, 1 model selected > select /D:969-971 27 atoms, 26 bonds, 3 residues, 1 model selected Drag select of 15 residues > select /D:969 7 atoms, 6 bonds, 1 residue, 1 model selected > select /D:969-971 27 atoms, 26 bonds, 3 residues, 1 model selected Drag select of 9 residues > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > select /B:1430-1475 372 atoms, 377 bonds, 46 residues, 1 model selected > select /B:1290-1475 1505 atoms, 1521 bonds, 186 residues, 1 model selected > select /B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:1-195 1452 atoms, 1470 bonds, 195 residues, 1 model selected > select /B:1475 10 atoms, 9 bonds, 1 residue, 1 model selected > select /B:1242-1475 1892 atoms, 1911 bonds, 234 residues, 1 model selected > select /B:1475 10 atoms, 9 bonds, 1 residue, 1 model selected > select /B:91-1475 10982 atoms, 11053 bonds, 1385 residues, 1 model selected > select /B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:1-990 7795 atoms, 7849 bonds, 990 residues, 1 model selected > select /B:1475 10 atoms, 9 bonds, 1 residue, 1 model selected > select /B:1474-1475 20 atoms, 20 bonds, 2 residues, 1 model selected > select /B:1-4,1474-1475 51 atoms, 50 bonds, 6 residues, 1 model selected > select /B:1-2 16 atoms, 15 bonds, 2 residues, 1 model selected > select /B:1-672 5292 atoms, 5336 bonds, 672 residues, 1 model selected > select /B 11657 atoms, 11738 bonds, 1475 residues, 1 model selected > rainbow sel > select clear > select > /B:4-28,31-59,64-103,107-132,140-151,153-158,161-179,182-200,208-211,216-303,305-428,430-531,537-573,579-694,698-834,837-977,981-1149,1151-1384,1388-1417,1421-1448,1450-1474 11166 atoms, 11217 bonds, 1411 residues, 1 model selected > select /B:1428-1430 26 atoms, 26 bonds, 3 residues, 1 model selected > select /B:1330-1430 818 atoms, 826 bonds, 101 residues, 1 model selected > select /B:1386 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:1311-1386 625 atoms, 628 bonds, 76 residues, 1 model selected > hbonds sel reveal true 96 hydrogen bonds found > select clear > select /B:1327-1328 14 atoms, 13 bonds, 2 residues, 1 model selected > select /B:1327-1328 14 atoms, 13 bonds, 2 residues, 1 model selected > select /B:1335-1336 19 atoms, 18 bonds, 2 residues, 1 model selected > select /B:1335-1337 27 atoms, 26 bonds, 3 residues, 1 model selected > select /B:1344 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:1344 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:1345 11 atoms, 10 bonds, 1 residue, 1 model selected > select /B:1345 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:666 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:666-847 1472 atoms, 1500 bonds, 182 residues, 1 model selected > select /A:662 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:662-987 2621 atoms, 2678 bonds, 326 residues, 1 model selected > select /B:1337 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:1337-1345 78 atoms, 77 bonds, 5 pseudobonds, 9 residues, 2 models selected > select /B:1323 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:1323-1370 404 atoms, 406 bonds, 49 pseudobonds, 48 residues, 2 models selected > select /B:1325 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:1325 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:1328 5 atoms, 4 bonds, 1 residue, 1 model selected > select /B:1328-1330 22 atoms, 21 bonds, 3 residues, 1 model selected > select /B:1362 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:1362-1363 16 atoms, 15 bonds, 2 residues, 1 model selected Drag select of 1 atoms, 1 residues, 1 bonds Drag select of 2 atoms, 3 residues, 2 bonds > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:967 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:967-968 10 atoms, 9 bonds, 2 residues, 1 model selected Drag select of 1 atoms, 1 bonds > select /A:921 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:921-923 31 atoms, 30 bonds, 3 residues, 1 model selected > select clear Drag select of 66 residues > select /A 7856 atoms, 8003 bonds, 987 residues, 1 model selected > select /D 7855 atoms, 7969 bonds, 1020 residues, 1 model selected > color sel red > select clear > select /A:191 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A 7856 atoms, 8003 bonds, 987 residues, 1 model selected > color bfactor sel 7856 atoms, 987 residues, atom bfactor range 21.2 to 90.7 > hbonds sel reveal true 994 hydrogen bonds found > select /A 7856 atoms, 8003 bonds, 955 pseudobonds, 987 residues, 2 models selected > color (#!1 & sel) red > color (#!1 & sel) lime > color (#!1 & sel) yellow > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > select /B:1460-1475 131 atoms, 132 bonds, 16 residues, 1 model selected > select /B:1321-1475 1253 atoms, 1267 bonds, 155 residues, 1 model selected > select /B:1430 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:1430-1447 140 atoms, 139 bonds, 18 residues, 1 model selected > select /B:1134-1149 132 atoms, 131 bonds, 16 residues, 1 model selected > select /B:837-1149 2446 atoms, 2452 bonds, 313 residues, 1 model selected > select /B:305 7 atoms, 7 bonds, 1 residue, 1 model selected > select /B:305-612 2448 atoms, 2459 bonds, 308 residues, 1 model selected > select /D 7855 atoms, 7969 bonds, 1020 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > select /A 7856 atoms, 8003 bonds, 955 pseudobonds, 987 residues, 2 models selected > select /B 11657 atoms, 11738 bonds, 1475 residues, 1 model selected > select /D 7855 atoms, 7969 bonds, 1020 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /D Alignment identifier is 1/D > select /D:36 7 atoms, 7 bonds, 1 residue, 1 model selected > select /D:36-258 1764 atoms, 1785 bonds, 223 residues, 1 model selected > ui tool show ""Color Actions"" > color sel aquamarine > select /D:464 7 atoms, 6 bonds, 1 residue, 1 model selected > select /D:464-686 1749 atoms, 1780 bonds, 223 residues, 1 model selected > color sel light sea green > select clear > select /D:789 9 atoms, 8 bonds, 1 residue, 1 model selected > select /D:789-995 1573 atoms, 1591 bonds, 207 residues, 1 model selected > select /D:789 9 atoms, 8 bonds, 1 residue, 1 model selected > select /D:789-1017 1738 atoms, 1758 bonds, 229 residues, 1 model selected > color sel cornflower blue > select clear Drag select of 10 residues > close > open > /Users/juliendumont/Downloads/fold_2024_05_27_14_25/fold_2024_05_27_14_25_model_0.cif Chain information for fold_2024_05_27_14_25_model_0.cif #1 --- Chain | Description A | . B C | . D E | . > hide atoms > show cartoons > select /A 7856 atoms, 8003 bonds, 987 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:939 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:933-939 61 atoms, 61 bonds, 7 residues, 1 model selected > select /A:597-598 14 atoms, 13 bonds, 2 residues, 1 model selected > select /A:597-600 28 atoms, 27 bonds, 4 residues, 1 model selected > select /A:570 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:570-572 31 atoms, 30 bonds, 3 residues, 1 model selected > select /A:508-509 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:508-510 25 atoms, 24 bonds, 3 residues, 1 model selected Drag select of 3 residues Drag select of 13 residues > ui tool show ""Show Sequence Viewer"" > sequence chain /D Alignment identifier is 1/D > select /D:969 7 atoms, 6 bonds, 1 residue, 1 model selected > select /D:969-971 27 atoms, 26 bonds, 3 residues, 1 model selected > hbonds sel reveal true 11 hydrogen bonds found Drag select of 7 residues > select /B 5465 atoms, 5520 bonds, 693 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > select /B:173-174 20 atoms, 19 bonds, 2 residues, 1 model selected > select /B:171-174 34 atoms, 33 bonds, 4 residues, 1 model selected Drag select of 1 atoms, 9 residues > ui tool show ""Show Sequence Viewer"" > sequence chain /E Alignment identifier is 1/E > select /E:969 7 atoms, 6 bonds, 1 residue, 1 model selected > select /E:969-971 27 atoms, 26 bonds, 3 residues, 1 model selected > hbonds sel reveal true 12 hydrogen bonds found Drag select of 5 atoms, 7 residues > select /B:171 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:171-174 34 atoms, 33 bonds, 4 residues, 1 model selected Drag select of 4 atoms, 8 residues > select /B:213 10 atoms, 10 bonds, 1 residue, 1 model selected > select /B:213-216 37 atoms, 38 bonds, 4 residues, 1 model selected Drag select of 5 atoms, 8 residues > select /C 5465 atoms, 5520 bonds, 693 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /C Alignment identifier is 1/C Drag select of 3 atoms, 4 residues > select /C:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C 5465 atoms, 5520 bonds, 693 residues, 1 model selected > select /B 5465 atoms, 5520 bonds, 693 residues, 1 model selected > rainbow sel > select clear > select /B 5465 atoms, 5520 bonds, 693 residues, 1 model selected > color sel cyan > select /D 7855 atoms, 7969 bonds, 1020 residues, 1 model selected > rainbow sel > select /E 7855 atoms, 7969 bonds, 8 pseudobonds, 1020 residues, 2 models selected > rainbow sel > select clear > select /B 5465 atoms, 5520 bonds, 693 residues, 1 model selected > rainbow sel > select /C 5465 atoms, 5520 bonds, 693 residues, 1 model selected > rainbow sel > select clear > select /A:2-32 234 atoms, 238 bonds, 31 residues, 1 model selected > select /A:2-347 2807 atoms, 2856 bonds, 346 residues, 1 model selected > select /A:921 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:921-923 31 atoms, 30 bonds, 3 residues, 1 model selected Drag select of 7 residues Drag select of 47 residues Drag select of 11 residues > select /A 7856 atoms, 8003 bonds, 987 residues, 1 model selected > hbonds sel reveal true 997 hydrogen bonds found > hide sel atoms > select clear > show atoms > hide atoms > select /A 7856 atoms, 8003 bonds, 964 pseudobonds, 987 residues, 2 models selected > show sel atoms > style sel stick Changed 7856 atom styles > select clear Drag select of 19 residues Drag select of 16 atoms, 28 residues, 3 pseudobonds, 12 bonds > hbonds sel reveal true 44 hydrogen bonds found > select clear Drag select of 2 atoms, 19 residues, 1 bonds > hbonds sel reveal true 35 hydrogen bonds found > style sel stick Changed 146 atom styles > select clear > select /A:661-662 18 atoms, 17 bonds, 2 residues, 1 model selected > select /A:661-987 2628 atoms, 2685 bonds, 327 residues, 1 model selected > select /E:464-465 16 atoms, 15 bonds, 2 residues, 1 model selected > select /E:464-471 62 atoms, 61 bonds, 8 residues, 1 model selected > select /E:670 8 atoms, 7 bonds, 1 residue, 1 model selected > select /E:464-670 1609 atoms, 1633 bonds, 207 residues, 1 model selected > close > open > /Users/juliendumont/Downloads/fold_2024_05_28_10_01/fold_2024_05_28_10_01_model_0.cif Chain information for fold_2024_05_28_10_01_model_0.cif #1 --- Chain | Description A B | . C D | . E F | . > hide atoms > show cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:667 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:667-771 845 atoms, 859 bonds, 105 residues, 1 model selected > select /A:923 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:923 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:921 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:921-923 31 atoms, 30 bonds, 3 residues, 1 model selected > hbonds sel reveal true 4 hydrogen bonds found > style sel stick Changed 31 atom styles > select /B 7856 atoms, 8003 bonds, 987 residues, 1 model selected > select /C 5465 atoms, 5520 bonds, 693 residues, 1 model selected > select /E 6246 atoms, 6335 bonds, 813 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /E Alignment identifier is 1/E > select /E:812-813 18 atoms, 18 bonds, 2 residues, 1 model selected > select /E:812-813 18 atoms, 18 bonds, 2 residues, 1 model selected > select /E:762 7 atoms, 6 bonds, 1 residue, 1 model selected > select /E:762-764 27 atoms, 26 bonds, 3 residues, 1 model selected > hbonds sel reveal true 11 hydrogen bonds found > style sel stick Changed 27 atom styles > select /A:551 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:551-987 3481 atoms, 3549 bonds, 437 residues, 1 model selected > select /A:721-722 14 atoms, 14 bonds, 2 residues, 1 model selected > select /A:721-723 20 atoms, 20 bonds, 3 residues, 1 model selected > select /A:885 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:885-900 116 atoms, 118 bonds, 16 residues, 1 model selected > select /A:967 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:967-985 144 atoms, 146 bonds, 19 residues, 1 model selected > select /A:726 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:726-740 136 atoms, 138 bonds, 15 residues, 1 model selected > select /A:951 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:951-964 124 atoms, 127 bonds, 14 residues, 1 model selected > select /A:884 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:884-900 128 atoms, 131 bonds, 17 residues, 1 model selected > select /A:927 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:927-938 103 atoms, 104 bonds, 12 residues, 1 model selected > select /A:776 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:776-800 210 atoms, 215 bonds, 25 residues, 1 model selected > select /A:801 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:801-808 60 atoms, 60 bonds, 8 residues, 1 model selected > select /A:559 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:559-587 214 atoms, 216 bonds, 29 residues, 1 model selected > hbonds sel reveal true 45 hydrogen bonds found > style sel stick Changed 214 atom styles > select clear Drag select of 1 atoms, 9 residues > select /E:744 7 atoms, 6 bonds, 1 residue, 1 model selected > select /E:744-746 23 atoms, 22 bonds, 3 residues, 1 model selected > style sel stick Changed 23 atom styles Drag select of 47 residues > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > ui tool show ""Show Sequence Viewer"" > sequence chain /C Alignment identifier is 1/C > select /C:692-693 20 atoms, 20 bonds, 2 residues, 1 model selected > select /C:365-693 2645 atoms, 2668 bonds, 329 residues, 1 model selected > select /C:681 7 atoms, 6 bonds, 1 residue, 1 model selected > select /C:681-683 20 atoms, 20 bonds, 3 residues, 1 model selected > select /C:693 10 atoms, 9 bonds, 1 residue, 1 model selected Drag select of 3 atoms, 10 residues > select /C:693 10 atoms, 9 bonds, 1 residue, 1 model selected > select /C:575-693 953 atoms, 966 bonds, 119 residues, 1 model selected > color sel red > select /C:220 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C:220-225 54 atoms, 54 bonds, 6 residues, 1 model selected > select /C:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:1-227 1711 atoms, 1737 bonds, 227 residues, 1 model selected > color sel blue > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain /D Alignment identifier is 1/D > select /D:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /D:1-227 1711 atoms, 1737 bonds, 227 residues, 1 model selected > color sel orange red > select /D:578 11 atoms, 11 bonds, 1 residue, 1 model selected > select /D:578-693 934 atoms, 947 bonds, 116 residues, 1 model selected > color sel cornflower blue > select clear > select /D:578 11 atoms, 11 bonds, 1 residue, 1 model selected > select /D:578-693 934 atoms, 947 bonds, 116 residues, 1 model selected > color sel orange red > select /D:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /D:1-227 1711 atoms, 1737 bonds, 227 residues, 1 model selected > color sel light sea green > color sel medium blue > select clear Drag select of 84 residues > select add /E:404 633 atoms, 5 bonds, 85 residues, 1 model selected > select /D:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /D:1-227 1711 atoms, 1737 bonds, 227 residues, 1 model selected > color sel cyan > ui tool show ""Color Actions"" > color sel royal blue > select clear > select /D:221 11 atoms, 11 bonds, 1 residue, 1 model selected > select /D:221-225 45 atoms, 45 bonds, 5 residues, 1 model selected > open > /Users/juliendumont/Downloads/fold_2024_05_28_10_38/fold_2024_05_28_10_38_model_0.cif Chain information for fold_2024_05_28_10_38_model_0.cif #2 --- Chain | Description A | . B | . > 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 fold_2024_05_28_10_01_model_0.cif, chain A (#1) with fold_2024_05_28_10_38_model_0.cif, chain A (#2), sequence alignment score = 4101.4 RMSD between 156 pruned atom pairs is 0.619 angstroms; (across all 987 pairs: 55.116) > 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 fold_2024_05_28_10_01_model_0.cif, chain A (#1) with fold_2024_05_28_10_38_model_0.cif, chain A (#2), sequence alignment score = 4101.4 RMSD between 156 pruned atom pairs is 0.619 angstroms; (across all 987 pairs: 55.116) Drag select of 152 residues > close > open > /Users/juliendumont/Downloads/fold_2024_05_28_10_38/fold_2024_05_28_10_38_model_0.cif > format mmcif Chain information for fold_2024_05_28_10_38_model_0.cif #1 --- Chain | Description A | . B | . > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > select /B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:1-30 235 atoms, 242 bonds, 30 residues, 1 model selected > select /B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B 2688 atoms, 2752 bonds, 343 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /B Destroying pre-existing alignment with identifier 1/B Alignment identifier is 1/B > select /B:311 5 atoms, 4 bonds, 1 residue, 1 model selected > select /B:212-311 793 atoms, 811 bonds, 100 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A 7856 atoms, 8003 bonds, 987 residues, 1 model selected > select /A:527 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:527-681 1222 atoms, 1242 bonds, 155 residues, 1 model selected > select /A:360-361 17 atoms, 16 bonds, 2 residues, 1 model selected > select /A:360-524 1260 atoms, 1283 bonds, 165 residues, 1 model selected > close > open > /Users/juliendumont/Downloads/fold_2024_05_27_13_34/fold_2024_05_27_13_34_model_0.cif > format mmcif Chain information for fold_2024_05_27_13_34_model_0.cif #1 --- Chain | Description A | . B C | . D | . > close > open > /Users/juliendumont/Downloads/fold_2024_05_27_14_25/fold_2024_05_27_14_25_model_0.cif > format mmcif Chain information for fold_2024_05_27_14_25_model_0.cif #1 --- Chain | Description A | . B C | . D E | . > hide atoms > show cartoons > close > open > /Users/juliendumont/Downloads/fold_2024_05_28_10_01/fold_2024_05_28_10_01_model_0.cif > format mmcif Chain information for fold_2024_05_28_10_01_model_0.cif #1 --- Chain | Description A B | . C D | . E F | . > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > ui tool show ""Show Sequence Viewer"" > sequence chain /C Alignment identifier is 1/C > select /C:225-226 18 atoms, 17 bonds, 2 residues, 1 model selected > select /C:1-226 1703 atoms, 1729 bonds, 226 residues, 1 model selected > color sel red > select /C:693 10 atoms, 9 bonds, 1 residue, 1 model selected > select /C:578-693 934 atoms, 947 bonds, 116 residues, 1 model selected > color sel light sea green > select clear > select /C:578 11 atoms, 11 bonds, 1 residue, 1 model selected > select /C:578-693 934 atoms, 947 bonds, 116 residues, 1 model selected > color sel lime > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain /E Alignment identifier is 1/E > select /E:618 14 atoms, 15 bonds, 1 residue, 1 model selected > select /E:618-813 1493 atoms, 1511 bonds, 196 residues, 1 model selected > select /E:558-608 398 atoms, 402 bonds, 51 residues, 1 model selected > select /E:558-813 1958 atoms, 1982 bonds, 256 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_2024_05_28_10_01_model_0.cif_E SES surface #1.1: minimum, -22.26, mean 0.93, maximum 19.60 To also show corresponding color key, enter the above coulombic command and add key true Drag select of fold_2024_05_28_10_01_model_0.cif_E SES surface, 196353 of 736080 triangles, 39134 atoms > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_2024_05_28_10_01_model_0.cif_A SES surface #1.2: minimum, -30.37, mean -3.38, maximum 12.01 Coulombic values for fold_2024_05_28_10_01_model_0.cif_B SES surface #1.3: minimum, -25.92, mean -3.46, maximum 12.49 Coulombic values for fold_2024_05_28_10_01_model_0.cif_C SES surface #1.4: minimum, -25.96, mean -4.92, maximum 12.62 Coulombic values for fold_2024_05_28_10_01_model_0.cif_D SES surface #1.5: minimum, -26.40, mean -4.94, maximum 12.12 Coulombic values for fold_2024_05_28_10_01_model_0.cif_E SES surface #1.1: minimum, -22.26, mean 0.93, maximum 19.60 Coulombic values for fold_2024_05_28_10_01_model_0.cif_F SES surface #1.6: minimum, -22.86, mean 0.86, maximum 19.92 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select /E:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /E:1-218 1723 atoms, 1744 bonds, 218 residues, 1 model selected > select /E:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /E:1-268 2091 atoms, 2116 bonds, 268 residues, 1 model selected > color bfactor sel 2091 atoms, 268 residues, 1 surfaces, atom bfactor range 21.9 to 87.7 Drag select of fold_2024_05_28_10_01_model_0.cif_E SES surface, fold_2024_05_28_10_01_model_0.cif_A SES surface, fold_2024_05_28_10_01_model_0.cif_B SES surface, fold_2024_05_28_10_01_model_0.cif_C SES surface, fold_2024_05_28_10_01_model_0.cif_D SES surface, fold_2024_05_28_10_01_model_0.cif_F SES surface, 39134 atoms > color bfactor sel 39134 atoms, 4986 residues, 6 surfaces, atom bfactor range 20.7 to 89 > open > /Users/juliendumont/Downloads/fold_2024_05_28_12_55/fold_2024_05_28_12_55_model_0.cif Chain information for fold_2024_05_28_12_55_model_0.cif #2 --- Chain | Description A | . > close > open > /Users/juliendumont/Downloads/fold_2024_05_28_12_55/fold_2024_05_28_12_55_model_0.cif > format mmcif Chain information for fold_2024_05_28_12_55_model_0.cif #1 --- Chain | Description A | . > close > open > /Users/juliendumont/Downloads/fold_2024_05_28_10_01/fold_2024_05_28_10_01_model_0.cif > format mmcif Chain information for fold_2024_05_28_10_01_model_0.cif #1 --- Chain | Description A B | . C D | . E F | . > hide atoms > select /A 7856 atoms, 8003 bonds, 987 residues, 1 model selected > show sel surfaces > hide sel surfaces > show sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:985-986 17 atoms, 16 bonds, 2 residues, 1 model selected > select /A:985-987 27 atoms, 26 bonds, 3 residues, 1 model selected > open > /Users/juliendumont/Downloads/fold_2024_05_28_12_55/fold_2024_05_28_12_55_model_0.cif Chain information for fold_2024_05_28_12_55_model_0.cif #2 --- Chain | Description A | . > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #1/A:278 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:278-329 417 atoms, 424 bonds, 52 residues, 1 model selected > select #2/A:301 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/A:301-536 1790 atoms, 1821 bonds, 236 residues, 1 model selected > select #1/A:301 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:301-537 1798 atoms, 1829 bonds, 237 residues, 1 model selected > select #1/A:529 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:529-530 14 atoms, 13 bonds, 2 residues, 1 model selected > select #2/A:651-652 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2/A:651-987 2711 atoms, 2768 bonds, 337 residues, 1 model selected > select #1/A:651 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:651-987 2711 atoms, 2768 bonds, 337 residues, 1 model selected > ui tool show Matchmaker ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8.dev202404150449 (2024-04-15) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2,4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 64 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0) OS Loader Version: 580~2215 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 4 days, 23 hours, 46 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) 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: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.16 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 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: 1.56.1 ChimeraX-AtomicLibrary: 14.0.3 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.dev202404150449 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: 1.2 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: 2.14.1 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: 1.13.4 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: 1.4.1 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: 1.37.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.3 fonttools: 4.51.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 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: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.6 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 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: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.0 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.11.0 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 can't reproduce Tom Goddard all ChimeraX