id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14494 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.1-arm64-arm-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000002ef713000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002ee707000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002ed6fb000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002ec6ef000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002eb6e3000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002ea6d7000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002e96cb000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002e86bf000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002e76b3000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002e66a7000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002e569b000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002e468f000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002e3683000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002e2677000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002e166b000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002e065f000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002df653000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001e0585ec0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in File ""/Applications/ChimeraX-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.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-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1004 in find_matches File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1001 in evaluate File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1091 in evaluate File ""/Applications/ChimeraX-1.7.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-1.7.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-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2499 in _parse_arg File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2640 in _process_positional_arguments File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2864 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3468 in __call__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2929 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw (total: 60) {""app_name"":""ChimeraX"",""timestamp"":""2024-01-28 23:50:08.00 -0800"",""app_version"":""1.7.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.7.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.1 (23B2073)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""20F6BE02-9AC4-48DE-9BFD-73F9680C0D68""} { ""uptime"" : 670000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac15,10"", ""coalitionID"" : 14361, ""osVersion"" : { ""train"" : ""macOS 14.1"", ""build"" : ""23B2073"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-01-28 23:49:58.7343 -0800"", ""codeSigningMonitor"" : 1, ""incident"" : ""20F6BE02-9AC4-48DE-9BFD-73F9680C0D68"", ""pid"" : 80158, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-01-26 16:48:38.9519 -0800"", ""procStartAbsTime"" : 14743438243490, ""procExitAbsTime"" : 16296490907592, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.0"",""CFBundleVersion"":""1.7.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""83522F7A-B239-5B86-904C-63BD8ADD44D5"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""87812259-AF0E-8539-4F2F-A6A431E997DD"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""wakeTime"" : 5643, ""sleepWakeUUID"" : ""B7D8E0C5-481B-4C22-87DC-B2CBD144BBC8"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. 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University of California. All rights reserved. > open /Users/woori/Downloads/view_alphafold_hairpin_sk2o_sf.cxs Log from Fri Jan 26 16:25:48 2024UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/woori/Downloads/hsk2o_2M.pdb format pdb Chain information for hsk2o_2M.pdb #1 --- Chain | Description A C E G | No description available B D F H | No description available > hide atoms > show cartoons > open /Users/woori/Downloads/charmm-gui-0553074370/step5_assembly.pdb Summary of feedback from opening /Users/woori/Downloads/charmm- gui-0553074370/step5_assembly.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON JAN, 18. 2024. JOB Ignored bad PDB record found on line 2 REMARK INPUT GENERATION Ignored bad PDB record found on line 3 REMARK DATE: 1/18/24 20:53: 9 CREATED BY USER: apache Ignored bad PDB record found on line 307118 TER 307115 CLA 381 Chain information for step5_assembly.pdb #2 --- Chain | Description ? | No description available > hide #1 models > hide #2 atoms > show #2 cartoons > show #1 models > hide #2 models > select add #1 33923 atoms, 34116 bonds, 2195 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/C #1/E #1/G Alignment identifier is 1 > select clear > select #1/A:2-3/C:527-528/E:1052-1053/G:1577-1578 164 atoms, 160 bonds, 8 residues, 1 model selected > select #1/A:1-2/C:526-527/E:1051-1052/G:1576-1577 180 atoms, 180 bonds, 8 residues, 1 model selected > select > #1/A:1-2,324-379/C:526-527,849-904/E:1051-1052,1374-1429/G:1576-1577,1899-1954 4000 atoms, 4016 bonds, 232 residues, 1 model selected > select #1 /A 6190 atoms, 6250 bonds, 379 residues, 1 model selected > select #1 /b,c,d,e,f,d,h 21300 atoms, 21468 bonds, 1342 residues, 1 model selected > hide sel > hide sel cartoons > select #1 /g 6190 atoms, 6250 bonds, 379 residues, 1 model selected > hide sel cartoons > select clear > select #1/A:379/C:904/E:1429/G:1954 60 atoms, 56 bonds, 4 residues, 1 model selected > select #1/A:324-379/C:849-904/E:1374-1429/G:1899-1954 3820 atoms, 3836 bonds, 224 residues, 1 model selected > select #1/A:283-284/C:808-809/E:1333-1334/G:1858-1859 128 atoms, 124 bonds, 8 residues, 1 model selected > select #1/A:283-379/C:808-904/E:1333-1429/G:1858-1954 6640 atoms, 6680 bonds, 388 residues, 1 model selected > select #1/A:281/C:806/E:1331/G:1856 76 atoms, 72 bonds, 4 residues, 1 model selected > select #1/A:281-379/C:806-904/E:1331-1429/G:1856-1954 6772 atoms, 6812 bonds, 396 residues, 1 model selected > save /Users/woori/Downloads/seq_hsk2o format fasta alignment 1 > select #1/A:280/C:805/E:1330/G:1855 60 atoms, 56 bonds, 4 residues, 1 model selected > select #1/A:226-280/C:751-805/E:1276-1330/G:1801-1855 3260 atoms, 3284 bonds, 220 residues, 1 model selected > select #1/A:280-281/C:805-806/E:1330-1331/G:1855-1856 136 atoms, 132 bonds, 8 residues, 1 model selected > select #1/A:192-281/C:717-806/E:1242-1331/G:1767-1856 5500 atoms, 5556 bonds, 360 residues, 1 model selected > select #1/A:191-192/C:716-717/E:1241-1242/G:1766-1767 100 atoms, 100 bonds, 8 residues, 1 model selected > select #1/A:188-192/C:713-717/E:1238-1242/G:1763-1767 300 atoms, 300 bonds, 20 residues, 1 model selected > select > #1/A:2-82,87-90,93-106,129-131,135-158,160-162,165-174,180-190,192-214,227-238,251-278,283-319,324-361,363-378/C:527-607,612-615,618-631,654-656,660-683,685-687,690-699,705-715,717-739,752-763,776-803,808-844,849-886,888-903/E:1052-1132,1137-1140,1143-1156,1179-1181,1185-1208,1210-1212,1215-1224,1230-1240,1242-1264,1277-1288,1301-1328,1333-1369,1374-1411,1413-1428/G:1577-1657,1662-1665,1668-1681,1704-1706,1710-1733,1735-1737,1740-1749,1755-1765,1767-1789,1802-1813,1826-1853,1858-1894,1899-1936,1938-1953 20144 atoms, 20272 bonds, 1216 residues, 1 model selected > select #1/A:191/C:716/E:1241/G:1766 44 atoms, 40 bonds, 4 residues, 1 model selected > select #1/A:160-191/C:685-716/E:1210-1241/G:1735-1766 2076 atoms, 2084 bonds, 128 residues, 1 model selected > select #1/A:100-107/C:625-632/E:1150-1157/G:1675-1682 480 atoms, 476 bonds, 32 residues, 1 model selected > select #1/A:99-107/C:624-632/E:1149-1157/G:1674-1682 556 atoms, 552 bonds, 36 residues, 1 model selected > select #1/A:160/C:685/E:1210/G:1735 88 atoms, 84 bonds, 4 residues, 1 model selected > select #1/A:160-191/C:685-716/E:1210-1241/G:1735-1766 2076 atoms, 2084 bonds, 128 residues, 1 model selected > select #1/A:159/C:684/E:1209/G:1734 44 atoms, 40 bonds, 4 residues, 1 model selected > select #1/A:92-159/C:617-684/E:1142-1209/G:1667-1734 4468 atoms, 4532 bonds, 272 residues, 1 model selected > select #1/A:91/C:616/E:1141/G:1666 68 atoms, 64 bonds, 4 residues, 1 model selected > select #1/A:1-91/C:526-616/E:1051-1141/G:1576-1666 6020 atoms, 6076 bonds, 364 residues, 1 model selected > select #1/A:64-65/C:589-590/E:1114-1115/G:1639-1640 104 atoms, 100 bonds, 8 residues, 1 model selected > select #1/A:56-65/C:581-590/E:1106-1115/G:1631-1640 628 atoms, 624 bonds, 40 residues, 1 model selected > select #1/A:84-85/C:609-610/E:1134-1135/G:1659-1660 88 atoms, 84 bonds, 8 residues, 1 model selected > select #1/A:1-85/C:526-610/E:1051-1135/G:1576-1660 5596 atoms, 5644 bonds, 340 residues, 1 model selected > open /Users/woori/Downloads/AF-Q9H2S1-F1-model_v4.pdb AF-Q9H2S1-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for small conductance calcium- activated potassium channel protein 2 (Q9H2S1) [more info...] Chain information for AF-Q9H2S1-F1-model_v4.pdb #3 --- Chain | Description | UniProt A | small conductance calcium-activated potassium channel protein 2 | KCNN2_HUMAN 1-579 > delete #1, 2 > open /Users/woori/Downloads/hsk2o_2M.pdb Chain information for hsk2o_2M.pdb #1 --- Chain | Description A C E G | No description available B D F H | No description available > mmaker #1 to 3 > matchmaker #1 to 3 Invalid ""to"" argument: invalid atoms specifier > mmaker #1 to #3 /A 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-Q9H2S1-F1-model_v4.pdb, chain A (#3) with hsk2o_2M.pdb, chain E (#1), sequence alignment score = 1901.9 RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs: 4.437) > show cartoons > hide atoms > hide #3 models > show #3 models > open /Users/woori/Downloads/AF-Q9H2S1-F1-model_v4.pdb AF-Q9H2S1-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for small conductance calcium- activated potassium channel protein 2 (Q9H2S1) [more info...] Chain information for AF-Q9H2S1-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | small conductance calcium-activated potassium channel protein 2 | KCNN2_HUMAN 1-579 > open /Users/woori/Downloads/AF-Q9H2S1-F1-model_v4.pdb AF-Q9H2S1-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for small conductance calcium- activated potassium channel protein 2 (Q9H2S1) [more info...] Chain information for AF-Q9H2S1-F1-model_v4.pdb #4 --- Chain | Description | UniProt A | small conductance calcium-activated potassium channel protein 2 | KCNN2_HUMAN 1-579 > open /Users/woori/Downloads/AF-Q9H2S1-F1-model_v4.pdb AF-Q9H2S1-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for small conductance calcium- activated potassium channel protein 2 (Q9H2S1) [more info...] Chain information for AF-Q9H2S1-F1-model_v4.pdb #5 --- Chain | Description | UniProt A | small conductance calcium-activated potassium channel protein 2 | KCNN2_HUMAN 1-579 > mmaker #3 to #1 /B 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 hsk2o_2M.pdb, chain B (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#3), sequence alignment score = 63.2 RMSD between 7 pruned atom pairs is 1.290 angstroms; (across all 122 pairs: 38.453) > mmaker #3 to #1 /C 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 hsk2o_2M.pdb, chain C (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#3), sequence alignment score = 1896.2 RMSD between 186 pruned atom pairs is 1.091 angstroms; (across all 379 pairs: 5.394) > mmaker #4 to #1 /E 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 hsk2o_2M.pdb, chain E (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#4), sequence alignment score = 1901.9 RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs: 4.437) > mmaker #4 to #1 /E 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 hsk2o_2M.pdb, chain E (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#4), sequence alignment score = 1901.9 RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs: 4.437) > mmaker #4 to #1 /F 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 hsk2o_2M.pdb, chain F (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#4), sequence alignment score = 63.2 RMSD between 8 pruned atom pairs is 1.529 angstroms; (across all 122 pairs: 38.041) > mmaker #4 to #1 /E 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 hsk2o_2M.pdb, chain E (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#4), sequence alignment score = 1901.9 RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs: 4.437) > mmaker #5 to #1 /G 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 hsk2o_2M.pdb, chain G (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#5), sequence alignment score = 1859.3 RMSD between 184 pruned atom pairs is 1.254 angstroms; (across all 379 pairs: 4.882) > hide #2 models > hide #3 models > hide #4 models > hide #5 models > show #2 models > show #3 models > show #4 models > hide #4 models > show #4 models > hide #4 models > mmaker #4 to #1 /E 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 hsk2o_2M.pdb, chain E (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#4), sequence alignment score = 1901.9 RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs: 4.437) > mmaker #2 to #1 /A 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 hsk2o_2M.pdb, chain A (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#2), sequence alignment score = 1893.5 RMSD between 195 pruned atom pairs is 1.230 angstroms; (across all 379 pairs: 6.673) > mmaker #3 to #1 /C 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 hsk2o_2M.pdb, chain C (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#3), sequence alignment score = 1896.2 RMSD between 186 pruned atom pairs is 1.091 angstroms; (across all 379 pairs: 5.394) > mmaker #4 to #1 /E 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 hsk2o_2M.pdb, chain E (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#4), sequence alignment score = 1901.9 RMSD between 198 pruned atom pairs is 1.224 angstroms; (across all 379 pairs: 4.437) > mmaker #5 to #1 /G 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 hsk2o_2M.pdb, chain G (#1) with AF-Q9H2S1-F1-model_v4.pdb, chain A (#5), sequence alignment score = 1859.3 RMSD between 184 pruned atom pairs is 1.254 angstroms; (across all 379 pairs: 4.882) > show #4 models > show #5 models > hide #3 models > hide #4 models > hide #5 models > select #1 /b,c,d,e,f,g,h 27490 atoms, 27718 bonds, 1721 residues, 1 model selected > hide sel > hide sel cartoons > select clear > select #1/A:136 16 atoms, 15 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/C #1/E #1/G Alignment identifier is 1 > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A #2/A #4/A #5/A Alignment identifier is 2 > select #1/A:136 16 atoms, 15 bonds, 1 residue, 1 model selected > select add #2/A:254 23 atoms, 21 bonds, 2 residues, 2 models selected > save /Users/woori/Downloads/seq_sk2_alphafold format fasta alignment 2 > select > #3/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554 > #2/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554 > #4/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554 > #5/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554 11648 atoms, 11792 bonds, 1444 residues, 4 models selected > select #3/A:234-240,247-253 #2/A:234-240,247-253 #4/A:234-240,247-253 > #5/A:234-240,247-253 436 atoms, 444 bonds, 56 residues, 4 models selected > select > #3/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554 > #2/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554 > #4/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554 > #5/A:110-158,165-200,205-208,211-225,254-276,278-281,283-291,298-308,310-333,345-356,369-396,401-438,445-546,548-550,552-554 11648 atoms, 11792 bonds, 1444 residues, 4 models selected > select clear > select #1/A:41 10 atoms, 9 bonds, 1 residue, 1 model selected > select #2/A:158 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select #2/A:158 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:159 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:165 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:243 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select clear [Repeated 1 time(s)] > select #2/A:362 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > select #2/A:363 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A:245 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select #2/A:242 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:241 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear [Repeated 2 time(s)] > select #2/A:246 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select #2/A:245 12 atoms, 12 bonds, 1 residue, 1 model selected > select clear [Repeated 2 time(s)] > select #3/A:234-240,247-253 #2/A:234-240,247-253 #4/A:234-240,247-253 > #5/A:234-240,247-253 436 atoms, 444 bonds, 56 residues, 4 models selected > select clear > select #3/A:234-240,247-253 #2/A:234-240,247-253 #4/A:234-240,247-253 > #5/A:234-240,247-253 436 atoms, 444 bonds, 56 residues, 4 models selected > select clear > select #2/A:247 7 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:234 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:240 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A:245@CA 1 atom, 1 residue, 1 model selected > hide sel atoms > select #2/A:362 4 atoms, 3 bonds, 1 residue, 1 model selected Drag select of 11 atoms, 13 residues, 4 bonds > hide sel atoms > select clear > select #1/A:244 7 atoms, 6 bonds, 1 residue, 1 model selected > style sel ball Changed 7 atom styles > show sel atoms [Repeated 1 time(s)] > style sel ball Changed 7 atom styles > show sel atoms > style sel stick Changed 7 atom styles > show sel atoms > hide sel atoms > show sel atoms > show sel cartoons > show sel atoms > select clear > select #2/A:240 11 atoms, 10 bonds, 1 residue, 1 model selected > style sel ball Changed 11 atom styles > style sel sphere Changed 11 atom styles > select #2 :363 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 8 atom styles > select #2/A:243@CA 1 atom, 1 residue, 1 model selected > style sel sphere Changed 1 atom style > style sel stick Changed 1 atom style > select #2/A:243@CA 1 atom, 1 residue, 1 model selected > select up 11 atoms, 11 bonds, 1 residue, 1 model selected > style sel sphere Changed 11 atom styles > show #3 models > hide #3 models > show #3 models > hide #3 models > select #1 :363 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1 :245 12 atoms, 11 bonds, 1 residue, 1 model selected > style sel stick Changed 12 atom styles > style sel sphere Changed 12 atom styles > hide #2 models > show sel atoms > show #2 models > select #1 :245, 770, 1295, 1820 48 atoms, 44 bonds, 4 residues, 1 model selected > select #1 :245, 770, 1295, 1820 48 atoms, 44 bonds, 4 residues, 1 model selected > show sel atoms > open /Users/woori/Downloads/rank-001-modified-hsk2o-mmseq2-enc.pdb Chain information for rank-001-modified-hsk2o-mmseq2-enc.pdb #6 --- Chain | Description A B C D | No description available E F G H | No description available > show sel cartoons > hide sel atoms > show sel atoms > select clear > show #1-2,6 cartoons > hide #1-2,6 atoms > mmaker #6 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 hsk2o_2M.pdb, chain E (#1) with rank-001-modified- hsk2o-mmseq2-enc.pdb, chain A (#6), sequence alignment score = 1882.7 RMSD between 293 pruned atom pairs is 1.019 angstroms; (across all 379 pairs: 4.110) > select /b,c,d,e,f,g,h 41974 atoms, 42433 bonds, 3538 residues, 2 models selected > hide sel cartoons > select #6 /e 1173 atoms, 1185 bonds, 149 residues, 1 model selected > show sel cartoons > select #6 /c 3264 atoms, 3325 bonds, 407 residues, 1 model selected > show sel cartoons > select #6 /a,b,d,e,f,g,h 14484 atoms, 14715 bonds, 1817 residues, 1 model selected > hide sel cartoons > hide #2 models > delete #2,3,4,5 > mmaker #6 /C :157-144 to #1 /a :149-136 No 'to' model specified > mmaker #6 /C :157-144 to #1 /A :149-136 No 'to' model specified > align #6 /C :157-144 toAtoms #1 /A :149-136 No atoms paired for alignment > align #6 /C :157-144 & #1 /A :149-136 Missing required ""to_atoms"" argument > align #6 /C :157-144 toAtoms #1 /A :149-136 No atoms paired for alignment > ui tool show Matchmaker > help help:user/tools/matchmaker.html > align #6 /C :157-144 toAtoms #1 /A :149-136 No atoms paired for alignment > align #6 /C :144-157 toAtoms #1 /A :136-149 Unequal number of atoms to pair, 118 and 249 > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A #6/B #6/C #6/D Alignment identifier is 2 > select #6/A-D:144-145 60 atoms, 56 bonds, 8 residues, 1 model selected > select #6/A-D:144-161 600 atoms, 608 bonds, 72 residues, 1 model selected > select #6/A-D:157 48 atoms, 48 bonds, 4 residues, 1 model selected > select #6/A-D:144-157 472 atoms, 480 bonds, 56 residues, 1 model selected > align #6 /C :144-157 toAtoms #1 /A :136-149 Unequal number of atoms to pair, 118 and 249 > align #6 /C :144-157 toAtoms #1 /A :136-149 Unequal number of atoms to pair, 118 and 249 > select #6 /C :144-157 118 atoms, 120 bonds, 14 residues, 1 model selected > select #1 /A :136-149 249 atoms, 251 bonds, 14 residues, 1 model selected > mmaker #6 /C :144-157 to #1 /A :136-149 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 hsk2o_2M.pdb, chain A (#1) with rank-001-modified- hsk2o-mmseq2-enc.pdb, chain C (#6), sequence alignment score = 72.8 RMSD between 14 pruned atom pairs is 0.481 angstroms; (across all 14 pairs: 0.481) > select clear > select #1/A:93 21 atoms, 21 bonds, 1 residue, 1 model selected > select add #6/C:115 26 atoms, 25 bonds, 2 residues, 2 models selected > select add #1/A:107 36 atoms, 34 bonds, 3 residues, 2 models selected > mmaker #6 /C :101-115 to #1 /A :93-107 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 hsk2o_2M.pdb, chain A (#1) with rank-001-modified- hsk2o-mmseq2-enc.pdb, chain C (#6), sequence alignment score = 79.4 RMSD between 15 pruned atom pairs is 0.253 angstroms; (across all 15 pairs: 0.253) > select up 798 atoms, 812 bonds, 57 residues, 2 models selected > mmaker #6 /C :101-115, 144-157 to #1 /A :93-107, 136-149 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 hsk2o_2M.pdb, chain A (#1) with rank-001-modified- hsk2o-mmseq2-enc.pdb, chain C (#6), sequence alignment score = 152.2 RMSD between 29 pruned atom pairs is 0.499 angstroms; (across all 29 pairs: 0.499) > select #1 /A :93-107, 136-149 507 atoms, 511 bonds, 29 residues, 1 model selected > select #1 /A :108-135 425 atoms, 434 bonds, 28 residues, 1 model selected > select #1 /A :107-135 435 atoms, 444 bonds, 29 residues, 1 model selected > select #1 /A :106-135 446 atoms, 455 bonds, 30 residues, 1 model selected > select #1 /A :106-136 462 atoms, 471 bonds, 31 residues, 1 model selected > select #1 /A :106-137 474 atoms, 483 bonds, 32 residues, 1 model selected > select #1 /A :106-137, #6 /c :114-145 Expected a keyword > select #1 /A :106-137 and #6 /c :114-145 Expected a keyword > select #1 /A :106-137 & #6 /c :114-145 Nothing selected > select #1 /A :106-137 474 atoms, 483 bonds, 32 residues, 1 model selected > select #6 /c :114-145 246 atoms, 255 bonds, 32 residues, 1 model selected > select #1 /A :106-137 474 atoms, 483 bonds, 32 residues, 1 model selected > select #1 /A :106-137 474 atoms, 483 bonds, 32 residues, 1 model selected > select clear > hide #1 models > select #6/C:133 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #6/C:130 22 atoms, 21 bonds, 2 residues, 1 model selected > show sel atoms > style sel sphere Changed 22 atom styles > style sel ball Changed 22 atom styles > color sel byhetero > select clear > select #6/C:253 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > show sel atoms > color sel byhetero > select clear > select #6/C:252 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 4 atom styles > color sel byhetero > show sel atoms [Repeated 1 time(s)] > style sel ball Changed 4 atom styles > show sel atoms > style sel sphere Changed 4 atom styles > style sel ball Changed 4 atom styles > style sel stick Changed 4 atom styles > style sel sphere Changed 4 atom styles > style sel ball Changed 4 atom styles > show sel atoms > select add #6/C:248 10 atoms, 8 bonds, 2 residues, 1 model selected > select up 87 atoms, 88 bonds, 12 residues, 1 model selected > select down 10 atoms, 8 bonds, 2 residues, 1 model selected > select up 87 atoms, 88 bonds, 12 residues, 1 model selected > select down 10 atoms, 8 bonds, 2 residues, 1 model selected > select add #6/C:251 22 atoms, 20 bonds, 3 residues, 1 model selected > select add #6/C:250 26 atoms, 23 bonds, 4 residues, 1 model selected > select add #6/C:249 34 atoms, 30 bonds, 5 residues, 1 model selected > show sel atoms > style sel ball Changed 34 atom styles > color sel byhetero [Repeated 1 time(s)] > show sel atoms > select O 6466 atoms, 4398 residues, 2 models selected > select clear > select #6/C:253@CA 1 atom, 1 residue, 1 model selected > select add #6/C:252 5 atoms, 3 bonds, 2 residues, 1 model selected > select add #6/C:251@CA 6 atoms, 3 bonds, 3 residues, 1 model selected > select add #6/C:250 10 atoms, 6 bonds, 4 residues, 1 model selected > select add #6/C:249 18 atoms, 13 bonds, 5 residues, 1 model selected > select add #6/C:248 24 atoms, 18 bonds, 6 residues, 1 model selected > select add #6/C:247 32 atoms, 25 bonds, 7 residues, 1 model selected > select sel & O 6 atoms, 5 residues, 1 model selected > color sel & O red > hide sel cartoons > select #6 /b,c,d 9792 atoms, 9975 bonds, 1221 residues, 1 model selected > select #6 /a,b,d 9792 atoms, 9975 bonds, 1221 residues, 1 model selected > show sel cartoons > select clear > select #6 :114-145 2012 atoms, 2052 bonds, 256 residues, 1 model selected > select ~sel 49659 atoms, 50088 bonds, 4163 residues, 2 models selected > select #6 :1-113, 146-407 15736 atoms, 15972 bonds, 1968 residues, 1 model selected > delete sel > select #6 /e,f,g,h 1028 atoms, 1032 bonds, 128 residues, 1 model selected > show sel cartoons > open /Users/woori/Downloads/rank-001-modified-hsk2o-mmseq2-enc.pdb Chain information for rank-001-modified-hsk2o-mmseq2-enc.pdb #2 --- Chain | Description A B C D | No description available E F G H | No description available > hide #2 models > show #2 models > hide #6 models > hide #2 atoms > show #2 cartoons > select #6 /e,f,g,h 1028 atoms, 1032 bonds, 128 residues, 1 model selected > show #2 cartoons [Repeated 2 time(s)] > show #2 atoms > show #2 cartoons > hide #2 atoms > select #6 /e,f,g,h 1028 atoms, 1032 bonds, 128 residues, 1 model selected > show #2 atoms > hide #2 atoms > show #2 cartoons > show #6 models > delete #6 /e,f,g,h > hide #2 models > mmaker #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 hsk2o_2M.pdb, chain E (#1) with rank-001-modified- hsk2o-mmseq2-enc.pdb, chain A (#2), sequence alignment score = 1882.7 RMSD between 293 pruned atom pairs is 1.019 angstroms; (across all 379 pairs: 4.110) > show #2 models > hide #2 models > select #6 :130, 133 88 atoms, 84 bonds, 8 residues, 1 model selected > style sel ball Changed 88 atom styles > show sel atoms > color sel byhetero > select clear > show #1 models > select #1 :228-257 444 atoms, 449 bonds, 30 residues, 1 model selected > select #1 /a,c,e,g :228-257 444 atoms, 449 bonds, 30 residues, 1 model selected > show sel cartoons [Repeated 1 time(s)] > select #1 33923 atoms, 34116 bonds, 2195 residues, 1 model selected > show sel cartoons > select clear > select #1 :228-257 444 atoms, 449 bonds, 30 residues, 1 model selected > select #1 :228-257, 753-782, 1278-1307, 1803-1832 1788 atoms, 1804 bonds, 124 residues, 1 model selected > select #1 :1-226, 257-379, 526-751, 782-904, 1051-1276, 1307-1429, > 1575-1801, 1832-1954 23148 atoms, 23292 bonds, 1460 residues, 1 model selected > hide sel cartoons > select ~sel & ##selected 10775 atoms, 10824 bonds, 735 residues, 1 model selected > select up 10784 atoms, 10824 bonds, 744 residues, 1 model selected > select #1 :b,d,f,h Nothing selected > hide #1,6 cartoons > show #1,6 cartoons > select #1 :1-226, 257-379, 526-751, 782-904, 1051-1276, 1307-1429, > 1575-1801, 1832-1954 23148 atoms, 23292 bonds, 1460 residues, 1 model selected > hide sel cartoons > select up 23494 atoms, 23642 bonds, 1485 residues, 1 model selected > select down 23148 atoms, 23292 bonds, 1460 residues, 1 model selected > select down 10775 atoms, 10824 bonds, 735 residues, 1 model selected > select #1 /b,d,f,h 8920 atoms, 8968 bonds, 584 residues, 1 model selected > hide sel cartoons > select #1/C:764 19 atoms, 18 bonds, 1 residue, 1 model selected > select add #1/C:752 39 atoms, 38 bonds, 2 residues, 1 model selected > select up 370 atoms, 375 bonds, 24 residues, 1 model selected > select down 39 atoms, 38 bonds, 2 residues, 1 model selected > select #1/A:227-228/C:752-753/E:1277-1278/G:1802-1803 156 atoms, 156 bonds, 8 residues, 1 model selected > select #1/A:227-237/C:752-762/E:1277-1287/G:1802-1812 716 atoms, 724 bonds, 44 residues, 1 model selected > hide sel cartoons > select #1/C:781 16 atoms, 15 bonds, 1 residue, 1 model selected > select add #1/C:772 32 atoms, 30 bonds, 2 residues, 1 model selected > select #1/A:247-248/C:772-773/E:1297-1298/G:1822-1823 120 atoms, 120 bonds, 8 residues, 1 model selected > select #1/A:247-256/C:772-781/E:1297-1306/G:1822-1831 564 atoms, 568 bonds, 40 residues, 1 model selected > hide sel cartoons > save /Users/woori/Downloads/view_alphafold_hairpin_sk2o_sf.cxs > select #1/G:1819 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #1/G:1815 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A:240/C:765/E:1290/G:1815 44 atoms, 40 bonds, 4 residues, 1 model selected > select #1/A:240-244/C:765-769/E:1290-1294/G:1815-1819 260 atoms, 260 bonds, 20 residues, 1 model selected > show sel atoms > style sel ball Changed 260 atom styles > color sel byhetero > hide sel cartoons > select clear > select #1/A:242/C:767/E:1292/G:1817 28 atoms, 24 bonds, 4 residues, 1 model selected > select #1/A:242-244/C:767-769/E:1292-1294/G:1817-1819 140 atoms, 140 bonds, 12 residues, 1 model selected > select #1/A:240-241/C:765-766/E:1290-1291/G:1815-1816 120 atoms, 116 bonds, 8 residues, 1 model selected > select #1/A:240-241/C:765-766/E:1290-1291/G:1815-1816 120 atoms, 116 bonds, 8 residues, 1 model selected > hide sel cartoons > show sel cartoons > hide sel atoms > select clear > save /Users/woori/Downloads/view_alphafold_hairpin_sk2o_sf.cxs \u2014\u2014\u2014 End of log from Fri Jan 26 16:25:48 2024 \u2014\u2014\u2014 opened ChimeraX session > show #1,6 cartoons > show #2 models > select clear > ui tool show ""Change Chain IDs"" > select add #6 984 atoms, 1020 bonds, 128 residues, 1 model selected > ui tool show ""Change Chain IDs"" > changechains sel A E Chain IDs of 32 residues changed > changechains sel C A Chain IDs of 32 residues changed > changechains sel B C Chain IDs of 32 residues changed > changechains sel D G Chain IDs of 32 residues changed > changechains sel D G No residues specified have any of the 'from' chain IDs > select subtract #6 Nothing selected > hide #2 models > select #1 :1-226, 257-379, 526-751, 782-904, 1051-1276, 1307-1429, > 1575-1801, 1832-1954 23148 atoms, 23292 bonds, 1460 residues, 1 model selected > hide sel cartoons > select up 23494 atoms, 23642 bonds, 1485 residues, 1 model selected > select down 23148 atoms, 23292 bonds, 1460 residues, 1 model selected > select down 23148 atoms, 23292 bonds, 1460 residues, 1 model selected > select #1 /b,d,f,h 8920 atoms, 8968 bonds, 584 residues, 1 model selected > hide sel cartoons > save /Users/woori/Desktop/revised_chainid_truncated_hairpinloop.pdb models > #6 > select #1/A:227 20 atoms, 20 bonds, 1 residue, 1 model selected > select add #1/A:238 40 atoms, 40 bonds, 2 residues, 1 model selected > select #1/A:227-228/C:752-753/E:1277-1278/G:1802-1803 156 atoms, 156 bonds, 8 residues, 1 model selected > select #1/A:227-239/C:752-764/E:1277-1289/G:1802-1814 872 atoms, 884 bonds, 52 residues, 1 model selected > hide sel cartoons > select #1/A:247 16 atoms, 15 bonds, 1 residue, 1 model selected > select #1/A:246/C:771/E:1296/G:1821 68 atoms, 64 bonds, 4 residues, 1 model selected > select #1/A:246-253/C:771-778/E:1296-1303/G:1821-1828 452 atoms, 456 bonds, 32 residues, 1 model selected > hide sel cartoons > select #1/A:256-257/C:781-782/E:1306-1307/G:1831-1832 108 atoms, 104 bonds, 8 residues, 1 model selected > select #1/A:251-257/C:776-782/E:1301-1307/G:1826-1832 376 atoms, 376 bonds, 28 residues, 1 model selected > hide sel cartoons > select #1/A:240-241/C:765-766/E:1290-1291/G:1815-1816 120 atoms, 116 bonds, 8 residues, 1 model selected > select #1/A:240-245/C:765-770/E:1290-1295/G:1815-1820 308 atoms, 308 bonds, 24 residues, 1 model selected > hide sel atoms > select > #1/A:2-82,87-90,93-106,129-131,135-158,160-162,165-174,180-190,192-214,227-238,251-278,283-319,324-361,363-378/C:527-607,612-615,618-631,654-656,660-683,685-687,690-699,705-715,717-739,752-763,776-803,808-844,849-886,888-903/E:1052-1132,1137-1140,1143-1156,1179-1181,1185-1208,1210-1212,1215-1224,1230-1240,1242-1264,1277-1288,1301-1328,1333-1369,1374-1411,1413-1428/G:1577-1657,1662-1665,1668-1681,1704-1706,1710-1733,1735-1737,1740-1749,1755-1765,1767-1789,1802-1813,1826-1853,1858-1894,1899-1936,1938-1953 20144 atoms, 20272 bonds, 1216 residues, 1 model selected > select #1/A:240-245/C:765-770/E:1290-1295/G:1815-1820 308 atoms, 308 bonds, 24 residues, 1 model selected > select clear > select #1/A:245/C:770/E:1295/G:1820 48 atoms, 44 bonds, 4 residues, 1 model selected > select #1/A:244-245/C:769-770/E:1294-1295/G:1819-1820 76 atoms, 72 bonds, 8 residues, 1 model selected > show sel atoms > style sel ball Changed 76 atom styles > color sel byhetero > hide sel cartoons > select clear > select #6/A:130 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ARG rotLib Dunbrack rank-001-modified-hsk2o-mmseq2-enc.pdb #6/A ARG 130: phi -98.2, psi 128.8 trans Changed 600 bond radii > select clear > ui mousemode right zoom > select #!6/A:130@NH1 1 atom, 1 residue, 1 model selected > select add #1/G:1820@OD2 2 atoms, 2 residues, 2 models selected > distance sel Distance between rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/A ARG 130 NH1 and hsk2o_2M.pdb #1/G ASP 1820 OD2: 4.375Å > select clear > select #!6/C:130@CA 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ARG rotLib Dunbrack rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/C ARG 130: phi -99.6, psi 129.3 trans Changed 600 bond radii > ui mousemode right translate > select #6.2.60/A:1@NH2 1 atom, 1 residue, 1 model selected > select add #1/A:245@OD2 2 atoms, 2 residues, 2 models selected > distance sel Distance between rotamer 60 #6.2.60/A ARG 1 NH2 and hsk2o_2M.pdb #1/A ASP 245 OD2: 2.990Å > select #6.2.58/A:1@NH2 1 atom, 1 residue, 1 model selected > select add #1/A:245@OD2 2 atoms, 2 residues, 2 models selected > distance sel Distance between rotamer 58 #6.2.58/A ARG 1 NH2 and hsk2o_2M.pdb #1/A ASP 245 OD2: 3.615Å > select up 21 atoms, 19 bonds, 2 residues, 2 models selected > select up 180 atoms, 180 bonds, 13 residues, 2 models selected > select up 6199 atoms, 6258 bonds, 380 residues, 2 models selected > select down 180 atoms, 180 bonds, 13 residues, 2 models selected > swapaa #!6/C:130 ARG criteria 60 rotLib Dunbrack retain false Using Dunbrack library rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/C ARG 130: phi -99.6, psi 129.3 trans Applying ARG rotamer (chi angles: 57.4 85.0 174.5 173.5) to rank-001-modified- hsk2o-mmseq2-enc.pdb #!6/C ARG 130 > select #1/A:245@O 1 atom, 1 residue, 1 model selected > select add #!6/C:130@NH1 2 atoms, 2 residues, 2 models selected > distance sel Distance between hsk2o_2M.pdb #1/A ASP 245 O and rank-001-modified- hsk2o-mmseq2-enc.pdb #!6/C ARG 130 NH1: 5.651Å > select #1/A:245@OD2 1 atom, 1 residue, 1 model selected > select add #!6/C:130@NH2 2 atoms, 2 residues, 2 models selected > distance sel Distance between hsk2o_2M.pdb #1/A ASP 245 OD2 and rank-001-modified- hsk2o-mmseq2-enc.pdb #!6/C ARG 130 NH2: 2.990Å > ui tool show Rotamers > swapaa interactive sel ALA rotLib Dunbrack No rotamers for ALA in Dunbrack rotamer library > select up 23 atoms, 21 bonds, 2 residues, 2 models selected > select clear > select #!6/C:130 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ARG rotLib Dunbrack rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/C ARG 130: phi -99.6, psi 129.3 trans Changed 600 bond radii > select clear > select #6.2.30/A:1@NH2 1 atom, 1 residue, 1 model selected > select add #1/A:245@O 2 atoms, 2 residues, 2 models selected > distance sel Distance between rotamer 30 #6.2.30/A ARG 1 NH2 and hsk2o_2M.pdb #1/A ASP 245 O: 5.181Å > select add #6.2.11/A:1@NH2 3 atoms, 3 residues, 3 models selected > select subtract #1/A:245@O 2 atoms, 2 residues, 2 models selected > select add #1/A:245@O 3 atoms, 3 residues, 3 models selected > distance sel Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 3 atoms and 0 measurable objects > select clear > select add #1/A:245@O 1 atom, 1 residue, 1 model selected > select add #6.2.11/A:1@NH2 2 atoms, 2 residues, 2 models selected > distance sel Distance between hsk2o_2M.pdb #1/A ASP 245 O and rotamer 11 #6.2.11/A ARG 1 NH2: 5.048Å > select clear > select #1/A:245@O 1 atom, 1 residue, 1 model selected > distance sel Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 1 atoms and 0 measurable objects > select clear > select add #1/A:245@O 1 atom, 1 residue, 1 model selected > select add #6.2.51/A:1@NH2 2 atoms, 2 residues, 2 models selected > distance sel Distance between hsk2o_2M.pdb #1/A ASP 245 O and rotamer 51 #6.2.51/A ARG 1 NH2: 4.367Å > select add #6.2.65/A:1@NH2 3 atoms, 3 residues, 3 models selected > select clear > select #6.2.65/A:1@NH2 1 atom, 1 residue, 1 model selected > select add #1/A:245@O 2 atoms, 2 residues, 2 models selected > distance sel Distance between rotamer 65 #6.2.65/A ARG 1 NH2 and hsk2o_2M.pdb #1/A ASP 245 O: 4.232Å > select #6.2.7/A:1@NH1 1 atom, 1 residue, 1 model selected > select add #1/A:245@O 2 atoms, 2 residues, 2 models selected > distance sel Distance between rotamer 7 #6.2.7/A ARG 1 NH1 and hsk2o_2M.pdb #1/A ASP 245 O: 4.575Å > select clear > select #!6/G:130 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ARG rotLib Dunbrack rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/G ARG 130: phi -100.0, psi 129.7 trans Changed 600 bond radii > select #1/E:1295@OD2 1 atom, 1 residue, 1 model selected > select add #6.3.60/A:1@NH1 2 atoms, 2 residues, 2 models selected > distance sel Distance between hsk2o_2M.pdb #1/E ASP 1295 OD2 and rotamer 60 #6.3.60/A ARG 1 NH1: 6.113Å > select clear > select #1/E:1295@OD2 1 atom, 1 residue, 1 model selected > select add #6.3.39/A:1@NH1 2 atoms, 2 residues, 2 models selected > distance sel Distance between hsk2o_2M.pdb #1/E ASP 1295 OD2 and rotamer 39 #6.3.39/A ARG 1 NH1: 6.134Å > select #6.3.66/A:1@NH1 1 atom, 1 residue, 1 model selected > select add #1/E:1295@OD2 2 atoms, 2 residues, 2 models selected > distance sel Distance between rotamer 66 #6.3.66/A ARG 1 NH1 and hsk2o_2M.pdb #1/E ASP 1295 OD2: 6.759Å > select up 21 atoms, 19 bonds, 2 residues, 2 models selected > select up 180 atoms, 180 bonds, 13 residues, 2 models selected > select up 6199 atoms, 6258 bonds, 380 residues, 2 models selected > select up 33932 atoms, 34124 bonds, 2196 residues, 2 models selected > select up 34598 atoms, 34716 bonds, 2270 residues, 76 models selected > select up 34598 atoms, 34716 bonds, 2270 residues, 77 models selected > swapaa #!6/G:130 ARG criteria 60 rotLib Dunbrack retain false Using Dunbrack library rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/G ARG 130: phi -100.0, psi 129.7 trans Applying ARG rotamer (chi angles: 57.4 85.0 174.5 173.5) to rank-001-modified- hsk2o-mmseq2-enc.pdb #!6/G ARG 130 > select add #!6/G:130@NH1 33924 atoms, 34116 bonds, 2196 residues, 2 models selected > select clear > select add #1/E:1295@OD2 1 atom, 1 residue, 1 model selected > select add #!6/G:130@NH1 2 atoms, 2 residues, 2 models selected > distance sel Distance between hsk2o_2M.pdb #1/E ASP 1295 OD2 and rank-001-modified- hsk2o-mmseq2-enc.pdb #!6/G ARG 130 NH1: 6.113Å > select clear > select #!6/E:130@CA 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ARG rotLib Dunbrack rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/E ARG 130: phi -98.8, psi 128.7 trans Changed 600 bond radii > select clear > select #6.3.60/A:1@NH1 1 atom, 1 residue, 1 model selected > select add #1/C:770@OD2 2 atoms, 2 residues, 2 models selected > distance sel Distance between rotamer 60 #6.3.60/A ARG 1 NH1 and hsk2o_2M.pdb #1/C ASP 770 OD2: 5.454Å > select clear > select add #6.3.39/A:1@NH1 1 atom, 1 residue, 1 model selected > select add #1/C:770@OD2 2 atoms, 2 residues, 2 models selected > distance sel Distance between rotamer 39 #6.3.39/A ARG 1 NH1 and hsk2o_2M.pdb #1/C ASP 770 OD2: 5.293Å > show #2 models > select clear > ui tool show ""Show Sequence Viewer"" > select #2 :248-255 228 atoms, 228 bonds, 32 residues, 1 model selected > select #2 :1-247,255-407 17548 atoms, 17832 bonds, 2196 residues, 1 model selected > hide sel cartoons > select #2 :248 24 atoms, 20 bonds, 4 residues, 1 model selected > select #2 :256 28 atoms, 28 bonds, 4 residues, 1 model selected > select #2 :258 28 atoms, 24 bonds, 4 residues, 1 model selected > select #2 :251 48 atoms, 48 bonds, 4 residues, 1 model selected > select #2 :250 16 atoms, 12 bonds, 4 residues, 1 model selected > select #2 :252 16 atoms, 12 bonds, 4 residues, 1 model selected > select #2 :253 32 atoms, 28 bonds, 4 residues, 1 model selected > show sel atoms > style sel ball Changed 32 atom styles > select clear > swapaa #!6/A:130 ARG criteria 60 rotLib Dunbrack retain false Using Dunbrack library rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/A ARG 130: phi -98.2, psi 128.8 trans Applying ARG rotamer (chi angles: 57.4 85.0 174.5 173.5) to rank-001-modified- hsk2o-mmseq2-enc.pdb #!6/A ARG 130 > swapaa #!6/C:130 ARG criteria 65 rotLib Dunbrack retain false Using Dunbrack library rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/C ARG 130: phi -99.6, psi 129.3 trans Applying ARG rotamer (chi angles: 59.3 92.1 71.9 -159.5) to rank-001-modified- hsk2o-mmseq2-enc.pdb #!6/C ARG 130 > select #1/C:770@OD2 1 atom, 1 residue, 1 model selected > select add #6.3.37/A:1@NH2 2 atoms, 2 residues, 2 models selected > distance sel Distance between hsk2o_2M.pdb #1/C ASP 770 OD2 and rotamer 37 #6.3.37/A ARG 1 NH2: 6.498Å > select #6.3.65/A:1@NH1 1 atom, 1 residue, 1 model selected > select add #1/C:770@OD2 2 atoms, 2 residues, 2 models selected > distance sel Distance between rotamer 65 #6.3.65/A ARG 1 NH1 and hsk2o_2M.pdb #1/C ASP 770 OD2: 5.726Å > select down 2 atoms, 2 residues, 2 models selected > select down 2 atoms, 2 residues, 2 models selected > select down 2 atoms, 2 residues, 2 models selected > select down 2 atoms, 2 residues, 2 models selected > select down 2 atoms, 2 residues, 2 models selected > select down 2 atoms, 2 residues, 2 models selected > select down 2 atoms, 2 residues, 2 models selected > swapaa #!6/E:130 ARG criteria 65 rotLib Dunbrack retain false Using Dunbrack library rank-001-modified-hsk2o-mmseq2-enc.pdb #!6/E ARG 130: phi -98.8, psi 128.7 trans Applying ARG rotamer (chi angles: 59.3 92.1 71.9 -159.5) to rank-001-modified- hsk2o-mmseq2-enc.pdb #!6/E ARG 130 > select clear > save > /Users/woori/Desktop/revised_rotamer_revised_chainid_truncated_hairpinloop.pdb > models #6 > select clear Drag select of 2 atoms, 9 residues, 1 bonds > select up 99 atoms, 65 bonds, 10 residues, 2 models selected > show sel atoms > style sel ball Changed 99 atom styles > color sel byhetero > select clear > save /Users/woori/Downloads/view_alphafold_revised_hairpin_sk2o_sf.cxs > hide #6 models Drag select of 47 atoms, 22 residues, 43 bonds > select clear Drag select of 44 atoms, 22 residues, 39 bonds > hide sel cartoons > hide sel atoms Drag select of 4 atoms, 2 bonds > hide sel atoms Drag select of 24 atoms, 11 residues, 22 bonds > hide sel atoms > hide sel cartoons > hide #2 models > show sel & #1 cartoons > select clear > show #1 cartoons > hide #1 atoms > select :272 32 atoms, 27 bonds, 5 residues, 2 models selected > select #1/A:272/C:797/E:1322/G:1847 64 atoms, 60 bonds, 4 residues, 1 model selected > select #1/A:272/C:797/E:1322/G:1847 64 atoms, 60 bonds, 4 residues, 1 model selected > open /Users/woori/Downloads/hsk2n_2M.pdb Chain information for hsk2n_2M.pdb #4 --- Chain | Description A C E G | No description available B D F H | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/C #1/E #1/G #4/A #4/C #4/E #4/G Alignment identifier is 3 > select #4 :390 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1 :272, 727, 1322, 1847 59 atoms, 55 bonds, 4 residues, 1 model selected > show sel cartoons > hide sel atoms > hide #!3 models > hide #3.1 models > hide #4 models > select #1 :272, 797, 1322, 1847 64 atoms, 60 bonds, 4 residues, 1 model selected > show sel atoms > open > /Users/woori/Downloads/expanse_result/sk4_control_pore_restraint/6cno_2M_v2.pdb Summary of feedback from opening /Users/woori/Downloads/expanse_result/sk4_control_pore_restraint/6cno_2M_v2.pdb --- warning | PDB SEQRES record for chain H is incomplete. Ignoring input sequence records as basis for sequence. Chain information for 6cno_2M_v2.pdb #5 --- Chain | Description A B C D | No description available E F G H | No description available > delete #4 > delete #3 > show #2 models > hide #2 models > show #2 models > hide #2 models > hide #1 models > hide #5 models > show #5 models > ui tool show ""Show Sequence Viewer"" > sequence chain #5/A #5/B #5/C #5/D Alignment identifier is 3 > select > #5/A:2-42,47-81,88-91,94-108,117-123,126-128,140-162,169-178,184-193,196-218,229-240,253-281,289-322,326-360,365-377/B:380-420,425-459,466-469,472-486,495-501,504-506,518-540,547-556,562-571,574-596,607-618,631-659,667-700,704-738,743-755/C:758-798,803-837,844-847,850-864,873-879,882-884,896-918,925-934,940-949,952-974,985-996,1009-1037,1045-1078,1082-1116,1121-1133/D:1136-1176,1181-1215,1222-1225,1228-1242,1251-1257,1260-1262,1274-1296,1303-1312,1318-1327,1330-1352,1363-1374,1387-1415,1423-1456,1460-1494,1499-1511 9264 atoms, 9404 bonds, 1176 residues, 1 model selected > select clear > show #5 cartoons > hide #5 atoms > select #5 :274 7 atoms, 6 bonds, 1 residue, 1 model selected > delete #5 > show #1 models > show #2 models > ui mousemode right rotate > hide #1-2 atoms > show #1-2 cartoons > hide #2 models > show #6 models > show #2 models > hide #6 models > show #6 models > hide #6 models > show #6 models > hide #6 models > show #6 models > hide #2 models > show #2 models > hide #2 models > delete #2 > select #1/A:108/C:633/E:1158/G:1683 76 atoms, 72 bonds, 4 residues, 1 model selected > select #1/A:108/C:633/E:1158/G:1683 76 atoms, 72 bonds, 4 residues, 1 model selected > select #1/A:108-135/C:633-660/E:1158-1185/G:1683-1710 1700 atoms, 1736 bonds, 112 residues, 1 model selected > color sel red > select clear > open /Users/woori/Downloads/rank-001-modified-hsk2o-mmseq2-enc.pdb Chain information for rank-001-modified-hsk2o-mmseq2-enc.pdb #2 --- Chain | Description A B C D | No description available E F G H | No description available > show cartoons > hide atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #6/E #6/C #6/A #6/G #2/A #2/B #2/C #2/D Alignment identifier is 2 > select #6/E,C,A,G:124 #2/A-D:124 56 atoms, 48 bonds, 8 residues, 2 models selected > select #6/E,C,A,G:124-143 #2/A-D:124-143 1248 atoms, 1288 bonds, 160 residues, 2 models selected 2 [ID: 2] region 8 chains [124-143] RMSD: 62.767 > mmaker #2 :124-143 to #6 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M3 Max OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,10 Model Number: MRX53LL/A Chip: Apple M3 Max Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 36 GB System Firmware Version: 10151.41.12 OS Loader Version: 10151.41.12 Software: System Software Overview: System Version: macOS 14.1 (23B2073) Kernel Version: Darwin 23.1.0 Time since boot: 37 days, 18 hours, 46 minutes Graphics/Displays: Apple M3 Max: Chipset Model: Apple M3 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 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: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 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: 1.1 ChimeraX-CheckWaters: 1.3.2 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: 1.7 ChimeraX-CoreFormats: 1.2 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: 1.1.3 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: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 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-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 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: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 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: 2.2.2 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: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 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: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX