id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15662 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.5-arm64-arm-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000002bd383000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002bc377000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002bb36b000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002ba35f000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b9353000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b8347000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b733b000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b632f000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b5323000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b4317000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b330b000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002b08cf000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002af8c3000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002ae8b7000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002ad8ab000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001fdbe2080 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/orderedset.py"", line 47 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 178 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 341 in add_trigger File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1063 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1129 in __copy__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/copy.py"", line 84 in copy File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py"", line 96 in clone_seq File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py"", line 60 in matches_to_gapped_seqs File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py"", line 55 in nw File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py"", line 78 in align File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py"", line 406 in match File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py"", line 742 in cmd_match File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.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.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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, lxml._elementpath, lxml.etree (total: 66) {""app_name"":""ChimeraX"",""timestamp"":""2024-07-24 13:26:33.00 -0700"",""app_version"":""1.7.1"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.7.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.5 (22G74)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""05DC573B-CEBD-4587-9A34-2C2E894C0174""} { ""uptime"" : 190000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,6"", ""coalitionID"" : 4194, ""osVersion"" : { ""train"" : ""macOS 13.5"", ""build"" : ""22G74"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-07-24 13:26:31.4335 -0700"", ""incident"" : ""05DC573B-CEBD-4587-9A34-2C2E894C0174"", ""pid"" : 50437, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-07-24 09:07:45.0700 -0700"", ""procStartAbsTime"" : 4277518533293, ""procExitAbsTime"" : 4638133256056, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.1"",""CFBundleVersion"":""1.7.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""D4A651AD-227C-55E0-B00C-C264D8671D4C"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""8BF27F0C-B423-AB5C-E06A-84A1CD5778C3"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 10260, ""sleepWakeUUID"" : ""128D6A82-13C9-42A2-984E-DA64DBBD2BDB"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. Bytes before following region: 105556740144983\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 6000d8000000-6000e0000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""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"":50437}, ""vmregioninfo"" : ""0xa9 is not in any region. Bytes before following region: 105556740144983\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 6000d8000000-6000e0000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""warnings"":0}, ""faultingThread"" : 0, ""threads"" : 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""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62c751b6bcb0435c2153fe92"", ""factorPackIds"" : { ""SIRI_UNDERSTANDING_ASR_ASSISTANT"" : ""6552c036dc598031005cc0f4"", ""SIRI_UNDERSTANDING_MORPHUN"" : ""64e514ddc83b9a3d50649ddc"" }, ""deploymentId"" : 240000366 }, { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 }, { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle > lighting soft > graphics silhouettes true UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/benjaminadler/Downloads/fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer/fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif Chain information for fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif #1 --- Chain | Description A B C D E F | . > hide atoms > show cartoons > color bfactor 16890 atoms, 2208 residues, atom bfactor range 14.3 to 91.2 > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_A SES surface #1.1: minimum, -13.37, mean 0.11, maximum 15.43 Coulombic values for fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_B SES surface #1.2: minimum, -15.92, mean 0.14, maximum 15.37 Coulombic values for fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_C SES surface #1.3: minimum, -19.48, mean 0.12, maximum 15.34 Coulombic values for fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_D SES surface #1.4: minimum, -15.77, mean 0.12, maximum 15.40 Coulombic values for fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_E SES surface #1.5: minimum, -17.76, mean 0.17, maximum 15.02 Coulombic values for fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_F SES surface #1.6: minimum, -12.37, mean 0.10, maximum 15.17 To also show corresponding color key, enter the above coulombic command and add key true > rainbow > open > /Users/benjaminadler/Downloads/fold_2024_05_30_11_34_goslar_gp218_gp061_innerbody_3mer/fold_2024_05_30_11_34_goslar_gp218_gp061_innerbody_3mer_model_0.cif Chain information for fold_2024_05_30_11_34_goslar_gp218_gp061_innerbody_3mer_model_0.cif #2 --- Chain | Description A B C | . D E F | . > hide #!1 models > open > /Users/benjaminadler/Downloads/fold_2024_05_30_11_17_goslar_gp218_gp219_innerbody_redo_3mer/fold_2024_05_30_11_17_goslar_gp218_gp219_innerbody_redo_3mer_model_0.cif Chain information for fold_2024_05_30_11_17_goslar_gp218_gp219_innerbody_redo_3mer_model_0.cif #3 --- Chain | Description A B C | . D E F | . > hide #2 models > open > /Users/benjaminadler/Downloads/fold_goslar_gp219_6mer/fold_goslar_gp219_6mer_model_0.cif Chain information for fold_goslar_gp219_6mer_model_0.cif #4 --- Chain | Description A B C D E F | . > hide #3 models > hide #4 atoms > show #4 cartoons > lighting soft > close #3 > close > open > /Users/benjaminadler/Downloads/fold_goslar_gp219_gp061_6_6mer/fold_goslar_gp219_gp061_6_6mer_model_0.cif Chain information for fold_goslar_gp219_gp061_6_6mer_model_0.cif #1 --- Chain | Description A B C D E F | . G H I J K L | . > open > /Users/benjaminadler/Downloads/fold_goslar_gp219_gp061_6_6mer/fold_goslar_gp219_gp061_6_6mer_model_1.cif Chain information for fold_goslar_gp219_gp061_6_6mer_model_1.cif #2 --- Chain | Description A B C D E F | . G H I J K L | . > open > /Users/benjaminadler/Downloads/fold_goslar_gp219_gp061_6_6mer/fold_goslar_gp219_gp061_6_6mer_model_2.cif Chain information for fold_goslar_gp219_gp061_6_6mer_model_2.cif #3 --- Chain | Description A B C D E F | . G H I J K L | . > hide #3 models > hide #2 models > hide #1 models > show #2 models > hide #2 models > show #3 models > show #1 models > hide #3 models > color bfactor #1 31848 atoms, 4098 residues, atom bfactor range 19.7 to 91.1 > rainbow #1 > show #1 surfaces > color #!1 bychain > open > /Users/benjaminadler/Downloads/fold_goslar_gp060_6mer/fold_goslar_gp060_6mer_model_0.cif Chain information for fold_goslar_gp060_6mer_model_0.cif #4 --- Chain | Description A B C D E F | . > hide #!1 models > open > /Users/benjaminadler/Downloads/fold_goslar_gp061_gp060_6_6mer/fold_goslar_gp061_gp060_6_6mer_model_0.cif Chain information for fold_goslar_gp061_gp060_6_6mer_model_0.cif #5 --- Chain | Description A B C D E F | . G H I J K L | . > hide #4 models > show #!1 models > mmaker #5 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_goslar_gp219_gp061_6_6mer_model_0.cif, chain G (#1) with fold_goslar_gp061_gp060_6_6mer_model_0.cif, chain A (#5), sequence alignment score = 1826.2 RMSD between 250 pruned atom pairs is 0.780 angstroms; (across all 368 pairs: 7.641) > show #5#!1 surfaces > hide #!1 models > open > /Users/benjaminadler/Downloads/fold_goslar_gp219_gp061_gp060_2_2_2mer/fold_goslar_gp219_gp061_gp060_2_2_2mer_model_0.cif Chain information for fold_goslar_gp219_gp061_gp060_2_2_2mer_model_0.cif #6 --- Chain | Description A B | . C D | . E F | . > hide #!5 models > open > /Users/benjaminadler/Downloads/fold_goslar_gp061_gp060_6_6mer/fold_goslar_gp061_gp060_6_6mer_model_0.cif Chain information for fold_goslar_gp061_gp060_6_6mer_model_0.cif #7 --- Chain | Description A B C D E F | . G H I J K L | . > hide #6 models > show #!1 models > hide #7 models > show #!5 models > select #5/G:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/H:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/F:1 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel magenta > hide #!1 models > select #5 31236 atoms, 31674 bonds, 4008 residues, 1 model selected > rainbow sel > color bfactor sel 31236 atoms, 4008 residues, 12 surfaces, atom bfactor range 15.6 to 89.6 > open > /Users/benjaminadler/Downloads/fold_goslar_gp219_gp061_gp060_2_6_2mer/fold_goslar_gp219_gp061_gp060_2_6_2mer_model_0.cif Chain information for fold_goslar_gp219_gp061_gp060_2_6_2mer_model_0.cif #8 --- Chain | Description A B | . C D E F G H | . I J | . > hide #!5 models > open > /Users/benjaminadler/Downloads/fold_phikz_gp089full/fold_phikz_gp089full_model_0.cif Chain information for fold_phikz_gp089full_model_0.cif #9 --- Chain | Description A | . > close > open > /Users/benjaminadler/Downloads/fold_phikz_gp089full/fold_phikz_gp089full_model_0.cif Chain information for fold_phikz_gp089full_model_0.cif #1 --- Chain | Description A | . > select #1:1-122 922 atoms, 934 bonds, 122 residues, 1 model selected > color sel magenta > select down 922 atoms, 934 bonds, 122 residues, 1 model selected > select up 934 atoms, 947 bonds, 123 residues, 1 model selected > select #1:156-387 1845 atoms, 1873 bonds, 232 residues, 1 model selected > color sel cyan > open > /Users/benjaminadler/Downloads/fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer/fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif Chain information for fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif #2 --- Chain | Description A B C D E F | . > mmaker #1 to #2/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 fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif, chain A (#2) with fold_phikz_gp089full_model_0.cif, chain A (#1), sequence alignment score = 595.9 RMSD between 168 pruned atom pairs is 1.014 angstroms; (across all 349 pairs: 16.722) > select #2 16890 atoms, 17094 bonds, 2208 residues, 1 model selected > hide sel atoms > select #2/A 2815 atoms, 2849 bonds, 368 residues, 1 model selected > show sel cartoons > select #2/A:116 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:115 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:1-115 880 atoms, 890 bonds, 115 residues, 1 model selected > color sel lime > lighting soft > graphics silhouettes false > graphics silhouettes true > select all 19922 atoms, 20177 bonds, 2595 residues, 2 models selected > lighting soft > graphics silhouettes false > graphics silhouettes true > open > /Users/benjaminadler/Downloads/fold_goslar_gp061n_12mer/fold_goslar_gp061n_12mer_model_0.cif Chain information for fold_goslar_gp061n_12mer_model_0.cif #3 --- Chain | Description A B C D E F G H I J K L | . > close #3 > select #0 Nothing selected > hide #2 models > show #2 models > save > /Users/benjaminadler/Desktop/Proteolysis_compare__PHIKZ_gp089__Goslar_gp061.cxs > includeMaps true > close #2 > close > open > /Users/benjaminadler/Downloads/fold_phikz_gp129full_portal/fold_phikz_gp129full_portal_model_0.cif Chain information for fold_phikz_gp129full_portal_model_0.cif #1 --- Chain | Description A | . > select #1:1-262 2060 atoms, 2090 bonds, 262 residues, 1 model selected > color sel magenta > select #1:263-896 4985 atoms, 5079 bonds, 634 residues, 1 model selected > color sel cyan > open > /Users/benjaminadler/Downloads/fold_2024_05_16_20_23_goslar_gp036_5mer/fold_2024_05_16_20_23_goslar_gp036_5mer_model_0.cif Chain information for fold_2024_05_16_20_23_goslar_gp036_5mer_model_0.cif #2 --- Chain | Description A B C D E | . > select #2 38085 atoms, 38730 bonds, 4845 residues, 1 model selected > lighting soft > select all 45130 atoms, 45900 bonds, 5741 residues, 2 models selected > lighting soft > graphics silhouettes false > graphics silhouettes true > hide sel atoms > select #2/A 7617 atoms, 7746 bonds, 969 residues, 1 model selected > show sel cartoons > mmaker #2/A 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_phikz_gp129full_portal_model_0.cif, chain A (#1) with fold_2024_05_16_20_23_goslar_gp036_5mer_model_0.cif, chain A (#2), sequence alignment score = 1517.2 RMSD between 324 pruned atom pairs is 1.156 angstroms; (across all 852 pairs: 24.105) > select #2/A:323 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 98 atoms, 99 bonds, 11 residues, 1 model selected Alignment identifier is 2/A > select #2/A:307 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:307-309 24 atoms, 23 bonds, 3 residues, 1 model selected > select #2/A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:319 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:319 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:363 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:361-363 22 atoms, 21 bonds, 3 residues, 1 model selected > select #2/A:318-319 17 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:317-319 24 atoms, 23 bonds, 3 residues, 1 model selected > select #2/A:313 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:313-315 25 atoms, 24 bonds, 3 residues, 1 model selected > select #2/A:319 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:317-319 24 atoms, 23 bonds, 3 residues, 1 model selected > select #2/A:319 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:1-319 2525 atoms, 2567 bonds, 319 residues, 1 model selected > select #2/A:969 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:320-969 5092 atoms, 5178 bonds, 650 residues, 1 model selected > select #2/A:1-319 2525 atoms, 2567 bonds, 319 residues, 1 model selected > color sel lime > select #2/A:320-969 5092 atoms, 5178 bonds, 650 residues, 1 model selected > color sel orange > select #2:1-319 12625 atoms, 12835 bonds, 1595 residues, 1 model selected > color sel lime > select #2:320-969 25460 atoms, 25890 bonds, 3250 residues, 1 model selected > color sel orange > select #2 38085 atoms, 38730 bonds, 4845 residues, 1 model selected > show sel cartoons > select #0 Nothing selected > select #1:1-262 2060 atoms, 2090 bonds, 262 residues, 1 model selected > color sel magenta > select #1:263-896 4985 atoms, 5079 bonds, 634 residues, 1 model selected > color sel cyan > select #2:1-319 12625 atoms, 12835 bonds, 1595 residues, 1 model selected > color sel lime > select #2:320-969 25460 atoms, 25890 bonds, 3250 residues, 1 model selected > color sel orange > select #0 Nothing selected > hide #1 models > show #1 models > save > /Users/benjaminadler/Desktop/Proteolysis_compare__PHIKZ_gp129__Goslar_gp036.cxs > close > open > /Users/benjaminadler/Desktop/Proteolysis_compare__PHIKZ_gp089__Goslar_gp061.cxs > format session opened ChimeraX session > select ~sel & ##selected Nothing selected > select #2 16890 atoms, 17094 bonds, 2208 residues, 1 model selected > show sel cartoons > select #0 Nothing selected > hide #2 models > show #2 models > mmaker #1 to #2/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 fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif, chain F (#2) with fold_phikz_gp089full_model_0.cif, chain A (#1), sequence alignment score = 598.9 RMSD between 167 pruned atom pairs is 1.017 angstroms; (across all 349 pairs: 16.765) > select #2/F:112 8 atoms, 7 bonds, 1 residue, 1 model selected Alignment identifier is 2/F > select #2/F:115 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/F:113-115 22 atoms, 21 bonds, 3 residues, 1 model selected > select #2/F:119 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/F:119-120 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/F:115 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/F:1-115 880 atoms, 890 bonds, 115 residues, 1 model selected > hide #1 models > open > /Users/benjaminadler/Downloads/fold_phikz_gp089n_gp089c_6_6mer/fold_phikz_gp089n_gp089c_6_6mer_model_0.cif Chain information for fold_phikz_gp089n_gp089c_6_6mer_model_0.cif #3 --- Chain | Description A B C D E F | . G H I J K L | . > mmaker #3 to #2 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_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif, chain F (#2) with fold_phikz_gp089n_gp089c_6_6mer_model_0.cif, chain G (#3), sequence alignment score = 465.8 RMSD between 134 pruned atom pairs is 1.033 angstroms; (across all 226 pairs: 6.475) > hide sel atoms > select add #2 16890 atoms, 17094 bonds, 2208 residues, 1 model selected > select subtract #2 Nothing selected > select add #3 16608 atoms, 16848 bonds, 2124 residues, 1 model selected > hide sel atoms > show sel cartoons > show #1 models > hide #1 models > select #3/H 1845 atoms, 1873 bonds, 232 residues, 1 model selected > color sel cyan > hide #3 models > show #3 models > select #3 16608 atoms, 16848 bonds, 2124 residues, 1 model selected > hide sel cartoons > select up 16608 atoms, 16848 bonds, 2124 residues, 1 model selected > select #3/H 1845 atoms, 1873 bonds, 232 residues, 1 model selected > show sel cartoons > select #2/F:215 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/F:215-217 18 atoms, 17 bonds, 3 residues, 1 model selected > select #2:215-217 108 atoms, 102 bonds, 18 residues, 1 model selected > select #2/F:148 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/F:148-150 22 atoms, 21 bonds, 3 residues, 1 model selected > open ""/Users/benjaminadler/Downloads/fold_phikz_gp092_2mer > (1)/fold_phikz_gp092_2mer_model_0.cif"" Chain information for fold_phikz_gp092_2mer_model_0.cif #4 --- Chain | Description A B | . > close > open ""/Users/benjaminadler/Downloads/fold_phikz_gp092_2mer > (1)/fold_phikz_gp092_2mer_model_0.cif"" Chain information for fold_phikz_gp092_2mer_model_0.cif #1 --- Chain | Description A B | . > select #1:86-440 5782 atoms, 5878 bonds, 710 residues, 1 model selected > color sel cyan > open > /Users/benjaminadler/Downloads/fold_phikz_gp093full/fold_phikz_gp093full_model_0.cif Chain information for fold_phikz_gp093full_model_0.cif #2 --- Chain | Description A | . > hide #1 models > close > open > /Users/benjaminadler/Downloads/fold_phikz_gp093full/fold_phikz_gp093full_model_0.cif > format mmcif Chain information for fold_phikz_gp093full_model_0.cif #1 --- Chain | Description A | . > open > /Users/benjaminadler/Downloads/fold_goslar_gp058_6mer/fold_goslar_gp058_6mer_model_0.cif Chain information for fold_goslar_gp058_6mer_model_0.cif #2 --- Chain | Description A B C D E F | . > hide atoms > show cartoons > mmaker #1 to #2/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 fold_goslar_gp058_6mer_model_0.cif, chain A (#2) with fold_phikz_gp093full_model_0.cif, chain A (#1), sequence alignment score = 350.9 RMSD between 40 pruned atom pairs is 0.975 angstroms; (across all 368 pairs: 27.410) > hide #2 models > select #1:1-86 649 atoms, 651 bonds, 86 residues, 1 model selected > color sel magenta > select #1:87-440 2692 atoms, 2725 bonds, 349 residues, 1 model selected > color sel cyan > select #1:1-85 641 atoms, 643 bonds, 85 residues, 1 model selected > color sel magenta > select #1:86-440 2700 atoms, 2733 bonds, 350 residues, 1 model selected > color sel cyan > show #2 models > select #0 Nothing selected Alignment identifier is 1/A Alignment identifier is 1 > select #2/A-F:21 30 atoms, 24 bonds, 6 residues, 1 model selected > select #2/A-F:21-23 114 atoms, 108 bonds, 18 residues, 1 model selected > select #1/A:90 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:90-92 22 atoms, 21 bonds, 3 residues, 1 model selected > select #2/A-F:48 42 atoms, 36 bonds, 6 residues, 1 model selected > select #2/A-F:48-50 126 atoms, 120 bonds, 18 residues, 1 model selected > select #2/A-F:68 30 atoms, 24 bonds, 6 residues, 1 model selected > select #2/A-F:68-70 132 atoms, 126 bonds, 18 residues, 1 model selected > select #2/A-F:70 54 atoms, 48 bonds, 6 residues, 1 model selected > select #2/A-F:70-440 16812 atoms, 17046 bonds, 2226 residues, 1 model selected > select #2 19794 atoms, 20064 bonds, 2640 residues, 1 model selected > hide sel cartoons > select #2/A 3299 atoms, 3344 bonds, 440 residues, 1 model selected > show sel cartoons > select #2/A:154 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 539 atoms, 552 bonds, 64 residues, 1 model selected > hide #1 models > select #0 Nothing selected > show #1 models > rainbow > color bychain > select #1 color sel white Expected a keyword > select #1 3341 atoms, 3377 bonds, 435 residues, 1 model selected > color sel white > select #2 19794 atoms, 20064 bonds, 2640 residues, 1 model selected > rainbow sel > select #1:86-440 2700 atoms, 2733 bonds, 350 residues, 1 model selected > color sel magenta > select #2/A:112 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 551 atoms, 552 bonds, 73 residues, 1 model selected > select #2/A-F:108 30 atoms, 24 bonds, 6 residues, 1 model selected > select #2/A-F:108-110 126 atoms, 120 bonds, 18 residues, 1 model selected > select #2/A-F:102 48 atoms, 42 bonds, 6 residues, 1 model selected > select #2/A-F:102-104 144 atoms, 138 bonds, 18 residues, 1 model selected > select #2/A-F:84 54 atoms, 48 bonds, 6 residues, 1 model selected > select #2/A-F:82-84 144 atoms, 138 bonds, 18 residues, 1 model selected > select #2/A-F:102 48 atoms, 42 bonds, 6 residues, 1 model selected > select #2/A-F:102-104 144 atoms, 138 bonds, 18 residues, 1 model selected > select #2/A-F:82 42 atoms, 36 bonds, 6 residues, 1 model selected > select #2/A-F:82-84 144 atoms, 138 bonds, 18 residues, 1 model selected > select #2/A-F:84 54 atoms, 48 bonds, 6 residues, 1 model selected > select #2/A-F:84-91 378 atoms, 372 bonds, 48 residues, 1 model selected > select all 23135 atoms, 23441 bonds, 3075 residues, 2 models selected > show sel cartoons > lighting soft > graphics silhouettes false > graphics silhouettes true > select #1:1-85 641 atoms, 643 bonds, 85 residues, 1 model selected > color sel magenta > select #1:86-440 2700 atoms, 2733 bonds, 350 residues, 1 model selected > color sel cyan > select #2:1-82 3576 atoms, 3606 bonds, 492 residues, 1 model selected > color sel lime > select #2:83-440 16218 atoms, 16452 bonds, 2148 residues, 1 model selected > color sel orange > select #0 Nothing selected > select #2/C:124 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 142 atoms, 142 bonds, 18 residues, 1 model selected > select #2/A-F:123 30 atoms, 24 bonds, 6 residues, 1 model selected > select #2/A-F:123-125 138 atoms, 132 bonds, 18 residues, 1 model selected > select #2/A-F:146 42 atoms, 42 bonds, 6 residues, 1 model selected > select #2/A-F:146-149 198 atoms, 204 bonds, 24 residues, 1 model selected > select #2/A-F:139 66 atoms, 66 bonds, 6 residues, 1 model selected > select #2/A-F:139 66 atoms, 66 bonds, 6 residues, 1 model selected > select #2/A-F:147 36 atoms, 30 bonds, 6 residues, 1 model selected > select #2/A-F:147-149 156 atoms, 156 bonds, 18 residues, 1 model selected > select #0 Nothing selected > save > /Users/benjaminadler/Desktop/Proteolysis_compare__PHIKZ_gp093__Goslar_gp058.cxs > close #1 > close > open > /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_6_6mer_v2/fold_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif Chain information for fold_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif #1 --- Chain | Description A B C D E F | . G H I J K L | . > open > /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_6_6mer_v2/fold_goslar_gp061n_gp061c_6_6mer_v2_model_1.cif Chain information for fold_goslar_gp061n_gp061c_6_6mer_v2_model_1.cif #2 --- Chain | Description A B C D E F | . G H I J K L | . > open > /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_6_6mer_v2/fold_goslar_gp061n_gp061c_6_6mer_v2_model_2.cif Chain information for fold_goslar_gp061n_gp061c_6_6mer_v2_model_2.cif #3 --- Chain | Description A B C D E F | . G H I J K L | . > mmaker #3 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_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif, chain I (#1) with fold_goslar_gp061n_gp061c_6_6mer_v2_model_2.cif, chain G (#3), sequence alignment score = 1059.2 RMSD between 144 pruned atom pairs is 0.571 angstroms; (across all 219 pairs: 5.640) > 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 fold_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif, chain I (#1) with fold_goslar_gp061n_gp061c_6_6mer_v2_model_1.cif, chain G (#2), sequence alignment score = 1071.2 RMSD between 141 pruned atom pairs is 0.743 angstroms; (across all 219 pairs: 3.312) > hide #2 models > hide #3 models > hide #1 models > show #2 models > hide #2 models > show #3 models > show #1 models > hide #3 models > open > /Users/benjaminadler/Downloads/fold_goslar_gp061_gp060_6_6mer/fold_goslar_gp061_gp060_6_6mer_model_0.cif Chain information for fold_goslar_gp061_gp060_6_6mer_model_0.cif #4 --- Chain | Description A B C D E F | . G H I J K L | . > hide #1 models > show #4 cartoons > hide #4 atoms > color bfactor #4 31236 atoms, 4008 residues, atom bfactor range 15.6 to 89.6 > coulombic #4 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_A SES surface #4.1: minimum, -16.78, mean -0.14, maximum 12.28 Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_B SES surface #4.2: minimum, -16.38, mean -0.14, maximum 12.37 Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_C SES surface #4.3: minimum, -14.95, mean -0.16, maximum 12.36 Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_D SES surface #4.4: minimum, -15.34, mean -0.14, maximum 12.45 Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_E SES surface #4.5: minimum, -15.92, mean -0.13, maximum 12.50 Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_F SES surface #4.6: minimum, -19.73, mean -0.14, maximum 12.40 Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_G SES surface #4.7: minimum, -22.91, mean -1.62, maximum 15.80 Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_H SES surface #4.8: minimum, -18.42, mean -1.59, maximum 14.82 Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_I SES surface #4.9: minimum, -18.39, mean -1.57, maximum 12.68 Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_J SES surface #4.10: minimum, -18.95, mean -1.63, maximum 15.49 Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_K SES surface #4.11: minimum, -18.43, mean -1.60, maximum 13.82 Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_L SES surface #4.12: minimum, -19.73, mean -1.60, maximum 13.45 To also show corresponding color key, enter the above coulombic command and add key true > color #!4 bychain > show #1 models > hide #1 models > show #3 models > hide #3 models > show #1 models > mmaker #4 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_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif, chain I (#1) with fold_goslar_gp061_gp060_6_6mer_model_0.cif, chain B (#4), sequence alignment score = 990.2 RMSD between 99 pruned atom pairs is 0.561 angstroms; (across all 219 pairs: 17.222) > hide #1 models > hide #!4 models > show #1 models > ui mousemode right distance > distance #1/C:4@CB #1/F:4@CB Distance between fold_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif #1/C SER 4 CB and /F SER 4 CB: 29.757Å > close > open > /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_0.cif Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_0.cif #1 --- Chain | Description A B C D E F | . G H I J K L | . M N O P Q R | . > color bychain > hide atoms > show cartoons > color bfactor 29754 atoms, 3804 residues, atom bfactor range 14.6 to 87.5 > color bychain > show surfaces > select #1A,B,C,D,E,F Expected an objects specifier or a keyword > select #1/A,B,C,D,E,F 5286 atoms, 5346 bonds, 690 residues, 1 model selected > color sel purple > select #1/G,H,I,J,K,L 10122 atoms, 10248 bonds, 1314 residues, 1 model selected > color sel magenta > select #1/K,L,M,N,O,P 12938 atoms, 13136 bonds, 1638 residues, 1 model selected > color sel red > select up 29754 atoms, 30174 bonds, 3804 residues, 7 models selected > select up 29754 atoms, 30174 bonds, 3804 residues, 19 models selected > select #1/G,H,I,J,K,L 10122 atoms, 10248 bonds, 1314 residues, 1 model selected > color sel magenta > select #1/M,N,O,P,Q,R 14346 atoms, 14580 bonds, 1800 residues, 1 model selected > COLOR SEL RED Unknown command: COLOR SEL RED > color sel red > lighting soft > select #0 Nothing selected > open > /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_1.cif Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_1.cif #2 --- Chain | Description A B C D E F | . G H I J K L | . M N O P Q R | . > open > /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_2.cif Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_2.cif #3 --- Chain | Description A B C D E F | . G H I J K L | . M N O P Q R | . > hide #!1 models > hide #3 models > show #3 models > show #!1 models > mmaker #3 to #1 ===== Log before crash end ===== Log: Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle > lighting soft > graphics silhouettes true UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_0.cif Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_0.cif #1 --- Chain | Description A B C D E F | . G H I J K L | . M N O P Q R | . > open > /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_1.cif Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_1.cif #2 --- Chain | Description A B C D E F | . G H I J K L | . M N O P Q R | . > open > /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_2.cif Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_2.cif #3 --- Chain | Description A B C D E F | . G H I J K L | . M N O P Q R | . OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 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: Mac14,6 Model Number: MNWA3LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 8422.141.2 OS Loader Version: 8422.141.2 Software: System Software Overview: System Version: macOS 13.5 (22G74) Kernel Version: Darwin 22.6.0 Time since boot: 11 days, 6 hours, 30 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 38 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 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: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 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: 1.7.1 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: 2.6.1 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: 1.5.14 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: 1.0.4 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: 1.12.4 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: 1.33.3 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: 0.2.1 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: 4.47.2 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: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 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: 10.2.0 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: 1.0.8 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: 0.5.0 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: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX