id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17540 Crash accessing StructureSeq.structure chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000031b07f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031a073000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000319067000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031805b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031704f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000316043000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000315037000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031402b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031301f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000312013000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000311007000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001ed1a4840 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 91 in get_prop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1255 in _changes_cb File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1069 in proxy_handler File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py"", line 54 in check_for_changes File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py"", line 77 in File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3318 in command_trigger File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 144 in __exit__ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3203 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py"", line 225 in delete File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py"", line 308 in _key_closed File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/model.py"", line 105 in delete File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py"", line 1013 in close File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py"", line 678 in reset_state File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 625 in reset File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 837 in restore File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 1166 in open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 37 in open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 497 in remember_data_format File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 527 in collated_open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 215 in provider_open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 132 in cmd_open File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py"", line 334 in _qt_safe File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.mlp._mlp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 67) {""app_name"":""ChimeraX"",""timestamp"":""2025-05-02 20:14:54.00 -0400"",""app_version"":""1.9.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""AB3027BD-1991-4961-BD40-1B7020463C9A""} { ""uptime"" : 990000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro17,1"", ""coalitionID"" : 135451, ""osVersion"" : { ""train"" : ""macOS 15.3.2"", ""build"" : ""24D81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-05-02 20:14:43.0944 -0400"", ""codeSigningMonitor"" : 1, ""incident"" : ""AB3027BD-1991-4961-BD40-1B7020463C9A"", ""pid"" : 94997, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-04-30 21:05:48.5398 -0400"", ""procStartAbsTime"" : 22094712152673, ""procExitAbsTime"" : 23861696360603, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.9.0"",""CFBundleVersion"":""1.9.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""94790132-3312-58DA-A8CA-17E26FEA0A65"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""3D29B87B-2012-CFF9-597B-275E5FAEBE1F"", ""lowPowerMode"" : 1, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""93464843-BCEA-47F0-B491-00902AFC0FC1"", ""wakeTime"" : 247, ""sleepWakeUUID"" : ""CC6E2AAC-F34E-4612-8132-6D003C5DCA33"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xfffffffffffffff8 is not in any region. Bytes after previous region: 18446638519461216249 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [ 55.6M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END"", ""exception"" : {""codes"":""0x0000000000000001, 0xfffffffffffffff8"",""rawCodes"":[1,-8],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0xfffffffffffffff8""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":94997}, ""vmregioninfo"" : ""0xfffffffffffffff8 is not in any region. 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: ""e97abe8cf26a1bd7e23199cd8bbf015cb43beea0"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""639124e81d92412bfb4880b3"", ""factorPackIds"" : { }, ""deploymentId"" : 240000012 }, { ""rolloutId"" : ""661464ecda55e5192b100804"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6zz6 6zz6 title: Cryo-EM structure of S.cerevisiae cohesin-Scc2-DNA complex [more info...] Chain information for 6zz6 #1 --- Chain | Description | UniProt A | Structural maintenance of chromosomes protein 1,Structural maintenance of chromosomes protein 1,Structural maintenance of chromosomes protein 1 | SMC1_YEAST 2-71 87-195 1044-1224 B | Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3,Structural maintenance of chromosomes protein 3 | SMC3_YEAST 2-228 997-1071 1104-1222 C | Sister chromatid cohesion protein 1,Sister chromatid cohesion protein 1,Sister chromatid cohesion protein 1 | SCC1_YEAST 67-103 502-510 519-555 D | Sister chromatid cohesion protein 2 | SCC2_YEAST 1-1493 F | DNA (34-MER) | G | DNA (34-MER) | Non-standard residues in 6zz6 #1 --- ATP — adenosine-5'-triphosphate MG — magnesium ion > show :ATP atoms > style stick Changed 16597 atom styles > preset custom pretty-chain Using preset: Custom / Pretty-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain > hide atoms > show cartoons > hide #1/C:102-503 cartoons > hide #1/B:228-998 cartoons > select /C:67-555 639 atoms, 644 bonds, 83 residues, 1 model selected > select /B:0-1222 3368 atoms, 3413 bonds, 423 residues, 1 model selected > select :ATP 62 atoms, 66 bonds, 2 residues, 1 model selected > select :ATP 62 atoms, 66 bonds, 2 residues, 1 model selected > show select Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show selection Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show > hide #1/C:102-503 cartoons > hide #1/B:228-998 cartoons > hide #1/C:102-503 cartoons > hide sel atoms > hide > open emdb:11585 Summary of feedback from opening 11585 fetched from emdb --- note | Fetching map header 11585 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-11585/header/emd-11585.xml Opened emdb 11585 as #2, grid size 320,320,320, pixel 1.07, shown at level 0.016, step 2, values float32, fit PDB 6zz6 > volume #2 step 1 > volume #2 level 0.02954 > select /B:0-1222 3368 atoms, 3413 bonds, 423 residues, 1 model selected > volume #2 level 0.02534 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #2 level 0.0202 > hide #!1 models > show #!1 models > hide #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > select /B:1040 5 atoms, 4 bonds, 1 residue, 1 model selected > select /B:1040-1222 1203 atoms, 1221 bonds, 151 residues, 1 model selected > select /B:0 4 atoms, 3 bonds, 1 residue, 1 model selected > select /B:0-1 11 atoms, 11 bonds, 2 residues, 1 model selected > select /B:56-57 17 atoms, 16 bonds, 2 residues, 1 model selected > select /B:56-67 105 atoms, 105 bonds, 12 residues, 1 model selected > select /B:1222 11 atoms, 10 bonds, 1 residue, 1 model selected > select /B:1150-1222 605 atoms, 614 bonds, 73 residues, 1 model selected > select /B:0-1 11 atoms, 11 bonds, 2 residues, 1 model selected > select /B:0-1222 3368 atoms, 3413 bonds, 423 residues, 1 model selected > select clear > select /B:0-1 11 atoms, 11 bonds, 2 residues, 1 model selected > select /B:0-67 552 atoms, 563 bonds, 68 residues, 1 model selected > select /B:0-1 11 atoms, 11 bonds, 2 residues, 1 model selected > select /B:0-219 1740 atoms, 1762 bonds, 220 residues, 1 model selected > volume #2 level 0.07251 > hide #!1 models > show #!1 models > volume #2 level 0.08372 > hide #!1 models > show #!1 models > volume #2 level 0.006659 > volume #2 level 0.02954 > hide #!2 models > select clear > view name horizontal_dna > view horizontal_dna > save model.png transparentBackground true > show #!2 models > select /C:67-555 639 atoms, 644 bonds, 83 residues, 1 model selected > select clear > view horizontal_dna > volume #2 level 0.02581 > color zone #2 near #1 distance 4.5 > color zone #2 near #1 distance 6 > color zone #2 near #1 distance 8 > color zone #2 near #1 distance 10 > color zone #2 near #1 distance 12 > hide #!1 models > save map.png transparentBackground true > save map.png transparentBackground true height 432 width 432 > hide #!2 models > show #!1 models > save model.png transparentBackground true height 432 width 432 > save /Users/asaeed/Desktop/p1.cxs > mlp Map values for surface ""6zz6_A SES surface"": minimum -28.52, mean -4.572, maximum 23.22 Map values for surface ""6zz6_B SES surface"": minimum -29.48, mean -4.999, maximum 25.71 Map values for surface ""6zz6_C SES surface"": minimum -23.45, mean -2.221, maximum 23.28 Map values for surface ""6zz6_D SES surface"": minimum -28.11, mean -3.537, maximum 24.35 To also show corresponding color key, enter the above mlp command and add key true > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /A LEU 192 /A ASN 1087 /A SER 1088 /A ALA 1224 /B ARG 225 /B ASN 226 /B ARG 227 /B LYS 228 /B GLU 1000 /B ARG 1222 /C ALA 555 /D THR 221 /D THR 222 /D ASN 223 /D CYS 224 /D LEU 225 /D THR 226 /D LYS 227 /D LEU 228 /D GLN 229 /D MET 230 /D THR 231 /D ILE 232 /D LYS 233 /D ASN 234 /D ILE 235 /D THR 236 /D LEU 250 /D LEU 251 /D ARG 252 /D LEU 253 /D LEU 254 /D ASP 255 /D VAL 256 /D MET 257 /D VAL 258 /D CYS 259 /D ASN 260 /D ILE 261 /D LYS 262 /D ARG 278 /D TYR 279 /D ILE 280 /D LEU 282 /D LEU 283 /D SER 284 /D THR 285 /D ILE 286 /D VAL 287 /D LEU 288 /D PHE 289 /D ASN 290 /D ILE 291 /D GLU 304 /D SER 305 /D TYR 306 /D ILE 307 /D MET 308 /D GLU 309 /D PRO 310 /D VAL 311 /D ASN 312 /D PHE 313 /D LEU 314 /D SER 315 /D ASP 316 /D LEU 317 /D ILE 318 /D GLU 319 /D SER 320 /D LEU 321 /D LYS 322 /D SER 386 /D VAL 436 /D ARG 623 /D ILE 647 /D ILE 648 /D THR 649 /D VAL 650 /D ASP 651 /D ASN 652 /D GLU 653 /D LEU 654 /D LYS 655 /D LYS 656 /D ILE 657 /D LEU 658 /D GLU 659 /D GLN 660 /D ILE 661 /D LYS 662 /D ASP 846 /D GLN 847 /D SER 1183 /D LEU 1413 /D GLU 1448 /D SER 1449 /D GLU 1450 /D LEU 1451 /D LYS 1452 /D ASN 1453 /D LYS 1454 /D GLN 1455 /D PHE 1466 /D SER 1467 /D GLN 1469 /D LEU 1470 /D GLU 1471 /D ASN 1472 /D ILE 1473 /D GLU 1474 /D GLN 1475 /G DT 32 /G DT 33 /G DT 34 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 6zz6_A SES surface #1.4: minimum, -19.65, mean -0.08, maximum 15.82 Coulombic values for 6zz6_B SES surface #1.5: minimum, -22.45, mean -0.31, maximum 16.93 Coulombic values for 6zz6_C SES surface #1.6: minimum, -17.05, mean -0.37, maximum 10.79 Coulombic values for 6zz6_D SES surface #1.7: minimum, -21.57, mean -0.20, maximum 18.67 Coulombic values for 6zz6_F SES surface #1.8: minimum, -17.78, mean -10.21, maximum -2.35 Coulombic values for 6zz6_G SES surface #1.9: minimum, -16.67, mean -10.72, maximum -0.86 To also show corresponding color key, enter the above coulombic command and add key true > hide /G/F > hide /G/F cartoons > hide /G/F surfaces > open /Users/asaeed/Downloads/6ZZ6D_With_ConSurf.pdb 6ZZ6D_With_ConSurf.pdb title: Cryo-em structure of S.cerevisiae cohesin-SCC2-DNA complex [more info...] Chain information for 6ZZ6D_With_ConSurf.pdb #3 --- Chain | Description | UniProt A | structural maintenance of chromosomes protein 1,structural maintenance of chromosomes protein 1,structural maintenance of chromosomes protein 1 | SMC1_YEAST 2-71 87-195 1044-1224 B | structural maintenance of chromosomes protein 3,structural maintenance of chromosomes protein 3,structural maintenance of chromosomes protein 3 | SMC3_YEAST 2-228 997-1071 1104-1222 C | sister chromatid cohesion protein 1,sister chromatid cohesion protein 1,sister chromatid cohesion protein 1 | SCC1_YEAST 67-103 502-510 519-555 D | sister chromatid cohesion protein 2 | SCC2_YEAST 1-1493 F | DNA (34-mer) | G | DNA (34-mer) | Non-standard residues in 6ZZ6D_With_ConSurf.pdb #3 --- ATP — adenosine-5'-triphosphate MG — magnesium ion > hide #!1 models > hide #!3 atoms > show #!3 cartoons > color byattribute bfactor #3/D palette cyanmaroon key true > key cyan-white-maroon :1 :5 :9 showTool true > ui mousemode right ""color key"" 8264 atoms, 1050 residues, atom bfactor range 1 to 9 > key pos 0.573994,0.342945 size 0.182897,0.0337527 > key pos 0.623206,0.276819 size 0.108357,0.0840229 > key pos 0.818856,0.0332416 size 0.158438,0.0260102 > ui tool show ""Show Sequence Viewer"" > sequence chain #1/D #3/D Alignment identifier is 1 > select > #1/D:222-236,251-262,279-291,305-322,338-352,356-373,387-406,409-424,444-456,459-466,475-506,510-524,531-548,555-579,598-616,618-634,648-662,679-688,691-709,712-730,736-749,751-765,768-778,783-801,803-817,822-845,850-866,870-883,892-917,928-942,949-962,967-981,987-1001,1006-1022,1027-1049,1060-1075,1092-1104,1110-1147,1151-1175,1204-1221,1224-1242,1245-1258,1261-1302,1312-1320,1325-1341,1356-1368,1373-1398,1414-1434,1449-1454,1467-1473 > #3/D:222-236,251-262,279-291,305-322,338-352,356-373,387-406,409-424,444-456,459-466,475-506,510-524,531-548,555-579,598-616,618-634,648-662,679-688,691-709,712-730,736-749,751-765,768-778,783-801,803-817,822-845,850-866,870-883,892-917,928-942,949-962,967-981,987-1001,1006-1022,1027-1049,1060-1075,1092-1104,1110-1147,1151-1175,1204-1221,1224-1242,1245-1258,1261-1302,1312-1320,1325-1341,1356-1368,1373-1398,1414-1434,1449-1454,1467-1473 13816 atoms, 13958 bonds, 1750 residues, 2 models selected > select #1/D:712-713 #3/D:712-713 34 atoms, 32 bonds, 4 residues, 2 models selected > select #1/D:712-718 #3/D:712-718 116 atoms, 114 bonds, 14 residues, 2 models selected Sister Chromatid Cohesion Protein 2 [ID: 1] region 2 chains [712-718] RMSD: 0.000 > select #1/D:712 #3/D:712 18 atoms, 16 bonds, 2 residues, 2 models selected > select #1/D:712-801 #3/D:712-801 1460 atoms, 1476 bonds, 180 residues, 2 models selected Sister Chromatid Cohesion Protein 2 [ID: 1] region 2 chains [712-801] RMSD: 0.000 > view horizontal_dna > select clear > view horizontal_dna > preset custom pretty-chain Using preset: Custom / Pretty-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain > color byattribute bfactor #3/D palette cyanmaroon key true > key cyan-white-maroon :1 :5 :9 showTool true 8264 atoms, 1050 residues, atom bfactor range 1 to 9 > transparency 70 /A/B/C/F/G target c Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency /A/B/C/F/G 70 target c > view horizontal_dna > transparency /A/B/C/F/G 90 target c > transparency /A/B/C/F/G 80 target c > key pos 0.779884,0.115759 size 0.166889,0.0224714 > view horizontal_dna > key pos 0.620338,0.126824 size 0.150025,0.0204763 > key pos 0.681009,0.128003 size 0.142288,0.0202173 > key pos 0.680875,0.148742 size 0.141757,0.0224854 > save cons1.png transparentBackground true height 432 width 432 > turn y 90 > turn y -180 > turn y 10 > save cons2.png transparentBackground true height 432 width 432 > view horizontal_dna > turn y -60 > view name horizontal_dna2 > save /Users/asaeed/Desktop/p2.cxs > ui mousemode right translate > close session > open /Users/asaeed/Downloads/integrative_model.cxs Opened emdb 11585 as #2, grid size 320,320,320, pixel 1.07, shown at level 0.0238, step 1, values float32 Opened emdb 12880 as #3, grid size 200,200,200, pixel 1.72, shown at level 0.0788, step 1, values float32 Opened emdb 12887 as #4, grid size 200,200,200, pixel 1.96, shown at level 0.03, step 1, values float32 opened ChimeraX session > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!3 models > show #!4 models > hide #!4 models > preset custom pretty-chain Using preset: Custom / Pretty-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain > open /Users/asaeed/Desktop/p1.cxs Opened emdb 11585 as #2, grid size 320,320,320, pixel 1.07, shown at level 0.0258, step 1, values float32 opened ChimeraX session > show #!2 models > hide #!1 models > preset custom pretty-chain Using preset: Custom / Pretty-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain > close session > open /Users/asaeed/Downloads/integrative_model.cxs format session Opened emdb 11585 as #2, grid size 320,320,320, pixel 1.07, shown at level 0.0238, step 1, values float32 Opened emdb 12880 as #3, grid size 200,200,200, pixel 1.72, shown at level 0.0788, step 1, values float32 Opened emdb 12887 as #4, grid size 200,200,200, pixel 1.96, shown at level 0.03, step 1, values float32 opened ChimeraX session > preset custom pretty-chain Using preset: Custom / Pretty-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain > hide #!2 models > hide #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > open /Users/asaeed/Downloads/fold_pds5/fold_pds5_model_0.cif Chain information for fold_pds5_model_0.cif #5 --- Chain | Description A | . Computing secondary structure > select add #5 10381 atoms, 10584 bonds, 1277 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #5,1,0,0,165.4,0,1,0,-57.096,0,0,1,151.53 > view matrix models #5,1,0,0,246.2,0,1,0,89.912,0,0,1,160.07 > view matrix models #5,1,0,0,187.86,0,1,0,164.6,0,0,1,195.12 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.71903,-0.61958,-0.31484,185.61,-0.070055,0.3861,-0.91979,165.2,0.69144,0.68342,0.23421,202.8 > view matrix models > #5,0.10461,-0.93938,0.32654,178.15,-0.6175,-0.31874,-0.7191,159.55,0.77958,-0.12642,-0.61341,205.9 > hide #!1 models > hide #!4 models > hide #!3 models > show #!1 models > view matrix models > #5,0.34322,0.67218,0.65603,177.63,-0.40763,-0.52265,0.74878,162.53,0.84619,-0.52442,0.094617,207.55 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.34322,0.67218,0.65603,134.34,-0.40763,-0.52265,0.74878,137.58,0.84619,-0.52442,0.094617,203.68 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.7194,0.33669,0.60754,140.03,-0.34453,-0.58652,0.733,138.55,0.60313,-0.73664,-0.30594,201.02 > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models > #5,0.7194,0.33669,0.60754,157.43,-0.34453,-0.58652,0.733,137.59,0.60313,-0.73664,-0.30594,184.72 > view matrix models > #5,0.7194,0.33669,0.60754,155.68,-0.34453,-0.58652,0.733,150.34,0.60313,-0.73664,-0.30594,187.33 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.72178,0.40666,0.56006,155.56,-0.3267,-0.51319,0.79366,150.4,0.61017,-0.75582,-0.23755,187.45 > view matrix models > #5,0.67757,0.26918,0.68443,155.27,-0.5856,-0.36556,0.72349,146.68,0.44495,-0.89102,-0.090058,185.56 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.67757,0.26918,0.68443,156.5,-0.5856,-0.36556,0.72349,155.27,0.44495,-0.89102,-0.090058,186.95 > mmaker #5 to #1 Computing secondary structure 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 6zz6, chain D (#1) with fold_pds5_model_0.cif, chain A (#5), sequence alignment score = 781.2 RMSD between 12 pruned atom pairs is 1.435 angstroms; (across all 937 pairs: 31.321) > select clear > color bfactor #5 palette alphafold 10381 atoms, 1277 residues, atom bfactor range 13.2 to 97.7 > mmaker #5:365-800 to #1 Computing secondary structure 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 6zz6, chain D (#1) with fold_pds5_model_0.cif, chain A (#5), sequence alignment score = 372.5 RMSD between 10 pruned atom pairs is 1.356 angstroms; (across all 377 pairs: 26.014) > open /Users/asaeed/Desktop/p1.cxs Opened emdb 11585 as #2, grid size 320,320,320, pixel 1.07, shown at level 0.0258, step 1, values float32 opened ChimeraX session > turn y -60 > ui mousemode right clip > view > undo > ui mousemode right windowing > ui mousemode right ""contour level"" > ui mousemode right ""move planes"" > ui mousemode right zone > ui mousemode right ""color key"" > hide #3 target m > ui tool show ""Side View"" > view name horizontal_dna2 > save model2.png transparentBackground true height 432 width 432 > hide #!1 models > show #!2 models > select ~sel & ##selected Nothing selected > save map2.png transparentBackground true height 432 width 432 > open /Users/asaeed/Desktop/p2.cxs > ui mousemode right zone ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MJ123LL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 44 days, 17 hours, 12 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG ULTRAWIDE: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 160.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Core duplicate all ChimeraX