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Opened 6 months ago
Closed 6 months ago
#17540 closed defect (duplicate)
Crash accessing StructureSeq.structure
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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. 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",
"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,
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===== 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
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash accessing StructureSeq.structure |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Duplicate of #17013