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Opened 6 hours ago
#19870 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x00000003486af000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003476a3000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000346697000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034568b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034467f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000343673000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000342667000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034165b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000034064f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033f643000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033e637000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033d62b000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033c61f000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033b613000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000033a607000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000002004060c0 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imaging, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 55)
{"app_name":"ChimeraX","timestamp":"2026-02-19 17:13:13.00 +0000","app_version":"1.10.0","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.6 (24G84)","roots_installed":0,"name":"ChimeraX","incident_id":"0EA31C16-DA0B-4EE0-A7E2-D85C89A7BA44"}
{
"uptime" : 23000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 2887,
"osVersion" : {
"train" : "macOS 15.6",
"build" : "24G84",
"releaseType" : "User"
},
"captureTime" : "2026-02-19 17:05:23.6964 +0000",
"codeSigningMonitor" : 1,
"incident" : "0EA31C16-DA0B-4EE0-A7E2-D85C89A7BA44",
"pid" : 2514,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-02-19 11:04:29.0292 +0000",
"procStartAbsTime" : 135691827840,
"procExitAbsTime" : 564616304259,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"44A2F365-9E12-538B-8DC9-FD5ED37321BC","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B97F65CB-AB70-2664-1BC6-992D64AA7B45",
"lowPowerMode" : 1,
"appleIntelligenceStatus" : {"reasons":["siriAssetIsNotReady","notOptedIn","assetIsNotReady"],"state":"unavailable"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "662559AD-112B-4C5D-95D3-6A5066F19C47",
"wakeTime" : 4328,
"sleepWakeUUID" : "0F015813-E933-4684-9CD8-671F49A42D23",
"sip" : "enabled",
"vmRegionInfo" : "0x20078836c5f0 is not in any region. Bytes after previous region: 34735685813745 Bytes before following region: 70336394115600\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000a0078836c5f0","rawCodes":[1,175954210506224],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000a0078836c5f0 -> 0x000020078836c5f0 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":2514},
"vmregioninfo" : "0x20078836c5f0 is not in any region. Bytes after previous region: 34735685813745 Bytes before following region: 70336394115600\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5100567192},{"value":99},{"value":104},{"value":5904761040},{"value":1027},{"value":8742178245366393788},{"value":8742178236780661628},{"value":14757395258967641293},{"value":4294967286},{"value":5100567122},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8611288408},{"value":0},{"value":11},{"value":259},{"value":8594153888,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4333454896,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8555319296,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":8555319296,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6749108364},"cpsr":{"value":1073745920},"fp":{"value":5100567264},"sp":{"value":5100567232},"esr":{"value":1442840704,"description":" Address size 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===== Log before crash start =====
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/hmed/Downloads/cryosparc_P98_J17_006_volume_map_sharp.mrc
Opened cryosparc_P98_J17_006_volume_map_sharp.mrc as #1, grid size
480,480,480, pixel 0.831, shown at level 0.147, step 2, values float32
> volume #1 level 0.447
> volume #1 step 1
> volume #1 level 0.4855
> lighting soft
> set bgColor white
> open /Users/hmed/Downloads/9EWQ.pdb /Users/hmed/Downloads/8E6K.pdb
> /Users/hmed/Downloads/8E6K.cif "/Users/hmed/Downloads/8E6J 1.pdb"
> /Users/hmed/Downloads/9KOD.pdb
9EWQ.pdb title:
Influenza virus neuraminidase N1 NC13 ectodomain with A tetrabrachio- domain
stalk [more info...]
Chain information for 9EWQ.pdb #2
---
Chain | Description
A B C D | neuraminidase
8E6K.pdb title:
2H08 fab In complex with influenza virus neuraminidase from A/brevig
mission/1/1918 (H1N1) [more info...]
Chain information for 8E6K.pdb #3
---
Chain | Description | UniProt
A B C D | neuraminidase | NRAM_I18A0 82-470
E F G H | 2H08 fragment antigen binding heavy chain |
I J K L | 2H08 fragment antigen binding light chain |
Non-standard residues in 8E6K.pdb #3
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
8E6K.cif title:
2H08 Fab in complex with influenza virus neuraminidase from A/Brevig
Mission/1/1918 (H1N1) [more info...]
Chain information for 8E6K.cif #4
---
Chain | Description | UniProt
A B C D | Neuraminidase | NRAM_I18A0 82-470
E F G H | 2H08 fragment antigen binding heavy chain |
I J K L | 2H08 fragment antigen binding light chain |
Non-standard residues in 8E6K.cif #4
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
8E6J 1.pdb title:
3H03 fab In complex with influenza virus neuraminidase from A/brevig
mission/1/1918 (H1N1) [more info...]
Chain information for 8E6J 1.pdb #5
---
Chain | Description | UniProt
A B C D | neuraminidase | NRAM_I18A0 82-470
E F G H | 3H03 fragment antigen binding heavy chain |
I J K L | 3H03 fragment antigen binding light chain |
9KOD.pdb title:
Neuraminidase of A/dairy cow/minnesota/24_016288-003/2024 (DCMN24 N1) In
complex with cav-F6 fab [more info...]
Chain information for 9KOD.pdb #6
---
Chain | Description
A B C D | neuraminidase
E G I K | cav-F6 heavy chain
F H J L | cav-F6 κ chain
Non-standard residues in 9KOD.pdb #6
---
CA — calcium ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> show cartoons
> hide atoms
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #5 models
> hide #!6 models
> hide #5 models
> show #4 models
> show #3 models
> hide #4 models
> show #2 models
> hide #3 models
> select add #2
11904 atoms, 12254 bonds, 1540 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.13135,0.10157,-0.98612,380.79,0.35371,0.93407,0.049093,-66.226,0.92609,-0.34235,-0.15861,88.915
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.13135,0.10157,-0.98612,387.26,0.35371,0.93407,0.049093,-67.115,0.92609,-0.34235,-0.15861,112.3
> view matrix models
> #2,-0.13135,0.10157,-0.98612,380.66,0.35371,0.93407,0.049093,-68.91,0.92609,-0.34235,-0.15861,110.6
> view matrix models
> #2,-0.13135,0.10157,-0.98612,380.43,0.35371,0.93407,0.049093,-66.765,0.92609,-0.34235,-0.15861,110.83
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 9EWQ.pdb (#2) to map cryosparc_P98_J17_006_volume_map_sharp.mrc
(#1) using 11904 atoms
average map value = 0.2725, steps = 72
shifted from previous position = 2.66
rotated from previous position = 4.86 degrees
atoms outside contour = 8459, contour level = 0.48546
Position of 9EWQ.pdb (#2) relative to
cryosparc_P98_J17_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.09281877 0.17057375 -0.98096344 357.40958835
0.33443205 0.93332040 0.13064543 -75.28601928
0.93783787 -0.31593927 -0.14367498 98.90011257
Axis -0.22590289 -0.97061714 0.08288699
Axis point 143.75589202 0.00000000 204.32008668
Rotation angle (degrees) 98.71888807
Shift along axis 0.53157525
> view matrix models
> #2,-0.092819,0.17057,-0.98096,350.34,0.33443,0.93332,0.13065,-77.276,0.93784,-0.31594,-0.14367,98.688
> fitmap #2 inMap #1
Fit molecule 9EWQ.pdb (#2) to map cryosparc_P98_J17_006_volume_map_sharp.mrc
(#1) using 11904 atoms
average map value = 0.2736, steps = 76
shifted from previous position = 5.11
rotated from previous position = 4.72 degrees
atoms outside contour = 8442, contour level = 0.48546
Position of 9EWQ.pdb (#2) relative to
cryosparc_P98_J17_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.10049857 0.09039277 -0.99082248 374.45820913
0.34018612 0.93896558 0.05115698 -63.64741394
0.93497243 -0.33192285 -0.12511506 99.27621483
Axis -0.19353804 -0.97294229 0.12619958
Axis point 149.50844549 0.00000000 212.25594943
Rotation angle (degrees) 98.24023898
Shift along axis 1.98197032
> volume flip #1
Opened cryosparc_P98_J17_006_volume_map_sharp.mrc z flip as #7, grid size
480,480,480, pixel 0.831, shown at step 1, values float32
> fitmap #2 inMap #7
Fit molecule 9EWQ.pdb (#2) to map cryosparc_P98_J17_006_volume_map_sharp.mrc z
flip (#7) using 11904 atoms
average map value = 0.2632, steps = 100
shifted from previous position = 3.59
rotated from previous position = 5.27 degrees
atoms outside contour = 8542, contour level = 0.48546
Position of 9EWQ.pdb (#2) relative to
cryosparc_P98_J17_006_volume_map_sharp.mrc z flip (#7) coordinates:
Matrix rotation and translation
-0.05253495 0.06180782 -0.99670451 374.33565591
0.27018465 0.96173761 0.04539838 -52.84835005
0.96137419 -0.26690926 -0.06722436 68.34519241
Axis -0.15664353 -0.98210966 0.10451516
Axis point 159.25609690 0.00000000 207.46075764
Rotation angle (degrees) 94.53171170
Shift along axis 0.40872691
> view matrix models
> #2,-0.052535,0.061808,-0.9967,375.34,0.27018,0.96174,0.045398,-58.207,0.96137,-0.26691,-0.067224,68.988
> fitmap #2 inMap #7
Fit molecule 9EWQ.pdb (#2) to map cryosparc_P98_J17_006_volume_map_sharp.mrc z
flip (#7) using 11904 atoms
average map value = 0.2515, steps = 68
shifted from previous position = 1.12
rotated from previous position = 1.17 degrees
atoms outside contour = 8618, contour level = 0.48546
Position of 9EWQ.pdb (#2) relative to
cryosparc_P98_J17_006_volume_map_sharp.mrc z flip (#7) coordinates:
Matrix rotation and translation
-0.03762832 0.06642827 -0.99708144 371.47542737
0.28323263 0.95757968 0.05310779 -60.88035135
0.95831278 -0.28040764 -0.05484676 69.08170078
Axis -0.16713832 -0.97992859 0.10864960
Axis point 158.24674010 0.00000000 208.73177237
Rotation angle (degrees) 93.86740467
Shift along axis 5.07631637
> view matrix models
> #2,-0.037628,0.066428,-0.99708,371.83,0.28323,0.95758,0.053108,-58.797,0.95831,-0.28041,-0.054847,73.062
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.11024,0.10966,0.98784,-18.559,-0.4764,-0.86645,0.14935,440.56,0.87229,-0.48707,-0.043275,129.51
> view matrix models
> #2,-0.053039,-0.046928,0.99749,43.662,-0.25359,-0.96552,-0.058908,452.78,0.96586,-0.25607,0.03931,49.983
> fitmap #2 inMap #7
Fit molecule 9EWQ.pdb (#2) to map cryosparc_P98_J17_006_volume_map_sharp.mrc z
flip (#7) using 11904 atoms
average map value = 1.152, steps = 72
shifted from previous position = 4.51
rotated from previous position = 3.24 degrees
atoms outside contour = 2044, contour level = 0.48546
Position of 9EWQ.pdb (#2) relative to
cryosparc_P98_J17_006_volume_map_sharp.mrc z flip (#7) coordinates:
Matrix rotation and translation
-0.00987940 -0.01052014 0.99989586 22.93547162
-0.25270803 -0.96745955 -0.01267574 445.77948485
0.96749215 -0.25280694 0.00689940 54.88121692
Axis -0.70092864 0.09458450 -0.70693197
Axis point 11.53851492 225.70514329 0.00000000
Rotation angle (degrees) 170.13687580
Shift along axis -12.70958685
> fitmap #2 inMap #7
Fit molecule 9EWQ.pdb (#2) to map cryosparc_P98_J17_006_volume_map_sharp.mrc z
flip (#7) using 11904 atoms
average map value = 1.152, steps = 40
shifted from previous position = 0.00978
rotated from previous position = 0.0132 degrees
atoms outside contour = 2048, contour level = 0.48546
Position of 9EWQ.pdb (#2) relative to
cryosparc_P98_J17_006_volume_map_sharp.mrc z flip (#7) coordinates:
Matrix rotation and translation
-0.00987601 -0.01049475 0.99989616 22.93170695
-0.25248749 -0.96751748 -0.01264874 445.74002113
0.96754976 -0.25258619 0.00690542 54.83382387
Axis -0.70093429 0.09449421 -0.70693844
Axis point 11.53491689 225.68001116 0.00000000
Rotation angle (degrees) 170.14499369
Shift along axis -12.71790661
> view matrix models
> #2,-0.15828,-0.027182,0.98702,58.214,-0.42118,-0.90226,-0.092391,480.56,0.89306,-0.43034,0.13137,83.169
> fitmap #2 inMap #1
Fit molecule 9EWQ.pdb (#2) to map cryosparc_P98_J17_006_volume_map_sharp.mrc
(#1) using 11904 atoms
average map value = 0.3066, steps = 132
shifted from previous position = 0.463
rotated from previous position = 9.05 degrees
atoms outside contour = 8152, contour level = 0.48546
Position of 9EWQ.pdb (#2) relative to
cryosparc_P98_J17_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.00301887 -0.02731687 0.99962227 24.50012686
-0.40343203 -0.91463407 -0.02621274 467.71513425
0.91500464 -0.40335877 -0.00825934 98.29065867
Axis -0.69930419 0.15689801 -0.69739276
Axis point 0.00000000 245.41797874 -9.20044743
Rotation angle (degrees) 164.35607923
Shift along axis -12.29665966
> hide #!1 models
> show #!7 models
> fitmap #2 inMap #1
Fit molecule 9EWQ.pdb (#2) to map cryosparc_P98_J17_006_volume_map_sharp.mrc
(#1) using 11904 atoms
average map value = 0.3066, steps = 40
shifted from previous position = 0.00635
rotated from previous position = 0.00657 degrees
atoms outside contour = 8148, contour level = 0.48546
Position of 9EWQ.pdb (#2) relative to
cryosparc_P98_J17_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.00296760 -0.02721697 0.99962515 24.46847205
-0.40345309 -0.91462799 -0.02610047 467.70309669
0.91499552 -0.40337931 -0.00826652 98.29402159
Axis -0.69931820 0.15686816 -0.69738543
Axis point 0.00000000 245.41132949 -9.19630927
Rotation angle (degrees) 164.35075058
Shift along axis -12.29234096
> fitmap #2 inMap #7
Fit molecule 9EWQ.pdb (#2) to map cryosparc_P98_J17_006_volume_map_sharp.mrc z
flip (#7) using 11904 atoms
average map value = 0.3252, steps = 60
shifted from previous position = 0.739
rotated from previous position = 2.25 degrees
atoms outside contour = 7878, contour level = 0.48546
Position of 9EWQ.pdb (#2) relative to
cryosparc_P98_J17_006_volume_map_sharp.mrc z flip (#7) coordinates:
Matrix rotation and translation
-0.00174977 0.00576348 0.99998186 18.30333898
-0.38393894 -0.92334678 0.00464997 460.04815818
0.92335683 -0.38392384 0.00382847 90.49230864
Axis -0.69933430 0.13790562 -0.70136551
Axis point 10.68718086 237.97767186 0.00000000
Rotation angle (degrees) 163.87004477
Shift along axis -12.82510838
> view matrix models
> #2,0.012789,-0.022289,0.99967,21.06,-0.38553,-0.92256,-0.015637,463.81,0.92261,-0.38521,-0.020392,95.196
> view matrix models
> #2,0.062532,0.022652,0.99779,2.4693,-0.36642,-0.92941,0.044063,450.76,0.92835,-0.36836,-0.049817,95.903
> view matrix models
> #2,0.05903,0.040139,0.99745,-0.26653,-0.23537,-0.97046,0.052983,431.2,0.97011,-0.23789,-0.047839,61.125
> fitmap #2 inMap #7
Fit molecule 9EWQ.pdb (#2) to map cryosparc_P98_J17_006_volume_map_sharp.mrc z
flip (#7) using 11904 atoms
average map value = 1.152, steps = 72
shifted from previous position = 0.258
rotated from previous position = 4.99 degrees
atoms outside contour = 2045, contour level = 0.48546
Position of 9EWQ.pdb (#2) relative to
cryosparc_P98_J17_006_volume_map_sharp.mrc z flip (#7) coordinates:
Matrix rotation and translation
-0.00989525 -0.01050721 0.99989584 22.94019453
-0.25268689 -0.96746519 -0.01266708 445.77120526
0.96749751 -0.25278591 0.00691828 54.88872601
Axis -0.70092318 0.09457293 -0.70693893
Axis point 11.53572521 225.70140825 0.00000000
Rotation angle (degrees) 170.13731151
Shift along axis -12.72440343
> select subtract #2
Nothing selected
> transparency #7.1 50
> graphics silhouettes true
> show #2 atoms
> color #2 #daeeefff
> ui tool show "Side View"
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2:119
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #2:178
36 atoms, 32 bonds, 4 residues, 1 model selected
> select #2:98
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/A:89
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:89-92
31 atoms, 32 bonds, 4 residues, 1 model selected
> select #2/A:90
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:89-90
20 atoms, 21 bonds, 2 residues, 1 model selected
> color sel lime
> select #2/A:29
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:29-30
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:38
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:38-39
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/A:40
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:40
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:29
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:29-31
27 atoms, 28 bonds, 3 residues, 1 model selected
> select #2/A:62-63
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:62-63
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:89
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:89-90
20 atoms, 21 bonds, 2 residues, 1 model selected
> select #2/A:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:109-110
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/A:133
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:133
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> open 8gav fromDatabase pdb format mmcif
Summary of feedback from opening 8gav fetched from pdb
---
note | Fetching compressed mmCIF 8gav from http://files.rcsb.org/download/8gav.cif
8gav title:
Structure of human NDS.3 Fab in complex with influenza virus neuraminidase
from A/Darwin/09/2021 (H3N2) [more info...]
Chain information for 8gav #8
---
Chain | Description | UniProt
A | Neuraminidase | A0A8F5JTQ6_9INFA 83-469
H | Fab NDS.3, heavy chain |
L | Fab NDS.3, light chain |
Non-standard residues in 8gav #8
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
8gav mmCIF Assemblies
---
1| complete point assembly
2| point asymmetric unit
3| point asymmetric unit, std point frame
> mmaker #8 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9EWQ.pdb, chain A (#2) with 8gav, chain A (#8), sequence alignment
score = 1086
RMSD between 328 pruned atom pairs is 0.889 angstroms; (across all 380 pairs:
1.562)
> ui tool show "Fit in Map"
> fitmap #8 inMap #7
Fit molecule 8gav (#8) to map cryosparc_P98_J17_006_volume_map_sharp.mrc z
flip (#7) using 4772 atoms
average map value = 0.516, steps = 120
shifted from previous position = 0.427
rotated from previous position = 0.875 degrees
atoms outside contour = 2875, contour level = 0.48546
Position of 8gav (#8) relative to cryosparc_P98_J17_006_volume_map_sharp.mrc z
flip (#7) coordinates:
Matrix rotation and translation
-0.00251203 0.03493684 0.99938637 45.29122065
-0.70320371 -0.71061390 0.02307430 428.34348486
0.71098399 -0.70271423 0.02635280 193.39791159
Axis -0.67539430 0.26837751 -0.68688867
Axis point 21.20795431 249.29029248 0.00000000
Rotation angle (degrees) 147.49947978
Shift along axis -48.47450813
> close #1
> select add #2
11904 atoms, 12254 bonds, 1540 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #8 models
> color A red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> hide #!7 models
> color /A red
> color /B blue
> color /C cyan
> color /D green
> color /A paleblue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /A lightblue
> color /B lightblue
> color /A blue
> color bychain pallette Paired-12
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color chains pallette Paired-12
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color random pallette Paired-12
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color random bonds pallette Paired-12
Expected ',' or a keyword
> color random bonds, pallette Paired-12
Missing or invalid "what" argument: Should be one of 'All', 'atoms', 'bonds',
'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or
'surfaces'
> runscript |~/apps/viridis_colormaps.py
Missing or invalid "scriptFile" argument: File '|~/apps/viridis_colormaps.py'
does not exist
> runscript ~/apps/viridis_colormaps.py
Missing or invalid "scriptFile" argument: File
'/Users/hmed/apps/viridis_colormaps.py' does not exist
> pwd
Current working directory is: /Users/hmed/Desktop
> pwd
Current working directory is: /Users/hmed/Desktop
> runscript /Users/hmed/apps/viridis_colormaps.py
Missing or invalid "scriptFile" argument: File
'/Users/hmed/apps/viridis_colormaps.py' does not exist
> runscript /Users/hmed/apps/viridis_colormaps/viridis_colormaps.py
Missing or invalid "scriptFile" argument: File
'/Users/hmed/apps/viridis_colormaps/viridis_colormaps.py' does not exist
> runscript /Users/hmed/apps/chimerax_viridis/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> color #2 bychain
> color #2 bychain pallette inferno
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #2 bychain palette inferno
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sequential #2 bychain palette inferno
Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword
> lighting soft msMapSize 64
> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1
> cartoon style strand modeHelix default arrows true xsection rectangle width
> 2 thickness 1
> cartoon style helix modeHelix default arrows false xsection oval width 1.6
> thickness 1.2
> graphics silhouettes width 3
> graphics silhouettes true
> lighting_lumi
Unknown command: lighting_lumi
> rainbow Template target c palette ^PuBu-5
Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword
> rainbow chains target c palette ^pubu-5
> hide #2 atoms
> rainbow chains target c palette inferno
Fetching compressed palette rubo from
https://www.colourlovers.com/api/palettes?keywords=rubo&format=json&numResults=100
Could not find palette rubo at COLOURlovers.com using keyword search
> rainbow chains target c palette turbo
> show #!7 models
> select #2/A:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:217
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:217
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:219-220
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:219-221
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #2/A:205
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:205
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:343
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:343-344
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:342
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:342
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:372
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:371-372
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/A:342
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:342
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:312
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:312
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/A:278
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:278
11 atoms, 10 bonds, 1 residue, 1 model selected
> select :29,62,89,90,1009,133,138,188,205
2155 atoms, 1997 bonds, 270 residues, 6 models selected
> show sel & #2 atoms
> color sel & #2 byhetero
> color (#2 & sel) hot pink
> color sel & #2 byhetero
> select :28,61,62,135,187,203,278,312
1771 atoms, 1635 bonds, 219 residues, 6 models selected
> color (#2 & sel) lime
> style sel & #2 stick
Changed 336 atom styles
> show sel & #2 atoms
> color sel & #2 byhetero
> select add #8
6464 atoms, 6458 bonds, 827 residues, 6 models selected
> select add #2
18032 atoms, 18400 bonds, 2335 residues, 6 models selected
> select add #3
36624 atoms, 37560 bonds, 4751 residues, 6 models selected
> select subtract #3
17692 atoms, 18084 bonds, 2291 residues, 5 models selected
> select subtract #2
5788 atoms, 5830 bonds, 751 residues, 4 models selected
> select add #4
24380 atoms, 24990 bonds, 3167 residues, 4 models selected
> select subtract #4
5448 atoms, 5514 bonds, 707 residues, 3 models selected
> select add #5
24112 atoms, 24738 bonds, 3131 residues, 3 models selected
> select subtract #5
5104 atoms, 5194 bonds, 663 residues, 2 models selected
> select add #6
23920 atoms, 24590 bonds, 34 pseudobonds, 3103 residues, 3 models selected
> select subtract #6
4772 atoms, 4894 bonds, 619 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
4772 atoms, 4894 bonds, 619 residues, 1 model selected
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> mmaker #3-6 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9EWQ.pdb, chain A (#2) with 8E6K.pdb, chain A (#3), sequence
alignment score = 1889
RMSD between 382 pruned atom pairs is 0.556 angstroms; (across all 385 pairs:
0.722)
Matchmaker 9EWQ.pdb, chain A (#2) with 8E6K.cif, chain A (#4), sequence
alignment score = 1889
RMSD between 382 pruned atom pairs is 0.556 angstroms; (across all 385 pairs:
0.722)
Matchmaker 9EWQ.pdb, chain A (#2) with 8E6J 1.pdb, chain A (#5), sequence
alignment score = 1896.2
RMSD between 382 pruned atom pairs is 0.517 angstroms; (across all 385 pairs:
0.692)
Matchmaker 9EWQ.pdb, chain A (#2) with 9KOD.pdb, chain A (#6), sequence
alignment score = 1924.4
RMSD between 385 pruned atom pairs is 0.352 angstroms; (across all 385 pairs:
0.352)
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #5 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #8 models
> hide #8 models
> show #4 models
> hide #5 models
> hide #4 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> show #8 models
> hide #8 models
> show #8 models
> show #2 models
> select subtract #8
Nothing selected
> save /Users/hmed/Documents/dongdong/fluN1experiments/allon2A11.cxs
> save /Users/hmed/Documents/dongdong/fluN1experiments/P98_J17z.mrc models #7
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHF3B/A
Chip: Apple M2 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 9 hours, 6 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 19
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.6.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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