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Opened 4 hours ago
#19822 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-26.2-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Thread 0x0000000309067000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000030805b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000030704f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000306043000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000305037000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000030402b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000030301f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000302013000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000301007000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017f18f000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017e183000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017d177000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017c16b000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x000000020c55ec40 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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.surface._surface, chimerax.pdb_lib._load_libs, PIL._imaging, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 54)
{"app_name":"ChimeraX","timestamp":"2026-02-08 22:01:19.00 +0100","app_version":"1.11.1","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.11.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.2 (25C56)","roots_installed":0,"name":"ChimeraX","incident_id":"D793BAF7-D6AA-478F-A62B-B33127E9E6D8"}
{
"uptime" : 54000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,13",
"coalitionID" : 3373,
"osVersion" : {
"train" : "macOS 26.2",
"build" : "25C56",
"releaseType" : "User"
},
"captureTime" : "2026-02-08 21:33:31.4624 +0100",
"codeSigningMonitor" : 2,
"incident" : "D793BAF7-D6AA-478F-A62B-B33127E9E6D8",
"pid" : 4550,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-02-04 18:09:37.2661 +0100",
"procStartAbsTime" : 820531604660,
"procExitAbsTime" : 1308839771098,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.1","CFBundleVersion":"1.11.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"1B3251B3-5DBA-50CE-86B9-A9714C216A41","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "32A898DB-B5C3-553E-2DED-9686897E8549",
"appleIntelligenceStatus" : {"reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguageInfo(system: en-GB, siri: en)","selectedLanguageDoesNotMatchSelectedSiriLanguage"],"state":"unavailable"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "9B688AAE-DFA6-402D-A0D6-7ED6B12FEB8F",
"wakeTime" : 1304,
"sleepWakeUUID" : "18F5CA44-9DAD-448D-B20A-9EBF2940EE71",
"sip" : "enabled",
"vmRegionInfo" : "0xb00003a00 is in 0x8ee000000-0xbe3c00000; bytes after start: 8891939328 bytes before end: 3820996095
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_SMALL 6a4400000-6a4800000 [ 4096K] rw-\/rwx SM=PRV
GAP OF 0x249800000 BYTES
---> commpage (reserved) 8ee000000-be3c00000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL be3c00000-be4000000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000b00003a00","rawCodes":[2,47244655104],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000b00003a00"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":4550},
"vmregioninfo" : "0xb00003a00 is in 0x8ee000000-0xbe3c00000; bytes after start: 8891939328 bytes before end: 3820996095
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_SMALL 6a4400000-6a4800000 [ 4096K] rw-\/rwx SM=PRV
GAP OF 0x249800000 BYTES
---> commpage (reserved) 8ee000000-be3c00000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL be3c00000-be4000000 [ 4096K] 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":6171137992},{"value":99},{"value":95},{"value":0},{"value":0},{"value":8637254813136906748},{"value":8637254821664720316},{"value":14757395258967641293},{"value":4294967286},{"value":6171137922},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8819689872},{"value":0},{"value":10},{"value":259},{"value":8796892448 ,"symbolLocation":224,"symbol": "_main_thread"},{"value":0},{"value":1},{"value":4319004216 ,"symbolLocation":0,"symbol": "faulthandler_handlers"},{"value":1},{"value":4296902544},{"value":4315691832 ,"symbolLocation":0,"symbol": "cfunction_call"},{"value":4389676632}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6969088136},"cpsr":{"value":1073741824},"fp":{"value":6171138064},"sp":{"value":6171138032},"esr":{"value":1442840704,"description":"(Syscall)"},"pc":{"value":6968849840,"matchesCrashFrame":1},"far":{"value":0}},"id":503175,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[
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{"imageOffset":8457876,"symbol": "__47+[NSCGSSpace addTileResizeNotificationHandler:]_block_invoke" ,"symbolLocation":284,"imageIndex":140},
{"imageOffset":353408,"symbol": "__CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__" ,"symbolLocation":128,"imageIndex":144},
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{"imageOffset":216980,"symbol": "_CFXNotificationPost" ,"symbolLocation":740,"imageIndex":144},
{"imageOffset":10535840,"symbol": "-[NSNotificationCenter postNotificationName:object:userInfo:]" ,"symbolLocation":88,"imageIndex":145},
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/paulminges/Library/CloudStorage/OneDrive-
> Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
> Target Development/Structure_Analysis/MMP-10.pdb"
MMP-10.pdb title:
Alphafold monomer V2.0 prediction for stromelysin-2 (P09238) [more info...]
Chain information for MMP-10.pdb #1
---
Chain | Description | UniProt
A | stromelysin-2 | MMP10_HUMAN 1-476
Computing secondary structure
> set bgColor white
> set bgColor black
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> rainbow
> sequence chain #1/A
Alignment identifier is 1/A
> select
> /A:21-41,55-69,80-87,126-143,211-222,245-247,252-262,328-330,346-348,375-378,425-427,470-474
837 atoms, 837 bonds, 106 residues, 1 model selected
> select /A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:1-12
95 atoms, 96 bonds, 12 residues, 1 model selected
> select /A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:1-95
758 atoms, 769 bonds, 95 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-98
779 atoms, 791 bonds, 98 residues, 1 model selected
> color sel bychain
> color sel bypolymer
> color sel bychain
> color sel bypolymer
> rainbow sel
> color sel bypolymer
> color sel bynucleotide
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> color #1 #7ad600ff
> color #1 #2fd605ff
> select /A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:1-99
790 atoms, 803 bonds, 99 residues, 1 model selected
> color #1 #942192ff
> select /A:1-99
790 atoms, 803 bonds, 99 residues, 1 model selected
> color #1 #ff9300ff
> select
> /A:21-41,55-69,80-87,126-143,211-222,245-247,252-262,328-330,346-348,375-378,425-427,470-474
837 atoms, 837 bonds, 106 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-99
790 atoms, 803 bonds, 99 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-99
790 atoms, 803 bonds, 99 residues, 1 model selected
> color sel gray
> select /A:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:2-50
391 atoms, 398 bonds, 49 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-99
790 atoms, 803 bonds, 99 residues, 1 model selected
> label sel attribute label_specifier
> undo
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-99
790 atoms, 803 bonds, 99 residues, 1 model selected
> ~label sel residues
> ui windowfill toggle
> volume style surface
No volumes specified
> select /A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A
3833 atoms, 3955 bonds, 476 residues, 1 model selected
> volume style surface
No volumes specified
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for MMP-10.pdb_A SES surface #1.1: minimum, -19.89, mean
-3.03, maximum 9.23
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for MMP-10.pdb_A SES surface #1.1: minimum, -19.89, mean
-3.03, maximum 9.23
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "MMP-10.pdb_A SES surface": minimum -31.22, mean
-4.877, maximum 23.98
To also show corresponding color key, enter the above mlp command and add key
true
> style sel stick
Changed 3833 atom styles
> style sel stick
Changed 3833 atom styles
> style sel stick
Changed 3833 atom styles
> style sel stick
Changed 3833 atom styles
> color sel byhetero
> color sel bynucleotide
> color sel bychain
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 3833 atom styles
> style sel sphere
Changed 3833 atom styles
> style sel ball
Changed 3833 atom styles
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A
3833 atoms, 3955 bonds, 476 residues, 1 model selected
> style sel stick
Changed 3833 atom styles
> style sel ball
Changed 3833 atom styles
> style sel stick
Changed 3833 atom styles
> cartoon (#!1 & sel)
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A
3833 atoms, 3955 bonds, 476 residues, 1 model selected
> cartoon style (#!1 & sel) xsection oval modeHelix default
> color all grey
> hide surfaces
> show cartoons
> hide all
> name "Signal Peptide" :1-17
Not registering illegal selector name "Signal Peptide"
> name "Signal Peptide" :1-17
Not registering illegal selector name "Signal Peptide"
> name "Signal Peptide" :1-17
Not registering illegal selector name "Signal Peptide"
> name list
There are no user-defined specifier names.
> name list
There are no user-defined specifier names.
> list models
Unknown command: list models
> list models
Unknown command: list models
> select /A:1-2
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A
3833 atoms, 3955 bonds, 476 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-20
153 atoms, 157 bonds, 20 residues, 1 model selected
> select clear
> select /A:140
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:140-222
654 atoms, 678 bonds, 83 residues, 1 model selected
> ui hideFloating toggle
> select clear
> name"Signal Peptide":1-17
incomplete quoted text
> name "Signal Peptide" :1-17
Not registering illegal selector name "Signal Peptide"
> color "Signal Peptide" orange
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color "Signal Peptide" red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> name list
There are no user-defined specifier names.
> ui windowfill toggle
> name SignalPeptide : 1-17
> name list
SignalPeptide : 1-17
> name ProPeptide : 18-98
> color "SignalPeptide" lightgrey
> color "ProPeptide" lightgrey
> transparency "ProPeptide" 50
> transparency "ProPeptide" 5
> transparency "ProPeptide" 50 target c
> transparency "SignalPeptide" 50 target c
> name Main 99-476
"99-476": invalid atom specifier
> name"Main": 99-476
incomplete quoted text
> name Main : 99-476
> color "Main" green
> select /A:100
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:100-476
3043 atoms, 3151 bonds, 377 residues, 1 model selected
> close session
> open "/Users/paulminges/Library/CloudStorage/OneDrive-
> Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
> Target
> Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_job_request.json"
Failed opening file /Users/paulminges/Library/CloudStorage/OneDrive-
Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
Target
Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_job_request.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/paulminges/Library/CloudStorage/OneDrive-
Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
Target
Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_job_request.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open "/Users/paulminges/Library/CloudStorage/OneDrive-
> Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
> Target
> Development/Structure_Analysis/MMP-10_01-476/AF-P09238-F1-model_v6.cif"
Chain information for AF-P09238-F1-model_v6.cif #1
---
Chain | Description | UniProt
A | Stromelysin-2 | MMP10_HUMAN 1-476
Color AF-P09238-F1-model_v6.cif by residue attribute pLDDT_score
> color bfactor palette alphafold
3833 atoms, 476 residues, atom bfactor range 31 to 98.6
> ui windowfill toggle
> open "/Users/paulminges/Library/CloudStorage/OneDrive-
> Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
> Target
> Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_full_data_0.json"
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/paulminges/Library/CloudStorage/OneDrive-
Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
Target
Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_full_data_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open "/Users/paulminges/Library/CloudStorage/OneDrive-
> Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
> Target
> Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_model_0.cif"
Chain information for fold_2026_02_06_14_30_model_0.cif #2
---
Chain | Description
A | .
Computing secondary structure
> open "/Users/paulminges/Library/CloudStorage/OneDrive-
> Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
> Target
> Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_model_0.cif"
> format mmcif
Chain information for fold_2026_02_06_14_30_model_0.cif #3
---
Chain | Description
A | .
Computing secondary structure
> list models
Unknown command: list models
> hide #1
> ui tool show "Model Panel"
> ui tool show "Selection Inspector"
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac16,13
Model Number: MC6L4D/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 24 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 6 days, 21 hours, 46 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
N27p:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2880 x 1864 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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