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Opened 3 months ago
Closed 3 months ago
#18314 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x000000031884b000 (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 0x000000031783f000 (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 0x0000000316833000 (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 0x0000000315827000 (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 0x000000031481b000 (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 0x000000031380f000 (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 0x0000000312803000 (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 0x00000003117f7000 (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 0x00000003107eb000 (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 0x000000030f7df000 (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 0x000000030e7d3000 (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 0x00000001f582df00 (most recent call first):
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.pdb_lib._load_libs, 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.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 58)
{"app_name":"ChimeraX","timestamp":"2025-07-29 16:51:09.00 -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 15.5 (24F74)","roots_installed":0,"name":"ChimeraX","incident_id":"A65231B3-A146-4F02-AA54-FFD08DC50C68"}
{
"uptime" : 1500000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 59935,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-07-29 16:50:40.8340 -0400",
"codeSigningMonitor" : 1,
"incident" : "A65231B3-A146-4F02-AA54-FFD08DC50C68",
"pid" : 80185,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-02 08:58:54.6328 -0400",
"procStartAbsTime" : 7327647763882,
"procExitAbsTime" : 36576682345767,
"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":"503EE9E6-7239-55B2-81B8-4723E7B88941","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4F9CB563-7192-3CF3-091D-498E8D85E0A9",
"lowPowerMode" : 1,
"appleIntelligenceStatus" : {"state":"available"},
"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" : "6D070026-B97C-433F-8EE9-8A995EFAED2F",
"wakeTime" : 1102,
"sleepWakeUUID" : "5A9402B5-EADA-42BA-93A7-0E54E3D4755B",
"sip" : "enabled",
"vmRegionInfo" : "0x2e9ff48b58c8 is not in any region. Bytes after previous region: 50783501113545 Bytes before following region: 54288578815800\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, 0x00002e9ff48b58c8","rawCodes":[1,51264537450696],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00002e9ff48b58c8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":80185},
"vmregioninfo" : "0x2e9ff48b58c8 is not in any region. Bytes after previous region: 50783501113545 Bytes before following region: 54288578815800\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" : 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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: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/eric/Documents/Kardon Lab/ALAS2 ClustalOWS Alignment.fa" format
> fasta
Summary of feedback from opening /Users/eric/Documents/Kardon Lab/ALAS2
ClustalOWS Alignment.fa
---
notes | Alignment identifier is ALAS2 ClustalOWS Alignment.fa
Showing conservation header ("seq_conservation" residue attribute) for
alignment ALAS2 ClustalOWS Alignment.fa
Opened 250 sequences from ALAS2 ClustalOWS Alignment.fa
> open "/Users/eric/Documents/Kardon Lab/ALAS2 ClustalOWS Alignment.fa" format
> fasta
Summary of feedback from opening /Users/eric/Documents/Kardon Lab/ALAS2
ClustalOWS Alignment.fa
---
notes | Destroying pre-existing alignment with identifier ALAS2 ClustalOWS Alignment.fa
Alignment identifier is ALAS2 ClustalOWS Alignment.fa
Showing conservation header ("seq_conservation" residue attribute) for
alignment ALAS2 ClustalOWS Alignment.fa
Opened 250 sequences from ALAS2 ClustalOWS Alignment.fa
> open /Users/eric/Documents/ChimeraX/ALAS2-PD2-Heme-Confidence-Hbond.cxs
> format session
opened ChimeraX session
> hide #!2 models
> hide #!4 models
> hide #!3 models
> hide #!5 models
> open "/Users/eric/Documents/Kardon Lab/ALAS2 ClustalOWS Alignment.fa" format
> fasta
Summary of feedback from opening /Users/eric/Documents/Kardon Lab/ALAS2
ClustalOWS Alignment.fa
---
notes | Alignment identifier is ALAS2 ClustalOWS Alignment.fa
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_0.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_1.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_2.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_3.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_4.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment ALAS2 ClustalOWS Alignment.fa
Opened 250 sequences from ALAS2 ClustalOWS Alignment.fa
> open /Users/eric/Documents/ChimeraX/ALAS2-PD2-Heme-Confidence-Hbond.cxs
> format session
opened ChimeraX session
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> open "/Users/eric/Documents/Kardon Lab/ALAS2 ClustalOWS Alignment.fa"
Summary of feedback from opening /Users/eric/Documents/Kardon Lab/ALAS2
ClustalOWS Alignment.fa
---
notes | Alignment identifier is ALAS2 ClustalOWS Alignment.fa
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_0.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_1.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_2.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_3.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_4.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment ALAS2 ClustalOWS Alignment.fa
Opened 250 sequences from ALAS2 ClustalOWS Alignment.fa
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_conservation #!1-5 target absc palette
> -2,blue:0,white:1,red
33940 atoms, 4260 residues, atom seq_conservation range -2.02 to 1.29
> select #1/A:41 #2/A:41 #3/A:41 #4/A:41 #5/A:41
45 atoms, 40 bonds, 5 residues, 5 models selected
> select #1/A:41-42 #2/A:41-42 #3/A:41-42 #4/A:41-42 #5/A:41-42
85 atoms, 80 bonds, 10 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[319-320] RMSD: 0.590
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_conservation #!1-5 target absc palette
> -1.84075,blue:-0.364,white:0.581296,red
33940 atoms, 4260 residues, atom seq_conservation range -2.02 to 1.29
> select #1/A:42 #2/A:42 #3/A:42 #4/A:42 #5/A:42
40 atoms, 35 bonds, 5 residues, 5 models selected
> select #1/A:42 #2/A:42 #3/A:42 #4/A:42 #5/A:42
40 atoms, 35 bonds, 5 residues, 5 models selected
> select #1/A:42 #2/A:42 #3/A:42 #4/A:42 #5/A:42
40 atoms, 35 bonds, 5 residues, 5 models selected
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!5 models
> show #!1 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file
> /Users/eric/Documents/ChimeraX/fold_alas2_pd2_heme_2025_06_13_12_35/fold_alas2_pd2_heme_2025_06_13_12_35_full_data_0.json
> color #1/A:174 lime
> color #1/A:382 magenta
> color #1/B:102-108 lime
> color #1/A:31-44 magenta
> ui tool show "Render/Select by Attribute"
> open "/Users/eric/Documents/Kardon Lab/POLDIP2.msf"
Summary of feedback from opening /Users/eric/Documents/Kardon Lab/POLDIP2.msf
---
notes | Alignment identifier is POLDIP2.msf
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_0.cif chain B to
Homo/1-385 with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_1.cif chain B to
Homo/1-385 with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_2.cif chain B to
Homo/1-385 with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_3.cif chain B to
Homo/1-385 with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_4.cif chain B to
Homo/1-385 with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment POLDIP2.msf
Opened 17 sequences from POLDIP2.msf
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_conservation #!1-5 target absc palette
> -2.015,blue:-0.0875,white:1,red
33940 atoms, 4260 residues, atom seq_conservation range -2.02 to 1.84
> select clear
Drag select of 1 residues
> select #1/A:41 #2/A:41 #3/A:41 #4/A:41 #5/A:41
45 atoms, 40 bonds, 5 residues, 5 models selected
> select #1/A:41-42 #2/A:41-42 #3/A:41-42 #4/A:41-42 #5/A:41-42
85 atoms, 80 bonds, 10 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[319-320] RMSD: 0.590
> select #1A
Expected an objects specifier or a keyword
> select #1/A
4149 atoms, 4247 bonds, 534 residues, 1 model selected
> ui tool show "Side View"
> Color Green
Unknown command: Color Green
> color sel forest green
> select #1/B
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> color sel red
> select #1/A
4149 atoms, 4247 bonds, 534 residues, 1 model selected
> color sel blue
> select clear
> select #1/C
43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!1 & sel) byelement
> undo
> color (#!1 & sel) orange
> select clear
> hide #6 models
> set bgColor white
> set bgColor black
> set bgColor white
> select #1/C
43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!1 & sel) magenta
> color (#!1 & sel) forest green
> select clear
> select #1
6788 atoms, 6967 bonds, 24 pseudobonds, 852 residues, 3 models selected
> color (#!1 & sel) gray
> select #1/C
43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!1 & sel) forest green
> select clear
Drag select of 1 residues
> open "/Users/eric/Documents/Kardon Lab/ALAS2 ClustalOWS Alignment.fa"
Summary of feedback from opening /Users/eric/Documents/Kardon Lab/ALAS2
ClustalOWS Alignment.fa
---
notes | Alignment identifier is ALAS2 ClustalOWS Alignment.fa
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_0.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_1.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_2.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_3.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_4.cif chain A to
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment ALAS2 ClustalOWS Alignment.fa
Opened 250 sequences from ALAS2 ClustalOWS Alignment.fa
> select #1/A:16-17 #2/A:16-17 #3/A:16-17 #4/A:16-17 #5/A:16-17
80 atoms, 80 bonds, 10 residues, 5 models selected
> select #1/A:16-19 #2/A:16-19 #3/A:16-19 #4/A:16-19 #5/A:16-19
170 atoms, 180 bonds, 20 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[294-297] RMSD: 0.937
> color (#!1 & sel) blue
> show #6 models
> ui tool show "Side View"
> hide #6 models
> select clear
> select #1/B:164
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select #1/C
43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected
> hide sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel atoms
> select #1/A 1-70
Expected a keyword
> select #1/A,1-70
4149 atoms, 4247 bonds, 534 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select #1/A:16 #2/A:16 #3/A:16 #4/A:16 #5/A:16
50 atoms, 50 bonds, 5 residues, 5 models selected
> select #1/A:9-16 #2/A:9-16 #3/A:9-16 #4/A:9-16 #5/A:9-16
305 atoms, 320 bonds, 40 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[287-294] RMSD: 1.369
> select #1/B,1-100
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select #1/C
43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected
> color (#!1 & sel) red
> select clear
> select #1/A:17 #2/A:17 #3/A:17 #4/A:17 #5/A:17
30 atoms, 25 bonds, 5 residues, 5 models selected
> select #1/A:17 #2/A:17 #3/A:17 #4/A:17 #5/A:17
30 atoms, 25 bonds, 5 residues, 5 models selected
> select #1/A:17-20 #2/A:17-20 #3/A:17-20 #4/A:17-20 #5/A:17-20
160 atoms, 165 bonds, 20 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific,
mitochondrial..G3QI29_GORGO/1-587 5-aminolevulinate synthase [295-298] RMSD:
0.842
> select #1/A:25 #2/A:25 #3/A:25 #4/A:25 #5/A:25
45 atoms, 40 bonds, 5 residues, 5 models selected
> select #1/A:25-31 #2/A:25-31 #3/A:25-31 #4/A:25-31 #5/A:25-31
265 atoms, 260 bonds, 35 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[303-309] RMSD: 0.832
> select #1/A, 164-end
6788 atoms, 6967 bonds, 24 pseudobonds, 852 residues, 3 models selected
> hide sel atoms
> undo
> select #1/A
4149 atoms, 4247 bonds, 534 residues, 1 model selected
> hide sel atoms
> select #1/A:17 #2/A:17 #3/A:17 #4/A:17 #5/A:17
30 atoms, 25 bonds, 5 residues, 5 models selected
> select #1/A:17-18 #2/A:17-18 #3/A:17-18 #4/A:17-18 #5/A:17-18
65 atoms, 65 bonds, 10 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[295-296] RMSD: 0.944
> select #1/A:16 #2/A:16 #3/A:16 #4/A:16 #5/A:16
50 atoms, 50 bonds, 5 residues, 5 models selected
> select #1/A:16-19 #2/A:16-19 #3/A:16-19 #4/A:16-19 #5/A:16-19
170 atoms, 180 bonds, 20 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[294-297] RMSD: 0.937
> show sel & #!1 cartoons
> show sel & #!1 atoms
> select #1/B
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> select up
6788 atoms, 6967 bonds, 852 residues, 1 model selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select #1/A,117-end
6788 atoms, 6967 bonds, 24 pseudobonds, 852 residues, 3 models selected
> hide sel atoms
> show sel atoms
> select #1/A
4149 atoms, 4247 bonds, 534 residues, 1 model selected
> undo
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select #1/B
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> color sel yellow
> color sel orange red
> color sel byelement
> undo
> color sel #ff9300ff
> color sel #945200ff
> color sel #aa7942ff
> select #1/A
4149 atoms, 4247 bonds, 534 residues, 1 model selected
> color sel black
> select clear
> select #1/A:16 #2/A:16 #3/A:16 #4/A:16 #5/A:16
50 atoms, 50 bonds, 5 residues, 5 models selected
> select #1/A:16-19 #2/A:16-19 #3/A:16-19 #4/A:16-19 #5/A:16-19
170 atoms, 180 bonds, 20 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[294-297] RMSD: 0.937
> select clear
> select #1/A:16 #2/A:16 #3/A:16 #4/A:16 #5/A:16
50 atoms, 50 bonds, 5 residues, 5 models selected
> select #1/A:16 #2/A:16 #3/A:16 #4/A:16 #5/A:16
50 atoms, 50 bonds, 5 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[294] RMSD: 1.088
> show sel & #!1 atoms
> hide sel & #!1 atoms
> show sel & #!1 atoms
> color (#!1 & sel) yellow
> select #1/A:19 #2/A:19 #3/A:19 #4/A:19 #5/A:19
55 atoms, 55 bonds, 5 residues, 5 models selected
> select #1/A:19 #2/A:19 #3/A:19 #4/A:19 #5/A:19
55 atoms, 55 bonds, 5 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[297] RMSD: 0.739
> show sel & #!1 atoms
> color (#!1 & sel) yellow
> hide #1/b
> select #1/b
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> hide sel cartoons
> undo
> redo
> select #1/a
4149 atoms, 4247 bonds, 534 residues, 1 model selected
> color sel black
> select up
6788 atoms, 6967 bonds, 852 residues, 1 model selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select up
33940 atoms, 34835 bonds, 477 pseudobonds, 4260 residues, 6 models selected
> select #1/b
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> select #1/A:41-42 #2/A:41-42 #3/A:41-42 #4/A:41-42 #5/A:41-42
85 atoms, 80 bonds, 10 residues, 5 models selected
> select #1/A:41-42 #2/A:41-42 #3/A:41-42 #4/A:41-42 #5/A:41-42
85 atoms, 80 bonds, 10 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[319-320] RMSD: 0.590
> show sel & #!1 atoms
> show #6 models
Drag select of 10 residues
> show sel atoms
Drag select of 2 atoms, 7 residues, 1 bonds
Drag select of 2 residues
> show sel atoms
> select #1/b
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> hide sel atoms
Drag select of 2 residues
> show sel atoms
> show sel cartoons
> select #1/b
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel atoms
> select clear
Drag select of 1 residues
> show sel atoms
> select clear
> select #1/A:41 #2/A:41 #3/A:41 #4/A:41 #5/A:41
45 atoms, 40 bonds, 5 residues, 5 models selected
> select #1/A:41-42 #2/A:41-42 #3/A:41-42 #4/A:41-42 #5/A:41-42
85 atoms, 80 bonds, 10 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[319-320] RMSD: 0.590
> color (#!1 & sel) yellow
Drag select of 1 residues
> color sel forest green
> ui tool show "Color Actions"
Drag select of 2 residues
> select clear
Drag select of 1 residues
> color sel forest green
> show sel atoms
> select #1/b: 260-end
472 atoms, 491 bonds, 58 residues, 1 model selected
> hide sel cartoons
> select #1/b: 1-226
1855 atoms, 1908 bonds, 226 residues, 1 model selected
> hide sel cartoons
> select #1/b
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> ui tool show "Selection Inspector"
> ui tool show "Color Actions"
> color sel #000000ff
> color sel #aa7942ff
> select clear
> select #1/b
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> show sel cartoons
> select #1/A:42 #2/A:42 #3/A:42 #4/A:42 #5/A:42
40 atoms, 35 bonds, 5 residues, 5 models selected
> select #1/A:42 #2/A:42 #3/A:42 #4/A:42 #5/A:42
40 atoms, 35 bonds, 5 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[320] RMSD: 0.707
> color (#!1 & sel) byelement
> select #1/A:41
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byelement
> select add #1/A:41@CD
1 atom, 3 bonds, 1 residue, 1 model selected
> open "/Users/eric/Documents/Kardon Lab/POLDIP2.msf"
Summary of feedback from opening /Users/eric/Documents/Kardon Lab/POLDIP2.msf
---
notes | Alignment identifier is POLDIP2.msf
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_0.cif chain B to
Homo/1-385 with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_1.cif chain B to
Homo/1-385 with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_2.cif chain B to
Homo/1-385 with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_3.cif chain B to
Homo/1-385 with 0 mismatches
Associated fold_alas2_pd2_heme_2025_06_13_12_35_model_4.cif chain B to
Homo/1-385 with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment POLDIP2.msf
Opened 17 sequences from POLDIP2.msf
Drag select of 1 bonds
Drag select of 4 atoms, 3 residues, 4 bonds
Drag select of 1 atoms, 2 residues, 1 bonds
Drag select of 3 atoms, 4 bonds
> select #1/a
4149 atoms, 4247 bonds, 534 residues, 1 model selected
> color sel gray
> color sel dark gray
> color sel dim gray
> select clear
> select #1/A:41 #2/A:41 #3/A:41 #4/A:41 #5/A:41
45 atoms, 40 bonds, 5 residues, 5 models selected
> select #1/A:41-42 #2/A:41-42 #3/A:41-42 #4/A:41-42 #5/A:41-42
85 atoms, 80 bonds, 10 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[319-320] RMSD: 0.590
> select clear
Drag select of 1 residues
> select #1/B:251
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:251
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel byelement
> undo
> color sel magenta
> color sel medium blue
Drag select of 1 residues
> color sel byelement
> select #1/B:231@CZ
1 atom, 1 residue, 1 model selected
> select #1/B:231@CZ
1 atom, 1 residue, 1 model selected
> select add #1/B:231@CD
1 atom, 3 bonds, 1 residue, 1 model selected
> select add #1/B:231@CZ
2 atoms, 3 bonds, 1 residue, 1 model selected
> color sel forest green
> select clear
> color sel lime
> color sel forest green
> select clear
Drag select of 2 residues, 2 bonds
Drag select of 1 residues
> color sel forest green
Drag select of 1 residues
> color sel forest green
> select #1/B:231@NH2
1 atom, 1 residue, 1 model selected
> select #1/B:231@NH1
1 atom, 1 residue, 1 model selected
> select add #1/B:231@NH2
2 atoms, 1 residue, 1 model selected
> select add #1/B:231@NE
3 atoms, 1 pseudobond, 1 residue, 2 models selected
> color (#!1 & sel) cornflower blue
> undo
> color (#!1 & sel) byelement
> select #1/B:251@CA
1 atom, 1 residue, 1 model selected
> color sel forest green
> select clear
> select #1/B:251@CB
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms, 1 residues
> color sel byelement
> color sel forest green
> undo
> select down
7 atoms, 1 residue, 1 model selected
> select down
7 atoms, 1 residue, 1 model selected
> select up
104 atoms, 105 bonds, 14 residues, 1 model selected
> select down
7 atoms, 1 residue, 1 model selected
> select up
104 atoms, 105 bonds, 14 residues, 1 model selected
> select down
7 atoms, 1 residue, 1 model selected
> select up
104 atoms, 105 bonds, 14 residues, 1 model selected
> select down
7 atoms, 1 residue, 1 model selected
> select up
104 atoms, 105 bonds, 14 residues, 1 model selected
> select down
7 atoms, 1 residue, 1 model selected
> color sel forest green
> select #1/b: 1-226
1855 atoms, 1908 bonds, 226 residues, 1 model selected
> hide sel cartoons
> select up
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> select down
1855 atoms, 1908 bonds, 226 residues, 1 model selected
> select #1/b: 260-end
472 atoms, 491 bonds, 58 residues, 1 model selected
> hide sel cartoons
Drag select of 2 atoms, 2 residues, 1 bonds
> color sel byelement
> select clear
Drag select of 1 residues
> select #1/b: 260-end
472 atoms, 491 bonds, 58 residues, 1 model selected
> select clear
> select #1/b
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #00fdffff
> color sel #aa7942ff
Drag select of 2 residues
> select clear
Drag select of 1 residues
> select clear
> select #1/B:231@NH2
1 atom, 1 residue, 1 model selected
> select #1/B:231@NH1
1 atom, 1 residue, 1 model selected
> select add #1/B:231@NH2
2 atoms, 1 residue, 1 model selected
> select #1/B:231@NE
1 atom, 1 residue, 1 model selected
> select add #1/B:231@NH1
2 atoms, 1 residue, 1 model selected
> select add #1/B:231@NH2
3 atoms, 2 pseudobonds, 1 residue, 2 models selected
> color (#!1 & sel) byelement
> select #1/A:42@CG
1 atom, 1 residue, 1 model selected
> select add #1/A:41@CD
2 atoms, 2 bonds, 2 residues, 1 model selected
> select add #1/A:41@CG
3 atoms, 3 bonds, 2 residues, 1 model selected
> select subtract #1/A:41@CG
2 atoms, 3 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select add #1/A:41@CG
3 atoms, 3 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select clear
> select add #1/A:41@CA
1 atom, 1 residue, 1 model selected
> select subtract #1/A:41
Nothing selected
Drag select of 2 residues
> color sel forest green
> select #1/A:41@OE2
1 atom, 1 residue, 1 model selected
> select add #1/A:41@OE1
2 atoms, 1 residue, 1 model selected
> color sel byelement
> select add #1/A:42@OD2
3 atoms, 2 residues, 1 model selected
> select add #1/A:42@OD1
4 atoms, 2 residues, 1 model selected
> color sel byelement
> select clear
> select #1/b
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> hide sel atoms
> select #1/A:19@CG
1 atom, 1 residue, 1 model selected
> select #1/A:41-42 #2/A:41-42 #3/A:41-42 #4/A:41-42 #5/A:41-42
85 atoms, 80 bonds, 10 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[319-320] RMSD: 0.590
> select #1/A:16-19,41-42 #2/A:16-19,41-42 #3/A:16-19,41-42 #4/A:16-19,41-42
> #5/A:16-19,41-42
255 atoms, 260 bonds, 30 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[319-320] + 1 other block RMSD: 0.837
> color (#!1 & sel) forest green
> select #1/A:16-19,41-42 #2/A:16-19,41-42 #3/A:16-19,41-42 #4/A:16-19,41-42
> #5/A:16-19,41-42
255 atoms, 260 bonds, 30 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[319-320] + 2 other blocks RMSD: 0.865
> color (#!1 & sel) byelement
> select clear
> select #1/A:16@CB
1 atom, 1 residue, 1 model selected
> select #1/A:16@CG
1 atom, 1 residue, 1 model selected
> select add #1/A:16@CB
2 atoms, 1 residue, 1 model selected
> select add #1/A:16@CE1
3 atoms, 1 residue, 1 model selected
> select add #1/A:16@CD2
4 atoms, 1 residue, 1 model selected
> color sel forest green
> select #1/A:16
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:16
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:16
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel forest green
> undo
> select #1/A:16-19,41-42 #2/A:16-19,41-42 #3/A:16-19,41-42 #4/A:16-19,41-42
> #5/A:16-19,41-42
255 atoms, 260 bonds, 30 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[319-320] + 2 other blocks RMSD: 0.865
> color (#!1 & sel) forest green
> select #1/A:16@ND1
1 atom, 1 residue, 1 model selected
> select #1/A:16@NE2
1 atom, 1 residue, 1 model selected
> select add #1/A:16@ND1
2 atoms, 1 residue, 1 model selected
> select add #1/A:17@SG
3 atoms, 2 residues, 1 model selected
> select add #1/A:18@N
4 atoms, 3 residues, 1 model selected
> select subtract #1/A:18
3 atoms, 2 residues, 1 model selected
> select add #1/A:18@N
4 atoms, 3 residues, 1 model selected
> select subtract #1/A:18@N
3 atoms, 2 residues, 1 model selected
> select add #1/A:18@N
4 atoms, 3 residues, 1 model selected
> select subtract #1/A:18@N
3 atoms, 2 residues, 1 model selected
> select add #1/A:18@CD
4 atoms, 3 residues, 1 model selected
> select subtract #1/A:18@CD
3 atoms, 2 residues, 1 model selected
> select add #1/A:18@N
4 atoms, 3 residues, 1 model selected
> color sel byelement
> select #1/A:16-19,41-42 #2/A:16-19,41-42 #3/A:16-19,41-42 #4/A:16-19,41-42
> #5/A:16-19,41-42
255 atoms, 260 bonds, 30 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[319-320] + 2 other blocks RMSD: 0.865
> select #1/A:16-19,41-42 #2/A:16-19,41-42 #3/A:16-19,41-42 #4/A:16-19,41-42
> #5/A:16-19,41-42
255 atoms, 260 bonds, 30 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[319-320] + 2 other blocks RMSD: 0.865
> select #1/A:21 #2/A:21 #3/A:21 #4/A:21 #5/A:21
40 atoms, 35 bonds, 5 residues, 5 models selected
> select #1/A:21-23 #2/A:21-23 #3/A:21-23 #4/A:21-23 #5/A:21-23
115 atoms, 110 bonds, 15 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[299-301] RMSD: 0.681
> select #1/A:17 #2/A:17 #3/A:17 #4/A:17 #5/A:17
30 atoms, 25 bonds, 5 residues, 5 models selected
> select #1/A:17-18 #2/A:17-18 #3/A:17-18 #4/A:17-18 #5/A:17-18
65 atoms, 65 bonds, 10 residues, 5 models selected
ALAS2 ClustalOWS Alignment.fa [ID: ALAS2 ClustalOWS Alignment.fa] region
HEM0_HUMAN/1-587 5-aminolevulinate synthase, erythroid-specific, mitochondrial
[295-296] RMSD: 0.944
> color (#!1 & sel) dim gray
> select clear
> select #1/A:18@N
1 atom, 1 residue, 1 model selected
> select #1/A:17@SG
1 atom, 1 residue, 1 model selected
> select add #1/A:18@N
2 atoms, 2 residues, 1 model selected
> color sel byelement
> select #1/a 1-4
Expected a keyword
> select #1/a: 1-4
30 atoms, 29 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #1/a: 1-4
30 atoms, 29 bonds, 4 residues, 1 model selected
> show sel cartoons
> select #1/b
2596 atoms, 2674 bonds, 317 residues, 1 model selected
> show sel cartoons
===== Log before crash end =====
Log:
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: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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 Air
Model Identifier: Mac14,2
Model Number: MN6Y3LL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 34 days, 9 hours, 33 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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 , 3 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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