![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#16166 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-15.0.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700015cb7000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700014cb4000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700013cb1000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700012cae000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700011cab000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700010ca8000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070000fca5000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070000eca2000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070000dc9f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070000cc9c000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070000bc99000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff8590dd680 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, 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, chimerax.alignment_algs._sw, chimerax.atom_search.ast, chimerax.mlp._mlp (total: 61)
{"app_name":"ChimeraX","timestamp":"2024-10-22 20:30:11.00 +0200","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.0.1 (24A348)","roots_installed":0,"name":"ChimeraX","incident_id":"F2A28E97-092B-4E43-BE01-758BD92D4952"}
{
"uptime" : 170000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 33195,
"osVersion" : {
"train" : "macOS 15.0.1",
"build" : "24A348",
"releaseType" : "User"
},
"captureTime" : "2024-10-22 20:30:06.8903 +0200",
"codeSigningMonitor" : 0,
"incident" : "F2A28E97-092B-4E43-BE01-758BD92D4952",
"pid" : 65670,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-22 13:03:03.5629 +0200",
"procStartAbsTime" : 143296172430760,
"procExitAbsTime" : 170118900011225,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"2D1D3C45-E2CD-50DC-B3E4-890A9DF5387C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C9E08316-F481-AE51-0088-DBB74F890D4B",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "2194C047-8FAD-41BF-8CA3-F8D5FCF9AA3D",
"wakeTime" : 28867,
"bridgeVersion" : {"build":"22P353","train":"9.0"},
"sleepWakeUUID" : "FCD48EA3-1FA2-4401-B872-B80F0F18927D",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4468326400\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10a554000-10a558000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":65670},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4468326400\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10a554000-10a558000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"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 =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/lau/Documentos/Ongoing/TPS1_binding/sugarpocket_TPS1_CDF5_tags_andco.cxs
Log from Mon Oct 21 20:08:42 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/lau/Downloads/fold_mcherry_tps1xcdf5_gfp_seed1/fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif
Chain information for fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif #1
---
Chain | Description
A | .
B | .
> select /A:1-1239
9787 atoms, 10006 bonds, 1239 residues, 1 model selected
> color sel yellow
> select /B:1-644
5012 atoms, 5126 bonds, 644 residues, 1 model selected
> color sel medium blue
> select /B:1-644
5012 atoms, 5126 bonds, 644 residues, 1 model selected
> color sel yellow
> select /A:1-1239
9787 atoms, 10006 bonds, 1239 residues, 1 model selected
> color sel medium blue
> select #1 /B
5012 atoms, 5126 bonds, 644 residues, 1 model selected
> ui tool show Contacts
> contacts sel saveFile /Users/lau/Desktop/mCherry-TPS1_CDF5-GFP resSeparation
> 10 interModel false intraMol false ignoreHiddenModels true color #ffffff
> dashes 5 radius 0.105 reveal true
337 contacts
> open
> /Users/lau/Downloads/fold_mcherry_tps1xcdf5_gfp_seed1/fold_mcherry_tps1xcdf5_gfp_seed1_model_1.cif
Chain information for fold_mcherry_tps1xcdf5_gfp_seed1_model_1.cif #2
---
Chain | Description
A | .
B | .
> open
> /Users/lau/Downloads/fold_mcherry_tps1xcdf5_gfp_seed1/fold_mcherry_tps1xcdf5_gfp_seed1_model_2.cif
Chain information for fold_mcherry_tps1xcdf5_gfp_seed1_model_2.cif #3
---
Chain | Description
A | .
B | .
> open
> /Users/lau/Downloads/fold_mcherry_tps1xcdf5_gfp_seed1/fold_mcherry_tps1xcdf5_gfp_seed1_model_3.cif
Chain information for fold_mcherry_tps1xcdf5_gfp_seed1_model_3.cif #4
---
Chain | Description
A | .
B | .
> open
> /Users/lau/Downloads/fold_mcherry_tps1xcdf5_gfp_seed1/fold_mcherry_tps1xcdf5_gfp_seed1_model_4.cif
Chain information for fold_mcherry_tps1xcdf5_gfp_seed1_model_4.cif #5
---
Chain | Description
A | .
B | .
> ui tool show Matchmaker
> matchmaker #2-5 to #1
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 fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_1.cif, chain A (#2), sequence alignment
score = 6348.1
RMSD between 769 pruned atom pairs is 0.687 angstroms; (across all 1239 pairs:
24.967)
Matchmaker fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_2.cif, chain A (#3), sequence alignment
score = 6361.9
RMSD between 769 pruned atom pairs is 0.850 angstroms; (across all 1239 pairs:
29.311)
Matchmaker fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_3.cif, chain A (#4), sequence alignment
score = 6379.9
RMSD between 615 pruned atom pairs is 0.854 angstroms; (across all 1239 pairs:
23.342)
Matchmaker fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_4.cif, chain A (#5), sequence alignment
score = 6369.1
RMSD between 658 pruned atom pairs is 0.865 angstroms; (across all 1239 pairs:
23.990)
> select /A
48935 atoms, 50030 bonds, 6195 residues, 5 models selected
> color sel medium blue
> select /B
25060 atoms, 25630 bonds, 3220 residues, 5 models selected
> color sel yellow
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> select add #2
34847 atoms, 35636 bonds, 4459 residues, 5 models selected
> select subtract #2
20048 atoms, 20504 bonds, 2576 residues, 4 models selected
> select add #3
29835 atoms, 30510 bonds, 3815 residues, 4 models selected
> select subtract #3
15036 atoms, 15378 bonds, 1932 residues, 3 models selected
> select add #4
24823 atoms, 25384 bonds, 3171 residues, 3 models selected
> select subtract #4
10024 atoms, 10252 bonds, 1288 residues, 2 models selected
> select add #5
19811 atoms, 20258 bonds, 2527 residues, 2 models selected
> select subtract #5
5012 atoms, 5126 bonds, 644 residues, 1 model selected
> show #2 models
> hide #!1 models
> select add #1
14799 atoms, 15132 bonds, 337 pseudobonds, 1883 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #2 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> show #!1 models
> show #2 models
> show #3 models
> show #4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select /B
25060 atoms, 25630 bonds, 3220 residues, 5 models selected
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> contacts sel saveFile /Users/lau/Desktop/mCherry-TPS1andCDF5-GFP
> resSeparation 10 interModel false intraMol false ignoreHiddenModels true
> color #ffffff dashes 5 radius 0.105 reveal true
2851 contacts
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> select #1 /A
9787 atoms, 10006 bonds, 1239 residues, 1 model selected
> select #1 /A:1-242
1910 atoms, 1955 bonds, 242 residues, 1 model selected
> select /A:1-242
9550 atoms, 9775 bonds, 1210 residues, 5 models selected
> color (#!1 & sel) lime
> select /A:1-242
9550 atoms, 9775 bonds, 1210 residues, 5 models selected
> color (#!1 & sel) purple
> select /B:400-644
9645 atoms, 9860 bonds, 1225 residues, 5 models selected
> color (#!1 & sel) lime
> select #1 /B:1-16
130 atoms, 130 bonds, 16 residues, 1 model selected
> open /Users/lau/Downloads/T6P-TPS1/pred.model_idx_0.cif
Summary of feedback from opening
/Users/lau/Downloads/T6P-TPS1/pred.model_idx_0.cif
---
warning | Atom C_1 is not in the residue template for LIG /A:1
note | Fetching CCD LIG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/LIG/LIG.cif
pred.model_idx_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.model_idx_0.cif #7
---
Chain | Description
B | protein-1-0
Non-standard residues in pred.model_idx_0.cif #7
---
LIG — (LIG)
Color pred.model_idx_0.cif by residue attribute pLDDT_score
> hide #6 models
> hide #!1 models
> select #7
7488 atoms, 7651 bonds, 943 residues, 1 model selected
> select #7 /A
27 atoms, 28 bonds, 1 residue, 1 model selected
> select #7 /B
7461 atoms, 7623 bonds, 942 residues, 1 model selected
> color sel medium blue
> show #!1 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #7 to #1
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 fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
pred.model_idx_0.cif, chain B (#7), sequence alignment score = 4543.2
RMSD between 459 pruned atom pairs is 0.645 angstroms; (across all 942 pairs:
34.889)
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #2-5,7 to #1
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 fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_1.cif, chain A (#2), sequence alignment
score = 6348.1
RMSD between 769 pruned atom pairs is 0.687 angstroms; (across all 1239 pairs:
24.967)
Matchmaker fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_2.cif, chain A (#3), sequence alignment
score = 6361.9
RMSD between 769 pruned atom pairs is 0.850 angstroms; (across all 1239 pairs:
29.311)
Matchmaker fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_3.cif, chain A (#4), sequence alignment
score = 6379.9
RMSD between 615 pruned atom pairs is 0.854 angstroms; (across all 1239 pairs:
23.342)
Matchmaker fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_4.cif, chain A (#5), sequence alignment
score = 6369.1
RMSD between 658 pruned atom pairs is 0.865 angstroms; (across all 1239 pairs:
23.990)
Matchmaker fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
pred.model_idx_0.cif, chain B (#7), sequence alignment score = 4543.2
RMSD between 459 pruned atom pairs is 0.645 angstroms; (across all 942 pairs:
34.889)
> hide #7 models
> show #7 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #2-5,7 to #1
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 fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_1.cif, chain A (#2), sequence alignment
score = 6348.1
RMSD between 769 pruned atom pairs is 0.687 angstroms; (across all 1239 pairs:
24.967)
Matchmaker fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_2.cif, chain A (#3), sequence alignment
score = 6361.9
RMSD between 769 pruned atom pairs is 0.850 angstroms; (across all 1239 pairs:
29.311)
Matchmaker fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_3.cif, chain A (#4), sequence alignment
score = 6379.9
RMSD between 615 pruned atom pairs is 0.854 angstroms; (across all 1239 pairs:
23.342)
Matchmaker fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_4.cif, chain A (#5), sequence alignment
score = 6369.1
RMSD between 658 pruned atom pairs is 0.865 angstroms; (across all 1239 pairs:
23.990)
Matchmaker fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1) with
pred.model_idx_0.cif, chain B (#7), sequence alignment score = 4543.2
RMSD between 459 pruned atom pairs is 0.645 angstroms; (across all 942 pairs:
34.889)
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #7 models
> select /A:1-242
9577 atoms, 9803 bonds, 1211 residues, 6 models selected
> color (#2-5#!1 & sel) lime
> color (#2-5#!1 & sel) purple
> select /B:400:644
84 atoms, 72 bonds, 12 residues, 6 models selected
> color (#2-5#!1 & sel) forest green
> select add #7
7558 atoms, 7711 bonds, 953 residues, 6 models selected
> select subtract #7
70 atoms, 60 bonds, 10 residues, 5 models selected
> select /B:400-644
11551 atoms, 11802 bonds, 1470 residues, 6 models selected
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sel lime green
[Repeated 3 time(s)]
> show #7 models
> hide #7 models
> show #7 models
> select /B
32521 atoms, 33253 bonds, 4162 residues, 6 models selected
> hide sel cartoons
> hide #7 models
> show #7 models
> select #7 /B
7461 atoms, 7623 bonds, 942 residues, 1 model selected
> select #7 /C
Nothing selected
> select #7 /A
27 atoms, 28 bonds, 1 residue, 1 model selected
> show sel surfaces
> color (#!7 & sel) red
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> select #7 /B
7461 atoms, 7623 bonds, 942 residues, 1 model selected
> show sel cartoons
> color sel medium blue
> select #7 /A
27 atoms, 28 bonds, 1 residue, 1 model selected
> transparency (#!7 & sel) 80
> transparency (#!7 & sel) 60
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> contacts sel saveFile /Users/lau/Desktop/TPS1_T6P resSeparation 10
> interModel false intraMol false ignoreHiddenModels true color #ffffff dashes
> 5 radius 0.105 reveal true
40 contacts
> label (#!7 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> hide #7.3 models
> close #7.3
> label (#!7 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> hide #7.3 models
> close #7.3
> select #7
7488 atoms, 7651 bonds, 40 pseudobonds, 943 residues, 2 models selected
> hide #7.2 models
> show #7.2 models
> label (#!7 & sel) text "{0.name} {0.number}{0.insertion_code}"
> hide #7.3 models
> close #7.3
> select #7 contacts
Expected a keyword
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #7 /B:92-559
3731 atoms, 3819 bonds, 468 residues, 1 model selected
> color sel blue
> ui tool show "Color Actions"
> color sel navy
> color sel steel blue
> color sel deep sky blue
> select #7 /B:1-92
740 atoms, 749 bonds, 92 residues, 1 model selected
> color sel cornflower blue
> color sel light sea green
> open /Users/lau/Downloads/Glu6P-UDPGlu-TPS1/Glu6P-UDPGlu-TPS1_0.cif
Summary of feedback from opening /Users/lau/Downloads/Glu6P-UDPGlu-
TPS1/Glu6P-UDPGlu-TPS1_0.cif
---
warnings | Atom O_1 is not in the residue template for LIG /A:1
Atom O_1 is not in the residue template for LIG /B:1
Glu6P-UDPGlu-TPS1_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Glu6P-UDPGlu-TPS1_0.cif #8
---
Chain | Description
C | protein-2-0
Non-standard residues in Glu6P-UDPGlu-TPS1_0.cif #8
---
LIG — (LIG)
Color Glu6P-UDPGlu-TPS1_0.cif by residue attribute pLDDT_score
> hide #8 models
> select #8 /C:1-92
740 atoms, 749 bonds, 92 residues, 1 model selected
> show #8 models
> hide #!7 models
> hide #7.1 models
> hide #7.2 models
> color sel light sea green
> select #8 /C:92-559
3731 atoms, 3819 bonds, 468 residues, 1 model selected
> color sel cyan
> select #8 /C:560-942
2999 atoms, 3062 bonds, 383 residues, 1 model selected
> color sel medium blue
> select #8 /A
16 atoms, 16 bonds, 1 residue, 1 model selected
> show sel surfaces
> select #8 /A /B
52 atoms, 54 bonds, 2 residues, 1 model selected
> show sel surfaces
> color (#!8 & sel) orange
> transparency (#!8 & sel) 60
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> contacts sel saveFile /Users/lau/Desktop/Glu6P-UDP-Glu-TPS1 resSeparation 10
> interModel false intraMol false ignoreHiddenModels true color #ffffff dashes
> 5 radius 0.105 reveal true
69 contacts
> color #8.3 #ff2600ff models
> open /Users/lau/Downloads/Glu6P-UDPGlu-TPS1_MSA/Glu6P-UDPGlu-TPS1_MSA_0.cif
Summary of feedback from opening /Users/lau/Downloads/Glu6P-UDPGlu-
TPS1_MSA/Glu6P-UDPGlu-TPS1_MSA_0.cif
---
warnings | Atom O_1 is not in the residue template for LIG /A:1
Atom O_1 is not in the residue template for LIG /B:1
Glu6P-UDPGlu-TPS1_MSA_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for Glu6P-UDPGlu-TPS1_MSA_0.cif #9
---
Chain | Description
C | protein-2-0
Non-standard residues in Glu6P-UDPGlu-TPS1_MSA_0.cif #9
---
LIG — (LIG)
Color Glu6P-UDPGlu-TPS1_MSA_0.cif by residue attribute pLDDT_score
> hide #!8 models
> hide #8.1 models
> hide #8.2 models
> hide #8.3 models
> select subtract #8.2
16 atoms, 16 bonds, 1 residue, 3 models selected
> select subtract #8.1
1 model selected
> select #9 /A /B
52 atoms, 54 bonds, 2 residues, 1 model selected
> show sel surfaces
> transparency (#!9 & sel) 80
> transparency (#!9 & sel) 50
> color (#!9 & sel) orange red
> transparency (#!9 & sel) 70
> transparency (#!9 & sel) 80
> transparency (#!9 & sel) 60
> select #9 /C:92-559
3731 atoms, 3819 bonds, 468 residues, 1 model selected
> color sel cyan
> select #9 /C:1-91
731 atoms, 740 bonds, 91 residues, 1 model selected
> color sel light sea green
> select clear
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!9 to #8
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 Glu6P-UDPGlu-TPS1_0.cif, chain C (#8) with Glu6P-UDPGlu-
TPS1_MSA_0.cif, chain C (#9), sequence alignment score = 4610.4
RMSD between 470 pruned atom pairs is 0.692 angstroms; (across all 942 pairs:
28.763)
> hide #!8 models
> open /Users/lau/Downloads/Glu6P-UDPGlu-TPS1_MSA/scores.model_idx_0.json
JSON file "/Users/lau/Downloads/Glu6P-UDPGlu-TPS1_MSA/scores.model_idx_0.json"
is not AlphaFold predicted aligned error data, expected a top level list
> undo
> hide #!8 models
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #9
7513 atoms, 7677 bonds, 944 residues, 1 model selected
> select #9 /B /C
7497 atoms, 7661 bonds, 943 residues, 1 model selected
> select #9 /A /B
52 atoms, 54 bonds, 2 residues, 1 model selected
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> contacts sel saveFile /Users/lau/Desktop/Glu6P-UDPGlu-TPS1_MSA resSeparation
> 10 interModel false intraMol false ignoreHiddenModels true color #ffffff
> dashes 5 radius 0.105 reveal true
113 contacts
> show #!1 models
> hide #!1 models
> show #!7 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #1/A to #9/C pairing ss
Parameters
---
Chain pairing | ss
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 Glu6P-UDPGlu-TPS1_MSA_0.cif, chain C (#9) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_0.cif, chain A (#1), sequence alignment
score = 4682.4
RMSD between 546 pruned atom pairs is 0.806 angstroms; (across all 942 pairs:
17.755)
> hide #!7 models
> show #!1 models
> hide #!9 models
> select add #9
7513 atoms, 7677 bonds, 113 pseudobonds, 944 residues, 4 models selected
> show #!9 models
> select #1 /B
5012 atoms, 5126 bonds, 5 pseudobonds, 644 residues, 2 models selected
> show sel cartoons
> select clear
> hide #!9 models
> hide #!1 models
> show #!2 models
> show #!9 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #2/A to #9/C pairing ss
Parameters
---
Chain pairing | ss
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 Glu6P-UDPGlu-TPS1_MSA_0.cif, chain C (#9) with
fold_mcherry_tps1xcdf5_gfp_seed1_model_1.cif, chain A (#2), sequence alignment
score = 4659.6
RMSD between 494 pruned atom pairs is 1.085 angstroms; (across all 942 pairs:
19.257)
> select #2 /B
5012 atoms, 5126 bonds, 6 pseudobonds, 644 residues, 2 models selected
> show sel cartoons
> select clear
> hide #!9 models
> show #6 models
> show #!7 models
> hide #6 models
> hide #2 models
> hide #1.1 models
> hide #!7 models
> show #!8 models
> show #!9 models
> show #!7 models
> hide #!8 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #7/B to #9/C pairing ss
Parameters
---
Chain pairing | ss
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 Glu6P-UDPGlu-TPS1_MSA_0.cif, chain C (#9) with
pred.model_idx_0.cif, chain B (#7), sequence alignment score = 4623
RMSD between 362 pruned atom pairs is 1.072 angstroms; (across all 942 pairs:
29.046)
> hide #!9 models
> show #7.1 models
> hide #!7 models
> show #!7 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!7 models
> show #!8 models
> hide #!9 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> hide #7.1 models
> show #!9 models
> hide #!8 models
> show #!1 models
> show #1.1 models
> hide #!1 models
> hide #1.1 models
> hide #3.1 models
> hide #4.1 models
> hide #5.1 models
> show #6 models
> show #2 models
> hide #2 models
> show #!3 models
> hide #!9 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #2 models
> select #2 /B:276-286
94 atoms, 100 bonds, 11 residues, 1 model selected
> hide #6 models
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #1/A #2/A #3/A #4/A #5/A
Alignment identifier is 1
> select #1/A:243 #2/A:243 #3/A:243 #4/A:243 #5/A:243
40 atoms, 35 bonds, 5 residues, 5 models selected
> select #1/A:243-244 #2/A:243-244 #3/A:243-244 #4/A:243-244 #5/A:243-244
75 atoms, 75 bonds, 10 residues, 5 models selected
. [ID: 1] region 5 chains [243-244] RMSD: 27.563
> select #1/A:243-244 #2/A:243-244 #3/A:243-244 #4/A:243-244 #5/A:243-244
75 atoms, 75 bonds, 10 residues, 5 models selected
> select #1/A:243-244 #2/A:243-244 #3/A:243-244 #4/A:243-244 #5/A:243-244
75 atoms, 75 bonds, 10 residues, 5 models selected
. [ID: 1] region 5 chains [243-244] RMSD: 27.563
> select #1/A:243-244 #2/A:243-244 #3/A:243-244 #4/A:243-244 #5/A:243-244
75 atoms, 75 bonds, 10 residues, 5 models selected
> select #1/A:243-244 #2/A:243-244 #3/A:243-244 #4/A:243-244 #5/A:243-244
75 atoms, 75 bonds, 10 residues, 5 models selected
. [ID: 1] region 5 chains [243-244] RMSD: 27.563
> select #2 /B:276-286
94 atoms, 100 bonds, 11 residues, 1 model selected
> show #6 models
> hide #2 models
> show #!1 models
> select
> #1/A:4-12,63-65,67-69,75-77,87-90,227-229,231-238,259-285,299-320,363-370,389-402,411-430,441-468,480-482,485-492,509-514,518-527,536-550,577-585,587-599,614-616,618-631,633-635,653-673,690-699,714-722,737-742,754-766,769-785,788-812,819-828,855-859,865-876,890-897,907-909,930-945,967-983,1009-1024,1041-1050,1145-1147,1167-1182
> #2/A:4-12,63-65,67-69,75-77,87-90,227-229,231-238,259-285,299-320,363-370,389-402,411-430,441-468,480-482,485-492,509-514,518-527,536-550,577-585,587-599,614-616,618-631,633-635,653-673,690-699,714-722,737-742,754-766,769-785,788-812,819-828,855-859,865-876,890-897,907-909,930-945,967-983,1009-1024,1041-1050,1145-1147,1167-1182
> #3/A:4-12,63-65,67-69,75-77,87-90,227-229,231-238,259-285,299-320,363-370,389-402,411-430,441-468,480-482,485-492,509-514,518-527,536-550,577-585,587-599,614-616,618-631,633-635,653-673,690-699,714-722,737-742,754-766,769-785,788-812,819-828,855-859,865-876,890-897,907-909,930-945,967-983,1009-1024,1041-1050,1145-1147,1167-1182
> #4/A:4-12,63-65,67-69,75-77,87-90,227-229,231-238,259-285,299-320,363-370,389-402,411-430,441-468,480-482,485-492,509-514,518-527,536-550,577-585,587-599,614-616,618-631,633-635,653-673,690-699,714-722,737-742,754-766,769-785,788-812,819-828,855-859,865-876,890-897,907-909,930-945,967-983,1009-1024,1041-1050,1145-1147,1167-1182
> #5/A:4-12,63-65,67-69,75-77,87-90,227-229,231-238,259-285,299-320,363-370,389-402,411-430,441-468,480-482,485-492,509-514,518-527,536-550,577-585,587-599,614-616,618-631,633-635,653-673,690-699,714-722,737-742,754-766,769-785,788-812,819-828,855-859,865-876,890-897,907-909,930-945,967-983,1009-1024,1041-1050,1145-1147,1167-1182
18440 atoms, 18625 bonds, 2265 residues, 5 models selected
> select #1/A:1 #2/A:1 #3/A:1 #4/A:1 #5/A:1
40 atoms, 35 bonds, 5 residues, 5 models selected
> select #1/A #2/A #3/A #4/A #5/A
48935 atoms, 50030 bonds, 6195 residues, 5 models selected
. [ID: 1] region 5 chains [1-1239] RMSD: 45.277
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 2 time(s)]
> save /Users/lau/Desktop/mCherry-GSGSGS-TPS1.fasta format fasta alignment 1
> hide #6 models
> hide #!1 models
> show #2 models
> select clear
> show #6 models
> show #!9 models
> hide #6 models
> hide #!9 models
> show #!8 models
> show #6 models
> hide #6 models
> show #6 models
> hide #2 models
> hide #6 models
> show #!1 models
> hide #!1 models
> show #2 models
> hide #!8 models
> show #!9 models
> hide #2 models
> show #!3 models
> hide #!9 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> open
> /Users/lau/Downloads/fold_2xmcherry_tps1_and_2xcdf5_gfp_seed1-2/fold_2xmcherry_tps1_and_2xcdf5_gfp_seed1_model_0.cif
Chain information for fold_2xmcherry_tps1_and_2xcdf5_gfp_seed1_model_0.cif #10
---
Chain | Description
A B | .
C D | .
> hide #!5 models
> select #10 /A/B
19574 atoms, 20012 bonds, 2478 residues, 1 model selected
> select #10 /A
9787 atoms, 10006 bonds, 1239 residues, 1 model selected
> select #10 /B
9787 atoms, 10006 bonds, 1239 residues, 1 model selected
> select #10 /C
5012 atoms, 5126 bonds, 644 residues, 1 model selected
> select #10 /D
5012 atoms, 5126 bonds, 644 residues, 1 model selected
> select #10 /A/B
19574 atoms, 20012 bonds, 2478 residues, 1 model selected
> color sel medium blue
> select #10 /C/D
10024 atoms, 10252 bonds, 1288 residues, 1 model selected
> color sel yellow
> select #10 /A
9787 atoms, 10006 bonds, 1239 residues, 1 model selected
> color sel cornflower blue
> select #10 /D
5012 atoms, 5126 bonds, 644 residues, 1 model selected
> color sel yellow
> color sel orange
> select clear
> open
> /Users/lau/Downloads/fold_2xmcherry_tps1_and_2xcdf5_gfp_seed1-2/fold_2xmcherry_tps1_and_2xcdf5_gfp_seed1_model_1.cif
Chain information for fold_2xmcherry_tps1_and_2xcdf5_gfp_seed1_model_1.cif #11
---
Chain | Description
A B | .
C D | .
> hide #10 models
> select #11 /A/B colour blue
Expected a keyword
> select #11 /A/B color blue
Expected a keyword
> select #11 /A/B
19574 atoms, 20012 bonds, 2478 residues, 1 model selected
> colour sel blue
> open
> /Users/lau/Downloads/fold_2xmcherry_tps1_and_2xcdf5_gfp_seed1-2/fold_2xmcherry_tps1_and_2xcdf5_gfp_seed1_model_2.cif
Chain information for fold_2xmcherry_tps1_and_2xcdf5_gfp_seed1_model_2.cif #12
---
Chain | Description
A B | .
C D | .
> hide #11 models
> select #12 /A/B
19574 atoms, 20012 bonds, 2478 residues, 1 model selected
> colour sel blue
> select #12
> /A/B:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
9983 atoms, 10188 bonds, 1266 residues, 1 model selected
> select #12
> /A:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
196 atoms, 182 bonds, 27 residues, 1 model selected
> color sel white
> select #12
> /B:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
196 atoms, 182 bonds, 27 residues, 1 model selected
> color sel white
> hide #12 models
> select add #12
29598 atoms, 30264 bonds, 3766 residues, 1 model selected
> select subtract #12
Nothing selected
> show #11 models
> hide #11 models
> show #10 models
> select #10
> /B:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
196 atoms, 182 bonds, 27 residues, 1 model selected
> hide #10 models
> show #10 models
> hide #10 models
> show #!1 models
> select add #10
29598 atoms, 30264 bonds, 3766 residues, 1 model selected
> select subtract #10
Nothing selected
> hide #!1 models
> show #2 models
> select #2
> /B:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
108 atoms, 99 bonds, 14 residues, 1 model selected
> select #2
> /A:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
196 atoms, 182 bonds, 27 residues, 1 model selected
> color sel white
> show #6 models
> select #2
> /A:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
196 atoms, 182 bonds, 27 residues, 1 model selected
> color sel red
> select clear
> select #2 /A 243-260
Expected a keyword
> select #2 /A:243-260
137 atoms, 140 bonds, 18 residues, 1 model selected
> select #2 /A:250-300
409 atoms, 411 bonds, 51 residues, 1 model selected
> color sel cornflower blue
> hide #6 models
> hide #2 models
> show #!9 models
> show #2 models
> hide #!9 models
> hide #2 models
> select add #2
14799 atoms, 15132 bonds, 352 pseudobonds, 1883 residues, 2 models selected
> show #10 models
> select subtract #2
Nothing selected
> hide #10 models
> show #11 models
> show #!8 models
> hide #11 models
> show #2 models
> hide #!8 models
> select #2 /A
9787 atoms, 10006 bonds, 1239 residues, 1 model selected
> show sel surfaces
[Repeated 1 time(s)]
> transparency (#!2 & sel) 70
Alignment identifier is 2/A
> select clear
> select #2/A:1088-1089
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:1088-1107
143 atoms, 142 bonds, 20 residues, 1 model selected
> open
> /Users/lau/Downloads/fold_1xtps1_2xcdf5_dna_at1g05630_1_promoter/fold_1xtps1_2xcdf5_dna_at1g05630_1_promoter_model_0.cif
Chain information for fold_1xtps1_2xcdf5_dna_at1g05630_1_promoter_model_0.cif
#13
---
Chain | Description
A | .
B | .
C | .
> hide #!2 models
> select #13 /A
7462 atoms, 7624 bonds, 942 residues, 1 model selected
> select #13 /A:800-900
770 atoms, 784 bonds, 101 residues, 1 model selected
> hide #13 models
> select add #13
11774 atoms, 12150 bonds, 1401 residues, 1 model selected
> select subtract #13
Nothing selected
> show #!2 models
> select #2
> /A:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
196 atoms, 182 bonds, 27 residues, 1 model selected
> color (#!2 & sel) white
> color (#!2 & sel) cyan
> show #6 models
> save
> /Users/lau/Documentos/Ongoing/TPS1_binding/sugarpocket_TPS1_CDF5_tags_andco.cxs
> includeMaps true
——— End of log from Mon Oct 21 20:08:42 2024 ———
opened ChimeraX session
> ui tool show Registration
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
laura.lp.iq@gmail.com has been invited to the ChimeraX announcements list
> select
> #2/A:17-27,30-41,46-55,96-104,109-119,122-132,151-158,161-171,177-188,198-209,215-226,334-339,345-349,355-359,374-381,404-407,474-478,497-502,530-533,558-561,564-570,604-611,639-646,681-684,702-705,729-733,747-749,832-836,880-885,903-906,911-914,950-953,957-961,991-996,999-1004,1032-1037,1148-1153,1162-1164
2121 atoms, 2130 bonds, 260 residues, 1 model selected
> hide #!2 models
> show #!1 models
> select add #2
14799 atoms, 15132 bonds, 352 pseudobonds, 1883 residues, 3 models selected
> select subtract #2
1 model selected
> show #!9 models
> hide #6 models
> hide #!1 models
> select #9
> /C:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
220 atoms, 204 bonds, 27 residues, 1 model selected
> select #2
> /C:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
Nothing selected
> select cear
Expected an objects specifier or a keyword
> select clear
> interfaces #!9 & ~solvent
1 buried areas: C B 479
> select #9 /C
7461 atoms, 7623 bonds, 942 residues, 1 model selected
> show sel surfaces
> transparency (#!9 & sel) 70
> hide #!9 models
> show #!7 models
> select #7 /B
7461 atoms, 7623 bonds, 942 residues, 1 model selected
> show sel surfaces
> transparency (#!7 & sel) 70
> ui tool show "Side View"
> select #7 /A
27 atoms, 28 bonds, 1 residue, 1 model selected
> show sel surfaces
> hide #!7 models
> select add #7
7488 atoms, 7651 bonds, 40 pseudobonds, 943 residues, 3 models selected
> select subtract #7
2 models selected
> show #10 models
> hide #10 models
> show #!1 models
> show #!7 models
> hide #!1 models
> show #!8 models
> hide #!7 models
> select #8 /A
16 atoms, 16 bonds, 1 residue, 1 model selected
> select #8 /C
7461 atoms, 7623 bonds, 942 residues, 1 model selected
> show sel surfaces
> transparency (#!8 & sel) 70
> select #8 /A/B
52 atoms, 54 bonds, 2 residues, 1 model selected
> show sel surfaces
> hide #!8 models
> show #!1 models
> show #1.1 models
> hide #1.1 models
> show #6 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> select #1 /A
9787 atoms, 10006 bonds, 1239 residues, 1 model selected
> show sel surfaces
> transparency (#!1 & sel) 70
> select #1
> /A:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
196 atoms, 182 bonds, 27 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide sel cartoons
> show sel cartoons
> lighting simple
> lighting soft
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sel deep sky blue
> show #!9 models
> select #1
> /A:363,364,365,367,419,428,480,482,504,535,574,610,612,617,647,649,650,688,689,694,711,712,713,714,715,716,719
196 atoms, 182 bonds, 27 residues, 1 model selected
> color (#!1 & sel) medium blue
> select clear
> hide #6 models
> hide #1.2 models
> show #1.2 models
> hide #!1 models
> hide #1.2 models
> show #1.2 models
> select #1
14799 atoms, 15132 bonds, 674 pseudobonds, 1883 residues, 3 models selected
> hide sel cartoons
> select #1
14799 atoms, 15132 bonds, 680 pseudobonds, 1883 residues, 4 models selected
> show sel cartoons
> select clear
> hide #!9 models
> show #!8 models
> hide #!1 models
> hide #1.2 models
> show #!1 models
> hide #!1 models
> hide #!8 models
> select #1
14799 atoms, 15132 bonds, 674 pseudobonds, 1883 residues, 3 models selected
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> select subtract #1.1
14799 atoms, 15132 bonds, 337 pseudobonds, 1883 residues, 3 models selected
> select add #1
14799 atoms, 15132 bonds, 674 pseudobonds, 1883 residues, 4 models selected
> select subtract #1
1 model selected
> show #!1 models
> show #6 models
> hide #!1 models
> show #!2 models
> hide #6 models
> hide #!2 models
> show #!2 models
> select #2
14799 atoms, 15132 bonds, 352 pseudobonds, 1883 residues, 2 models selected
> hide sel surfaces
> select clear
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #1.2 models
> hide #1.2 models
> show #!2 models
> hide #!1 models
> show #6 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> select #3
14799 atoms, 15132 bonds, 990 pseudobonds, 1883 residues, 3 models selected
> show sel cartoons
> select clear
> select #3 /B: 143-188
389 atoms, 402 bonds, 46 residues, 1 model selected
> select #3 /B: 29-125
717 atoms, 728 bonds, 97 residues, 1 model selected
> hide #3 models
> select add #3
14799 atoms, 15132 bonds, 986 pseudobonds, 1883 residues, 2 models selected
> select subtract #3
Nothing selected
> show #!4 models
> select #4
14799 atoms, 15132 bonds, 992 pseudobonds, 1883 residues, 3 models selected
> show sel cartoons
> select clear
> hide #4 models
> show #10 models
> show #11 models
> show #12 models
> show #13 models
> hide #6 models
> hide #13 models
> ui tool show "Modeller Comparative"
Populating font family aliases took 132 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
No alignments chosen for modeling
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #11-12 & sel to #10
No molecules/chains to match specified
> matchmaker #11-12 & sel to #10
No molecules/chains to match specified
> matchmaker #11-12 & sel to #10
No molecules/chains to match specified
> matchmaker #11-12 & sel to #10 & sel
No 'to' model specified
> matchmaker #11-12 & sel to #10 & sel
No 'to' model specified
> matchmaker #11 & sel to #10 & sel
No 'to' model specified
> matchmaker #3-4,11-13#!2,5,7-9 & sel to #10/A & sel pairing bs
No 'to' chains specified
> matchmaker #11/A & sel to #1/A & sel pairing ss
No 'to' chains specified
> hide #11 models
> show #11 models
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> contacts sel resSeparation 10 interModel false intraMol false color #ffffff
> dashes 5 radius 0.105 reveal true
No atoms match given atom specifier
> select clear
> hide #12 models
> hide #11 models
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> contacts sel saveFile /Users/lau/Desktop/2mCherryTPS1_2CDF5_eGFP_m0
> resSeparation 10 interModel false intraMol false color #ffffff dashes 5
> radius 0.105 reveal true
No atoms match given atom specifier
> hide #10 models
> show #11 models
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #11 models
> show #10 models
> select #10 /A
9787 atoms, 10006 bonds, 1239 residues, 1 model selected
> select #10 /B
9787 atoms, 10006 bonds, 1239 residues, 1 model selected
> select #10 /A/B
19574 atoms, 20012 bonds, 2478 residues, 1 model selected
> ui tool show Contacts
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> contacts sel saveFile /Users/lau/Desktop/mCherryTPS1_CDF5eGFP_m0
> resSeparation 10 interModel false intraMol false color #ffffff dashes 5
> radius 0.105 reveal true
1376 contacts
> hide #!10 models
> show #!10 models
> hide #!10 models
> select add #10
29598 atoms, 30264 bonds, 1376 pseudobonds, 3766 residues, 2 models selected
> select subtract #10
Nothing selected
> show #11 models
> hide #11 models
> show #12 models
> hide #12 models
> show #13 models
> hide #13 models
> show #!7 models
> mlp #!7
Map values for surface "pred.model_idx_0.cif_B SES surface": minimum -30.85,
mean -6.164, maximum 24.36
To also show corresponding color key, enter the above mlp command and add key
true
> transparency #7.1,3#!7 70
> transparency #7.1,3#!7 30
> ui tool show "Side View"
> ui tool show "Surface Color"
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> key delete
> ui mousemode right translate
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!1 models
> hide #!7.3 models
> hide #!7 models
> hide #7.1 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-23.0.21
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.0.0.0.0 (iBridge: 22.16.10353.0.0,0)
OS Loader Version: 582~1023
Software:
System Software Overview:
System Version: macOS 15.0.1 (24A348)
Kernel Version: Darwin 24.0.0
Time since boot: 6 days, 22 hours, 22 minutes
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2425:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 1CRC304
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
DELL P2425:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: BNPC304
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.55
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 13 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 , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This crash in the Qt 6.6 window toolkit happens when unplugging or plugging in an external display or waking from sleep. It seems to be fixed in Qt 6.7 which is used in the ChimeraX daily build. So use the daily build to avoid this crash.
Crash in Qt 6.6 in _NSViewHierarchyDidChangeBackingProperties.
Note:
See TracTickets
for help on using tickets.
Reported by Laura Lamelas