![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16892 closed defect (nonchimerax)
Graphics crash in glBufferSubData, macOS 14.1.1, M1 GPU
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001e3f49ec0 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2831 in update_buffer_data
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1912 in update_buffers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1924 in activate_bindings
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 814 in _draw_geometry
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 791 in draw_self
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1560 in
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1307 in draw_transparent
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1559 in draw_transparent
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 266 in _draw_scene
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
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.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 51)
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{
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"procRole" : "Foreground",
"version" : 2,
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"modelCode" : "MacBookAir10,1",
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"build" : "23B81",
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"captureTime" : "2025-02-18 17:08:10.0633 +0100",
"codeSigningMonitor" : 1,
"incident" : "8F769239-6080-4D1D-9BA6-024D6ED54264",
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"procLaunch" : "2025-02-18 16:45:31.8052 +0100",
"procStartAbsTime" : 20455826187811,
"procExitAbsTime" : 20488422035047,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "21FF33AE-7575-DB21-344D-FEA875389A1E",
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs_plus_asgards.cxs
Log from Tue Feb 11 18:53:35 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs.cxs
Log from Fri Oct 11 12:28:40 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.Log
from Fri Oct 11 10:32:57 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs.cxs
> format session
Log from Wed Oct 9 16:01:21 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs.cxs
> format session
Log from Wed Oct 9 14:23:06 2024
> view matrix
view matrix camera
0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.080881,-0.37107,0.92508,-0.072644,0.90711,-0.35721,-0.22259,0.86818,0.41304,0.85715,0.30771,-0.54666,#3,-0.13505,0.91861,0.37136,-0.48431,-0.90398,0.039221,-0.42577,-0.070453,-0.40568,-0.39321,0.82511,-0.43506,#4,-0.17213,-0.62081,0.76483,-0.20135,-0.4132,-0.65931,-0.62815,2.0948,0.89422,-0.42416,-0.14303,-0.50991,#5,0.83544,0.30561,-0.45678,-2.6285,-0.42479,-0.16827,-0.88952,0.13194,-0.34871,0.93717,-0.010762,2.0713,#6,0.3235,0.0013252,-0.94623,-1.3383,0.88725,-0.34793,0.30285,0.70119,-0.32882,-0.93752,-0.11373,1.7828,#7,-0.71108,-0.41305,-0.56899,-0.77743,0.68601,-0.58496,-0.43268,-0.10351,-0.15412,-0.69801,0.69931,0.37546,#8,-0.28718,0.85343,0.43495,0.29099,0.14526,-0.41002,0.90043,-0.24122,0.9468,0.32177,-0.0062164,-1.197
> windowsize size 600 600
Expected an integer >= 1 or a keyword
> windowsize 600 600
> save FmdF_M.jannaschi.png supersample 8 transparentBackground true
> show #2 models
> hide #1 models
> save FmdF_M.maripaludis.png supersample 8 transparentBackground true
> show #3 models
> hide #2 models
> save FmdF_M.formicicum.png supersample 8 transparentBackground true
> hide #3 models
> show #4 models
> save FmdF_M.kandleri.png supersample 8 transparentBackground true
> show #5 models
> hide #4 models
> save FmdF_M.fervidus.png supersample 8 transparentBackground true
> show #6 models
> hide #5 models
> save FmdF_conradii.png supersample 8 transparentBackground true
> hide #6 models
> show #5 models
> select add #5/A:205
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #5/A:208
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel yellow
> select clear
> save FmdF_M.fervidus.png supersample 8 transparentBackground true
> hide #5 models
> show #6 models
> save FmdF_M.conradii.png supersample 8 transparentBackground true
> hide #6 models
> show #7 models
> save FmdF_M.paludicola.png supersample 8 transparentBackground true
> hide #7 models
> show #7 models
> hide #7 models
> show #8 models
> save FmdF_M.mesophila.png supersample 8 transparentBackground true
> show #7 models
> hide #8 models
> hide #7 models
> show #7 models
> show #6 models
> show #8 models
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> true
Unknown command: true
> hide #8 models
> hide #7 models
> hide #6 models
> show #6 models
> hide #6 models
> show #1 models
> hide #1 models
> show #1 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #1 models
> show #3 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #3 models
> show #1 models
> save
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs.cxs
> includeMaps true
——— End of log from Wed Oct 9 14:23:06 2024 ———
opened ChimeraX session
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdFs_archaeoglobus/fold_archaeoglobus_fulgidus_fmdf/fold_archaeoglobus_fulgidus_fmdf_model_0.cif
> format mmcif
Chain information for fold_archaeoglobus_fulgidus_fmdf_model_0.cif #9
---
Chain | Description
A | .
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> mmaker #9 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_archaeoglobus_fulgidus_fmdf_model_0.cif, chain A (#9), sequence
alignment score = 528.4
RMSD between 43 pruned atom pairs is 1.264 angstroms; (across all 273 pairs:
8.377)
> color #9 forest green
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdFs_archaeoglobus/fold_archaeoglobus_sulfaticallidus_fmdf/fold_archaeoglobus_sulfaticallidus_fmdf_model_0.cif
> format mmcif
Chain information for fold_archaeoglobus_sulfaticallidus_fmdf_model_0.cif #10
---
Chain | Description
A | .
> mmaker #10 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_archaeoglobus_sulfaticallidus_fmdf_model_0.cif, chain A (#10),
sequence alignment score = 558
RMSD between 77 pruned atom pairs is 1.014 angstroms; (across all 292 pairs:
12.305)
> color #10 forest green
> select clear
> hide #10 models
> hide #1 models
> select add #9/A:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #9/A:175
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel yellow
> select clear
> hide #9 models
> show #10 models
> select add #10/A:184
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #10/A:187
12 atoms, 10 bonds, 2 residues, 1 model selected
> color sel yellow
> show sel atoms
> select clear
> save FmdF_A.sulfaticallidus.png supersample 8 transparentBackground true
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> save FmdF_A.sulfaticallidus.png supersample 8 transparentBackground true
> hide #10 models
> show #9 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:364
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A:282-364
627 atoms, 629 bonds, 83 residues, 1 model selected
> color sel dodgerblue bluetrue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel dodger blue
> select clear
> show #10 models
> hide #9 models
> ui tool show "Show Sequence Viewer"
> sequence chain #10/A
Alignment identifier is 10/A
> select #10/A:376
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:293-376
592 atoms, 596 bonds, 84 residues, 1 model selected
> color sel dodger blue
> select clear
> save FmdF_A.sulfaticallidus.png supersample 8 transparentBackground true
> open
> /Users/pasanseg/Downloads/fold_fmdf_sulfati_dimer/fold_fmdf_sulfati_dimer_model_0.cif
Chain information for fold_fmdf_sulfati_dimer_model_0.cif #11
---
Chain | Description
A B | .
> hide #10 models
> select :cys
2682 atoms, 2236 bonds, 447 residues, 11 models selected
> show sel atoms
> close #11
> save
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs.cxs
> includeMaps true
> show #10 models
> hide #10 models
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> show #10 models
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> select clear
> save
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs.cxs
> includeMaps true
[Repeated 1 time(s)]
——— End of log from Wed Oct 9 16:01:21 2024 ———
opened ChimeraX session
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdFs_classII/fold_methanoregula_boonei_fmdf_ok/fold_methanoregula_boonei_fmdf_ok_model_0.cif
Chain information for fold_methanoregula_boonei_fmdf_ok_model_0.cif #11
---
Chain | Description
A | .
> mmaker #11 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_methanoregula_boonei_fmdf_ok_model_0.cif, chain A (#11), sequence
alignment score = 751.9
RMSD between 146 pruned atom pairs is 1.002 angstroms; (across all 335 pairs:
9.922)
> color #11 forest green
> hide #10 models
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> save FmdF_boonei.png supersample 8 transparentBackground true
> hide #11 models
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdFS_classIIb/fold_fmdf_barkeri/fold_fmdf_barkeri_model_0.cif
Chain information for fold_fmdf_barkeri_model_0.cif #12
---
Chain | Description
A | .
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdFS_classIIb/fold_fmdf_m_acetivorans/fold_fmdf_m_acetivorans_model_0.cif
Chain information for fold_fmdf_m_acetivorans_model_0.cif #13
---
Chain | Description
A | .
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdFS_classIIb/fold_fmdf_methanohalophilus_mahii/fold_fmdf_methanohalophilus_mahii_model_0.cif
Chain information for fold_fmdf_methanohalophilus_mahii_model_0.cif #14
---
Chain | Description
A | .
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdFS_classIIb/fold_fmdf_methanolobus_halotolerans/fold_fmdf_methanolobus_halotolerans_model_0.cif
Chain information for fold_fmdf_methanolobus_halotolerans_model_0.cif #15
---
Chain | Description
A | .
> mmaker #12 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_fmdf_barkeri_model_0.cif, chain A (#12), sequence alignment score =
588.9
RMSD between 89 pruned atom pairs is 0.834 angstroms; (across all 302 pairs:
30.991)
> mmaker #13 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_fmdf_m_acetivorans_model_0.cif, chain A (#13), sequence alignment
score = 554.3
RMSD between 85 pruned atom pairs is 0.859 angstroms; (across all 298 pairs:
30.809)
> mmaker #14 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_fmdf_methanohalophilus_mahii_model_0.cif, chain A (#14), sequence
alignment score = 575
RMSD between 91 pruned atom pairs is 0.909 angstroms; (across all 295 pairs:
30.079)
> mmaker #15 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_fmdf_methanolobus_halotolerans_model_0.cif, chain A (#15), sequence
alignment score = 577.2
RMSD between 89 pruned atom pairs is 0.715 angstroms; (across all 297 pairs:
30.415)
> color #12 forestgreen
> color #13 forestgreen
> color #14 forestgreen
> color #15 forestgreen
> hide #13 models
> hide #14 models
> hide #15 models
> show #15 models
> show #14 models
> show #13 models
> hide #13 models
> hide #14 models
> hide #15 models
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
> select #12/A:346
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #12/A:253-346
688 atoms, 692 bonds, 94 residues, 1 model selected
> color sel dodger blue
> select clear
> hide #12 models
> show #13 models
> hide #13 models
> show #13 models
> ui tool show "Show Sequence Viewer"
> sequence chain #13/A
Alignment identifier is 13/A
> select #13/A:346
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #13/A:255-346
689 atoms, 697 bonds, 92 residues, 1 model selected
> color sel dodger blue
> select clear
> hide #13 models
> show #14 models
> ui tool show "Show Sequence Viewer"
> sequence chain #14/A
Alignment identifier is 14/A
> select #14/A:341
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #14/A:327-341
126 atoms, 128 bonds, 15 residues, 1 model selected
> select #14/A:308-341
246 atoms, 248 bonds, 34 residues, 1 model selected
> select #14/A:260-341
604 atoms, 610 bonds, 82 residues, 1 model selected
> color sel dodger blue
> select clear
> hide #14 models
> show #15 models
> ui tool show "Show Sequence Viewer"
> sequence chain #15/A
Alignment identifier is 15/A
> select #15/A:339
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:265-339
537 atoms, 539 bonds, 75 residues, 1 model selected
> select #15/A:339
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:301-339
288 atoms, 288 bonds, 39 residues, 1 model selected
> select #15/A:248-339
669 atoms, 673 bonds, 92 residues, 1 model selected
> color sel dodger blue
> select clear
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> hide #15 models
> show #12 models
> save FmdF_Mbarkeri.png supersample 8 transparentBackground true
> hide #12 models
> show #13 models
> save FmdF_Macetivorans.png supersample 8 transparentBackground true
> hide #13 models
> save FmdF_Mmahii.png supersample 8 transparentBackground true
> show #14 models
> save FmdF_Mmahii.png supersample 8 transparentBackground true
> hide #14 models
> show #15 models
> save FmdF_Mhalotolerans.png supersample 8 transparentBackground true
> save
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs.cxs
> includeMaps true
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> close #12
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdFS_classIIb/fold_methanococcoides_methylutens/fold_methanococcoides_methylutens_model_0.cif
Chain information for fold_methanococcoides_methylutens_model_0.cif #12
---
Chain | Description
A | .
> mmaker #15 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_fmdf_methanolobus_halotolerans_model_0.cif, chain A (#15), sequence
alignment score = 577.2
RMSD between 89 pruned atom pairs is 0.715 angstroms; (across all 297 pairs:
30.415)
> hide #12 models
> show #12 models
> show #14 models
> hide #15 models
> hide #14 models
> show #15 models
> hide #15 models
> mmaker #12 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_methanococcoides_methylutens_model_0.cif, chain A (#12), sequence
alignment score = 582.5
RMSD between 87 pruned atom pairs is 0.850 angstroms; (across all 290 pairs:
29.967)
> ui tool show "Show Sequence Viewer"
> sequence chain #15/A
Alignment identifier is 15/A
> select #15/A:339
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #15/A:314-339
188 atoms, 188 bonds, 26 residues, 1 model selected
> select #15/A:248-339
669 atoms, 673 bonds, 92 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
> select #12/A:340
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #12/A:248-340
674 atoms, 681 bonds, 93 residues, 1 model selected
> color sel dodger blue
> select clear
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> save FmdF_Mmethylutens.png supersample 8 transparentBackground true
> save
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs.cxs
> includeMaps true
> open
> /Users/pasanseg/Downloads/fold_2024_10_10_19_07/fold_2024_10_10_19_07_model_0.cif
Chain information for fold_2024_10_10_19_07_model_0.cif #16
---
Chain | Description
A | .
> hide #12 models
> mmaker #16 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_2024_10_10_19_07_model_0.cif, chain A (#16), sequence alignment
score = 831.2
RMSD between 181 pruned atom pairs is 1.060 angstroms; (across all 340 pairs:
11.323)
> show #10 models
> hide #10 models
> show #6 models
> hide #6 models
> close #16
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdFs_archaeoglobus/fold_archaeoglobus_veneficus_fmdf/fold_archaeoglobus_veneficus_fmdf_model_0.cif
Chain information for fold_archaeoglobus_veneficus_fmdf_model_0.cif #16
---
Chain | Description
A | .
> mmaker #16 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_archaeoglobus_veneficus_fmdf_model_0.cif, chain A (#16), sequence
alignment score = 704.9
RMSD between 121 pruned atom pairs is 1.372 angstroms; (across all 329 pairs:
15.708)
> close #16
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdFs_archaeoglobus/fold_archaeoglobus_neptunius_fmdf/fold_archaeoglobus_neptunius_fmdf_model_0.cif
Chain information for fold_archaeoglobus_neptunius_fmdf_model_0.cif #16
---
Chain | Description
A | .
> mmaker #16 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_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_archaeoglobus_neptunius_fmdf_model_0.cif, chain A (#16), sequence
alignment score = 574.3
RMSD between 73 pruned atom pairs is 0.889 angstroms; (across all 293 pairs:
8.959)
> select :cys
3462 atoms, 2891 bonds, 577 residues, 16 models selected
> select clear
> select add #16/A:185
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #16/A:182
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel yellow
> select clear
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> save
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs.cxs
> includeMaps true
——— End of log from Fri Oct 11 10:32:57 2024 ———
opened ChimeraX session
> select #12/A:340
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #12/A:239-340
752 atoms, 760 bonds, 102 residues, 1 model selected
> hide #16 models
> show #16 models
> ui tool show "Show Sequence Viewer"
> sequence chain #16/A
Alignment identifier is 16/A
> select #16/A:374
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #16/A:292-374
645 atoms, 648 bonds, 83 residues, 1 model selected
> color sel dodgerblue blueM
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel dodger blue
> select clear
> save FmdF_A.neptunis.png supersample 8 transparentBackground true
> save
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs.cxs
> includeMaps true
——— End of log from Fri Oct 11 12:28:40 2024 ———
opened ChimeraX session
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdF_Asgard/asgard_wp_162306737_promethearchaeum_syntrophicum/fold_asgard_wp_162306737_promethearchaeum_syntrophicum_model_0.cif
Chain information for
fold_asgard_wp_162306737_promethearchaeum_syntrophicum_model_0.cif #17
---
Chain | Description
A | .
Computing secondary structure
> mmaker #17 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_asgard_wp_162306737_promethearchaeum_syntrophicum_model_0.cif, chain
A (#17), sequence alignment score = 339.6
RMSD between 70 pruned atom pairs is 0.975 angstroms; (across all 190 pairs:
38.477)
> hide #16 models
> hide #17 models
> show #16 models
> hide #16 models
> show #17 models
> select #17:cys
109 atoms, 91 bonds, 18 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #17
2023 atoms, 2070 bonds, 251 residues, 1 model selected
> color sel forest green target c
> select clear
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> save FmdF_P.syntrophicum.png supersample 8 transparentBackground true
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> windowsize 600 600
> view matrix camera
> 0.076945,-0.90146,-0.42597,-83.885,0.041172,0.42975,-0.90201,-179.09,0.99618,0.051867,0.070182,26.769
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> save FmdF_P.syntrophicum.png supersample 8 transparentBackground true
> hide #17 models
> save
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/figures/FmdFs_other_species/fmdfs_plus_asgards.cxs
> includeMaps true
——— End of log from Tue Feb 11 18:53:35 2025 ———
opened ChimeraX session
> open
> /Users/pasanseg/Nextcloud/Mvh_Hdr_MvhB_HcgG_complex_provisional/AF3_organism_list_trials/AF3/FmdF_Asgard/asgard_uyp43905_ca_lokiarchaeum_ossiferum/fold_asgard_uyp43905_ca_lokiarchaeum_ossiferum_model_0.cif
Chain information for
fold_asgard_uyp43905_ca_lokiarchaeum_ossiferum_model_0.cif #18
---
Chain | Description
A | .
Computing secondary structure
> windowsize 600 600
> mmaker #18 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_asgard_uyp43905_ca_lokiarchaeum_ossiferum_model_0.cif, chain A
(#18), sequence alignment score = 336.7
RMSD between 67 pruned atom pairs is 1.199 angstroms; (across all 185 pairs:
37.035)
> color sel byhetero
> select :cys
3673 atoms, 3067 bonds, 612 residues, 18 models selected
> color sel byhetero
> select clear
> select :cys
3673 atoms, 3067 bonds, 612 residues, 18 models selected
> show sel atoms
> select clear
> windowsize 600 600
> mmaker #18 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_fmdf_methanocaldococcus_jannaschii_model_0.cif, chain A (#1)
with fold_asgard_uyp43905_ca_lokiarchaeum_ossiferum_model_0.cif, chain A
(#18), sequence alignment score = 336.7
RMSD between 67 pruned atom pairs is 1.199 angstroms; (across all 185 pairs:
37.035)
===== Log before crash end =====
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: Z1250006KD/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 32 days, 4 hours, 48 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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 , 8 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in glBufferSubData |
comment:2 by , 8 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash in glBufferSubData → Graphics crash in glBufferSubData, macOS 14.1.1, M1 GPU |
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Unusual graphics crash in Mac M1 OpenGL driver. Does not appear large maps were involved.