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Opened 21 months ago
Closed 21 months ago
#14597 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.6-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070001ef66000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001bf5d000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000070001cf60000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007000186c5000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000112204600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py", line 576 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1613 in remove_deleted_pointers
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 134 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 894 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 253 in filter
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 813 in selected_items
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/selection.py", line 46 in items
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/select.py", line 170 in report_selection
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/select.py", line 62 in select
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/region_browser.py", line 1763 in _select_on_structures
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/region_browser.py", line 1585 in _mouse_up_cb
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 63)
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{
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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23
> CRAMP1 SANT domain residues mutagenesis/NPAT_CR1_full_SANT.cxs" format
> session
opened ChimeraX session
> ui tool show "AlphaFold Error Plot"
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_11/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> color sel bynucleotide
> select add #1
5621 atoms, 5724 bonds, 36 pseudobonds, 739 residues, 2 models selected
> color sel bynucleotide
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
> select #1/B:22
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:22
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:4-5
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/B:4-70
579 atoms, 596 bonds, 67 residues, 1 model selected
> select #1/B:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:5-61
489 atoms, 502 bonds, 57 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 to #1 & sel
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 best_model.pdb, chain B (#1) with best_model.pdb, chain A (#2),
sequence alignment score = 312
RMSD between 57 pruned atom pairs is 0.314 angstroms; (across all 57 pairs:
0.314)
> select #1/A:563
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:563-589
197 atoms, 197 bonds, 27 residues, 1 model selected
> select #1/A:563-589,658-664
254 atoms, 254 bonds, 34 residues, 1 model selected
> select #1/A:668
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:650-668
150 atoms, 154 bonds, 19 residues, 1 model selected
> select #1/A:660-661
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/A:660-661
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/A:661
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:661
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:665
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:665
8 atoms, 7 bonds, 1 residue, 1 model selected
> save "/Users/enaden/Documents/Cambridge Year 4/Part III Project/2024 2 12
> CRAMP1 DUF UBL mutants/DUF_SANT_align.cxs"
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_5/best_model.pdb
Chain information for best_model.pdb #3
---
Chain | Description
A | No description available
B | No description available
> hide #3 models
> hide #2 models
> hide #!1 models
> select add #1
5621 atoms, 5724 bonds, 36 pseudobonds, 739 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #1.1 models
> show #3 models
> color #3 bychain
> close #3
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_6/best_model.pdb
Chain information for best_model.pdb #3
---
Chain | Description
A | No description available
B | No description available
> color #3 bychain
> show #!1 models
> ui tool show Matchmaker
> select #1/B:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:5-17
112 atoms, 114 bonds, 13 residues, 1 model selected
> select #1/B:4-5
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/B:4-62
504 atoms, 517 bonds, 59 residues, 1 model selected
> select #1/B:3-4
20 atoms, 21 bonds, 2 residues, 1 model selected
> select #1/B:3-62
518 atoms, 533 bonds, 60 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #3 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 best_model.pdb, chain B (#1) with best_model.pdb, chain B (#3),
sequence alignment score = 380.8
RMSD between 70 pruned atom pairs is 0.754 angstroms; (across all 70 pairs:
0.754)
> show #2 models
> hide #2 models
> hide #!1 models
> show #!1 models
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
Destroying pre-existing alignment with identifier 1/B
Alignment identifier is 1/B
> select #1/A:55
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:55
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:658
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:658
7 atoms, 6 bonds, 1 residue, 1 model selected
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> close #3
> hide #!1 models
> show #2 models
> hide #2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> close #1
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_6/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> color #1 bychain
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:1-30
232 atoms, 234 bonds, 30 residues, 1 model selected
> close #1
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_7/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> color #1 bychain
> close #1
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_8/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> color #1 bychain
> close #1
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_9/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> color #1 bychain
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> select #1/A:17
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:17
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:5-11
59 atoms, 59 bonds, 7 residues, 1 model selected
> select #1/B:23
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:23-24
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/B:76
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:76
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:88
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/B:88
4 atoms, 3 bonds, 1 residue, 1 model selected
> close #1
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_10/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> color #1 bychain
> close #1
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_11/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
> color #1 bychain
> close #1
> close
> open "/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23
> CRAMP1 SANT domain residues
> mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> color bychain
Alignment identifier is 1/A
Alignment identifier is 1/B
> select /B:11
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:11
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide #1 models
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_7/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
> color #2 bychain
> hide #2 target m
> close #2
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_6/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
> color #2 bychain
Alignment identifier is 1/B
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A
261 atoms, 263 bonds, 33 residues, 1 model selected
> close #2
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_5/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
> color #2 bychain
> close #2
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_8/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
> color #2 bychain
> close #2
> show #1 models
> select /B:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:6-8
26 atoms, 25 bonds, 3 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:658
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:658
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:563-564
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:532-563
233 atoms, 239 bonds, 32 residues, 1 model selected
> select /A:658
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:658-664
57 atoms, 57 bonds, 7 residues, 1 model selected
> select /A:665-666
18 atoms, 18 bonds, 2 residues, 1 model selected
> select /A:665-666
18 atoms, 18 bonds, 2 residues, 1 model selected
> select /A:658
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:658-665
65 atoms, 65 bonds, 8 residues, 1 model selected
> select /A:669
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:662-669
69 atoms, 70 bonds, 8 residues, 1 model selected
> select /A:639
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:639-669
254 atoms, 259 bonds, 31 residues, 1 model selected
> select /A:669
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:648-669
174 atoms, 179 bonds, 22 residues, 1 model selected
> select /A:639-640
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:639-643
44 atoms, 43 bonds, 5 residues, 1 model selected
> select /A:669
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:648-669
174 atoms, 179 bonds, 22 residues, 1 model selected
> ui tool show AlphaFold
> alphafold predict
> LPSSFPAGMDVDKFLLSLHYDE,ESWSTEDKNTFFEGLYEHGKDFEAIQNNIALKYKKKGKPASMVKNKEQVRHFYYRTWHKITKYIDFD
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> close
AlphaFold prediction finished
Results in /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_12
> open /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_12/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> color bychain
> alphafold pae #1 file
> /Users/enaden/Downloads/ChimeraX/AlphaFold/prediction_12/best_model_pae.json
> alphafold contacts
Missing or invalid "residues" argument: empty atom specifier
> alphafold contacts /AA
No residues specified for alphafold contacts
> alphafold contacts /A
Alignment identifier is 1/A
Alignment identifier is 1/B
> select /A:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> open "/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23
> CRAMP1 SANT domain residues
> mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model.pdb"
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> select #1/B:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:5-67
545 atoms, 560 bonds, 63 residues, 1 model selected
> select #1/B:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:5-67
545 atoms, 560 bonds, 63 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 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 best_model.pdb, chain B (#1) with best_model.pdb, chain B (#2),
sequence alignment score = 362.2
RMSD between 66 pruned atom pairs is 0.528 angstroms; (across all 67 pairs:
0.627)
> color sel bychain
> hide #!1 models
> color #2 bychain
> alphafold contacts /A /B
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> select add #1
754 atoms, 776 bonds, 12 pseudobonds, 89 residues, 2 models selected
> select subtract #1
Nothing selected
> alphafold contacts /A /B
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> close #1
> close
> open "/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23
> CRAMP1 SANT domain residues
> mutagenesis/AlphaFold/prediction_11/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
> close
> open "/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23
> CRAMP1 SANT domain residues
> mutagenesis/AlphaFold/SANT_NPAT_Cterm_short/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> color bychain
> alphafold pae #1 file "/Users/enaden/Documents/Cambridge Year 4/Part III
> Project/3_10_23 CRAMP1 SANT domain residues
> mutagenesis/AlphaFold/SANT_NPAT_Cterm_short/best_model_pae.json"
> alphafold contacts /A /B
Alignment identifier is 1/A
Alignment identifier is 1/B
> select /B:12
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:12
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:16
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:16-17
21 atoms, 21 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select /B:54
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:54
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:53
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:53
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> open "/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23
> CRAMP1 SANT domain residues
> mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model.pdb"
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
> hide #!1 models
> color #2 bychain
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 file "/Users/enaden/Documents/Cambridge Year 4/Part III
> Project/3_10_23 CRAMP1 SANT domain residues
> mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model_pae.json"
Number of residues in structure "best_model.pdb #1" is 89 which does not match
PAE matrix size 739.
This can happen if chains were deleted from the AlphaFold model or if the PAE
data was applied to a structure that was not the one predicted by AlphaFold.
Use the full-length AlphaFold model to show predicted aligned error.
> alphafold pae #1 file "/Users/enaden/Documents/Cambridge Year 4/Part III
> Project/3_10_23 CRAMP1 SANT domain residues
> mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model_pae.json"
Number of residues in structure "best_model.pdb #1" is 89 which does not match
PAE matrix size 739.
This can happen if chains were deleted from the AlphaFold model or if the PAE
data was applied to a structure that was not the one predicted by AlphaFold.
Use the full-length AlphaFold model to show predicted aligned error.
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file "/Users/enaden/Documents/Cambridge Year 4/Part III
> Project/3_10_23 CRAMP1 SANT domain residues
> mutagenesis/AlphaFold/SANT_NPAT_Cterm/best_model_pae.json"
> alphafold contacts /A /B
Interface PAE pseudobonds can only be computed for a single structure, got 2.
> close #1
> alphafold contacts /A /B
Alignment identifier is 2/A
Alignment identifier is 2/B
> select /B:12
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:12
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:53
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:53
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:56
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> close #2
> open "/Users/enaden/Documents/Cambridge Year 4/Part III Project/3_10_23
> CRAMP1 SANT domain residues
> mutagenesis/AlphaFold/SANT_NPAT_Cterm_short/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> color bychain
> open "/Users/enaden/Documents/Cambridge Year 4/Part III Project/2024 2 12
> CRAMP1 DUF UBL mutants/DUF_NPAT_Cterm/best_model.pdb"
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
> close #2
> open "/Users/enaden/Documents/Cambridge Year 4/Part III Project/2024 2 12
> CRAMP1 DUF UBL mutants/DUF/best_model.pdb"
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 2/A
> select #1/B:4-5
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/B:4-61
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.8.5
OpenGL renderer: Intel(R) UHD Graphics 617
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir8,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.6 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0)
OS Loader Version: 540.120.3~22
Software:
System Software Overview:
System Version: macOS 12.6 (21G115)
Kernel Version: Darwin 21.6.0
Time since boot: 17 days 19:00
Graphics/Displays:
Intel UHD Graphics 617:
Chipset Model: Intel UHD Graphics 617
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x87c0
Revision ID: 0x0002
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
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: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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