![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 17 months ago
Closed 17 months ago
#15372 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-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.8rc202405171936 (2024-05-17 19:36:10 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000003853a7000 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001facebac0 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py", line 575 in __init__
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1616 in remove_deleted_pointers
File "/Applications/ChimeraX-1.8-rc2024.05.17.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-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1065 in __init__
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2245 in process_changes
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2251 in changes
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 69 in draw_new_frame
File "/Applications/ChimeraX-1.8-rc2024.05.17.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-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 285 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
File "/Applications/ChimeraX-1.8-rc2024.05.17.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 58)
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===== Log before crash start =====
UCSF ChimeraX version: 1.8rc202405170741 (2024-05-17)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/maryam/Downloads/6k3f.pdb
6k3f.pdb title:
Crystal structure of β-arrestin 2 In complex with CXCR7 phosphopeptide [more
info...]
Chain information for 6k3f.pdb #1
---
Chain | Description | UniProt
A B C D E F | arrestin β-2 | ARRB2_RAT 1-356
U V W X Y Z | peptide from atypical chemokine receptor 3 | ACKR3_HUMAN 331-345
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 16746 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> ui tool show "Show Sequence Viewer"
> sequence chain /A /B /C /D /E /F
Alignment identifier is 1
> select clear
> select /A,C-D,F:280-350/B,E:280-346
3198 atoms, 3228 bonds, 418 residues, 1 model selected
> select /A,C-D,F:8-350/B,E:8-346
16176 atoms, 16535 bonds, 2 pseudobonds, 2038 residues, 2 models selected
> show (#!1 & sel) target ab
> hide (#!1 & sel) target a
> color (#!1 & sel) yellow
> undo
> select add #1
17270 atoms, 17104 bonds, 2 pseudobonds, 2629 residues, 2 models selected
> select subtract #1
Nothing selected
> open /Users/maryam/Downloads/8j9k.pdb
8j9k.pdb title:
Structure of basal β-ARRESTIN2 [more info...]
Chain information for 8j9k.pdb #2
---
Chain | Description | UniProt
B | FAB6 light chain |
C | arrestin β-2 | ARRB2_RAT 6-399
D | FAB6 heavy chain |
> 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 6k3f.pdb, chain D (#1) with 8j9k.pdb, chain C (#2), sequence
alignment score = 1568.9
RMSD between 194 pruned atom pairs is 1.276 angstroms; (across all 342 pairs:
2.819)
> open /Users/maryam/Downloads/8hst.pdb
8hst.pdb title:
The structure of rat β-ARRESTIN1 [more info...]
Chain information for 8hst.pdb #3
---
Chain | Description | UniProt
A B | arrestin β-1 | ARRB1_RAT 1-394
> hide #!1 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/U #1/V #1/W #1/X #1/Y #1/Z
Alignment identifier is 1
> open /Users/maryam/Downloads/8hsv.pdb
8hsv.pdb title:
The structure of rat β-ARRESTIN1 In complex with A rat MDM2 peptide [more
info...]
Chain information for 8hsv.pdb #4
---
Chain | Description | UniProt
A B | arrestin β-1 | ARRB1_RAT 1-394
E F | peptide from E3 ubiquitin-protein ligase MDM2 | D3ZVH5_RAT 210-227
Non-standard residues in 8hsv.pdb #4
---
SO4 — sulfate ion
> hide #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/E #4/F
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #3/B #4/A #4/B
Alignment identifier is 2
> select #3/A-B:394 #4/A-B:394
36 atoms, 32 bonds, 4 residues, 2 models selected
> select #3/A-B:4-394 #4/A-B:4-394
11506 atoms, 11742 bonds, 8 pseudobonds, 1448 residues, 4 models selected
Arrestin Β-1 [ID: 2] region 4 chains [1-414] RMSD: 47.103
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> open
> /Users/maryam/Downloads/fold_bai1_vdv_2024_06_02_04_50/fold_bai1_vdv_2024_06_02_04_50_model_0.cif
Chain information for fold_bai1_vdv_2024_06_02_04_50_model_0.cif #5
---
Chain | Description
A | .
> ui tool show Matchmaker
> matchmaker #!4 to #5
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_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with
8hsv.pdb, chain E (#4), sequence alignment score = 28.6
RMSD between 4 pruned atom pairs is 1.633 angstroms; (across all 15 pairs:
8.627)
> color #4 #711decff
> set bgColor white
> color #4 #49278aff
> color #4 #47268aff
> color #5 #ef6051ff
> color #5 #ef725fff
> color #5 #ef735fff
> color #5 #ef6150ff
> color #5 #232eefff
> color #5 #ef7c7bff
> color #5 #ef6056ff
> color #5 #ef7078ff
> color #5 #ef6b62ff
> color #4 #322896ff
> select add #4/A:502@O4
5759 atoms, 5880 bonds, 4 pseudobonds, 723 residues, 3 models selected
> select add #4/A:501@S
5760 atoms, 5883 bonds, 4 pseudobonds, 724 residues, 3 models selected
> select add #4/A:501@O3
5761 atoms, 5886 bonds, 4 pseudobonds, 724 residues, 3 models selected
> select add #4/A:501@O4
5762 atoms, 5886 bonds, 4 pseudobonds, 724 residues, 3 models selected
> select add #4/A:502@O1
5763 atoms, 5887 bonds, 4 pseudobonds, 724 residues, 3 models selected
> select subtract #4/A:502@O4
5762 atoms, 5887 bonds, 4 pseudobonds, 724 residues, 3 models selected
> select add #4/A:503@O3
5763 atoms, 5887 bonds, 4 pseudobonds, 725 residues, 3 models selected
> select add #4/A:503@O4
5764 atoms, 5886 bonds, 4 pseudobonds, 725 residues, 3 models selected
> select subtract #4/A:503@O4
5763 atoms, 5886 bonds, 4 pseudobonds, 725 residues, 3 models selected
> select add #4/B:502@O2
5764 atoms, 5889 bonds, 4 pseudobonds, 726 residues, 3 models selected
> select add #4/B:501@O2
5765 atoms, 5891 bonds, 4 pseudobonds, 727 residues, 3 models selected
> select add #4/E:219
5771 atoms, 5896 bonds, 4 pseudobonds, 728 residues, 3 models selected
> select add #4/E:218
5781 atoms, 5906 bonds, 4 pseudobonds, 729 residues, 3 models selected
> select add #4/E:216
5787 atoms, 5911 bonds, 4 pseudobonds, 730 residues, 3 models selected
> select add #4/E:215
5794 atoms, 5917 bonds, 4 pseudobonds, 731 residues, 3 models selected
> select add #4/E:214
5798 atoms, 5920 bonds, 4 pseudobonds, 732 residues, 3 models selected
> select add #4/E:213
5806 atoms, 5927 bonds, 4 pseudobonds, 733 residues, 3 models selected
> select add #4/E:211
5814 atoms, 5934 bonds, 4 pseudobonds, 734 residues, 3 models selected
> select add #4/E:212
5822 atoms, 5941 bonds, 4 pseudobonds, 735 residues, 3 models selected
> select add #4/E:217
5830 atoms, 5948 bonds, 4 pseudobonds, 736 residues, 3 models selected
> select add #4/E:220
5835 atoms, 5952 bonds, 4 pseudobonds, 737 residues, 3 models selected
> select add #4/E:221
5843 atoms, 5959 bonds, 4 pseudobonds, 738 residues, 3 models selected
> select add #4/E:222
5849 atoms, 5964 bonds, 4 pseudobonds, 739 residues, 3 models selected
> select add #4/E:223
5857 atoms, 5971 bonds, 4 pseudobonds, 740 residues, 3 models selected
> select add #4/E:224
5865 atoms, 5978 bonds, 4 pseudobonds, 741 residues, 3 models selected
> select add #4/E:225
5874 atoms, 5986 bonds, 4 pseudobonds, 742 residues, 3 models selected
> select add #4/F:225
5883 atoms, 5994 bonds, 4 pseudobonds, 743 residues, 3 models selected
> select add #4/F:224
5891 atoms, 6001 bonds, 4 pseudobonds, 744 residues, 3 models selected
> select add #4/F:223
5899 atoms, 6008 bonds, 4 pseudobonds, 745 residues, 3 models selected
> select add #4/F:221
5907 atoms, 6015 bonds, 4 pseudobonds, 746 residues, 3 models selected
> select add #4/F:222
5913 atoms, 6020 bonds, 4 pseudobonds, 747 residues, 3 models selected
> select add #4/F:216
5919 atoms, 6025 bonds, 4 pseudobonds, 748 residues, 3 models selected
> select add #4/F:214
5923 atoms, 6028 bonds, 4 pseudobonds, 749 residues, 3 models selected
> select add #4/F:215
5930 atoms, 6034 bonds, 4 pseudobonds, 750 residues, 3 models selected
> select add #4/F:213
5938 atoms, 6041 bonds, 4 pseudobonds, 751 residues, 3 models selected
> select add #4/F:212
5946 atoms, 6048 bonds, 4 pseudobonds, 752 residues, 3 models selected
> show (#!4 & sel) target ab
> hbonds sel & #!4 reveal true
7 hydrogen bonds found
> select sel : hbonds sel & #5#!4 reveal true
282 hydrogen bonds found
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:1-589
4439 atoms, 4559 bonds, 17 pseudobonds, 589 residues, 2 models selected
> delete :1-928
> delete :1208-1584
> open /Users/maryam/Downloads/8hsv.pdb
8hsv.pdb title:
The structure of rat β-ARRESTIN1 In complex with A rat MDM2 peptide [more
info...]
Chain information for 8hsv.pdb #1
---
Chain | Description | UniProt
A B | arrestin β-1 | ARRB1_RAT 1-394
E F | peptide from E3 ubiquitin-protein ligase MDM2 | D3ZVH5_RAT 210-227
Non-standard residues in 8hsv.pdb #1
---
SO4 — sulfate ion
> ui tool show Matchmaker
> matchmaker #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 8hsv.pdb, chain E (#1) with
fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5), sequence alignment
score = 16.6
RMSD between 4 pruned atom pairs is 1.484 angstroms; (across all 15 pairs:
12.815)
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B
Alignment identifier is 1
> select #1/A-B:394
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A-B:4-394
5748 atoms, 5866 bonds, 4 pseudobonds, 726 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> ui tool show Matchmaker
> matchmaker #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 8hsv.pdb, chain E (#1) with
fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5), sequence alignment
score = 16.6
RMSD between 4 pruned atom pairs is 1.484 angstroms; (across all 15 pairs:
12.815)
> select #5/A:971
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:971
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel yellow
> select #5/A:971
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:971
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> open /Users/maryam/Downloads/1rv1.pdb
1rv1.pdb title:
Crystal structure of human MDM2 with an imidazoline inhibitor [more info...]
Chain information for 1rv1.pdb #2
---
Chain | Description | UniProt
A B C | ubiquitin-protein ligase E3 MDM2 | MDM2_HUMAN 25-109
Non-standard residues in 1rv1.pdb #2
---
IMZ —
cis-[4,5-bis-(4-bromophenyl)-2-(2-ethoxy-4-methoxyphenyl)-4,5-dihydroimidazol-1-yl]-[4-(2-hydroxyethyl)piperazin-1-yl]methanone
> open /Users/maryam/Downloads/1ycr.pdb
1ycr.pdb title:
MDM2 bound to the transactivation domain of P53 [more info...]
Chain information for 1ycr.pdb #3
---
Chain | Description | UniProt
A | MDM2 | MDM2_HUMAN 17-125
B | P53 | P53_HUMAN 15-29
> open /Users/maryam/Downloads/4hfz.pdb
4hfz.pdb title:
Crystal structure of an MDM2/P53 peptide complex [more info...]
Chain information for 4hfz.pdb #4
---
Chain | Description | UniProt
A C | E3 ubiquitin-protein ligase MDM2 | MDM2_HUMAN 17-125
B D | cellular tumor antigen P53 | P53_HUMAN 15-29
Non-standard residues in 4hfz.pdb #4
---
SO4 — sulfate ion
> open /Users/maryam/Downloads/4hg7.pdb
4hg7.pdb title:
Crystal structure of an MDM2/nutlin-3A complex [more info...]
Chain information for 4hg7.pdb #7
---
Chain | Description | UniProt
A | E3 ubiquitin-protein ligase MDM2 | MDM2_HUMAN 17-108
Non-standard residues in 4hg7.pdb #7
---
NUT —
4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one
(nutlin 3A)
SO4 — sulfate ion
46 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/maryam/Downloads/6i3s.pdb
6i3s.pdb title:
Crystal structure of MDM2 In complex with compound 13. [more info...]
Chain information for 6i3s.pdb #8
---
Chain | Description | UniProt
A | E3 ubiquitin-protein ligase MDM2 | MDM2_HUMAN 18-111
Non-standard residues in 6i3s.pdb #8
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
H28 —
(3~{S},3'~{R},3'~{A}~{S},6'~{A}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-
phenyl)-1'-(cyclopropylmethyl)spiro[1~{H}-indole-3,2'-3~{A},6~{A}-dihydro-3~{H}-pyrrolo[3,4-B]pyrrole]-2,4'-dione
SO4 — sulfate ion
22 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/maryam/Downloads/6k3f.pdb
6k3f.pdb title:
Crystal structure of β-arrestin 2 In complex with CXCR7 phosphopeptide [more
info...]
Chain information for 6k3f.pdb #9
---
Chain | Description | UniProt
A B C D E F | arrestin β-2 | ARRB2_RAT 1-356
U V W X Y Z | peptide from atypical chemokine receptor 3 | ACKR3_HUMAN 331-345
> open /Users/maryam/Downloads/8goc.pdb
8goc.pdb title:
Structure of β-ARRESTIN2 In complex with A phosphopeptide corresponding to the
human vasopressin V2 receptor, V2R [more info...]
Chain information for 8goc.pdb #10
---
Chain | Description | UniProt
A B C | β-arrestin-2 | ARRB2_BOVIN 1-420
D H M | FAB30 heavy chain |
E L N | FAB30 light chain |
G U V | vasopressin V2 receptor | V2R_HUMAN 343-371
> hide #4 models
> show #4 models
> select add #9
17278 atoms, 17111 bonds, 2 pseudobonds, 2630 residues, 3 models selected
> select subtract #9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #9
17278 atoms, 17111 bonds, 2 pseudobonds, 2630 residues, 3 models selected
> select subtract #9
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> close #9
> hide #!10 models
> show #!10 models
> close #10
> ui tool show Matchmaker
> matchmaker #2-4,7-8#!1 to #5
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_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with
1rv1.pdb, chain C (#2), sequence alignment score = 35.9
RMSD between 14 pruned atom pairs is 1.528 angstroms; (across all 83 pairs:
16.069)
Matchmaker fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with
1ycr.pdb, chain A (#3), sequence alignment score = 31.6
RMSD between 12 pruned atom pairs is 1.257 angstroms; (across all 78 pairs:
15.063)
Matchmaker fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with
4hfz.pdb, chain C (#4), sequence alignment score = 29.3
RMSD between 14 pruned atom pairs is 1.338 angstroms; (across all 84 pairs:
15.804)
Matchmaker fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with
4hg7.pdb, chain A (#7), sequence alignment score = 29.8
RMSD between 13 pruned atom pairs is 1.233 angstroms; (across all 85 pairs:
15.415)
Matchmaker fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with
6i3s.pdb, chain A (#8), sequence alignment score = 16
RMSD between 11 pruned atom pairs is 0.785 angstroms; (across all 94 pairs:
20.863)
Matchmaker fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5) with
8hsv.pdb, chain E (#1), sequence alignment score = 16.6
RMSD between 4 pruned atom pairs is 1.484 angstroms; (across all 15 pairs:
12.815)
> zoom 3
> hide #!1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #4 models
> show #3 models
> show #5 models
> hide #4 models
> hide #3 models
> hide #7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> open "/Users/maryam/Downloads/fold_bai1_wt_2024_06_01_10_49
> 2/fold_bai1_wt_2024_06_01_10_49_model_0.cif"
Chain information for fold_bai1_wt_2024_06_01_10_49_model_0.cif #9
---
Chain | Description
A | .
> ui tool show Matchmaker
> 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 6i3s.pdb, chain A (#8) with
fold_bai1_wt_2024_06_01_10_49_model_0.cif, chain A (#9), sequence alignment
score = 28
RMSD between 16 pruned atom pairs is 0.909 angstroms; (across all 77 pairs:
16.729)
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #5 models
> hide #8 models
> show #9 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:928
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A:181-928
5723 atoms, 5860 bonds, 748 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/A:1206
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/A:1206-1584
2918 atoms, 3007 bonds, 379 residues, 1 model selected
> select #9/A:1207
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:1207-1210
26 atoms, 25 bonds, 4 residues, 1 model selected
> select #9/A:1206
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/A:1206-1584
2918 atoms, 3007 bonds, 379 residues, 1 model selected
> select #9/A:1540-1584
360 atoms, 368 bonds, 45 residues, 1 model selected
> select #9/A:1207-1584
2914 atoms, 3003 bonds, 378 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:1-180
1385 atoms, 1425 bonds, 180 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #8 models
> show #5 models
> ui tool show Matchmaker
> matchmaker #5,7#!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 6i3s.pdb, chain A (#8) with
fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5), sequence alignment
score = 16
RMSD between 11 pruned atom pairs is 0.785 angstroms; (across all 94 pairs:
20.863)
Matchmaker 6i3s.pdb, chain A (#8) with 4hg7.pdb, chain A (#7), sequence
alignment score = 434.4
RMSD between 83 pruned atom pairs is 0.742 angstroms; (across all 91 pairs:
1.240)
Matchmaker 6i3s.pdb, chain A (#8) with
fold_bai1_wt_2024_06_01_10_49_model_0.cif, chain A (#9), sequence alignment
score = 16
RMSD between 11 pruned atom pairs is 1.015 angstroms; (across all 94 pairs:
21.177)
> hide #!9 models
> show #!9 models
> hide #5 models
> select #9/A:971
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/A:971
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel target ab
> select #5/A:971
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:971
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #5 models
> show sel target ab
> tile
3 models tiled
> select clear
> select #9/A:971
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/A:971
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel yellow
> ui tool show Matchmaker
> matchmaker #5,7#!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 6i3s.pdb, chain A (#8) with
fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5), sequence alignment
score = 16
RMSD between 11 pruned atom pairs is 0.785 angstroms; (across all 94 pairs:
20.863)
Matchmaker 6i3s.pdb, chain A (#8) with 4hg7.pdb, chain A (#7), sequence
alignment score = 434.4
RMSD between 83 pruned atom pairs is 0.742 angstroms; (across all 91 pairs:
1.240)
Matchmaker 6i3s.pdb, chain A (#8) with
fold_bai1_wt_2024_06_01_10_49_model_0.cif, chain A (#9), sequence alignment
score = 16
RMSD between 11 pruned atom pairs is 1.015 angstroms; (across all 94 pairs:
21.177)
> hide #5 models
> hide #!9 models
> ui tool show Matchmaker
> 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 6i3s.pdb, chain A (#8) with
fold_bai1_wt_2024_06_01_10_49_model_0.cif, chain A (#9), sequence alignment
score = 16
RMSD between 11 pruned atom pairs is 1.015 angstroms; (across all 94 pairs:
21.177)
> show #!9 models
> move y -100
> move y +20
> move y +5
> hbonds sel reveal true
2 hydrogen bonds found
> hbonds sel reveal true
2 hydrogen bonds found
> select #8/A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:107
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:107-111
38 atoms, 37 bonds, 5 residues, 1 model selected
> select #8/A:111
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:18-111
774 atoms, 789 bonds, 94 residues, 1 model selected
> select sel : hbonds sel & #8#!9 reveal true
606 hydrogen bonds found
> open /Users/maryam/Downloads/7wcn.pdb
7wcn.pdb title:
Cryo-em structure of GPR119-GS complex with small molecule agonist AR231453
[more info...]
Chain information for 7wcn.pdb #10
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394
B | transducin β chain 1 | GBB1_HUMAN 13-351
C | G γ-I | GBG2_HUMAN 1-71
N | NB35 |
R | G-protein coupled receptor 119 | GP119_HUMAN 1-335
Non-standard residues in 7wcn.pdb #10
---
8WL — N-(2-fluoranyl-4-methylsulfonyl-
phenyl)-5-nitro-6-[4-(3-propan-2-yl-1,2,4-oxadiazol-5-yl)piperidin-1-yl]pyrimidin-4-amine
(AR231453)
> hide #!9 models
> hide #8 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8217 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> ui tool show "Show Sequence Viewer"
> show #!9 models
> show #5 models
> ui tool show Matchmaker
> matchmaker #5,7-8#!9 to #10
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 7wcn.pdb, chain R (#10) with
fold_bai1_vdv_2024_06_02_04_50_model_0.cif, chain A (#5), sequence alignment
score = 268.8
RMSD between 56 pruned atom pairs is 0.940 angstroms; (across all 258 pairs:
8.524)
Matchmaker 7wcn.pdb, chain A (#10) with 4hg7.pdb, chain A (#7), sequence
alignment score = 36.9
RMSD between 6 pruned atom pairs is 1.405 angstroms; (across all 68 pairs:
19.462)
Matchmaker 7wcn.pdb, chain A (#10) with 6i3s.pdb, chain A (#8), sequence
alignment score = 31.4
RMSD between 9 pruned atom pairs is 0.409 angstroms; (across all 79 pairs:
17.047)
Matchmaker 7wcn.pdb, chain R (#10) with
fold_bai1_wt_2024_06_01_10_49_model_0.cif, chain A (#9), sequence alignment
score = 271.6
RMSD between 55 pruned atom pairs is 0.883 angstroms; (across all 258 pairs:
8.528)
> hide #5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #10/A
Alignment identifier is 10/A
> sequence chain #10/B
Alignment identifier is 10/B
> sequence chain #10/C
Alignment identifier is 10/C
> sequence chain #10/N
Alignment identifier is 10/N
> select clear
> select #10/N
973 atoms, 994 bonds, 128 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #10/B:351
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/B:46-351
2346 atoms, 2393 bonds, 306 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> delete atoms #6,9-10
> delete bonds #6,9-10
> open /Users/maryam/Downloads/7wcn.pdb
7wcn.pdb title:
Cryo-em structure of GPR119-GS complex with small molecule agonist AR231453
[more info...]
Chain information for 7wcn.pdb #9
---
Chain | Description | UniProt
A | adenylate cyclase-stimulating G α protein | GNAS2_HUMAN 1-394
B | transducin β chain 1 | GBB1_HUMAN 13-351
C | G γ-I | GBG2_HUMAN 1-71
N | NB35 |
R | G-protein coupled receptor 119 | GP119_HUMAN 1-335
Non-standard residues in 7wcn.pdb #9
---
8WL — N-(2-fluoranyl-4-methylsulfonyl-
phenyl)-5-nitro-6-[4-(3-propan-2-yl-1,2,4-oxadiazol-5-yl)piperidin-1-yl]pyrimidin-4-amine
(AR231453)
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8217 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select #9/B:13-351
2606 atoms, 2653 bonds, 339 residues, 1 model selected
> sequence chain #9/B
Alignment identifier is 9/B
> select #9/B:351
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B
2606 atoms, 2653 bonds, 339 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/N:1-128
973 atoms, 994 bonds, 128 residues, 1 model selected
> sequence chain #9/N
Alignment identifier is 9/N
> select clear
> select #9/N
973 atoms, 994 bonds, 128 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/A:9-394
1947 atoms, 1983 bonds, 2 pseudobonds, 235 residues, 2 models selected
> sequence chain #9/A
Alignment identifier is 9/A
> sequence chain #9/B
Chains must have same sequence
> select #9/B:13-351
Nothing selected
> select #9/B:13-351
Nothing selected
> sequence chain #9/B
Chains must have same sequence
> sequence chain #9/C
Alignment identifier is 9/C
> select clear
> select #9/C
451 atoms, 457 bonds, 58 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #9/A:9-286
1048 atoms, 1062 bonds, 2 pseudobonds, 127 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Destroying pre-existing alignment with identifier 9/A
Alignment identifier is 9/A
> sequence chain #9/R
Alignment identifier is 9/R
> select clear
> select #9/R:5-300
2240 atoms, 2295 bonds, 1 pseudobond, 289 residues, 2 models selected
> delete atoms (#!9 & sel)
> delete bonds (#!9 & sel)
> select clear
> sequence chain #9/B
Chains must have same sequence
> select add #9/R:401@C26
1 atom, 13 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #9/R:401@O6
1 atom, 1 residue, 1 model selected
> select add #9/R:401@C8
2 atoms, 1 residue, 1 model selected
> select add #9/R:401@C1
3 atoms, 1 residue, 1 model selected
> select add #9/R:401@C16
4 atoms, 4 bonds, 1 residue, 1 model selected
> select add #9/R:401@O24
5 atoms, 8 bonds, 1 residue, 1 model selected
> select add #9/R:401@C23
6 atoms, 8 bonds, 1 residue, 1 model selected
> select add #9/R:401@O25
7 atoms, 8 bonds, 1 residue, 1 model selected
> select add #9/R:401@O31
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #9/R:401@N30
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #9/R:401@O32
10 atoms, 8 bonds, 1 residue, 1 model selected
> select add #9/R:401@C3
11 atoms, 8 bonds, 1 residue, 1 model selected
> select add #9/R:401@C10
12 atoms, 8 bonds, 1 residue, 1 model selected
> select add #9/R:401@C4
13 atoms, 8 bonds, 1 residue, 1 model selected
> select add #9/R:401@C9
14 atoms, 8 bonds, 1 residue, 1 model selected
> select add #9/R:401@N5
15 atoms, 9 bonds, 1 residue, 1 model selected
> select add #9/R:401@C14
16 atoms, 9 bonds, 1 residue, 1 model selected
> select add #9/R:401@C29
17 atoms, 9 bonds, 1 residue, 1 model selected
> select add #9/R:401@C27
18 atoms, 9 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #9/R:401@C20
1 atom, 1 residue, 1 model selected
> select add #9/R:401@C19
2 atoms, 1 residue, 1 model selected
> select add #9/R:401@C33
3 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@C34
4 atoms, 1 bond, 1 residue, 1 model selected
> select subtract #9/R:401@C34
3 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@C34
4 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@C7
5 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@N35
6 atoms, 1 bond, 1 residue, 1 model selected
> select subtract #9/R:401@C7
5 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@C7
6 atoms, 1 bond, 1 residue, 1 model selected
> select subtract #9/R:401@N35
5 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@C2
6 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@N13
7 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@C12
8 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@F28
9 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@N15
10 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@N11
11 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@N17
12 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@C18
13 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@C21
14 atoms, 1 bond, 1 residue, 1 model selected
> select add #9/R:401@S22
15 atoms, 1 bond, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #9/R:401@N35
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8rc202405170741 (2024-05-17)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
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: Mac15,6
Model Number: Z1AX00298LL/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 13 hours, 49 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
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: 0.1.4
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: 1.6.3
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
ChimeraX-AtomicLibrary: 14.0.5
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: 1.2.4
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: 1.0.4
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: 1.8rc202405170741
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: 1.2.3
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
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
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: 1.13.4
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: 3.0.3
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: 1.16.4
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
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
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: 4.51.0
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: 8.1.2
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
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: 3.0.43
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
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 17 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 , 17 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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