![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 hours ago
#20334 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.3.2-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000203847100 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, chimerax.surface._surface, PIL._imaging, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, pyKVFinder._pyKVFinder (total: 60)
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"procLaunch" : "2026-05-16 00:16:34.0988 +0800",
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"appleIntelligenceStatus" : {"reasons":["regionIneligible","countryLocationIneligible","selectedLanguageDoesNotMatchSelectedSiriLanguage","selectedLanguageDoesNotMatchSelectedSiriLanguageInfo(system: zh, siri: en-GB)"],"state":"unavailable"},
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4331618296
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 1022f4000-1022f8000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":39987},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4331618296
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/fahn/Desktop/2026-01/20240323_4u9l_TM1TM2loopRemodeling_for_Hattori-
> sensei
> 2/ColabFold/good_structures/d923_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"
> format pdb
Chain information for
d923_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1
---
Chain | Description
A B | No description available
Computing secondary structure
> select add #1
2684 atoms, 2712 bonds, 346 residues, 1 model selected
> hide sel atoms
> style sel ball
Changed 2684 atom styles
> select subtract #1
Nothing selected
> select add #1
2684 atoms, 2712 bonds, 346 residues, 1 model selected
> select subtract #1
Nothing selected
> color #1 #0096ffff
> color #1 #d4fb79ff
> color #1 #73fcd6ff
> color #1 #ff8ad8ff
> color #1 #ff7e79ff
> show cartoons
> show atoms
> hide atoms
> style stick
Changed 2684 atom styles
> style sphere
Changed 2684 atom styles
> volume planes z style image imageMode "full region"
No volumes specified
> volume showOutlineBox true
No volumes specified
> volume showOutlineBox true
No volumes specified
> view orient
> volume step 2
No volumes specified
> volume step 1
No volumes specified
> ui mousemode right "tape measure"
> marker segment #2 position 6.684,-4.699,6.742 toPosition 6.684,-4.699,6.742
> color yellow radius 0.1 label 0 labelHeight 0.2 labelColor yellow
> select add #1
2684 atoms, 2712 bonds, 346 residues, 1 model selected
> volume showOutlineBox true
No volumes specified
> ui mousemode right "tape measure"
> ui mousemode right windowing
> segmentations mouseModes true
> ui mousemode shift wheel 'resize segmentation cursor'
> ui mousemode right 'create segmentations'
> ui mousemode shift right 'erase segmentations'
> ui mousemode shift middle 'move segmentation cursor'
> select subtract #1
Nothing selected
> volume projectionMode 2d-xyz
No volumes specified
> volume appearance airways
No volumes specified
> ui mousemode right "crop volume"
> ui mousemode right "tape measure"
> segmentations mouseModes false
> ui mousemode shift wheel 'none'
> ui mousemode right 'windowing'
> ui mousemode shift right 'none'
> ui mousemode shift middle 'none'
> segmentations mouseModes true
> ui mousemode shift wheel 'resize segmentation cursor'
> ui mousemode right 'create segmentations'
> ui mousemode shift right 'erase segmentations'
> ui mousemode shift middle 'move segmentation cursor'
> ui mousemode right "tape measure"
> select clear
> select #1/A:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:117
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select #1/A:113
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right select
> ui mousemode right "tape measure"
> marker delete #2
> open /Users/fahn/Desktop/2026-01/SSRF-20251218_refine_10-dimer.pdb
Summary of feedback from opening
/Users/fahn/Desktop/2026-01/SSRF-20251218_refine_10-dimer.pdb
---
note | Combining 2 symmetry atoms into CA /C:2 CA
Chain information for SSRF-20251218_refine_10-dimer.pdb #2
---
Chain | Description
A E | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2/E to #1/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
d923_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B
(#1) with SSRF-20251218_refine_10-dimer.pdb, chain E (#2), sequence alignment
score = 876.3
RMSD between 173 pruned atom pairs is 0.473 angstroms; (across all 173 pairs:
0.473)
> open /Users/fahn/Desktop/2026-01/MgtE-sol-d940_refine_22-dimer.pdb
Chain information for MgtE-sol-d940_refine_22-dimer.pdb #3
---
Chain | Description
A C | No description available
54 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> ui tool show H-Bonds
> ui tool show Matchmaker
> open /Users/fahn/Desktop/2026-01/20240321_4u9l_redesign1_result_for_Hattori-
> sensei/ColabFold/good_designs/d940_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000_AB.pdb
Chain information for
d940_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000_AB.pdb #4
---
Chain | Description
A B | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #3/C to #4/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
d940_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000_AB.pdb, chain
B (#4) with MgtE-sol-d940_refine_22-dimer.pdb, chain C (#3), sequence
alignment score = 896.8
RMSD between 177 pruned atom pairs is 0.464 angstroms; (across all 177 pairs:
0.464)
> hide #1 models
> hide #2 models
> show #2 models
> hide #3 models
> hide #4 models
> show #3 models
> hide #2 models
> hide #3 models
> ui tool show Matchmaker
> matchmaker #4/B to #1/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
d923_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B
(#1) with
d940_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000_AB.pdb, chain
B (#4), sequence alignment score = 644.6
RMSD between 135 pruned atom pairs is 0.523 angstroms; (across all 173 pairs:
14.724)
> show #1 models
> show #2 models
> hide #2 models
> hide #1 models
> show #3 models
> show #4 models
> hide #4 models
> show #1 models
> hide #1 models
> hide #3 models
> show #4 models
> show #2 models
> hide #2 models
> show #1 models
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:8
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:8-35
229 atoms, 230 bonds, 28 residues, 1 model selected
> hide #1 models
> show #1 models
> hide #4 models
> hide #1 models
> show #4 models
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select #1/A:8
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:8-35
229 atoms, 230 bonds, 28 residues, 1 model selected
> select add #4
3025 atoms, 3060 bonds, 384 residues, 2 models selected
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> sequence chain #4/A,B
Alignment identifier is 1
> select #4/A:8/B:186
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #4/A:8-42/B:186-220
584 atoms, 588 bonds, 70 residues, 1 model selected
> show #1 models
> hide #1 models
> select #4/A:43-44/B:221-222
38 atoms, 40 bonds, 4 residues, 1 model selected
> select #4/A:43-45/B:221-223
56 atoms, 58 bonds, 6 residues, 1 model selected
> show #1 models
> hide #4 models
> select #1/A:8
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:8-35
229 atoms, 230 bonds, 28 residues, 1 model selected
> show #4 models
> select #1/A:40
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:40-69
225 atoms, 229 bonds, 30 residues, 1 model selected
> select
> #4/A:8-42,44-73,79-111,114-144,149-151,153-177/B:186-220,222-251,257-289,292-322,327-329,331-355
2474 atoms, 2494 bonds, 314 residues, 1 model selected
> select #4/A:44/B:222
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/A:44-73/B:222-251
434 atoms, 440 bonds, 60 residues, 1 model selected
> hide #1 models
> sequence chain #4/A,B
Alignment identifier is 1
> show #1 models
> select add #1
3118 atoms, 3152 bonds, 406 residues, 2 models selected
> select add #4
5480 atoms, 5542 bonds, 702 residues, 2 models selected
> hide #4 models
> select subtract #4
2684 atoms, 2712 bonds, 346 residues, 1 model selected
> sequence chain #1/A,B
Alignment identifier is 2
> select #4/A:8/B:186
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #4/A:8-42/B:186-220
584 atoms, 588 bonds, 70 residues, 1 model selected
> show #4 models
> select #4/A:44/B:222
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/A:44-73/B:222-251
434 atoms, 440 bonds, 60 residues, 1 model selected
> select #4/A:8/B:186
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #4/A:8-42/B:186-220
584 atoms, 588 bonds, 70 residues, 1 model selected
> select #1/A-B:8
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #1/A-B:8-36
482 atoms, 486 bonds, 58 residues, 1 model selected
> select #1/A-B:36
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #1/A-B:34-36
60 atoms, 60 bonds, 6 residues, 1 model selected
> select #1/A-B:8
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #1/A-B:8-35
458 atoms, 460 bonds, 56 residues, 1 model selected
> select #4/A:8-9/B:186-187
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #4/A:8-41/B:186-219
566 atoms, 570 bonds, 68 residues, 1 model selected
> select #1/A-B:8
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #1/A-B:8-35
458 atoms, 460 bonds, 56 residues, 1 model selected
> select #1/A-B:40
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A-B:40-68
434 atoms, 442 bonds, 58 residues, 1 model selected
> select #1/A-B:8
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #1/A-B:8-35
458 atoms, 460 bonds, 56 residues, 1 model selected
> hide #4 models
> select #1/A-B:40
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A-B:40-68
434 atoms, 442 bonds, 58 residues, 1 model selected
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #1 models
> show #1 models
> hide #4 models
> select #1/A-B:8-9
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #1/A-B:8-36
482 atoms, 486 bonds, 58 residues, 1 model selected
> select #1/A-B:40
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A-B:40-81
646 atoms, 654 bonds, 84 residues, 1 model selected
> select #1/A-B:73-74
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #1/A-B:68-74
114 atoms, 112 bonds, 14 residues, 1 model selected
> select #1/A-B:40
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A-B:40-67
416 atoms, 424 bonds, 56 residues, 1 model selected
> select #1/A-B:8
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #1/A-B:8-35
458 atoms, 460 bonds, 56 residues, 1 model selected
> hide #1 models
> show #4 models
> select #4/A:8-9/B:186-187
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #4/A:8-42/B:186-220
584 atoms, 588 bonds, 70 residues, 1 model selected
> select #4/A:44/B:222
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/A:44-73/B:222-251
434 atoms, 440 bonds, 60 residues, 1 model selected
> show #1 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #1 models
> show #4 models
> hide #4 models
> show #1 models
> hide #1 models
> show #4 models
> open /Applications/ChimeraX-1.11.1.app/
'/Applications/ChimeraX-1.11.1.app/' has no suffix
> show #1 models
> hide #1 models
> hide #4 models
> show #4 models
> show #2 models
> show #3 models
> hide #4 models
> select add #4
2796 atoms, 2830 bonds, 356 residues, 1 model selected
> select subtract #4
Nothing selected
> ui tool show Matchmaker
> matchmaker #3/C to #2/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker SSRF-20251218_refine_10-dimer.pdb, chain E (#2) with MgtE-
sol-d940_refine_22-dimer.pdb, chain C (#3), sequence alignment score = 635.4
RMSD between 135 pruned atom pairs is 0.755 angstroms; (across all 172 pairs:
14.868)
> select #1/B
1342 atoms, 1356 bonds, 173 residues, 1 model selected
> hide #2-3 cartoons
> show #2-3 cartoons
> hide #2 models
> hide #3 models
> show #3 models
> show #2 models
> select #3/C
1343 atoms, 1357 bonds, 178 residues, 1 model selected
> hide sel cartoons
> select #2/E
1331 atoms, 1345 bonds, 173 residues, 1 model selected
> hide sel cartoons
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #2 models
> hide #3 models
> show #1 models
> show #4 models
> save /Users/fahn/Desktop/vs.cxs
> close session
> open /Users/fahn/Desktop/vs.cxs format session
> view name session-start
opened ChimeraX session
> interfaces selAtoms
0 buried areas:
> hide #4 models
> hide #1 models
> show #2 models
> show #3 models
> hide #3 models
> show #3 models
> hide #2 models
> select #3/C
1343 atoms, 1357 bonds, 178 residues, 1 model selected
> hide sel atoms
> select #3/C
1343 atoms, 1357 bonds, 178 residues, 1 model selected
> hide #3 models
> show #3 models
> select ::name="SO4"
10 atoms, 10 bonds, 2 residues, 1 model selected
> select ::name="GOL"
32 atoms, 26 bonds, 6 residues, 1 model selected
> hide sel atoms
> select #3/C
1343 atoms, 1357 bonds, 178 residues, 1 model selected
> show sel cartoons
> select add #3
2905 atoms, 2740 bonds, 549 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
2905 atoms, 2740 bonds, 549 residues, 1 model selected
> marker segment #5 position 11.82,13.91,-2.299 toPosition 7.594,10.1,-3.389
> color yellow radius 0.1 label 5.793 labelHeight 0.5793 labelColor yellow
> hide #!5 models
> hide #!5 target m
> show #!5 models
> hide #!5 models
> hide #5.1 models
> ui tool show "Find Cavities"
> kvfinder #2-3
19 cavities found for SSRF-20251218_refine_10-dimer.pdb #2
SSRF-20251218_refine_10-dimer.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
2.1.1 | | 556.42 | 488.24 | 2576 | 6.12 | 1.63
2.1.11 | | 235.44 | 215.62 | 1090 | 0 | 0
2.1.15 | | 111.02 | 145.03 | 514 | 0 | 0
2.1.3 | | 60.91 | 71.95 | 282 | 2.47 | 0.85
2.1.2 | | 58.1 | 70.01 | 269 | 2.62 | 0.84
2.1.19 | | 26.14 | 35.19 | 121 | 1.2 | 0.46
2.1.13 | | 24.62 | 59.09 | 114 | 0 | 0
2.1.7 | | 21.17 | 39.07 | 98 | 0 | 0
2.1.9 | | 14.26 | 21.68 | 66 | 1.2 | 0.32
2.1.18 | | 12.74 | 23.11 | 59 | 1.2 | 0.31
2.1.6 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.14 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.17 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.8 | | 9.94 | 18.46 | 46 | 0.85 | 0.25
2.1.5 | | 8.64 | 19.12 | 40 | 1.34 | 0.55
2.1.10 | | 8.21 | 15.89 | 38 | 1.2 | 0.34
2.1.4 | | 7.56 | 17.2 | 35 | 1.34 | 0.5
2.1.12 | | 7.34 | 13.6 | 34 | 0.6 | 0.19
2.1.16 | | 5.4 | 12.94 | 25 | 0.6 | 0.12
Populating font family aliases took 40 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
13 cavities found for MgtE-sol-d940_refine_22-dimer.pdb #3
MgtE-sol-d940_refine_22-dimer.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
3.1.6 | | 1481.11 | 1075.87 | 6857 | 18.26 | 5.23
3.1.9 | | 41.04 | 56.06 | 190 | 2.68 | 0.7
3.1.8 | | 38.02 | 50.49 | 176 | 1.9 | 0.52
3.1.2 | | 33.26 | 50.42 | 154 | 0 | 0
3.1.13 | | 29.16 | 37.97 | 135 | 1.8 | 0.56
3.1.5 | | 23.33 | 39.8 | 108 | 0 | 0
3.1.7 | | 19.87 | 36.19 | 92 | 0 | 0
3.1.4 | | 19.01 | 38.34 | 88 | 0 | 0
3.1.12 | | 19.01 | 27.91 | 88 | 1.7 | 0.38
3.1.1 | | 17.5 | 40.83 | 81 | 2.16 | 0.9
3.1.11 | | 12.31 | 29.54 | 57 | 0 | 0
3.1.10 | | 8.21 | 15.58 | 38 | 1.2 | 0.39
3.1.3 | | 6.7 | 11.6 | 31 | 0.85 | 0.24
> show #1 models
> hide #1 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> view #2.1.1 @ zoom 0.75
moved plane near -40.53221842010549 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -40.53221842010549 [-0.96498108 -0.24989624 0.0797706 ]
> surface #2.1.1-19 transparency 50
> ~surface #2.1
> surface #2.1.1
> select #2.1.1
2576 atoms, 1 residue, 1 model selected
> show
> #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150
> view #!2.1.11 @ zoom 0.75
moved plane near -24.572493455153815 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -24.572493455153815 [-0.96498108 -0.24989624 0.0797706 ]
> ~surface #2.1
> surface #!2.1.11
> select #!2.1.11
1090 atoms, 1 residue, 1 model selected
> show #!2/A,E:49-50,52-54,57,153-154,156-157
> view #!2.1.1 @ zoom 0.75
moved plane near -50.8656777460205 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -50.8656777460205 [-0.96498108 -0.24989624 0.0797706 ]
> ~surface #2.1
> surface #!2.1.1
> select #!2.1.1
2576 atoms, 1 residue, 1 model selected
> show
> #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150
> view #!2.1.11 @ zoom 0.75
moved plane near -28.20274909595857 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -28.20274909595857 [-0.96498108 -0.24989624 0.0797706 ]
> ~surface #2.1
> surface #!2.1.11
> select #!2.1.11
1090 atoms, 1 residue, 1 model selected
> show #!2/A,E:49-50,52-54,57,153-154,156-157
> view #!2.1.1 @ zoom 0.75
moved plane near -50.8656777460205 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -50.8656777460205 [-0.96498108 -0.24989624 0.0797706 ]
> ~surface #2.1
> surface #!2.1.1
> select #!2.1.1
2576 atoms, 1 residue, 1 model selected
> show
> #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150
> view #3.1.6 @ zoom 0.75
moved plane near -48.861023411397944 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -48.861023411397944 [-0.96498108 -0.24989624 0.0797706 ]
> surface #3.1.1-13 transparency 50
> ~surface #3.1
> surface #3.1.6
> select #3.1.6
6857 atoms, 1 residue, 1 model selected
> show
> #!3/A:18-19,22-23,26,50-51,54-56,58-59,62-63,65-67,69-70,149-159,161-162/C:18-19,22-23,26,50-51,54-59,62-63,65-67,69-70,149-155,157-159,161-162
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #1 models
> show #!2 models
> hide #1 models
> show #!3 models
> hide #!2 models
> select add #3
11000 atoms, 2740 bonds, 562 residues, 16 models selected
> select subtract #3
13 models selected
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> view #!2.1.11 @ zoom 0.75
moved plane near -32.22259946335476 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -32.22259946335476 [-0.96498108 -0.24989624 0.0797706 ]
> ~surface #2.1
> surface #!2.1.11
> select #!2.1.11
1090 atoms, 1 residue, 1 model selected
> show #!2/A,E:49-50,52-54,57,153-154,156-157
> view #!2.1.1 @ zoom 0.75
moved plane near -53.53413084780411 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -53.53413084780411 [-0.96498108 -0.24989624 0.0797706 ]
> ~surface #2.1
> surface #!2.1.1
> select #!2.1.1
2576 atoms, 1 residue, 1 model selected
> show
> #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150
> select add #2
8285 atoms, 2700 bonds, 402 residues, 22 models selected
> select subtract #2
19 models selected
> select add #2
8285 atoms, 2700 bonds, 402 residues, 21 models selected
> select #2/E
1331 atoms, 1345 bonds, 173 residues, 1 model selected
> show sel cartoons
> select add #2
8285 atoms, 2700 bonds, 402 residues, 21 models selected
> select subtract #2
19 models selected
> view #!3.1.9 @ zoom 0.75
moved plane near -21.271883453837066 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -21.271883453837066 [-0.96498108 -0.24989624 0.0797706 ]
> ~surface #3.1
> surface #!3.1.9
> select #!3.1.9
190 atoms, 1 residue, 1 model selected
> show #!3/A:57,126-128,130-131,134,160-161,164-165,168
> view #!3.1.6 @ zoom 0.75
moved plane near -60.072447736261914 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -60.072447736261914 [-0.96498108 -0.24989624 0.0797706 ]
> ~surface #3.1
> surface #!3.1.6
> select #!3.1.6
6857 atoms, 1 residue, 1 model selected
> show
> #!3/A:18-19,22-23,26,50-51,54-56,58-59,62-63,65-67,69-70,149-159,161-162/C:18-19,22-23,26,50-51,54-59,62-63,65-67,69-70,149-155,157-159,161-162
> view #!2.1.11 @ zoom 0.75
moved plane near -32.22259946335476 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -32.22259946335476 [-0.96498108 -0.24989624 0.0797706 ]
> ~surface #2.1
> surface #!2.1.11
> select #!2.1.11
1090 atoms, 1 residue, 1 model selected
> show #!2/A,E:49-50,52-54,57,153-154,156-157
> view #!2.1.1 @ zoom 0.75
moved plane near -53.53413084780411 [-0.96498108 -0.24989624 0.0797706 ]
moved plane far -53.53413084780411 [-0.96498108 -0.24989624 0.0797706 ]
> ~surface #2.1
> surface #!2.1.1
> select #!2.1.1
2576 atoms, 1 residue, 1 model selected
> show
> #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150
> view #!2.1.11 @ zoom 0.75
moved plane near -34.46109721666628 [-0.14067287 0.33287003 -0.93242086]
moved plane far -34.46109721666628 [-0.14067287 0.33287003 -0.93242086]
> ~surface #2.1
> surface #!2.1.11
> select #!2.1.11
1090 atoms, 1 residue, 1 model selected
> show #!2/A,E:49-50,52-54,57,153-154,156-157
> view #!3.1.9 @ zoom 0.75
moved plane near -26.76603627620702 [-0.14067287 0.33287003 -0.93242086]
moved plane far -26.76603627620702 [-0.14067287 0.33287003 -0.93242086]
> ~surface #3.1
> surface #!3.1.9
> select #!3.1.9
190 atoms, 1 residue, 1 model selected
> show #!3/A:57,126-128,130-131,134,160-161,164-165,168
> show #!3 models
> hide #!2 models
> view #!3.1.6 @ zoom 0.75
moved plane near -57.88501970624285 [-0.13673975 0.28194493 -0.94963638]
moved plane far -57.88501970624285 [-0.13673975 0.28194493 -0.94963638]
> ~surface #3.1
> surface #!3.1.6
> select #!3.1.6
6857 atoms, 1 residue, 1 model selected
> show
> #!3/A:18-19,22-23,26,50-51,54-56,58-59,62-63,65-67,69-70,149-159,161-162/C:18-19,22-23,26,50-51,54-59,62-63,65-67,69-70,149-155,157-159,161-162
> view #!3.1.9 @ zoom 0.75
moved plane near -27.629945024598456 [-0.13673975 0.28194493 -0.94963638]
moved plane far -27.629945024598456 [-0.13673975 0.28194493 -0.94963638]
> ~surface #3.1
> surface #!3.1.9
> select #!3.1.9
190 atoms, 1 residue, 1 model selected
> show #!3/A:57,126-128,130-131,134,160-161,164-165,168
> view #!3.1.6 @ zoom 0.75
moved plane near -57.88501970624285 [-0.13673975 0.28194493 -0.94963638]
moved plane far -57.88501970624285 [-0.13673975 0.28194493 -0.94963638]
> ~surface #3.1
> surface #!3.1.6
> select #!3.1.6
6857 atoms, 1 residue, 1 model selected
> show
> #!3/A:18-19,22-23,26,50-51,54-56,58-59,62-63,65-67,69-70,149-159,161-162/C:18-19,22-23,26,50-51,54-59,62-63,65-67,69-70,149-155,157-159,161-162
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> view #!2.1.1 @ zoom 0.75
moved plane near -55.31161885335286 [-0.13673975 0.28194493 -0.94963638]
moved plane far -55.31161885335286 [-0.13673975 0.28194493 -0.94963638]
> ~surface #2.1
> surface #!2.1.1
> select #!2.1.1
2576 atoms, 1 residue, 1 model selected
> show
> #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150
> view #!2.1.11 @ zoom 0.75
moved plane near -33.83089111949969 [-0.13673975 0.28194493 -0.94963638]
moved plane far -33.83089111949969 [-0.13673975 0.28194493 -0.94963638]
> ~surface #2.1
> surface #!2.1.11
> select #!2.1.11
1090 atoms, 1 residue, 1 model selected
> show #!2/A,E:49-50,52-54,57,153-154,156-157
> view #!2.1.1 @ zoom 0.75
moved plane near -55.31161885335286 [-0.13673975 0.28194493 -0.94963638]
moved plane far -55.31161885335286 [-0.13673975 0.28194493 -0.94963638]
> ~surface #2.1
> surface #!2.1.1
> select #!2.1.1
2576 atoms, 1 residue, 1 model selected
> show
> #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150
> view #!2.1.11 @ zoom 0.75
moved plane near -33.83089111949969 [-0.13673975 0.28194493 -0.94963638]
moved plane far -33.83089111949969 [-0.13673975 0.28194493 -0.94963638]
> ~surface #2.1
> surface #!2.1.11
> select #!2.1.11
1090 atoms, 1 residue, 1 model selected
> show #!2/A,E:49-50,52-54,57,153-154,156-157
> view #!2.1.15 @ zoom 0.75
moved plane near -28.403875210640678 [-0.13673975 0.28194493 -0.94963638]
moved plane far -28.403875210640678 [-0.13673975 0.28194493 -0.94963638]
> ~surface #2.1
> surface #!2.1.15
> select #!2.1.15
514 atoms, 1 residue, 1 model selected
> show #!2/A:33,38,42,45-46,49/E:33,41-42,45-46,49,164-165
> view #!2.1.11 @ zoom 0.75
moved plane near -33.83089111949969 [-0.13673975 0.28194493 -0.94963638]
moved plane far -33.83089111949969 [-0.13673975 0.28194493 -0.94963638]
> ~surface #2.1
> surface #!2.1.11
> select #!2.1.11
1090 atoms, 1 residue, 1 model selected
> show #!2/A,E:49-50,52-54,57,153-154,156-157
> view #!2.1.1 @ zoom 0.75
moved plane near -55.31161885335286 [-0.13673975 0.28194493 -0.94963638]
moved plane far -55.31161885335286 [-0.13673975 0.28194493 -0.94963638]
> ~surface #2.1
> surface #!2.1.1
> select #!2.1.1
2576 atoms, 1 residue, 1 model selected
> show
> #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150
> view #!2.1.11 @ zoom 0.75
moved plane near -33.83089111949969 [-0.13673975 0.28194493 -0.94963638]
moved plane far -33.83089111949969 [-0.13673975 0.28194493 -0.94963638]
> ~surface #2.1
> surface #!2.1.11
> select #!2.1.11
1090 atoms, 1 residue, 1 model selected
> show #!2/A,E:49-50,52-54,57,153-154,156-157
> view #!3.1.9 @ zoom 0.75
moved plane near -27.629945024598456 [-0.13673975 0.28194493 -0.94963638]
moved plane far -27.629945024598456 [-0.13673975 0.28194493 -0.94963638]
> ~surface #3.1
> surface #!3.1.9
> select #!3.1.9
190 atoms, 1 residue, 1 model selected
> show #!3/A:57,126-128,130-131,134,160-161,164-165,168
> view #!3.1.6 @ zoom 0.75
moved plane near -57.88501970624285 [-0.13673975 0.28194493 -0.94963638]
moved plane far -57.88501970624285 [-0.13673975 0.28194493 -0.94963638]
> ~surface #3.1
> surface #!3.1.6
> select #!3.1.6
6857 atoms, 1 residue, 1 model selected
> show
> #!3/A:18-19,22-23,26,50-51,54-56,58-59,62-63,65-67,69-70,149-159,161-162/C:18-19,22-23,26,50-51,54-59,62-63,65-67,69-70,149-155,157-159,161-162
> show #!2 models
> hide #!3 models
> hide #!2/E,A:50,52-54,154
> hide #!3/A:55,58,67,149,152,156/C:55,57-58,67,149
> view #!2.1.1 @ zoom 0.75
moved plane near -45.87686358887427 [-0.13673975 0.28194493 -0.94963638]
moved plane far -45.87686358887427 [-0.13673975 0.28194493 -0.94963638]
> ~surface #2.1
> surface #!2.1.1
> select #!2.1.1
2576 atoms, 1 residue, 1 model selected
> show
> #!2/A:1,3,11,14-15,18,58,61-62,64-66,68,71,145-146,149/E:1,3,11,14-15,18,58,61-62,64-66,68,145-146,148-150
> view #!2.1.11 @ zoom 0.75
moved plane near -31.144026255720505 [-0.13673975 0.28194493 -0.94963638]
moved plane far -31.144026255720505 [-0.13673975 0.28194493 -0.94963638]
> ~surface #2.1
> surface #!2.1.11
> select #!2.1.11
1090 atoms, 1 residue, 1 model selected
> show #!2/A,E:49,57,153,156-157
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> marker delete #5
> ui windowfill toggle
> select #1/A-B:9
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/A-B:9
18 atoms, 16 bonds, 2 residues, 1 model selected
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #!2 models
> hide #!3 models
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> view #!3.1.9 @ zoom 0.75
moved plane near -36.97371809266014 [-0.50665092 0.48323984 -0.71399164]
moved plane far -36.97371809266014 [-0.50665092 0.48323984 -0.71399164]
> ~surface #3.1
> surface #!3.1.9
> select #!3.1.9
190 atoms, 1 residue, 1 model selected
> show #!3/A:127,130-131,134,160-161,164,168
> view #!3.1.6 @ zoom 0.75
moved plane near -77.06418463062619 [-0.50665092 0.48323984 -0.71399164]
moved plane far -77.06418463062619 [-0.50665092 0.48323984 -0.71399164]
> ~surface #3.1
> surface #!3.1.6
> select #!3.1.6
6857 atoms, 1 residue, 1 model selected
> show
> #!3/A:18-19,22-23,26,50-51,54,56,59,62-63,65-66,69-70,150-151,153-155,157-159,161-162/C:18-19,22-23,26,50-51,54,56,59,62-63,65-66,69-70,150-155,157-159,161-162
> view #!3.1.9 @ zoom 0.75
moved plane near -36.97371809266014 [-0.50665092 0.48323984 -0.71399164]
moved plane far -36.97371809266014 [-0.50665092 0.48323984 -0.71399164]
> ~surface #3.1
> surface #!3.1.9
> select #!3.1.9
190 atoms, 1 residue, 1 model selected
> show #!3/A:127,130-131,134,160-161,164,168
> view #!3.1.6 @ zoom 0.75
moved plane near -77.06418463062619 [-0.50665092 0.48323984 -0.71399164]
moved plane far -77.06418463062619 [-0.50665092 0.48323984 -0.71399164]
> ~surface #3.1
> surface #!3.1.6
> select #!3.1.6
6857 atoms, 1 residue, 1 model selected
> show
> #!3/A:18-19,22-23,26,50-51,54,56,59,62-63,65-66,69-70,150-151,153-155,157-159,161-162/C:18-19,22-23,26,50-51,54,56,59,62-63,65-66,69-70,150-155,157-159,161-162
> select #!2 & (#!2.1.11 @ select #!3 & (#!3.1.6 @ ~select #!2 & (#!2.1.11 @ ~select #!3 & (#!3.1.6 @ select #!2 & (#!2.1.11 @ select #!3 & (#!3.1.6 @ ~select #!2 & (#!2.1.11 @ ~select #!3 & (#!3.1.6 @ select #!2 & (#!2.1.11 @ select #!3 & (#!3.1.6 @ view sel
> volume showOutlineBox true
No volumes specified
> volume showOutlineBox true
No volumes specified
> volume showOutlineBox true
No volumes specified
> volume showOutlineBox true
No volumes specified
> volume showOutlineBox true
No volumes specified
> select add #3
11000 atoms, 2740 bonds, 562 residues, 15 models selected
> select subtract #3
13 models selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M5
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac17,3
Model Number: Z1L90002MCH/A
Chip: Apple M5
Total Number of Cores: 10 (4 Super and 6 Efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.2 (25D2150)
Kernel Version: Darwin 25.3.0
Time since boot: 22天19小时49分钟
Graphics/Displays:
Apple M5:
Chipset Model: Apple M5
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
narwhals: 2.21.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.4
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
plotly: 6.7.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.1
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.15.0
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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