id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15136	Crash in garbage collection	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-14.3.1-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x0000000200f10240 (most recent call first):
  Garbage-collecting
  File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2000 in save_state
  File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 219 in take_snapshot
  File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1417 in take_snapshot
  File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 296 in process
  File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 273 in discovery
  File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 636 in save
  File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 912 in save
  File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 95 in save
  File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 101 in provider_save
  File ""/Applications/ChimeraX-1.7.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 86 in cmd_save
  File ""/Applications/ChimeraX-1.7.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 62 in display
  File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 138 in show_save_file_dialog
  File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 127 in 
  File ""/Applications/ChimeraX-1.7.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.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.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.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, 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 (total: 61)


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}
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/JIP3-KLC.cxs""

Log from Tue Feb 20 11:59:33 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Manuscripts/Chaaban-
> JCS-2024/Adaptors/Adaptors/JIP3-linear.pdb""

Chain information for JIP3-linear.pdb #1  
---  
Chain | Description  
B C | No description available  
  

> ui tool show ""Show Sequence Viewer""

> sequence chain /B

Alignment identifier is 1/B  

> open ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Ammaar/AF/j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb""

Chain information for
j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb #2  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
  

> hide #1 models

> close session

> open ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Ammaar/AF/j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb""
> format pdb

Chain information for
j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
  

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> hide atoms

> show cartoons

> select /B/C

3200 atoms, 3262 bonds, 405 residues, 1 model selected  

> select /A/B

2510 atoms, 2530 bonds, 328 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #fffb00ff

> select /C/D

3890 atoms, 3994 bonds, 482 residues, 1 model selected  

> color sel #8efa00ff

> color sel #73fa79ff

> select /E/F

4776 atoms, 4866 bonds, 602 residues, 1 model selected  

> color sel #ff9300ff

> color sel #ff9941ff

> select /A:156

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /C/D

3890 atoms, 3994 bonds, 482 residues, 1 model selected  

> select clear

> select /C

1945 atoms, 1997 bonds, 241 residues, 1 model selected  

> select /D

1945 atoms, 1997 bonds, 241 residues, 1 model selected  

> hide sel cartoons

> select /F

2388 atoms, 2433 bonds, 301 residues, 1 model selected  

> select /E

2388 atoms, 2433 bonds, 301 residues, 1 model selected  

> hide sel cartoons

Drag select of 83 residues  

> hide sel cartoons

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/chaaban/Desktop/movie1.mp4

Movie saved to /Users/chaaban/Desktop/movie1.mp4  
  

> select /E

2388 atoms, 2433 bonds, 301 residues, 1 model selected  

> save ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/JIP1JIP3KLC.cxs""

> select /E

2388 atoms, 2433 bonds, 301 residues, 1 model selected  

> select /F

2388 atoms, 2433 bonds, 301 residues, 1 model selected  

> hide sel cartoons

> ui tool show ""Show Sequence Viewer""

> sequence chain /A

Alignment identifier is 1/A  

> select /A:55

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:55-59

45 atoms, 46 bonds, 5 residues, 1 model selected  

> color sel hot pink

> select clear

> save ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/JIP1JIP3KLC-J1J3spindly.cxs""

> close session

> open ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Kashish/DDJL.pdb""

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Kashish/DDJL.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 57 57 PRO V 4
ASP V 8 1 5  
Start residue of secondary structure not found: HELIX 58 58 PRO V 52 LYS V 58
1 7  
Start residue of secondary structure not found: HELIX 117 117 CYS T 742 PHE T
770 1 29  
Start residue of secondary structure not found: HELIX 120 120 PRO T 821 ILE T
852 1 32  
Start residue of secondary structure not found: HELIX 124 124 LEU T 1099 LYS T
1120 1 22  
5 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 130 130 GLN T 1274 HIS T
1281 1 8  
Start residue of secondary structure not found: HELIX 131 131 ASP T 1282 LEU T
1284 1 3  
Start residue of secondary structure not found: HELIX 176 176 CYS S 742 PHE S
770 1 29  
Start residue of secondary structure not found: HELIX 178 178 PRO S 821 ILE S
852 1 32  
Start residue of secondary structure not found: HELIX 182 182 PRO S 1096 LYS S
1138 1 43  
Start residue of secondary structure not found: HELIX 183 183 SER S 1140 PRO S
1142 1 3  
20 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 157 15715 TYR o 327 CYS o
331 0  
Start residue of secondary structure not found: SHEET 158 15815 VAL o 335 PHE
o 340 0  
Start residue of secondary structure not found: SHEET 159 15915 LEU o 347 THR
o 352 0  
Start residue of secondary structure not found: SHEET 160 16016 ILE o 357 ASP
o 361 0  
Start residue of secondary structure not found: SHEET 161 16116 VAL o 384 GLY
o 391 0  
Start residue of secondary structure not found: SHEET 162 16216 HIS o 396 SER
o 402 0  
14 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 177 17717 GLU o 584 GLY o
588 0  
Start residue of secondary structure not found: SHEET 178 17817 ILE o 594 VAL
o 599 0  
Start residue of secondary structure not found: SHEET 253 25325 LEU h 265 PHE
h 271 0  
Start residue of secondary structure not found: SHEET 254 25425 LEU h 285 TRP
h 287 0  
Start residue of secondary structure not found: SHEET 255 25525 LEU h 294 TYR
h 299 0  
Start residue of secondary structure not found: SHEET 256 25625 GLY h 311 ASN
h 317 0  
End residue of secondary structure not found: SHEET 257 25725 TYR h 327 CYS h
331 0  
Start residue of secondary structure not found: SHEET 258 25825 VAL h 335 PHE
h 340 0  
Start residue of secondary structure not found: SHEET 259 25925 LEU h 347 THR
h 352 0  
Start residue of secondary structure not found: SHEET 260 26026 ILE h 357 ASP
h 361 0  
Start residue of secondary structure not found: SHEET 261 26126 VAL h 387 GLY
h 391 0  
Start residue of secondary structure not found: SHEET 262 26226 HIS h 396 ILE
h 401 0  
14 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 277 27727 GLU h 584 ASP h
589 0  
Start residue of secondary structure not found: SHEET 278 27827 ILE h 594 VAL
h 599 0  
Start residue of secondary structure not found: SHEET 489 48948 LEU p 265 PHE
p 271 0  
Start residue of secondary structure not found: SHEET 490 49049 LEU p 285 TRP
p 287 0  
Start residue of secondary structure not found: SHEET 491 49149 LEU p 294 TYR
p 299 0  
Start residue of secondary structure not found: SHEET 492 49249 GLY p 311 ASN
p 317 0  
End residue of secondary structure not found: SHEET 493 49349 TYR p 327 CYS p
331 0  
Start residue of secondary structure not found: SHEET 494 49449 VAL p 335 PHE
p 340 0  
Start residue of secondary structure not found: SHEET 495 49549 LEU p 347 THR
p 352 0  
Start residue of secondary structure not found: SHEET 496 49649 ILE p 357 ASP
p 361 0  
Start residue of secondary structure not found: SHEET 497 49749 VAL p 384 GLY
p 391 0  
Start residue of secondary structure not found: SHEET 498 49849 HIS p 396 SER
p 402 0  
14 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 513 51351 GLU p 584 ASP p
589 0  
Start residue of secondary structure not found: SHEET 514 51451 ILE p 594 VAL
p 599 0  
Start residue of secondary structure not found: SHEET 530 53053 LEU g 265 PHE
g 271 0  
Start residue of secondary structure not found: SHEET 531 53153 LEU g 285 TRP
g 287 0  
Start residue of secondary structure not found: SHEET 532 53253 LEU g 294 TYR
g 299 0  
Start residue of secondary structure not found: SHEET 533 53353 GLY g 311 ASN
g 317 0  
End residue of secondary structure not found: SHEET 534 53453 TYR g 327 CYS g
331 0  
Start residue of secondary structure not found: SHEET 535 53553 VAL g 335 PHE
g 340 0  
Start residue of secondary structure not found: SHEET 536 53653 LEU g 347 THR
g 352 0  
Start residue of secondary structure not found: SHEET 537 53753 ILE g 357 ASP
g 361 0  
Start residue of secondary structure not found: SHEET 538 53853 VAL g 384 GLY
g 391 0  
Start residue of secondary structure not found: SHEET 539 53953 HIS g 396 SER
g 402 0  
14 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 554 55455 GLU g 584 ASP g
589 0  
Start residue of secondary structure not found: SHEET 555 55555 ILE g 594 VAL
g 599 0  
  
Chain information for DDJL.pdb #1  
---  
Chain | Description  
1 2 | No description available  
3 4 | No description available  
A B D E F G I | No description available  
C | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
W | No description available  
X | No description available  
Y | No description available  
a b d i | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
j | No description available  
k l v y | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s t w z | No description available  
u | No description available  
x | No description available  
  

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> hide atoms

> show cartoons

> select /x/X

2981 atoms, 2975 bonds, 600 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel yellow

> color sel #fffc79ff

> color sel #fffb00ff

> select clear

> select

161768 atoms, 161675 bonds, 32552 residues, 1 model selected  

> select /x/X

2981 atoms, 2975 bonds, 600 residues, 1 model selected  

> select ~sel

158787 atoms, 158700 bonds, 31952 residues, 1 model selected  

> color sel light sea green

> select clear

> ui tool show ""Show Sequence Viewer""

> sequence chain /X

Alignment identifier is 1/X  

> select /X:393

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /X:382

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /X:382-386

25 atoms, 24 bonds, 5 residues, 1 model selected  

> color sel hot pink

> select clear

> select /X:518-551

170 atoms, 169 bonds, 34 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel light gray

> select /x:518-551

170 atoms, 169 bonds, 34 residues, 1 model selected  

> color sel light gray

> select clear

[Repeated 1 time(s)]

> save ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/DDJL-J3spindly.cxs""

> open ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Ammaar/AF/j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb""

Chain information for
j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb #2  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
  

> mmaker #2 to #1/x

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 DDJL.pdb, chain x (#1) with
j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 351.7  
RMSD between 5 pruned atom pairs is 1.401 angstroms; (across all 109 pairs:
75.543)  
  

> mmaker #2 to #1/X

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 DDJL.pdb, chain X (#1) with
j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb, chain A
(#2), sequence alignment score = 535.7  
RMSD between 59 pruned atom pairs is 0.840 angstroms; (across all 145 pairs:
83.719)  
  

> hide atoms

> show cartoons

> preset custom pretty

Using preset: Custom / Pretty  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000

  

> hide #!1 models

> select #2/F

2388 atoms, 2433 bonds, 301 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select ~sel & ##selected

8788 atoms, 8957 bonds, 1111 residues, 1 model selected  

> select #2/D

1945 atoms, 1997 bonds, 241 residues, 1 model selected  

> hide sel cartoons

Drag select of 73 residues  

> hide sel cartoons

Drag select of 12 residues  

> hide sel cartoons

> select #2/D

1945 atoms, 1997 bonds, 241 residues, 1 model selected  

> show sel cartoons

> undo

[Repeated 6 time(s)]

> select #2/C

1945 atoms, 1997 bonds, 241 residues, 1 model selected  

> hide sel cartoons

Drag select of 82 residues  

> hide sel cartoons

> show #!1 models

> select #2/E

2388 atoms, 2433 bonds, 301 residues, 1 model selected  

> color sel orange

> select clear

> select #2/A/B

2510 atoms, 2530 bonds, 328 residues, 1 model selected  

> color sel yellow

> select clear

> select ~sel & ##selected

Nothing selected  

> select #2/D

1945 atoms, 1997 bonds, 241 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #73fa79ff

> select clear

> hide #!1 models

> show #!1 models

> hide #2 models

> show #2 models

> hide #!1 models

> ui tool show ""Show Sequence Viewer""

> sequence chain #2/B

Alignment identifier is 2/B  

> select #2/B:56

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/B:56-60

47 atoms, 48 bonds, 5 residues, 1 model selected  

> color sel hot pink

> select clear

> show #!1 models

> hide #2 models

> save ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/DDJL-J3spindly.cxs""

> open 6FUZ

Summary of feedback from opening 6FUZ fetched from pdb  
---  
notes | Fetching compressed mmCIF 6fuz from
http://files.rcsb.org/download/6fuz.cif  
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif  
  
6fuz title:  
Crystal structure of the TPR domain of KLC1 in complex with the C-terminal
peptide of JIP1 [more info...]  
  
Chain information for 6fuz #3  
---  
Chain | Description | UniProt  
A | Kinesin light chain 1,Kinesin light chain 1,C-Jun-amino-terminal kinase-
interacting protein 1 | Q5UE59_MOUSE 201-670  
N | nanobody |  
  
Non-standard residues in 6fuz #3  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  

> open 6EJN

Summary of feedback from opening 6EJN fetched from pdb  
---  
note | Fetching compressed mmCIF 6ejn from
http://files.rcsb.org/download/6ejn.cif  
  
6ejn title:  
The KLC2 TPR domain bound to the JIP3 leucine zipper domain [more info...]  
  
Chain information for 6ejn #4  
---  
Chain | Description | UniProt  
A B | Kinesin light chain 2 | Q91YS4_MOUSE 191-479  
C D | C-Jun-amino-terminal kinase-interacting protein 3 | JIP3_MOUSE 417-486  
  

> hide #!3 models

> hide #!4 models

> show #2 models

> hide #!1 models

> mmaker #3 to #2

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 j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain E (#2) with 6fuz, chain A (#3), sequence alignment score = 1402.4  
RMSD between 139 pruned atom pairs is 0.979 angstroms; (across all 244 pairs:
3.497)  
  

> mmaker #4 to #2

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 j1j3k1_6bb34_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain E (#2) with 6ejn, chain B (#4), sequence alignment score = 1306.6  
RMSD between 137 pruned atom pairs is 0.816 angstroms; (across all 255 pairs:
5.712)  
  

> show #!3 models

> hide #2 models

> show #2 models

> hide #2 models

> select #3/A

2147 atoms, 2174 bonds, 2 pseudobonds, 274 residues, 2 models selected  

> select ~sel & ##selected

873 atoms, 886 bonds, 119 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select clear

> preset custom pretty

Using preset: Custom / Pretty  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000

  
Drag select of 6 atoms, 267 residues, 2 pseudobonds, 5 bonds  

> hide sel atoms

> select clear

[Repeated 1 time(s)]

> select #3/A:704

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #3/A:705

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select add #3/A:706

23 atoms, 21 bonds, 3 residues, 1 model selected  

> select add #3/A:707

31 atoms, 28 bonds, 4 residues, 1 model selected  

> select add #3/A:708

39 atoms, 35 bonds, 5 residues, 1 model selected  

> select add #3/A:350

48 atoms, 43 bonds, 6 residues, 1 model selected  

> select subtract #3/A:350

39 atoms, 35 bonds, 5 residues, 1 model selected  

> select add #3/A:709

51 atoms, 47 bonds, 6 residues, 1 model selected  

> select add #3/A:710

59 atoms, 54 bonds, 7 residues, 1 model selected  

> select add #3/A:711

69 atoms, 63 bonds, 8 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #73fdffff

> color sel #73fa79ff

> select ~sel

181102 atoms, 181334 bonds, 3 pseudobonds, 35008 residues, 6 models selected  

> select subtract #4

175895 atoms, 176055 bonds, 1 pseudobond, 34349 residues, 4 models selected  

> select subtract #2

164719 atoms, 164665 bonds, 1 pseudobond, 32937 residues, 3 models selected  

> select subtract #1

2951 atoms, 2990 bonds, 1 pseudobond, 385 residues, 2 models selected  

> color (#!3 & sel) orange

> select clear

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> save ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/KCL-JIP1.cxs""

> show #!4 models

> hide #!3 models

> select #4/A/B

4277 atoms, 4351 bonds, 2 pseudobonds, 538 residues, 2 models selected  

> color (#!4 & sel) orange

> select #4/C/D

930 atoms, 928 bonds, 121 residues, 1 model selected  

> color sel yellow

> select clear

> save ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/JIP3-KLC.cxs""

——— End of log from Tue Feb 20 11:59:33 2024 ———

opened ChimeraX session  

> select #1/X:80-81

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/X:80-432

817 atoms, 815 bonds, 165 residues, 1 model selected  

> ui tool show ""Show Sequence Viewer""

> sequence chain #4/A #4/B

Alignment identifier is 1  

> select clear

> select #4/A:191-421/B:193-422

3687 atoms, 3754 bonds, 461 residues, 1 model selected  

> select clear

> select #4/A:191-195/B:193-195

64 atoms, 65 bonds, 8 residues, 1 model selected  

> select #4/A-B:193-195

48 atoms, 48 bonds, 6 residues, 1 model selected  

> select #4/A-B:193-196

58 atoms, 58 bonds, 8 residues, 1 model selected  

> select #4/A:191-192

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #4/A:191-194/B:193-194

50 atoms, 49 bonds, 6 residues, 1 model selected  

> select clear

> select #4/A-B:477

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #4/A-B:473-477

72 atoms, 70 bonds, 10 residues, 1 model selected  

> select clear

> select #4/A-B:473-477

72 atoms, 70 bonds, 10 residues, 1 model selected  

> select #4/A-B:236-237

34 atoms, 36 bonds, 4 residues, 1 model selected  

> select #4/A-B:236-238

50 atoms, 52 bonds, 6 residues, 1 model selected  

> select #4/A:421/B:421-422

21 atoms, 19 bonds, 3 residues, 1 model selected  

> select #4/A:414-421/B:414-422

145 atoms, 145 bonds, 17 residues, 1 model selected  

> close session

> open ""/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Presentations/2024-02-23 Lab Meeting/Media/JIP3-linear.pdb""

Chain information for JIP3-linear.pdb #1  
---  
Chain | Description  
B C | No description available  
  

> ui tool show ""Show Sequence Viewer""

> sequence chain /B /C

Alignment identifier is 1  
Drag select of 1 residues  
Drag select of 6 residues  

> select /B-C:320-321

32 atoms, 30 bonds, 4 residues, 1 model selected  

> select /B-C:320-579

4150 atoms, 4196 bonds, 520 residues, 1 model selected  

> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_0.cif

Chain information for fold_2024_05_08_20_40_model_0.cif #2  
---  
Chain | Description  
A B | .  
C | .  
D | .  
E | .  
F | .  
G | .  
H I | .  
  

> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_1.cif

Chain information for fold_2024_05_08_20_40_model_1.cif #3  
---  
Chain | Description  
A B | .  
C | .  
D | .  
E | .  
F | .  
G | .  
H I | .  
  

> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_2.cif

Chain information for fold_2024_05_08_20_40_model_2.cif #4  
---  
Chain | Description  
A B | .  
C | .  
D | .  
E | .  
F | .  
G | .  
H I | .  
  

> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_3.cif

Chain information for fold_2024_05_08_20_40_model_3.cif #5  
---  
Chain | Description  
A B | .  
C | .  
D | .  
E | .  
F | .  
G | .  
H I | .  
  

> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_4.cif

Chain information for fold_2024_05_08_20_40_model_4.cif #6  
---  
Chain | Description  
A B | .  
C | .  
D | .  
E | .  
F | .  
G | .  
H I | .  
  

> close session

> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_0.cif

Chain information for fold_2024_05_08_20_40_model_0.cif #1  
---  
Chain | Description  
A B | .  
C | .  
D | .  
E | .  
F | .  
G | .  
H I | .  
  

> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_1.cif

Chain information for fold_2024_05_08_20_40_model_1.cif #2  
---  
Chain | Description  
A B | .  
C | .  
D | .  
E | .  
F | .  
G | .  
H I | .  
  

> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_2.cif

Chain information for fold_2024_05_08_20_40_model_2.cif #3  
---  
Chain | Description  
A B | .  
C | .  
D | .  
E | .  
F | .  
G | .  
H I | .  
  

> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_3.cif

Chain information for fold_2024_05_08_20_40_model_3.cif #4  
---  
Chain | Description  
A B | .  
C | .  
D | .  
E | .  
F | .  
G | .  
H I | .  
  

> open
> /Users/chaaban/Downloads/fold_2024_05_08_20_40/fold_2024_05_08_20_40_model_4.cif

Chain information for fold_2024_05_08_20_40_model_4.cif #5  
---  
Chain | Description  
A B | .  
C | .  
D | .  
E | .  
F | .  
G | .  
H I | .  
  

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> hide #1 atoms

> show #1 cartoons

> show #2 models

> hide #1 models

> show #3 models

> show #4 models

> show #5 models

> hide #2-5 atoms

> show #2-5 cartoons

> hide #5 models

> hide #4 models

> hide #3 models

> select #2/A

1885 atoms, 1936 bonds, 232 residues, 1 model selected  

> select #2/A/B

3770 atoms, 3872 bonds, 464 residues, 1 model selected  

> show #3 models

> show #4 models

> hide #4 models

> show #5 models

> show #4 models

> show #1 models

> select /A/B

18850 atoms, 19360 bonds, 2320 residues, 5 models selected  

> color sel orange red

> select clear

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> select /C

7040 atoms, 7175 bonds, 910 residues, 5 models selected  

> select /C/D/E

45710 atoms, 46760 bonds, 5820 residues, 5 models selected  

> select /C/D/E/F

52930 atoms, 54095 bonds, 6770 residues, 5 models selected  

> select /C/D/E/F/G

68885 atoms, 70335 bonds, 8780 residues, 5 models selected  

> select /C/D/E/F

52930 atoms, 54095 bonds, 6770 residues, 5 models selected  

> color (#1 & sel) cornflower blue

> show #2 models

> select clear

> show #3 models

> show #4 models

> show #5 models

> select /C/D/E/F

52930 atoms, 54095 bonds, 6770 residues, 5 models selected  

> color sel cornflower blue

> select clear

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> select /G/H

26335 atoms, 26735 bonds, 3310 residues, 5 models selected  

> select /G

15955 atoms, 16240 bonds, 2010 residues, 5 models selected  

> select /h

10380 atoms, 10495 bonds, 1300 residues, 5 models selected  

> show #2 models

> show #3 models

> hide #3 models

> show #4 models

> show #3 models

> show #5 models

> select /G

15955 atoms, 16240 bonds, 2010 residues, 5 models selected  

> color sel cyan

> select /H/I

20760 atoms, 20990 bonds, 2600 residues, 5 models selected  

> color sel hot pink

> color sel yellow

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> select clear

> show #2 models

> hide #1 models

> show #3 models

> hide #2 models

> show #4 models

> hide #3 models

> show #5 models

> hide #4 models

> save /Users/chaaban/Downloads/fold_2024_05_08_20_40/chimerax.cxs


===== 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 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

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: Mac
      Model Identifier: Mac14,5
      Model Number: Z17J0018AB/A
      Chip: Unknown
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.81.1
      OS Loader Version: 10151.81.1

Software:

    System Software Overview:

      System Version: macOS 14.3.1 (23D60)
      Kernel Version: Darwin 23.3.0
      Time since boot: 36 days, 10 hours, 8 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL P2717H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
        DELL P2722H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.13
    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: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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-Clipper: 0.22.3
    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
    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-ISOLDE: 1.7
    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
    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: 1.5.13
    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: 1.0.3
    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: 1.12.3
    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: 1.33.2
    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: 0.2.0
    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: 4.47.0
    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: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    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: 10.0.1
    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: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    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: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
}}}
"	defect	closed	normal		Core		duplicate		Tom Goddard				all	ChimeraX