Can't save session because NewerVersionQuery not listed

[jiaxuan.cheng@…]

The following bug report has been submitted:
Platform:        macOS-13.6.6-arm64-arm-64bit
ChimeraX Version: 1.7.dev202309270131 (2023-09-27 01:31:04 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7.dev202309270131 (2023-09-27)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/jiaxuanc2/Desktop/VRC36/figure/overall-figure/overall-1.cxs
> format session

Opened VRC36-BG505.mrc as #2, grid size 360,360,360, pixel 0.83, shown at
level 0.047, step 1, values float32  
Opened VRC36-BG505-3.27A-C3.mrc as #3, grid size 360,360,360, pixel 0.83,
shown at level 0.0805, step 1, values float32  
Opened VRC36-BG505-3.27A-C3.mrc 1 as #4.2, grid size 360,360,360, pixel 0.83,
shown at level 0.0805, step 1, values float32  
Opened VRC36-BG505-3.27A-C3.mrc 2 as #4.3, grid size 360,360,360, pixel 0.83,
shown at level 0.063, step 1, values float32  
Opened VRC36-BG505.mrc 0 as #5.1, grid size 360,360,360, pixel 0.83, shown at
level 0.047, step 1, values float32  
Opened VRC36-BG505.mrc 1 as #5.2, grid size 360,360,360, pixel 0.83, shown at
level 0.047, step 1, values float32  
Opened VRC36-BG505.mrc 2 as #5.3, grid size 360,360,360, pixel 0.83, shown at
level 0.047, step 1, values float32  
Opened VRC36-BG505.mrc 3 as #5.4, grid size 360,360,360, pixel 0.83, shown at
level 0.0544, step 1, values float32  
Opened VRC36-BG505.mrc 4 as #5.5, grid size 360,360,360, pixel 0.83, shown at
level 0.00675, step 1, values float32  
Opened VRC36-BG505.mrc 5 as #5.6, grid size 360,360,360, pixel 0.83, shown at
level 0.0379, step 1, values float32  
Log from Mon Nov 6 16:49:48 2023UCSF ChimeraX version: 1.7.dev202309270131
(2023-09-27)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/jiaxuanc2/Desktop/VRC36/figure/VRC36.cxs

Opened VRC36-BG505.mrc as #2, grid size 360,360,360, pixel 0.83, shown at
level 0.0172, step 1, values float32  
Log from Mon Nov 6 15:56:25 2023UCSF ChimeraX version: 1.7.dev202309270131
(2023-09-27)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jiaxuanc2/Desktop/VRC36/figure/VRC36-BG505-for-overall-fig.pdb

Chain information for VRC36-BG505-for-overall-fig.pdb #1  
---  
Chain | Description  
A C E | No description available  
B D F | No description available  
G I K M O Q | No description available  
H J L N P R | No description available  
  

> show atoms

> hide atoms

> show atoms

> show cartoons

[Repeated 1 time(s)]

> hide atoms

> set bgColor white

> open /Users/jiaxuanc2/Desktop/VRC36/figure/P76_J522_sharp-3.73-EMhancer-
> HT.mrc

Opened P76_J522_sharp-3.73-EMhancer-HT.mrc as #2, grid size 360,360,360, pixel
0.83, shown at level 0.0274, step 2, values float32  

> volume #2 step 1

> hide #!2 models

> open
> /Users/jiaxuanc2/Desktop/VRC36/map_pdb_for_deposition/HT/P76_J522-EMhancer-
> HT.mrc

Opened P76_J522-EMhancer-HT.mrc as #3, grid size 360,360,360, pixel 0.83,
shown at level 0.0274, step 2, values float32  

> close #1

> close #2

> volume #3 step 1

> open /Users/jiaxuanc2/Desktop/VRC36/figure/VRC36-BG505.pdb

Chain information for VRC36-BG505.pdb #1  
---  
Chain | Description  
A C E | No description available  
B D F | No description available  
G I K M O Q | No description available  
H J L N P R | No description available  
  

> close #3

> open /Users/jiaxuanc2/Desktop/VRC36/figure/VRC36-BG505.mrc

Opened VRC36-BG505.mrc as #2, grid size 360,360,360, pixel 0.83, shown at
level 0.0274, step 2, values float32  

> hide #!2 models

> show cartoons

> show atoms

> hide atoms

> show atoms

> hide atoms

> show cartoons

> hide cartoons

[Repeated 1 time(s)]

> show cartoons

> hide atoms

> show atoms

> style stick

Changed 35934 atom styles  

> style ball

Changed 35934 atom styles  

> style stick

Changed 35934 atom styles  

> hide atoms

> show cartoons

> hide cartoons

> show cartoons

> show atoms

> hide atoms

> show surfaces

> hide surfaces

> show atoms

> ~hbonds

[Repeated 1 time(s)]

> hbonds reveal true

Skipping possible acceptor with bad geometry: /A NAG 1843 O7  
Wrong number of grandchild atoms for phi/psi acceptor /A NAG 1843 O7  
  
Skipping possible acceptor with bad geometry: /C NAG 1843 O7  
Wrong number of grandchild atoms for phi/psi acceptor /C NAG 1843 O7  
  
Skipping possible acceptor with bad geometry: /E NAG 1843 O7  
Wrong number of grandchild atoms for phi/psi acceptor /E NAG 1843 O7  
  
Skipping possible acceptor with bad geometry: /C NAG 1843 O7  
Wrong number of grandchild atoms for phi/psi acceptor /C NAG 1843 O7  
  
Skipping possible acceptor with bad geometry: /A NAG 1843 O7  
Wrong number of grandchild atoms for phi/psi acceptor /A NAG 1843 O7  
  
Skipping possible acceptor with bad geometry: /E NAG 1843 O7  
Wrong number of grandchild atoms for phi/psi acceptor /E NAG 1843 O7  
  
Skipping possible acceptor with bad geometry: /M PHE 27 O  
Wrong number of grandchild atoms for phi/psi acceptor /M PHE 27 O  
  
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: /I PHE 27 O  
Wrong number of grandchild atoms for phi/psi acceptor /I PHE 27 O  
  
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: /Q PHE 27 O  
Wrong number of grandchild atoms for phi/psi acceptor /Q PHE 27 O  
  
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: /M PHE 27 O  
Wrong number of grandchild atoms for phi/psi acceptor /M PHE 27 O  
  
Skipping possible acceptor with bad geometry: /I PHE 27 O  
Wrong number of grandchild atoms for phi/psi acceptor /I PHE 27 O  
  
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: /M PHE 27 O  
Wrong number of grandchild atoms for phi/psi acceptor /M PHE 27 O  
  
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: /Q PHE 27 O  
Wrong number of grandchild atoms for phi/psi acceptor /Q PHE 27 O  
  
[Repeated 2 time(s)]Skipping possible acceptor with bad geometry: /A NAG 1843
O7  
Wrong number of grandchild atoms for phi/psi acceptor /A NAG 1843 O7  
  
Skipping possible acceptor with bad geometry: /C NAG 1843 O7  
Wrong number of grandchild atoms for phi/psi acceptor /C NAG 1843 O7  
  
Skipping possible acceptor with bad geometry: /E NAG 1843 O7  
Wrong number of grandchild atoms for phi/psi acceptor /E NAG 1843 O7  
  
Skipping possible acceptor with bad geometry: /A NAG 1843 O7  
Wrong number of grandchild atoms for phi/psi acceptor /A NAG 1843 O7  
  
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: /I PHE 27 O  
Wrong number of grandchild atoms for phi/psi acceptor /I PHE 27 O  
  
Skipping possible acceptor with bad geometry: /C NAG 1843 O7  
Wrong number of grandchild atoms for phi/psi acceptor /C NAG 1843 O7  
  
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: /M PHE 27 O  
Wrong number of grandchild atoms for phi/psi acceptor /M PHE 27 O  
  
Skipping possible acceptor with bad geometry: /E NAG 1843 O7  
Wrong number of grandchild atoms for phi/psi acceptor /E NAG 1843 O7  
  
[Repeated 1 time(s)]Skipping possible acceptor with bad geometry: /Q PHE 27 O  
Wrong number of grandchild atoms for phi/psi acceptor /Q PHE 27 O  
  

Skipped 32 atom(s) with bad connectivities; see log for details  

3279 hydrogen bonds found  

> ~hbonds

> hide atoms

> show man

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show atoms man

Expected ',' or a keyword  

> show atoms, man

Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'  

> show atoms man

Expected ',' or a keyword  

> show atoms

> hide atoms

> show #1/A MAN

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show atoms

> show #1/A NAG

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #1/A atoms NAG

Expected ',' or a keyword  

> show #1/A atoms, NAG

Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'  

> hide atoms

Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 3  
Alignment identifier is 4  

> ui tool show "Selection Inspector"

> show atoms

> hide atoms

> show #1/A, NAG green

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #1/A, select green

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #1, A grey

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #1/A, A grey

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #1, A grey

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> color #1, A grey

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color /A & helix grey cartoons

> color /A grey cartoons

> color /A light grey cartoons

> show atoms

[Repeated 1 time(s)]

> hide atoms

> color /A,C,E light grey cartoons

> color /A,C,E darkred white cartoons

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color /A,C,E light grey cartoons

> color /B,D,F grey cartoons

> color /G,I,K,M cyan cartoons

> color /G,I,K,M,O,Q cyan cartoons

> color /H,J,L,N,P,R magenta cartoons

> style sphere

Changed 35934 atom styles  

> style sphere

Changed 35934 atom styles  

> show atoms

> style stick

Changed 35934 atom styles  

> style ball

Changed 35934 atom styles  

> hide atoms

> style ball

Changed 35934 atom styles  

> show atoms

[Repeated 1 time(s)]

> hide cartoons

> show cartoons

> hide atoms

> show atoms

> hide atoms

> select ::name="BMA"::name="MAN"::name="NAG"

2190 atoms, 2319 bonds, 177 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 2190 atom styles  

> color select green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select ::name="BMA"::name="MAN"::name="NAG"

2190 atoms, 2319 bonds, 177 residues, 1 model selected  

> color sel lime

> color sel byelement

> color sel lime

> select clear

Drag select of 2190 atoms, 4362 residues, 9 pseudobonds, 2319 bonds, 2
VRC36-BG505.mrc  

> color zone #2 near sel & #1 distance 4.98

> select add #1

35934 atoms, 36933 bonds, 9 pseudobonds, 4539 residues, 22 models selected  

> select subtract #2

35934 atoms, 36933 bonds, 9 pseudobonds, 4539 residues, 20 models selected  

> select add #2

35934 atoms, 36933 bonds, 9 pseudobonds, 4539 residues, 22 models selected  

> hide #!2 models

> show #!2 models

> ui tool show "Color Zone"

> color zone #2 near #1 distance 4.98

Drag select of 2190 atoms, 4362 residues, 9 pseudobonds, 2319 bonds, 2
VRC36-BG505.mrc  

> color zone #2 near #1 distance 4.98

> color single #2

> color zone #2 near #1 distance 4.98

> volume #2 step 1

> color single #2

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> color zone #2 near #1 distance 4.98

> color single #2

> volume #2 level 0.01718

> select clear

Drag select of 2190 atoms, 4362 residues, 9 pseudobonds, 2319 bonds, 2
VRC36-BG505.mrc  

> color zone #2 near #1 distance 4.98

> color single #2

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> color zone #2 near #1 distance 4.98

> color single #2

> select add #1

35934 atoms, 36933 bonds, 9 pseudobonds, 4539 residues, 22 models selected  

> color zone #2 near #1 distance 4.98

> color single #2

> save /Users/jiaxuanc2/Desktop/VRC36/figure/VRC36.cxs includeMaps true

——— End of log from Mon Nov 6 15:56:25 2023 ———

opened ChimeraX session  

> ui tool show "Color Zone"

> color single #2

> select clear

> color zone #2 near #1 distance 4.98

> color single #2

> color /H,J,L,N,P,R magenta cartoons

> color /G,I,K,M,O,Q cyan cartoons

> color /G,I,K,M,O,Q cyan

[Repeated 1 time(s)]

> color /B,D,F grey

> color /A,C,E light grey

> select ::name="BMA"::name="MAN"::name="NAG"

2190 atoms, 2319 bonds, 177 residues, 1 model selected  

> color sel lime

[Repeated 1 time(s)]

> select clear

> color zone #2 near #1 distance 4.98

> color single #2

> color zone #2 near #1 distance 4.98

> color single #2

> lighting simple

> lighting soft

> lighting full

> lighting simple

[Repeated 2 time(s)]

> lighting soft

> color zone #2 near #1 distance 4.98

[Repeated 1 time(s)]

> volume #2 level 0.01378

> color single #2

> color zone #2 near #1 distance 4.98

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting soft

> lighting flat

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> color single #2

> color zone #2 near #1 distance 4.98

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> ui tool show "Hide Dust"

> surface dust #2 size 4.98

> color /H,J,L,N,P,R magenta

> color single #2

> color zone #2 near #1 distance 4.98

> graphics silhouettes false

> volume #2 level 0.01893

> surface dust #2 size 2

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> hide #!1 models

> surface dust #2 size 4

> surface dust #2 size 5

> volume #2 level 0.01543

> volume #2 level 0.06801

> open
> /Users/jiaxuanc2/Desktop/VRC36/map_pdb_for_deposition/VRC36-BG505-3.27A-C3.mrc

Opened VRC36-BG505-3.27A-C3.mrc as #3, grid size 360,360,360, pixel 0.83,
shown at level 0.0487, step 2, values float32  

> volume #3 level 0.06272

> color zone #3 near #1 distance 4.98

> volume #3 step 1

> volume #3 level 0.08048

> surface dust #3 size 4.98

> volume splitbyzone #3

Opened VRC36-BG505-3.27A-C3.mrc 0 as #4.1, grid size 360,360,360, pixel 0.83,
shown at level 0.0805, step 1, values float32  
Opened VRC36-BG505-3.27A-C3.mrc 1 as #4.2, grid size 360,360,360, pixel 0.83,
shown at level 0.0805, step 1, values float32  
Opened VRC36-BG505-3.27A-C3.mrc 2 as #4.3, grid size 360,360,360, pixel 0.83,
shown at level 0.0805, step 1, values float32  
Opened VRC36-BG505-3.27A-C3.mrc 3 as #4.4, grid size 360,360,360, pixel 0.83,
shown at level 0.0805, step 1, values float32  
Opened VRC36-BG505-3.27A-C3.mrc 4 as #4.5, grid size 360,360,360, pixel 0.83,
shown at level 0.0805, step 1, values float32  
Opened VRC36-BG505-3.27A-C3.mrc 5 as #4.6, grid size 360,360,360, pixel 0.83,
shown at level 0.0805, step 1, values float32  

> close #4.6

> close #4.5

> close #4.4

> close #4.1

> surface dust #4.3 size 2

[Repeated 1 time(s)]

> surface dust #4.3 size 2.1

> surface dust #4.3 size 2.2

> surface dust #4.3 size 2.3

> surface dust #4.3 size 2.4

> surface dust #4.3 size 2.5

> surface dust #4.3 size 2.6

> surface dust #4.3 size 2.7

> surface dust #4.3 size 4

[Repeated 1 time(s)]

> surface dust #2 size 5

> volume #2 level 0.04698

> volume #4.3 level 0.06304

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> color zone #2 near #1 distance 4.98

> volume splitbyzone #2

Opened VRC36-BG505.mrc 0 as #5.1, grid size 360,360,360, pixel 0.83, shown at
level 0.047, step 1, values float32  
Opened VRC36-BG505.mrc 1 as #5.2, grid size 360,360,360, pixel 0.83, shown at
level 0.047, step 1, values float32  
Opened VRC36-BG505.mrc 2 as #5.3, grid size 360,360,360, pixel 0.83, shown at
level 0.047, step 1, values float32  
Opened VRC36-BG505.mrc 3 as #5.4, grid size 360,360,360, pixel 0.83, shown at
level 0.047, step 1, values float32  
Opened VRC36-BG505.mrc 4 as #5.5, grid size 360,360,360, pixel 0.83, shown at
level 0.047, step 1, values float32  
Opened VRC36-BG505.mrc 5 as #5.6, grid size 360,360,360, pixel 0.83, shown at
level 0.047, step 1, values float32  

> volume #5.5 level 0.004388

> volume #5.6 level 0.01797

> volume #5.5 level 0.006754

> volume #5.6 level 0.02341

> volume #5.6 level 0.03791

> surface dust #5.5 size 4.98

> surface dust #5.6 size 4.98

> surface dust #5.4 size 4.98

> surface dust #5.3 size 4.98

[Repeated 1 time(s)]

> surface dust #5.2 size 4.98

> ui tool show "Side View"

> volume #5.4 level 0.05444

> save /Users/jiaxuanc2/Desktop/VRC36/figure/VRC36.cxs includeMaps true

> save /Users/jiaxuanc2/Desktop/VRC36/figure/overall-figure/overall-1.png
> width 936 height 739 supersample 3 transparentBackground true

> save /Users/jiaxuanc2/Desktop/VRC36/figure/overall-figure/overall-1.cxs
> includeMaps true

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> save /Users/jiaxuanc2/Desktop/VRC36/figure/overall-figure/overall-1.cxs
> includeMaps true

——— End of log from Mon Nov 6 16:49:48 2023 ———

opened ChimeraX session  

> color #6/A,C,E grey

> open /Users/jiaxuanc2/Desktop/VRC36/figure/VRC36-BG505.pdb

Chain information for VRC36-BG505.pdb #6  
---  
Chain | Description  
A C E | No description available  
B D F | No description available  
G I K M O Q | No description available  
H J L N P R | No description available  
  

> hide #!6 atoms

> show #!6 cartoons

> color #6/A,C,E grey

> color #6/B,D,F black

> volume #5.6 transparency 0.6

> volume #5.5 transparency 0.6

> volume #5.4 transparency 0.6

> volume #5.2 transparency 0.6

> volume #4.3 transparency 0.6

> color #6/G,I,K,M,O,Q cyan

> color #6/H,J,L,N,P,R magenta

> save /Users/jiaxuanc2/Desktop/VRC36/figure/overall-figure/overall-3.cxs
> includeMaps true

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj  
raise RuntimeError(  
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x104aee5d0>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj  
raise RuntimeError(  
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x104aee5d0>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore  
  
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
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: MacBook Pro
      Model Identifier: Mac14,5
      Model Number: MPHG3LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 8422.141.2.700.1

Software:

    System Software Overview:

      System Version: macOS 13.6.6 (22G630)
      Kernel Version: Darwin 22.6.0
      Time since boot: 18 days, 20 hours, 35 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:
        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
        DELL P2723D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.0
    Babel: 2.12.1
    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: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.11.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.48
    ChimeraX-AtomicLibrary: 10.1
    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: 1.0.3
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.4
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202309270131
    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: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.1
    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: 1.5.12
    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: 1.11
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    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: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.10
    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: 1.12.2
    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: 1.32.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.4
    contourpy: 1.1.1
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.42.1
    funcparserlib: 1.0.1
    glfw: 2.6.2
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    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: 5.3.1
    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: 2.8.7
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.10.0
    prompt-toolkit: 3.0.39
    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: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.0
    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: 0.6.2
    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: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.0.5
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Zach Pearson]

FYI, this should have been fixed last October: ​https://github.com/RBVI/ChimeraX/commit/63d0cba961

[Greg Couch]

And the ChimeraX that has this problem is a daily build from 27 September 2023. Time to update.