atom_site.label_asym_id not allowing '.'

[psauer@…]

The following bug report has been submitted:
Platform:        macOS-13.6-arm64-arm-64bit
ChimeraX Version: 1.7.dev202310270152 (2023-10-27 01:52:18 UTC)
Description
Writing a cif file when the column 'atom_site.label_asym_id' contains the character '.' fails. However, opening such a file is not a problem. Ideally, one would be able to overwrite the column 'atom_site.label_asym_id' somehow or simply ignore it. The same file can be read by other programs.

Log:
> camera ortho

> cofr centerOfView

> alias cofron cofr centerofview showpivot true

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias paulclip cofr centerofview; style stick; surface cap false; clip near
> -2 far 6 position cofr; material transparentCastShadows false; lighting
> flat; graphics silhouettes false; transparency 70

> alias paullight material transparentCastShadows true; lighting soft;
> transparency 40; color sequential chain palette ^RdYlBu-11

> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; #disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.1; transparency 70;
> cofr centerofview; clip near -2 far 6 position cofr; #color ##~num_residues
> cornflower blue

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000

> alias map_unsphere surface unzone ##~num_residues

> alias default_mol_display ~disp; rib; rainbow chain palette ^RdYlBu-5;
> lighting soft

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

> alias caps_off surface cap false

> alias caps_on surface cap true

> alias paulvis lighting soft; material transparentcastshadows false; style
> stick; color /* #2b8cbe; color /X yellow; color byhetero; graphics
> silhouettes true; graphics silhouettes width 1; graphics silhouettes
> depthJump 0.1; transparency 60; hide H

> alias paullabel label /* residues color black height 0.8 bgcolor
> rgba(100%,100%,100%,0.6)

> buttonpanel Shortcuts rows 3 columns 5

> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"

> buttonpanel Shortcuts add Model_Panel command "tool show Models"

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add map_sphere command map_sphere_15

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add cofron command cofron

> buttonpanel Shortcuts add cofroff command cofroff

> buttonpanel Shortcuts add cootmode command cootmode

> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"

> buttonpanel Shortcuts add hidemaps command hidemaps

> buttonpanel Shortcuts add showmaps command showmaps

> buttonpanel Shortcuts add paulvis command paulvis

> buttonpanel Shortcuts add paullabel command paullabel

> buttonpanel Shortcuts add paulclip command paulclip

> buttonpanel Shortcuts add paullight command paullight

UCSF ChimeraX version: 1.7.dev202310270152 (2023-10-27)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/psauer/Documents/Processing/cif_file_testing/8GLP_step1.cif

Chain information for 8GLP_step1.cif #1  
---  
Chain | Description  
L5 | 28S rRNA  
L7 | 5S rRNA  
L8 | 5.8S rRNA  
LA | 60S ribosomal protein L8 (uL2)  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4  
LD | 60S ribosomal protein L5  
LE | 60S ribosomal protein L6  
LF | 60S ribosomal protein L7  
LG | 60S ribosomal protein L7a  
LH | 60S ribosomal protein L9  
LI | 60S ribosomal protein L10  
LJ | 60S ribosomal protein L11  
LL | 60S ribosomal protein L13  
LM | 60S ribosomal protein L14  
LN | 60S ribosomal protein L15  
LO | 60S ribosomal protein L13a  
LP | 60S ribosomal protein L17  
LQ | 60S ribosomal protein L18  
LR | 60S ribosomal protein L19  
LS | 60S ribosomal protein L18a  
LT | 60S ribosomal protein L21  
LU | 60S ribosomal protein L22  
LV | 60S ribosomal protein L23  
LW | 60S ribosomal protein L24  
LX | 60S ribosomal protein L23a  
LY | 60S ribosomal protein L26  
LZ | 60S ribosomal protein L27  
La | 60S ribosomal protein L27a  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L35a  
Lg | 60S ribosomal protein L34  
Lh | 60S ribosomal protein L35  
Li | 60S ribosomal protein L36  
Lj | 60S ribosomal protein L37  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | 60S ribosomal protein L40 (eL40)  
Ln | 60S ribosomal protein L41  
Lo | 60S ribosomal protein L36a  
Lp | 60S ribosomal protein L37a  
Lr | 60S ribosomal protein L28  
Pt | P-site tRNA  
S2 | 18S rRNA  
SA | 40S ribosomal protein SA  
SB | 40S ribosomal protein S3a  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein S12  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15a  
SX | 40S ribosomal protein S23 (uS12)  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | FAU ubiquitin-like and ribosomal protein S30  
Sf | Ubiquitin-40S ribosomal protein S27a  
Sg | Receptor of activated protein C kinase 1  
mR | mRNA  
  

> hbonds delete

> hide #!1 models

> show #!1 models

> hide atoms

> show atoms

> style stick

Changed 220720 atom styles  

> save
> /Users/psauer/Documents/Processing/cif_file_testing/8GLP_step1_deletehbonds.cif
> relModel #1

> close #1

> open
> /Users/psauer/Documents/Processing/20231011_IDB-872_projdir/J44_007_volume_map_sharp.mrc_masked.mrc

Summary of feedback from opening
/Users/psauer/Documents/Processing/20231011_IDB-872_projdir/J44_007_volume_map_sharp.mrc_masked.mrc  
---  
notes | open kw {}  
  
Opened J44_007_volume_map_sharp.mrc_masked.mrc as #1, grid size 512,512,512,
pixel 0.867, shown at level 0.875, step 2, values float32  

> volume #1 step 1

> volume #1 level 1.148

> lighting soft

> open
> /Users/psauer/Documents/Processing/20231011_IDB-872_projdir/cs_P1_J50_sharp_voxel_0.831_70A.mrc

Summary of feedback from opening
/Users/psauer/Documents/Processing/20231011_IDB-872_projdir/cs_P1_J50_sharp_voxel_0.831_70A.mrc  
---  
notes | open kw {}  
  
Opened cs_P1_J50_sharp_voxel_0.831_70A.mrc as #2, grid size 193,197,196, pixel
0.831,0.831,0.831, shown at level 3.63, step 1, values float32  

> volume #2 level 1.704

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-5.9631,0,1,0,-13.059,0,0,1,-7.2613

> fitmap #1 inMap #2

Fit map J44_007_volume_map_sharp.mrc_masked.mrc in map
cs_P1_J50_sharp_voxel_0.831_70A.mrc using 847667 points  
correlation = 0.1868, correlation about mean = 0.0662, overlap = 2.878e+05  
steps = 64, shift = 2.16, angle = 1.08 degrees  
  
Position of J44_007_volume_map_sharp.mrc_masked.mrc (#1) relative to
cs_P1_J50_sharp_voxel_0.831_70A.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99988215 -0.00879932 0.01257986 -6.71325472  
0.00893767 0.99989973 -0.01098374 -12.15166726  
-0.01248195 0.01109488 0.99986054 -8.48548763  
Axis 0.58382079 0.66270471 0.46901572  
Axis point -78.09376324 0.00000000 -207.40563756  
Rotation angle (degrees) 1.08345537  
Shift along axis -15.95213194  
  

> select clear

> select add #1

2 models selected  

> view matrix models
> #1,0.99925,0.032202,0.02135,-17.435,-0.03193,0.99941,-0.012937,-2.1642,-0.021754,0.012245,0.99969,-6.5543

> view matrix models
> #1,0.99925,0.032202,0.02135,-12.573,-0.03193,0.99941,-0.012937,-2.2098,-0.021754,0.012245,0.99969,-6.415

> view matrix models
> #1,0.99925,0.032202,0.02135,-14.553,-0.03193,0.99941,-0.012937,0.23301,-0.021754,0.012245,0.99969,-10.568

> view matrix models
> #1,0.99675,0.029416,0.074969,-25.953,-0.028762,0.99954,-0.0097816,-1.2658,-0.075223,0.0075935,0.99714,3.3589

> view matrix models
> #1,0.99675,0.029416,0.074969,-29.988,-0.028762,0.99954,-0.0097816,-0.25664,-0.075223,0.0075935,0.99714,3.0383

> fitmap #1 inMap #2

Fit map J44_007_volume_map_sharp.mrc_masked.mrc in map
cs_P1_J50_sharp_voxel_0.831_70A.mrc using 847667 points  
correlation = 0.2591, correlation about mean = 0.1472, overlap = 4.618e+05  
steps = 180, shift = 6.41, angle = 4.61 degrees  
  
Position of J44_007_volume_map_sharp.mrc_masked.mrc (#1) relative to
cs_P1_J50_sharp_voxel_0.831_70A.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999851 -0.00127691 0.00116260 -10.08354472  
0.00127669 0.99999917 0.00018919 -9.41097064  
-0.00116284 -0.00018770 0.99999931 -7.21404440  
Axis -0.10848002 0.66933130 0.73500183  
Axis point 1856.85814769 -8791.68499777 0.00000000  
Rotation angle (degrees) 0.09953061  
Shift along axis -10.50752995  
  

> select clear

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> close #1

> open
> /Users/psauer/Documents/Processing/20231011_IDB-872_projdir/J44_007_volume_map__masked.mrc

Summary of feedback from opening
/Users/psauer/Documents/Processing/20231011_IDB-872_projdir/J44_007_volume_map__masked.mrc  
---  
notes | open kw {}  
  
Opened J44_007_volume_map__masked.mrc as #1, grid size 512,512,512, pixel
0.831, shown at level 0.875, step 2, values float32  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> fitmap #1 inMap #2

Fit map J44_007_volume_map__masked.mrc in map
cs_P1_J50_sharp_voxel_0.831_70A.mrc using 167587 points  
correlation = 0.7809, correlation about mean = 0.7059, overlap = 3.771e+05  
steps = 60, shift = 0.034, angle = 0.0461 degrees  
  
Position of J44_007_volume_map__masked.mrc (#1) relative to
cs_P1_J50_sharp_voxel_0.831_70A.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999985 -0.00007718 0.00053399 -0.10630658  
0.00007686 0.99999982 0.00059788 -0.14616425  
-0.00053404 -0.00059784 0.99999968 0.21820893  
Axis -0.74238759 0.66310860 0.09564336  
Axis point 0.00000000 364.40461442 247.76295132  
Rotation angle (degrees) 0.04614138  
Shift along axis 0.00286815  
  

> volume #1 step 1

> volume #1 level 1.17

> volume #1 level 1.284

> volume #1 level 1.375

> open /Users/psauer/Documents/Processing/Compounds/1122/IDB-1122_test_3.cif

Summary of feedback from opening
/Users/psauer/Documents/Processing/Compounds/1122/IDB-1122_test_3.cif  
---  
warning | Unable to fetch template for '.': might have incorrect bonds  
  

> close #1-2

> cofron

> save /Users/psauer/Documents/Processing/Compounds/1122/IDB-1122_test_4.cif
> bestGuess true relModel #3

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 127, 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 138, 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 62, 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 49, 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 2908, 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 86, 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 2908, 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 101, 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/mmcif/__init__.py", line 123, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "src/mmcif_write.pyx", line 160, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 167, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 496, in
chimerax.mmcif.mmcif_write.save_structure.lambda4  
File "src/mmcif_write.pyx", line 496, in
chimerax.mmcif.mmcif_write.save_structure.lambda4  
File "src/mmcif_write.pyx", line 263, in
chimerax.mmcif.mmcif_write._chain_id_ordinal  
ValueError: not a legal chain id ., only a-z, A-Z, 0-9 allowed  
  
ValueError: not a legal chain id ., only a-z, A-Z, 0-9 allowed  
  
File "src/mmcif_write.pyx", line 263, in
chimerax.mmcif.mmcif_write._chain_id_ordinal  
  
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: Mac14,6
      Model Number: MNXA3LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.6 (22G120)
      Kernel Version: Darwin 22.6.0
      Time since boot: 11 days, 1 hour, 26 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 38
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        32GK650F:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 144.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.13.1
    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: 1.6.3
    charset-normalizer: 3.3.1
    ChimeraX-AddCharge: 1.5.12
    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: 12.0
    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: 1.3.1
    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.dev202310270152
    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: 1.13
    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: 2.0.2
    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: 1.12.2
    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: 1.33.2
    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-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: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.0
    filelock: 3.9.0
    fonttools: 4.43.1
    funcparserlib: 1.0.1
    glfw: 2.6.2
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.4
    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: 5.4.0
    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: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.11.0
    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: 2.4.1
    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: 6.3.3
    traitlets: 5.9.0
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.0.7
    wcwidth: 0.2.8
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Eric Pettersen]

Reported by Paul Sauer

[Greg Couch]

This looks like a duplicate of #9410. Please try today's daily build and confirm that the fix for that bug fixes your bug.

[Greg Couch]

Please reopen this ticket if you have any problems.