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Opened 4 hours ago
#19968 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26200
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
I wanted to save my file. I'm using SEQCROW bundle and I did the update and it seem that I cannot save my work.
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open C:\Users\sami.essid\AppData\Roaming\ChimeraX\m-aabbUrFe(0)-CO2_02.cxs
> format session
Log from Tue Mar 3 10:17:15 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\Users\sami.essid\Documents\ESSID\Calcul\GAUSSIAN\M8\a2UrFe-
> CO2\a2UrFe-0-CO2\a2UrFe-0-CO2_S_02.xyz format xyz
opened a2UrFe-0-CO2_S_02.xyz as an XYZ coordinate file
> set bgColor white
> preset seqcrow ball-stick-endcap
Using preset: SEQCROW / Ball-Stick-Endcap
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> ui mousemode right "structure eraser"
> ui mousemode right bond
> ui mousemode right "select fragment"
> ui mousemode right select
> select subtract /a:1@Fe1
123 atoms, 132 bonds, 1 residue, 1 model selected
> select subtract /a:1@C1
122 atoms, 130 bonds, 1 residue, 1 model selected
> select subtract /a:1@O1
121 atoms, 130 bonds, 1 residue, 1 model selected
> select subtract /a:1@O2
120 atoms, 130 bonds, 1 residue, 1 model selected
> ui tool show "Buried Volume"
> select clear
> select /a:1@O2
1 atom, 1 residue, 1 model selected
> color radial #1.2 center -1.3456,1.1810,-1.2263 palette rainbow range 0,4.00
> coordinateSystem #1
> transparency #1.2 30
model center %Vbur
a2UrFe-0-CO2_S_02 /a:1@O2 61.9
> select clear
> select subtract #1.1
Nothing selected
> select add #1.1
Nothing selected
> hide #1.2 models
> ui mousemode right distance
[Repeated 1 time(s)]
> distance /a:1@H33 /a:1@O1
Distance between /a UNK 1 H33 and O1: 1.956Å
> distance /a:1@O1 /a:1@H34
Distance between /a UNK 1 O1 and H34: 1.789Å
> distance /a:1@O1 /a:1@H35
Distance between /a UNK 1 O1 and H35: 1.714Å
> hide #2.1 models
> ui tool show Distances
> distance style color black
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style radius 0.09
[Repeated 2 time(s)]
> distance style radius 0.08
[Repeated 2 time(s)]
> distance style radius 0.07
[Repeated 2 time(s)]
> distance style radius 0.06
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> show #1.2 models
> transparency #!1.4 50
> transparency #!1.1 50
> transparency #!1.1 0
> transparency #!1.2 50
> ui mousemode right translate
> save C:/Users/sami.essid/AppData/Roaming/ChimeraX/m-aabbUrFe(0)-CO2_02.cxs
> ui mousemode right rotate
> transparency #!1.2 60
> transparency #!1.2 40
> transparency #!1.2 30
> transparency #!1.2 45
> ui mousemode right translate
> save C:\Users\sami.essid\Pictures\Steric_mapplot\m-aabbUrFe-CO2_02.png width
> 2000 height 1800 supersample 12
> save C:/Users/sami.essid/AppData/Roaming/ChimeraX/m-aabbUrFe(0)-CO2_02.cxs
> hide atoms
[Repeated 1 time(s)]
> show atoms
> hide atoms
> show atoms
> hide surfaces
> show surfaces
> hide surfaces
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> save C:\Users\sami.essid\Pictures\Steric_mapplot\m-aabbUrFe-CO2_02_test.png
> width 2000 height 1800 supersample 12
> save C:/Users/sami.essid/AppData/Roaming/ChimeraX/m-aabbUrFe(0)-CO2_02.cxs
——— End of log from Tue Mar 3 10:17:15 2026 ———
> view name session-start
opened ChimeraX session
> graphics silhouettes true
> ui tool show Distances
> distance style dashes 10
> 8
Unknown command: 8
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 6
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select /a:1@Fe1
1 atom, 1 residue, 1 model selected
> select /a:1@C1
1 atom, 1 residue, 1 model selected
> select /a:1@O1
1 atom, 1 residue, 1 model selected
> select add /a:1@C1
2 atoms, 1 residue, 2 models selected
> select add /a:1@O2
3 atoms, 1 residue, 2 models selected
> select add /a:1@Fe1
4 atoms, 1 residue, 2 models selected
> ui mousemode right "select fragment"
> ui mousemode right select
> select subtract /a:1@Fe1
123 atoms, 132 bonds, 1 residue, 2 models selected
> select subtract /a:1@C1
122 atoms, 130 bonds, 1 residue, 2 models selected
> select subtract /a:1@O2
121 atoms, 130 bonds, 1 residue, 2 models selected
> select subtract /a:1@O1
120 atoms, 130 bonds, 1 residue, 2 models selected
> ui tool show "Buried Volume"
> select clear
> select /a:1@C1
1 atom, 1 residue, 1 model selected
> ui mousemode right rotate
> color radial #1.4 center -0.5381,1.2181,-0.2866 palette rainbow range 0,4.00
> coordinateSystem #1
> transparency #1.4 30
model center %Vbur
a2UrFe-0-CO2_S_02 /a:1@C1 70.8
> select subtract #1.1
1 atom, 1 residue, 2 models selected
> select add #1.1
1 atom, 1 residue, 2 models selected
> select subtract #1.3
1 model selected
> hide #1.3 models
> show #1.3 models
> hide #!1.4 models
> show #!1.4 models
> hide #1.4.1 models
> hide #1.2 models
> show #1.2 models
> color #1.2 red
> hide #1.2 models
> hide #1.3 models
> hide #1.1 models
> hide #!1 models
> show #!1 models
> ui tool show Distances
> distance style radius 0.02
[Repeated 2 time(s)]
> distance style radius 0.01
[Repeated 2 time(s)]
> distance style dashes 6
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 9
[Repeated 2 time(s)]
> distance style dashes 10
[Repeated 2 time(s)]
> distance style radius 0.02
[Repeated 2 time(s)]
> distance style dashes 9
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style radius 0.03
[Repeated 2 time(s)]
> distance style radius 0.02
[Repeated 2 time(s)]
> ui mousemode right translate
> transparency #1.4 40
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right select
> select clear
> ui mousemode right translate
> save C:\Users\sami.essid\Pictures\Steric_mapplot\m-aabUrFe-CO2_02_C-
> centeredfin.png width 1920 height 1440 supersample 20
> hide #!1.4 models
> ui mousemode right select
> select /a:1@O2
1 atom, 1 residue, 1 model selected
> ui mousemode right rotate
> color radial #1.5 center -1.3456,1.1810,-1.2263 palette rainbow range 0,4.00
> coordinateSystem #1
> transparency #1.5 30
model center %Vbur
a2UrFe-0-CO2_S_02 /a:1@O2 61.7
> hide #!2 models
> hide #!1.5 models
> show #!2 models
> show #!1.5 models
> hide #1.5.1 models
> transparency #1.5 40
> ui mousemode right select
> select clear
[Repeated 1 time(s)]
> save C:\Users\sami.essid\Pictures\Steric_mapplot\m-aabUrFe-CO2_02_O-
> centeredfin.png width 1920 height 1440 supersample 20
> select clear
> ui mousemode right select
> ui mousemode right translate
> save C:\Users\sami.essid\Pictures\Steric_mapplot\m-aabUrFe-CO2_02_O-
> centered_bis.png width 1920 height 1440 supersample 20
> hide #!1.5 models
> show #!1.4 models
> save C:\Users\sami.essid\Pictures\Steric_mapplot\m-aabUrFe-CO2_02_C-
> centered_bis.png width 1920 height 1440 supersample 20
> save C:/Users/sami.essid/AppData/Roaming/ChimeraX/m-aabbUrFe(0)-CO2_02.cxs
Traceback (most recent call last):
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state
return _copy(data)
^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 230, in _copy
return convert(data)
^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 339, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 307, in _add_obj
uid = self.unique_name.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 176, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of VoidLabels class in SEQCROW 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 "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001F1CF0969D0>: Unable to restore objects of VoidLabels class in
SEQCROW bundle because the class name is not listed in the name to class table
for session restore
ValueError: error processing: 'models' -> : Unable to restore objects of
VoidLabels class in SEQCROW bundle because the class name is not listed in the
name to class table for session restore
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 341, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 232, in copy_state
return _copy(data)
^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 217, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\state.py", line 230, in _copy
return convert(data)
^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 339, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 307, in _add_obj
uid = self.unique_name.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 176, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of VoidLabels class in SEQCROW 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 "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 185, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1420, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider
what(session)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 38, in _file_save
show_save_file_dialog(session)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 144, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 68, in display
run(session, cmd)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000001F1CF0969D0>: Unable to restore objects of VoidLabels class in
SEQCROW bundle because the class name is not listed in the name to class table
for session restore
ValueError: error processing: 'models' -> : Unable to restore objects of
VoidLabels class in SEQCROW bundle because the class name is not listed in the
name to class table for session restore
File "C:\Users\sami.essid\AppData\Local\Programs\ChimeraX 1.11\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 571.59
OpenGL renderer: NVIDIA T400 4GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.9
Locale: fr_FR.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: Precision 3660
OS: Microsoft Windows 11 Professionnel (Build 26200)
Memory: 16,853,479,424
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i5-13500
OSLanguage: en-US
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.11.12
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pywin32: 311
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.14.0
Send2Trash: 2.0.0
SEQCROW: 1.9.5a1
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
WMI: 1.5.1
yarl: 1.22.0
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