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Opened 3 hours ago
#20231 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
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Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Creating a scene when in spotlight mode, then trying to save the session cxs file crashes
Log:
> cd "C:\Users\s437557\OneDrive - University of Texas
> Southwestern\Lab\Experiments\20260227_CCMC_Doc2bIDR_Binder_CryoEM_CR70-73\OneDrive_1_4-23-2026"
Current working directory is: C:\Users\s437557\OneDrive - University of Texas
Southwestern\Lab\Experiments\20260227_CCMC_Doc2bIDR_Binder_CryoEM_CR70-73\OneDrive_1_4-23-2026
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\\\Users\\\s437557\\\OneDrive - University of Texas
> Southwestern\\\Lab\\\Experiments\\\20260227_CCMC_Doc2bIDR_Binder_CryoEM_CR70-73\\\OneDrive_1_4-23-2026\\\cryosparc_P68_J26_007_volume_map_DeepEMEnhanced.mrc"
Opened cryosparc_P68_J26_007_volume_map_DeepEMEnhanced.mrc as #1, grid size
480,480,480, pixel 0.825, shown at level 0.000156, step 2, values float32
> volume #1 level 0.2224
> open "C:/Users/s437557/OneDrive - University of Texas
> Southwestern/Lab/Experiments/20260227_CCMC_Doc2bIDR_Binder_CryoEM_CR70-73/OneDrive_1_4-23-2026/fold_cr64_ggsggsggsgg_doc2b1_124_ccmc_model_0_Isolde.pdb"
Chain information for fold_cr64_ggsggsggsgg_doc2b1_124_ccmc_model_0_Isolde.pdb
#2
---
Chain | Description
A | No description available
B | No description available
> transparency 50
> color bychain
> show heteroatom
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show atoms
> color byhetero
> hide H
> clipper associate #1 #2
The toModel argument must be provided!
> clipper associate #1 toModel #2
Opened cryosparc_P68_J26_007_volume_map_DeepEMEnhanced.mrc as #1.1.1.1, grid
size 480,480,480, pixel 0.825, shown at level 0.214, step 1, values float32
Chain information for fold_cr64_ggsggsggsgg_doc2b1_124_ccmc_model_0_Isolde.pdb
#1.2
---
Chain | Description
A | No description available
B | No description available
> hide H
> transparency 50
> volume style surface
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> radius 10
Unknown command: clipper radius 10
> clipper spotlight radius 10
> clipper spotlight radius 15
> clipper spotlight radius 14
> select clear
> ui tool show Scenes
> scenes save Binder_Interface_Spotlight
> save "C:/Users/s437557/OneDrive - University of Texas
> Southwestern/Lab/Experiments/20260227_CCMC_Doc2bIDR_Binder_CryoEM_CR70-73/OneDrive_1_4-23-2026/Cryosparc_P68_J26_007_Sharp_Model0_Isolde_DeepEM_Spotlight.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\s437557\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\clipper\maps\mask_handler.py", line 333, in take_snapshot
'mask': self.mask,
^^^^^^^^^
AttributeError: 'ZoneMask' object has no attribute 'mask'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>:
Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
ValueError: error processing: 'scenes' -> -> : Error while saving session data
for 'scenes' -> ->
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\s437557\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\clipper\maps\mask_handler.py", line 333, in take_snapshot
'mask': self.mask,
^^^^^^^^^
AttributeError: 'ZoneMask' object has no attribute 'mask'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 133, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 144, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 68, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>:
Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
ValueError: error processing: 'scenes' -> -> : Error while saving session data
for 'scenes' -> ->
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> scenes restore Binder_Interface_Spotlight
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\tool.py", line 161, in scene_selected_cb
run(self.session, f"scene restore {StringArg.unparse(scene_name)}")
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\cmd.py", line 61, in restore_scene
session.scenes.restore_scene(scene_name)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\manager.py", line 102, in restore_scene
self.get_scene(scene_name).restore_scene()
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\scene.py", line 198, in restore_scene
model.restore_scene(scene_data)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1920, in restore_scene
set_map_state(scene_data, self, notify=True)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\session.py", line 609, in set_map_state
v.rendering_options = rendering_options_from_state(s['rendering_options'])
~^^^^^^^^^^^^^^^^^^^^^
KeyError: 'rendering_options'
Error processing trigger "scene selected":
KeyError: 'rendering_options'
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\session.py", line 609, in set_map_state
v.rendering_options = rendering_options_from_state(s['rendering_options'])
~^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select clear
> volume #1.1.1.1 level 0.03313
> select clear
> sequence chain #1.2/A
Alignment identifier is 1.2/A
> sequence chain #1.2/B
Alignment identifier is 1.2/B
> select /B:600
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:600-603
70 atoms, 71 bonds, 4 residues, 1 model selected
> style sel sphere
Changed 70 atom styles
> style sel stick
Changed 70 atom styles
> color (#1.2 & sel) magenta
> color (#1.2 & sel) white
> color (#1.2 & sel) byhetero
> select clear
[Repeated 1 time(s)]
> select /B:600
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:600-603
70 atoms, 71 bonds, 4 residues, 1 model selected
> color (#1.2 & sel) lime
> color (#1.2 & sel) byhetero
> select clear
> volume #1.1.1.1 level 0.06745
> volume #1.1.1.1 level 0.07515
> select clear
[Repeated 1 time(s)]
> sequence chain #1.2/A
Alignment identifier is 1.2/A
> sequence chain #1.2/B
Alignment identifier is 1.2/B
> select /B:601
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /B:601-602
36 atoms, 36 bonds, 2 residues, 1 model selected
> color (#1.2 & sel) hot pink
> undo
[Repeated 9 time(s)]
> select clear
[Repeated 1 time(s)]
> color bychain
> color byhetero
> select /B:600
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:600
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:600
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:600,603
34 atoms, 33 bonds, 2 residues, 1 model selected
> color (#1.2 & sel) lime
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> save "C:/Users/s437557/OneDrive - University of Texas
> Southwestern/Lab/Experiments/20260227_CCMC_Doc2bIDR_Binder_CryoEM_CR70-73/OneDrive_1_4-23-2026/Cryosparc_J26_Model0_Isoldepdb_DeepEM_Spotlight.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\s437557\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\clipper\maps\mask_handler.py", line 333, in take_snapshot
'mask': self.mask,
^^^^^^^^^
AttributeError: 'ZoneMask' object has no attribute 'mask'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>:
Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
ValueError: error processing: 'scenes' -> -> : Error while saving session data
for 'scenes' -> ->
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\s437557\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\clipper\maps\mask_handler.py", line 333, in take_snapshot
'mask': self.mask,
^^^^^^^^^
AttributeError: 'ZoneMask' object has no attribute 'mask'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 133, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 144, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 68, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>:
Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
ValueError: error processing: 'scenes' -> -> : Error while saving session data
for 'scenes' -> ->
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> save "C:/Users/s437557/OneDrive - University of Texas
> Southwestern/Lab/Experiments/20260227_CCMC_Doc2bIDR_Binder_CryoEM_CR70-73/OneDrive_1_4-23-2026/test.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\s437557\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\clipper\maps\mask_handler.py", line 333, in take_snapshot
'mask': self.mask,
^^^^^^^^^
AttributeError: 'ZoneMask' object has no attribute 'mask'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>:
Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
ValueError: error processing: 'scenes' -> -> : Error while saving session data
for 'scenes' -> ->
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\s437557\AppData\Local\UCSF\ChimeraX\1.11\Python311\site-
packages\chimerax\clipper\maps\mask_handler.py", line 333, in take_snapshot
'mask': self.mask,
^^^^^^^^^
AttributeError: 'ZoneMask' object has no attribute 'mask'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 133, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 144, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 68, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>:
Error while saving session data for 'scenes' ->
<chimerax.scenes.manager.SceneManager object at 0x0000013FE38E1B50> ->
<chimerax.clipper.maps.mask_handler.ZoneMask object at 0x0000013F8A1D1ED0>
ValueError: error processing: 'scenes' -> -> : Error while saving session data
for 'scenes' -> ->
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> ui tool show Scenes
> close
> open "C:/Users/s437557/OneDrive - University of Texas
> Southwestern/Lab/Experiments/20260227_CCMC_Doc2bIDR_Binder_CryoEM_CR70-73/OneDrive_1_4-23-2026/fold_cr64_ggsggsggsgg_doc2b1_124_ccmc_model_0_Isolde.pdb"
Chain information for fold_cr64_ggsggsggsgg_doc2b1_124_ccmc_model_0_Isolde.pdb
#1
---
Chain | Description
A | No description available
B | No description available
> open "C:/Users/s437557/OneDrive - University of Texas
> Southwestern/Lab/Experiments/20260227_CCMC_Doc2bIDR_Binder_CryoEM_CR70-73/OneDrive_1_4-23-2026/cryosparc_P68_J26_007_volume_map_DeepEMEnhanced.mrc"
Opened cryosparc_P68_J26_007_volume_map_DeepEMEnhanced.mrc as #2, grid size
480,480,480, pixel 0.825, shown at level 0.000156, step 2, values float32
> volume #2 level 0.2286
> color bychain
> clipper associate #2 toModel #1
Opened cryosparc_P68_J26_007_volume_map_DeepEMEnhanced.mrc as #1.1.1.1, grid
size 480,480,480, pixel 0.825, shown at level 0.214, step 1, values float32
Chain information for fold_cr64_ggsggsggsgg_doc2b1_124_ccmc_model_0_Isolde.pdb
#1.2
---
Chain | Description
A | No description available
B | No description available
> transparency 50
> volume style surface
> clipper spotlight radius 14
> select clear
[Repeated 1 time(s)]
> hide H
> sequence chain #1.2/A
Alignment identifier is 1.2/A
> sequence chain #1.2/B
Alignment identifier is 1.2/B
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:1-105
1678 atoms, 1693 bonds, 105 residues, 1 model selected
> select /A:1-114
1829 atoms, 1844 bonds, 114 residues, 1 model selected
> select /A:1-119
1905 atoms, 1920 bonds, 119 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> volume #1.1.1.1 level 0.0713
> select /B:600
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:600
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /B:600,603
34 atoms, 33 bonds, 2 residues, 1 model selected
> color (#1.2 & sel) lime
> color (#1.2 & sel) byhetero
> select clear
> save "C:/Users/s437557/OneDrive - University of Texas
> Southwestern/Lab/Experiments/20260227_CCMC_Doc2bIDR_Binder_CryoEM_CR70-73/OneDrive_1_4-23-2026/Cryosparc_P68_J26_007_Sharp_Model0_Isolde_Spotlight.cxs"
> select clear
[Repeated 1 time(s)]
> select /A:146@CG
1 atom, 1 residue, 1 model selected
> select clear
> select /A:146@CD2
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 5 time(s)]
> undo
[Repeated 9 time(s)]
> hide sel atoms
> show sel atoms
> select clear
> select /A:142
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:142
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:144
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:144-145
38 atoms, 38 bonds, 2 residues, 1 model selected
> select /A:146
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:146
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> volume style mesh
> save "C:/Users/s437557/OneDrive - University of Texas
> Southwestern/Lab/Experiments/20260227_CCMC_Doc2bIDR_Binder_CryoEM_CR70-73/OneDrive_1_4-23-2026/Cryosparc_P68_J26_007_Sharp_Model0_Isolde_Spotlight.cxs"
> scenes save ""
> scenes restore 2
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\tool.py", line 161, in scene_selected_cb
run(self.session, f"scene restore {StringArg.unparse(scene_name)}")
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\cmd.py", line 61, in restore_scene
session.scenes.restore_scene(scene_name)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\manager.py", line 102, in restore_scene
self.get_scene(scene_name).restore_scene()
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\scene.py", line 198, in restore_scene
model.restore_scene(scene_data)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1920, in restore_scene
set_map_state(scene_data, self, notify=True)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\session.py", line 609, in set_map_state
v.rendering_options = rendering_options_from_state(s['rendering_options'])
~^^^^^^^^^^^^^^^^^^^^^
KeyError: 'rendering_options'
Error processing trigger "scene selected":
KeyError: 'rendering_options'
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\session.py", line 609, in set_map_state
v.rendering_options = rendering_options_from_state(s['rendering_options'])
~^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> scenes restore 2
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\tool.py", line 161, in scene_selected_cb
run(self.session, f"scene restore {StringArg.unparse(scene_name)}")
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\cmd.py", line 61, in restore_scene
session.scenes.restore_scene(scene_name)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\manager.py", line 102, in restore_scene
self.get_scene(scene_name).restore_scene()
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\scene.py", line 198, in restore_scene
model.restore_scene(scene_data)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1920, in restore_scene
set_map_state(scene_data, self, notify=True)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\session.py", line 609, in set_map_state
v.rendering_options = rendering_options_from_state(s['rendering_options'])
~^^^^^^^^^^^^^^^^^^^^^
KeyError: 'rendering_options'
Error processing trigger "scene selected":
KeyError: 'rendering_options'
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\session.py", line 609, in set_map_state
v.rendering_options = rendering_options_from_state(s['rendering_options'])
~^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> scenes restore 2
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\tool.py", line 161, in scene_selected_cb
run(self.session, f"scene restore {StringArg.unparse(scene_name)}")
File "C:\Program Files\ChimeraX 1.11.1\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:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\cmd.py", line 61, in restore_scene
session.scenes.restore_scene(scene_name)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\manager.py", line 102, in restore_scene
self.get_scene(scene_name).restore_scene()
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\scenes\scene.py", line 198, in restore_scene
model.restore_scene(scene_data)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\volume.py", line 1920, in restore_scene
set_map_state(scene_data, self, notify=True)
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\session.py", line 609, in set_map_state
v.rendering_options = rendering_options_from_state(s['rendering_options'])
~^^^^^^^^^^^^^^^^^^^^^
KeyError: 'rendering_options'
Error processing trigger "scene selected":
KeyError: 'rendering_options'
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\map\session.py", line 609, in set_map_state
v.rendering_options = rendering_options_from_state(s['rendering_options'])
~^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.2134
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 3060
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 12,699,561,984
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz
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: 4.12.1
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: 2026.1.4
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-Clipper: 0.26.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
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: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
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: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
WMI: 1.5.1
yarl: 1.22.0
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