Save MD analysis GUI info in sessions

[alexandra.zahradnikova@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-111-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.12.dev202604290127 (2026-04-29 01:27:48 UTC)
Description
The session file that was originally saved on May 18, 2025 can be opened but cannot be saved again. The Log shows:

save /home/bmcuser/Documents/2026_SKBS/Devana/hwfs1delta_Vm100_1_10_closed_V2.cxs
Traceback (most recent call last):   File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 322, in process     data = sm.take_snapshot(obj, session, self.state_flags)            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/std_commands/coordset_gui.py", line 112, in take_snapshot     from chimerax.md_crds.gui import get_session_info ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui' (/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/md_crds/gui.py) The above exception was the direct cause of the following exception: Traceback (most recent call last):   File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 297, in discovery     self.processed[key] = self.process(obj, parents)                           ^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 329, in process     raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> [<chimerax.toolbar.tool.ToolbarTool object at 0x7908c00e3410>, <chimerax.sideview.tool.SideViewUI object at 0x79081afbc650>, <chimerax.cmd_line.tool.CommandLine object at 0x7908c07b6510>, <chimerax.model_panel.tool.ModelPanel object at 0x7909196ccd10>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at 0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>, <chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710> During handling of the above exception, another exception occurred: Traceback (most recent call last):   File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 1048, in save     session.save(output, version=version, include_maps=include_maps)   File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 731, in save     mgr.discovery(self._state_containers)   File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 301, in discovery     raise ValueError( ValueError: error processing: 'tools' -> [<chimerax.toolbar.tool.ToolbarTool object at 0x7908c00e3410>, <chimerax.sideview.tool.SideViewUI object at 0x79081afbc650>, <chimerax.cmd_line.tool.CommandLine object at 0x7908c07b6510>, <chimerax.model_panel.tool.ModelPanel object at 0x7909196ccd10>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at 0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>, <chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710>: Error while saving session data for 'tools' -> [<chimerax.toolbar.tool.ToolbarTool object at 0x7908c00e3410>, <chimerax.sideview.tool.SideViewUI object at 0x79081afbc650>, <chimerax.cmd_line.tool.CommandLine object at 0x7908c07b6510>, <chimerax.model_panel.tool.ModelPanel object at 0x7909196ccd10>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at 0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>, <chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710> ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] ->

File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(

See log for complete Python traceback.

Traceback (most recent call last):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 322, in process
    data = sm.take_snapshot(obj, session, self.state_flags)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/std_commands/coordset_gui.py", line 112, in take_snapshot
    from chimerax.md_crds.gui import get_session_info
ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui' (/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/md_crds/gui.py)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 297, in discovery
    self.processed[key] = self.process(obj, parents)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 329, in process
    raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' -> [<chimerax.toolbar.tool.ToolbarTool object at 0x7908c00e3410>, <chimerax.sideview.tool.SideViewUI object at 0x79081afbc650>, <chimerax.cmd_line.tool.CommandLine object at 0x7908c07b6510>, <chimerax.model_panel.tool.ModelPanel object at 0x7909196ccd10>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at 0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>, <chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 144, in show_save_file_dialog
    _dlg.display(session, **kw)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 68, in display
    run(session, cmd)
  File "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3245, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3245, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101, in provider_save
    saver_info.save(session, path, **provider_kw)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95, in save
    return cxs_save(session, path, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 1048, in save
    session.save(output, version=version, include_maps=include_maps)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 731, in save
    mgr.discovery(self._state_containers)
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 301, in discovery
    raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.toolbar.tool.ToolbarTool object at 0x7908c00e3410>, <chimerax.sideview.tool.SideViewUI object at 0x79081afbc650>, <chimerax.cmd_line.tool.CommandLine object at 0x7908c07b6510>, <chimerax.model_panel.tool.ModelPanel object at 0x7909196ccd10>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at 0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>, <chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710>: Error while saving session data for 'tools' -> [<chimerax.toolbar.tool.ToolbarTool object at 0x7908c00e3410>, <chimerax.sideview.tool.SideViewUI object at 0x79081afbc650>, <chimerax.cmd_line.tool.CommandLine object at 0x7908c07b6510>, <chimerax.model_panel.tool.ModelPanel object at 0x7909196ccd10>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at 0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>, <chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] -> <chimerax.std_commands.coordset_gui.CoordinateSetSlider object at 0x7908df33d710>

ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] ->

File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(


Log:
UCSF ChimeraX version: 1.12.dev202604290127 (2026-04-29)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> open /home/bmcuser/Documents/2026_SKBS/Devana/ions_Vm100_closed.cxs

Log from Tue Apr 8 21:23:47 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> F:/Simulations_F/Devana_F/hWFS1delta_closed_gromJob_737764/hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm200_gromJob_740764_743918_744982/hwfs1delta_Vm100_1_10.cxs

Log from Tue Apr 8 15:09:48 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> J:/Simulations_F/Devana_F/hWFS1delta_closed_gromJob_737764/hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm200_gromJob_740764_743918_744982/hwfs1delta_Vm100_1_10.cxs

Log from Sun Apr 6 18:08:17 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open F:/Simulations_F/Devana_F/hwfs1_gromJob_737764/hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918/step7_1.gro

Chain information for Title #1  
---  
Chain | Description  
? | No description available  
  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 2 time(s)]

> hide atoms

> show cartoons

> select ::name="POPC"

95006 atoms, 94297 bonds, 709 residues, 1 model selected  

> show sel atoms

> select clear

> select /?:880

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

> ui tool show Axes/Planes/Centroids

> define plane sel

Plane 'plane' placed at [89.96647059 88.81803922 93.73862745] with normal
[1.20792666e-01 2.40905629e-04 9.92677729e-01] and radius 56.0  

> close #1.1

> define plane sel padding 10

Plane 'plane' placed at [89.96647059 88.81803922 93.73862745] with normal
[1.20792666e-01 2.40905629e-04 9.92677729e-01] and radius 66.0  

> close #1.1

> define plane sel padding 20

Plane 'plane' placed at [89.96647059 88.81803922 93.73862745] with normal
[1.20792666e-01 2.40905629e-04 9.92677729e-01] and radius 76.0  

> select /?:453

59 atoms, 58 bonds, 5 residues, 1 model selected  

> define plane sel padding 20

Plane 'plane' placed at [92.58932203 87.80084746 69.83813559] with normal [
0.02232547 -0.03596117 0.99910378] and radius 90.8  

> select ::name="POPC"

95006 atoms, 94297 bonds, 709 residues, 1 model selected  

> hide sel atoms

> select clear

> select /?:549

79 atoms, 74 bonds, 5 residues, 1 model selected  

> select /?:502

47 atoms, 42 bonds, 5 residues, 1 model selected  

> close #1.1

> define plane sel padding 20

Plane 'plane' placed at [ 86.63914894 89.11744681 100.26212766] with normal
[-0.01808296 -0.06450767 0.99775336] and radius 89.5  

> close #1.1

> select /?:502@ca

4 atoms, 4 residues, 1 model selected  

> define plane sel padding 20

Plane 'plane' placed at [87.2475 87.685 97.065 ] with normal [-0.03181081
-0.02363679 0.99921438] and radius 88.5  

> select /?:477@ca

4 atoms, 4 residues, 1 model selected  

> close #1.1

> define plane sel padding 20

Plane 'plane' placed at [ 87.8975 87.455 105.9725] with normal [ 0.0178131
0.01799464 -0.99967939] and radius 91.0  

> hide sel cartoons

> undo

> select clear

> hide cartoons

> select ::name="CLA"

403 atoms, 403 residues, 1 model selected  

> style sel ball

Changed 403 atom styles  

> show sel atoms

> color sel yellow

> select clear

> select ::name="POT"

387 atoms, 387 residues, 1 model selected  

> show sel target ab

> style sel ball

Changed 387 atom styles  

> color sel orange

> select clear

> open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_1.xtc

Replaced existing frames of Title #1 with 11 new frames  

> open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_2.xtc replace false

Added 11 frames to Title #1  

> open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_3.xtc replace false

Added 11 frames to Title #1  

> open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_4.xtc replace false

Added 11 frames to Title #1  

> open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_5.xtc replace false

Added 11 frames to Title #1  

> ui tool show "Side View"

> save F:/Simulations_F/Devana_F/hwfs1_gromJob_737764/hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918/hwfs1delta_Vm100_1_5.cxs

> lighting shadows false

> select @@serial_number=47366

6 atoms, 6 residues, 1 model selected  

> style sel sphere

Changed 6 atom styles  

> select clear

> select @@serial_number=47366

6 atoms, 6 residues, 1 model selected  

> style sel ball

Changed 6 atom styles  

> select clear

> select @@serial_number=47237

6 atoms, 6 residues, 1 model selected  

> style sel sphere

Changed 6 atom styles  

> style sel ball

Changed 6 atom styles  

> select clear

> select @@serial_number=47349

6 atoms, 6 residues, 1 model selected  

> select clear

> select @@serial_number=47408

6 atoms, 6 residues, 1 model selected  

> select @@serial_number=47404

6 atoms, 6 residues, 1 model selected  

> select clear

> select @@serial_number=47293

6 atoms, 6 residues, 1 model selected  

> select #1.2

1 model selected  

> select @@serial_number=47215

6 atoms, 6 residues, 1 model selected  

> show sel cartoons

> select clear

> show cartoons

> select clear

> ui tool show "Side View"

> select ::name="TIP3"

419976 atoms, 279984 bonds, 139992 residues, 1 model selected  

> style sel stick

Changed 419976 atom styles  

> select ::name="TIP3"

419976 atoms, 279984 bonds, 139992 residues, 1 model selected  

> style sel stick

Changed 419976 atom styles  

> show sel atoms

> select clear

> show atoms

> style stick

Changed 567948 atom styles  

> select ::name="TIP3"

419976 atoms, 279984 bonds, 139992 residues, 1 model selected  

> hide sel atoms

[Repeated 1 time(s)]

> select clear

> hide atoms

> show cartoons

> select ::name="CLA"

403 atoms, 403 residues, 1 model selected  

> style sel ball

Changed 403 atom styles  

> show sel atoms

> select ::name="POT"

387 atoms, 387 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 387 atom styles  

> select clear

> open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_6.xtc replace false

Added 11 frames to Title #1  

> open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_7.xtc replace false

Added 11 frames to Title #1  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 2 time(s)]

> save F:/Simulations_F/Devana_F/hwfs1_gromJob_737764/hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918/hwfs1delta_Vm100_1_5.cxs

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 2 time(s)]

> open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_8.xtc replace false

Added 11 frames to Title #1  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 2 time(s)]

> open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918_744982\step7_9.xtc
> replace false

No such file/path:
F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm-
gui-2837532676_gromacs_Vm100_gromJob_740764_743918_744982\step7_9.xtc  

> open
> F:\Simulations_F\Devana_F\hwfs1_closed_gromJob_737764\hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918_744982\step7_9.xtc
> replace false

Added 11 frames to Title #1  

> open
> F:\Simulations_F\Devana_F\hwfs1_closed_gromJob_737764\hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918_744982\step7_10.xtc
> replace false

Added 11 frames to Title #1  

> save
> F:/Simulations_F/Devana_F/hwfs1_closed_gromJob_737764/hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm100_gromJob_740764_743918_744982/hwfs1delta_Vm100_1_10.cxs

——— End of log from Sun Apr 6 18:08:17 2025 ———

opened ChimeraX session  

> select ::name="CLA"

403 atoms, 403 residues, 1 model selected  

> ui tool show Axes/Planes/Centroids

> define centroid sel radius 10

Centroid 'centroid' placed at [85.24901131 86.62201386 93.5061334 ]  

> close #1.3

> select clear

> select @@serial_number=47570

6 atoms, 6 residues, 1 model selected  

> select clear

> select @@serial_number=47570

6 atoms, 6 residues, 1 model selected  

> select subtract /?:605

5 atoms, 5 residues, 1 model selected  

> style sel sphere

Changed 5 atom styles  

> ui tool show "Side View"

> select clear

> select add @@serial_number=47906

6 atoms, 6 residues, 1 model selected  

> style sel sphere

Changed 6 atom styles  

> style sel ball

Changed 6 atom styles  

> select add @@serial_number=47570

12 atoms, 12 residues, 1 model selected  

> style sel ball

Changed 12 atom styles  

> select @@serial_number=47237

6 atoms, 6 residues, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select : 1654

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

> style sel sphere

Changed 4 atom styles  

> select @@serial_number=47408

6 atoms, 6 residues, 1 model selected  

> select : 1825

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

> style sel sphere

Changed 4 atom styles  

> select : 1722

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

> style sel sphere

Changed 4 atom styles  

> select clear

> save
> J:/Simulations_F/Devana_F/hWFS1delta_closed_gromJob_737764/hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm200_gromJob_740764_743918_744982/hwfs1delta_Vm100_1_10.cxs

——— End of log from Tue Apr 8 15:09:48 2025 ———

opened ChimeraX session  

> save
> F:/Simulations_F/Devana_F/hWFS1delta_closed_gromJob_737764/hwfs1delta_charmm-
> gui-2837532676_gromacs_Vm200_gromJob_740764_743918_744982/ions.cxs

——— End of log from Tue Apr 8 21:23:47 2025 ———

> view name session-start

opened ChimeraX session  

> set bgColor white

> ui tool show "Side View"

> select ::name="TIP3"

419976 atoms, 279984 bonds, 139992 residues, 1 model selected  

> show sel atoms

> turn z 45

> turn z -45

> turn y -45

> turn x -1

> turn x 1

[Repeated 1 time(s)]

> turn y -1

[Repeated 1 time(s)]

> turn y 1

[Repeated 1 time(s)]

> turn x 5

> turn x -5

> turn z -5

> turn z 5

[Repeated 1 time(s)]

> turn z -1

[Repeated 2 time(s)]

> turn z .5

> hide sel atoms

> select ::name="POT"

387 atoms, 387 residues, 1 model selected  

> style sel ball

Changed 387 atom styles  

> select protein

52176 atoms, 52832 bonds, 3232 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark gray

> help help:user

> transparecy cartoons 50

Unknown command: transparecy cartoons 50  

> transparency cartoons 50

Missing or invalid "percent" argument: Expected a number  

> transparency sel 50

> transparency 50 ribbons

> transparency 0 ribbons

> hide sel cartoons

> select ::name="POT"

387 atoms, 387 residues, 1 model selected  

> style sel sphere

Changed 387 atom styles  

> color sel orange

> select ::name="TIP3"

419976 atoms, 279984 bonds, 139992 residues, 1 model selected  

> select ::name="CLA"

403 atoms, 403 residues, 1 model selected  

> style sel sphere

Changed 403 atom styles  

> color sel cornflower blue

> select clear

> select @@serial_number=47544

6 atoms, 6 residues, 1 model selected  

> select clear

> save
> /home/bmcuser/Documents/2026_SKBS/Devana/hwfs1delta_Vm100_1_10_closed_V2.cxs

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/std_commands/coordset_gui.py", line 112, in take_snapshot  
from chimerax.md_crds.gui import get_session_info  
ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui'
(/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/md_crds/gui.py)  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.toolbar.tool.ToolbarTool object at 0x7908c00e3410>,
<chimerax.sideview.tool.SideViewUI object at 0x79081afbc650>,
<chimerax.cmd_line.tool.CommandLine object at 0x7908c07b6510>,
<chimerax.model_panel.tool.ModelPanel object at 0x7909196ccd10>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at
0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>,
<chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x7908df33d710>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 1048, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' -> [<chimerax.toolbar.tool.ToolbarTool
object at 0x7908c00e3410>, <chimerax.sideview.tool.SideViewUI object at
0x79081afbc650>, <chimerax.cmd_line.tool.CommandLine object at
0x7908c07b6510>, <chimerax.model_panel.tool.ModelPanel object at
0x7909196ccd10>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at
0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>,
<chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x7908df33d710>: Error while saving session data for 'tools' ->
[<chimerax.toolbar.tool.ToolbarTool object at 0x7908c00e3410>,
<chimerax.sideview.tool.SideViewUI object at 0x79081afbc650>,
<chimerax.cmd_line.tool.CommandLine object at 0x7908c07b6510>,
<chimerax.model_panel.tool.ModelPanel object at 0x7909196ccd10>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at
0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>,
<chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x7908df33d710>  
  
ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , , ] ->  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/std_commands/coordset_gui.py", line 112, in take_snapshot  
from chimerax.md_crds.gui import get_session_info  
ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui'
(/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/md_crds/gui.py)  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.toolbar.tool.ToolbarTool object at 0x7908c00e3410>,
<chimerax.sideview.tool.SideViewUI object at 0x79081afbc650>,
<chimerax.cmd_line.tool.CommandLine object at 0x7908c07b6510>,
<chimerax.model_panel.tool.ModelPanel object at 0x7909196ccd10>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at
0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>,
<chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x7908df33d710>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 144, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 68, in display  
run(session, cmd)  
File "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 1048, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' -> [<chimerax.toolbar.tool.ToolbarTool
object at 0x7908c00e3410>, <chimerax.sideview.tool.SideViewUI object at
0x79081afbc650>, <chimerax.cmd_line.tool.CommandLine object at
0x7908c07b6510>, <chimerax.model_panel.tool.ModelPanel object at
0x7909196ccd10>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at
0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>,
<chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x7908df33d710>: Error while saving session data for 'tools' ->
[<chimerax.toolbar.tool.ToolbarTool object at 0x7908c00e3410>,
<chimerax.sideview.tool.SideViewUI object at 0x79081afbc650>,
<chimerax.cmd_line.tool.CommandLine object at 0x7908c07b6510>,
<chimerax.model_panel.tool.ModelPanel object at 0x7909196ccd10>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x7908df33d710>, <chimerax.color_actions.tool.ColorActions object at
0x7908f821df50>, <chimerax.log.tool.Log object at 0x7908def88390>,
<chimerax.shell.tool.ShellUI object at 0x7908b030f3d0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x7908df33d710>  
  
ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , , ] ->  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3
OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits)
OpenGL vendor: Mesa

Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:10.0
Manufacturer: Micro-Star International Co., Ltd.
Model: Desktop MPG Z890 Infinite X3 AI 2nd
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 Intel(R) Core(TM) Ultra 7 265KF
Cache Size: 30720 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       9.5Gi        44Gi       152Mi       8.2Gi        51Gi
	Swap:          2.0Gi       979Mi       1.0Gi

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2c05] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:5310]	
	Kernel modules: nvidiafb, nouveau

Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.1.2
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2026.4.22
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    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: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    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: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12.dev202604290127
    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: 1.2.1
    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: 1.8.2
    ChimeraX-Label: 1.4
    ChimeraX-LightingGUI: 1.0
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.3.1
    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-MatchAlign: 1.1
    ChimeraX-MatchMaker: 2.4
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.8
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    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: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    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: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.5
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.1
    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: 8.3.3
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.5
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    DateTime: 6.0
    debugpy: 1.8.20
    decorator: 5.2.1
    distro: 1.9.0
    docutils: 0.21.2
    et_xmlfile: 2.0.0
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.62.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.13
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    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: 6.7.1
    narwhals: 2.20.0
    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: 8.4.0
    OpenMM-CUDA-12: 8.4.0
    openpyxl: 3.1.5
    openvr: 1.26.701
    packaging: 25.0
    pandas: 3.0.2
    ParmEd: 4.2.2
    parso: 0.8.6
    pathlib: 1.0.1
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.9.6
    plotly: 6.7.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.3
    pydantic-settings: 2.14.0
    pydantic_core: 2.46.3
    pydata-sphinx-theme: 0.17.1
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    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: 6.10.2
    PyQt6-Qt6: 6.10.1
    PyQt6-WebEngine: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.1
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.27
    pytz: 2026.1.post1
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 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: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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: 3.4.1
    stack-data: 0.6.3
    starlette: 1.0.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.5
    tqdm: 4.67.3
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    Unidecode: 1.4.0
    urllib3: 2.6.3
    uvicorn: 0.46.0
    wcwidth: 0.6.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.23.0
    zope.interface: 8.4

[Eric Pettersen]

Hi Sasha,

Sorry for the problem. It was fixed about 10 days after the version you have, so if you update to a current daily build you should be able to save a session.

--Eric