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Opened 7 days ago
Closed 6 days ago
#20595 closed defect (duplicate)
Session save: cannot import name 'get_session_info' from 'chimerax.md_crds.gui'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.12.dev202604040008 (2026-04-04 00:08:08 UTC)
Description
gave this error when i tried to save a session file after morphing two coordinate sets.
Log:
UCSF ChimeraX version: 1.12.dev202604040008 (2026-04-04)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "L:\Graphics\BCRX001\GraphicsBackup\factor_D\morphing factorD\FD-
> bcx9930-8936.cxs" format session
Log from Wed Jul 8 10:13:53 2026 Startup Messages
---
warning | No presets found in custom preset folder L:/Graphics/BCRX001/GraphicsBackup/yahya-babu
UCSF ChimeraX version: 1.12.dev202604040008 (2026-04-04)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open L:/Graphics/BCRX001/GraphicsBackup/mar06_2026_bcx9930_factorD.pdb
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/mar06_2026_bcx9930_factorD.pdb
---
warnings | Ignored bad PDB record found on line 22
HELIX 1 1 HIS A 57 GLU A 59A 1 Generated by MOE 4
Ignored bad PDB record found on line 23
HELIX 2 2 ARG A 165 ASN A 169 1 Generated by MOE 5
Ignored bad PDB record found on line 24
HELIX 3 3 VAL A 231 TYR A 234 5 Generated by MOE 4
Ignored bad PDB record found on line 25
HELIX 4 4 ALA A 235 LEU A 242 1 Generated by MOE 8
Ignored bad PDB record found on line 26
SHEET 1 ARG A 20 GLU A 21 Generated by MOE
14 messages similar to the above omitted
Chain information for mar06_2026_bcx9930_factorD.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open L:/Graphics/BCRX001/GraphicsBackup/factor_D/FD-bcx8936-xray/fd-
> bcx8936-diffmap.pdb format swissdock
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/factor_D/FD-bcx8936-xray/fd-
bcx8936-diffmap.pdb
---
warnings | Ignored bad PDB record found on line 2
Ignored bad PDB record found on line 3
HELIX 1 1 HIS A 57 GLU A 60 1 Generated by MOE 4
Ignored bad PDB record found on line 4
Ignored bad PDB record found on line 5
HELIX 2 2 ASP A 61 ASP A 64 5 Generated by MOE 4
Ignored bad PDB record found on line 6
161 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (189 )
Ignored bad PDB record found on line 3818
Chain information for fd-bcx8936-diffmap.pdb #2
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker mar06_2026_bcx9930_factorD.pdb, chain A (#1) with fd-
bcx8936-diffmap.pdb, chain A (#2), sequence alignment score = 1116.9
RMSD between 218 pruned atom pairs is 0.562 angstroms; (across all 228 pairs:
0.978)
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker mar06_2026_bcx9930_factorD.pdb, chain A (#1) with fd-
bcx8936-diffmap.pdb, chain A (#2), sequence alignment score = 1116.9
RMSD between 218 pruned atom pairs is 0.562 angstroms; (across all 228 pairs:
0.978)
> delete H
> delete solvent
> cd "L:/Graphics/BCRX001/GraphicsBackup/factor_D/morphing factorD"
Current working directory is:
L:\Graphics\BCRX001\GraphicsBackup\factor_D\morphing factorD
> save "L:/Graphics/BCRX001/GraphicsBackup/factor_D/morphing factorD/FD-
> bcx9930-8936.cxs"
——— End of log from Wed Jul 8 10:13:53 2026 ———
> view name session-start
opened ChimeraX session
> close #2.1
> help help:user
> morph #2 #1 corkscrew frames 75
Expected a keyword
> help help:user
> morph #2 #1 method corkscrew frames 75 slider true
Computed 76 frame morph #3
> coordset #3 1,76
> close #3.1
> morph #2 #1 method corkscrew frames 75 slider true colorCore cornflower blue
Computed 76 frame morph #4
> coordset #4 1,76
> hide #3 models
> close #4.1
> morph #2 #1 method corkscrew frames 75 slider true colorCore cornflowerblue
> byhetero
Expected a keyword
> morph #2 #1 method corkscrew frames 75 slider true colorColor byhetero
Expected a keyword
> morph #2 #1 method corkscrew frames 75 slider true colorCore byhetero
Invalid "colorCore" argument: Invalid color name or specifier
> morph #2 #1 method corkscrew frames 75 slider true colorCore green
Computed 76 frame morph #5
> coordset #5 1,76
> close #4
> movie record
> movie encode C:\Users\Rkrishnan\Desktop\movie19.mp4 framerate 25.0
Movie saved to \C:Users\\...\Desktop\movie19.mp4
> split ligands
Split mar06_2026_bcx9930_factorD.pdb (#1) into 2 models
Split fd-bcx8936-diffmap.pdb (#2) into 2 models
Did not split Morph - fd-bcx8936-diffmap.pdb, has only one piece
[Repeated 1 time(s)] Chain information for mar06_2026_bcx9930_factorD.pdb #1.1
---
Chain | Description
A | No description available
Chain information for fd-bcx8936-diffmap.pdb #2.1
---
Chain | Description
A | No description available
> hide #!5 models
> hide #!2 models
> show #2.1 models
> hide #2.1 models
> cd "L:/Graphics/BCRX001/GraphicsBackup/factor_D/morphing factorD"
Current working directory is:
L:\Graphics\BCRX001\GraphicsBackup\factor_D\morphing factorD
> show #!5 models
> close #5.1
> save "L:/Graphics/BCRX001/GraphicsBackup/factor_D/morphing factorD/FD-
> bcx9930-8936-jul08A.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\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'
(C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\md_crds\gui.py)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\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 0x000001C092A4E610>,
<chimerax.log.tool.Log object at 0x000001C0B9609450>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0B30D9850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001C0B30D8910>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0B30D8910>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.toolbar.tool.ToolbarTool
object at 0x000001C092A4E610>, <chimerax.log.tool.Log object at
0x000001C0B9609450>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001C0B30D9850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001C0B30D8910>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0B30D8910>: Error while saving session data for 'tools' ->
[<chimerax.toolbar.tool.ToolbarTool object at 0x000001C092A4E610>,
<chimerax.log.tool.Log object at 0x000001C0B9609450>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0B30D9850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001C0B30D8910>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0B30D8910>
ValueError: error processing: 'tools' -> [, , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , ] ->
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\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'
(C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\md_crds\gui.py)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\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 0x000001C092A4E610>,
<chimerax.log.tool.Log object at 0x000001C0B9609450>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0B30D9850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001C0B30D8910>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0B30D8910>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 68, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.toolbar.tool.ToolbarTool
object at 0x000001C092A4E610>, <chimerax.log.tool.Log object at
0x000001C0B9609450>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001C0B30D9850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001C0B30D8910>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0B30D8910>: Error while saving session data for 'tools' ->
[<chimerax.toolbar.tool.ToolbarTool object at 0x000001C092A4E610>,
<chimerax.log.tool.Log object at 0x000001C0B9609450>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0B30D9850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001C0B30D8910>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0B30D8910>
ValueError: error processing: 'tools' -> [, , , , , , ] -> : Error while
saving session data for 'tools' -> [, , , , , , ] ->
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> close #3,5
> show #1.1 models
> show #2.2 models
> save "L:/Graphics/BCRX001/GraphicsBackup/factor_D/morphing factorD/FD-
> bcx9930-8936a.cxs"
> morph #1 #2
models have different number of chains, 1 (Morph -
mar06_2026_bcx9930_factorD.pdb #/A) and 0 ()
> morph #1.1 #2.1
Computed 51 frame morph #3
> coordset #3 1,51
> save "L:/Graphics/BCRX001/GraphicsBackup/factor_D/morphing factorD/FD-
> bcx9930-8936b.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\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'
(C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\md_crds\gui.py)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\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 0x000001C092A4E610>,
<chimerax.log.tool.Log object at 0x000001C0B9609450>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0C1599850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0C1599850>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.toolbar.tool.ToolbarTool
object at 0x000001C092A4E610>, <chimerax.log.tool.Log object at
0x000001C0B9609450>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001C0C1599850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0C1599850>: Error while saving session data for 'tools' ->
[<chimerax.toolbar.tool.ToolbarTool object at 0x000001C092A4E610>,
<chimerax.log.tool.Log object at 0x000001C0B9609450>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0C1599850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0C1599850>
ValueError: error processing: 'tools' -> [, , , , , ] -> : Error while saving
session data for 'tools' -> [, , , , , ] ->
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\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'
(C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\md_crds\gui.py)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\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 0x000001C092A4E610>,
<chimerax.log.tool.Log object at 0x000001C0B9609450>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0C1599850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0C1599850>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 68, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 731, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.12.dev202604040008\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' -> [<chimerax.toolbar.tool.ToolbarTool
object at 0x000001C092A4E610>, <chimerax.log.tool.Log object at
0x000001C0B9609450>, <chimerax.std_commands.coordset_gui.CoordinateSetSlider
object at 0x000001C0C1599850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0C1599850>: Error while saving session data for 'tools' ->
[<chimerax.toolbar.tool.ToolbarTool object at 0x000001C092A4E610>,
<chimerax.log.tool.Log object at 0x000001C0B9609450>,
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0C1599850>, <chimerax.help_viewer.tool.HelpUI object at
0x000001C0B2E8E6D0>, <chimerax.model_panel.tool.ModelPanel object at
0x000001C090F6C310>, <chimerax.cmd_line.tool.CommandLine object at
0x000001C0BAE35350>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001C0C1599850>
ValueError: error processing: 'tools' -> [, , , , , ] -> : Error while saving
session data for 'tools' -> [, , , , , ] ->
File "C:\Program Files\ChimeraX 1.12.dev202604040008\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 596.51
OpenGL renderer: NVIDIA RTX 4500 Ada Generation/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.9
Locale: en_US.cp1252
Qt version: PySide6 6.10.1, Qt 6.10.1
Qt runtime version: 6.10.1
Qt platform: windows
Manufacturer: LENOVO
Model: 30GUSJKD00
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 68,333,514,752
MaxProcessMemory: 137,438,953,344
CPU: 28 Intel(R) Core(TM) i7-14700
OSLanguage: en-US
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
build: 1.3.0
certifi: 2026.2.25
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
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: 2.3
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.dev202604040008
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: 1.3
ChimeraX-LightingGUI: 1.0
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-MatchMaker: 2.3
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: 1.5.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.4
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: 8.3.2
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.13.5
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.2.1
docutils: 0.21.2
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: 3.11
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
ipywidgets: 8.1.8
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
jupyterlab_widgets: 3.0.16
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
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
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.6
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.9.4
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: 2.13.1
pydantic_core: 2.41.5
pydata-sphinx-theme: 0.17.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.0
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
PySide6: 6.10.1
PySide6_Addons: 6.10.1
PySide6_Essentials: 6.10.1
pytest: 9.0.2
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.22
pywin32: 311
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
shiboken6: 6.10.1
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: 3.3.4
stack-data: 0.6.3
starlette: 1.0.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.5
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2026.1
urllib3: 2.6.3
uvicorn: 0.43.0
wcwidth: 0.6.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
WMI: 1.5.1
yarl: 1.23.0
Change History (2)
comment:1 by , 6 days ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Session save: cannot import name 'get_session_info' from 'chimerax.md_crds.gui' |
comment:2 by , 6 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Krish,
--Eric