Opened 7 months ago

Closed 7 months ago

#17582 closed defect (nonchimerax)

Problem saving session after adding trajectory coordinates

Reported by: alexandra.zahradnikova@… 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-10-10.0.19045
ChimeraX Version: 1.10.dev202504240337 (2025-04-24 03:37:50 UTC)
Description
Trying to save a very large session (1000 trajectories), 747043 atoms (from Gromacs simulation)
This is complete data, I will try saving the protein and ligands only
Analogous error was observed also with Chimerax 9 on a Linux system but will less log output

Log:
UCSF ChimeraX version: 1.10.dev202504240337 (2025-04-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7tdi fromDatabase pdb format mmcif

Summary of feedback from opening 7tdi fetched from pdb  
---  
note | Fetching compressed mmCIF 7tdi from http://files.rcsb.org/download/7tdi.cif  
  
7tdi title:  
Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in closed-
inactivated conformation class 2 (Dataset-A) [more info...]  
  
Chain information for 7tdi #1  
---  
Chain | Description | UniProt  
A B C D | Ryanodine receptor 1,Ryanodine receptor 1,RyR1 | RYR1_RABIT 1-1275 1565-2486 2704-2941 3614-5037  
  
Non-standard residues in 7tdi #1  
---  
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)  
CA — calcium ion  
ZN — zinc ion  
  

> open 7tdj fromDatabase pdb format mmcif

Summary of feedback from opening 7tdj fetched from pdb  
---  
note | Fetching compressed mmCIF 7tdj from http://files.rcsb.org/download/7tdj.cif  
  
7tdj title:  
Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in closed-
inactivated conformation class 1(Dataset-A) [more info...]  
  
Chain information for 7tdj #2  
---  
Chain | Description | UniProt  
A B C D | Ryanodine receptor 1,Ryanodine receptor 1,RyR1 | RYR1_RABIT 1-1275 1565-2486 2704-2941 3614-5037  
  
Non-standard residues in 7tdj #2  
---  
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)  
CA — calcium ion  
ZN — zinc ion  
  

> open 7tdk fromDatabase pdb format mmcif

Summary of feedback from opening 7tdk fetched from pdb  
---  
note | Fetching compressed mmCIF 7tdk from http://files.rcsb.org/download/7tdk.cif  
  
7tdk title:  
Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in closed-
inactivated conformation class 3 (Dataset-A) [more info...]  
  
Chain information for 7tdk #3  
---  
Chain | Description | UniProt  
A B C D | Ryanodine receptor 1,Ryanodine receptor 1,RyR1 | RYR1_RABIT 1-1275 1565-2486 2704-2941 3614-5037  
  
Non-standard residues in 7tdk #3  
---  
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)  
CA — calcium ion  
ZN — zinc ion  
  

> open 7tdg fromDatabase pdb format mmcif

7tdg title:  
Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in inactivated
conformation (Dataset-A) [more info...]  
  
Chain information for 7tdg #4  
---  
Chain | Description | UniProt  
A B C D | Ryanodine receptor 1,RyR1 | RYR1_RABIT 1-1275 1565-2486 2704-2941 3614-5037  
  
Non-standard residues in 7tdg #4  
---  
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)  
CA — calcium ion  
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)  
ZN — zinc ion  
  

> hide atoms

> show cartoons

[Repeated 1 time(s)]

> select A/

Expected an objects specifier or a keyword  

> select A/:

Expected an objects specifier or a keyword  

> select :A/1-3667

Nothing selected  

> select A:/1-3667

Expected an objects specifier or a keyword  

> select /A:1

Nothing selected  

> select /A:1-3000

72465 atoms, 73933 bonds, 48 pseudobonds, 10155 residues, 8 models selected  

> select A/:1-3667

Expected an objects specifier or a keyword  

> select /A:1-3667

83944 atoms, 85439 bonds, 56 pseudobonds, 12375 residues, 8 models selected  

> select ~sel

384781 atoms, 392074 bonds, 325 pseudobonds, 53845 residues, 16 models
selected  

> delete atoms (#!1-4 & sel)

> delete bonds (#!1-4 & sel)

> select :3668-4070

Nothing selected  

> select :3668-4070@ca

Nothing selected  

> select A/:3668-4070@ca

Expected an objects specifier or a keyword  

> select :A/3668-4070@ca

Nothing selected  

> close session

> cd J:

Current working directory is: J:\  

> cd Simulations_F/Devana_F

Current working directory is: J:\Simulations_F\Devana_F  

> cd 9_consecutive

Current working directory is: J:\Simulations_F\Devana_F\9_consecutive  

> ls *gro

Unknown command: ls *gro  

> dir *gro

Unknown command: dir *gro  

> open X:/Raw_Data/Simulations/Scripts/ChimeraX/Open_large_file.py

> open step6.6_equilibration.gro

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Chain information for Title #1  
---  
Chain | Description  
A D E | No description available  
B | No description available  
  

> open step7_1.xtc start 2

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executed Open_large_file.py  

> select ::name="TIP3"

542031 atoms, 361354 bonds, 180677 residues, 1 model selected  

> select clear

> save J:/Simulations_F/Devana_F/9_consecutive/9_consecutive_all.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\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 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1440, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 227, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 2049, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
SystemError: D:\a\1\s\Objects\listobject.c:338: bad argument to internal
function  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\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.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D1472F9D50>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D162041150>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D16206FB90>, <chimerax.log.tool.Log object at 0x000001D161F97FD0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710> -> <chimerax.atomic.structure.AtomicStructure object at
0x000001D118282050> 'Title'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core\session.py", line 1053, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' ->
[<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D1472F9D50>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D162041150>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D16206FB90>, <chimerax.log.tool.Log object at 0x000001D161F97FD0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710> -> <chimerax.atomic.structure.AtomicStructure object at
0x000001D118282050> 'Title': Error while saving session data for 'tools' ->
[<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D1472F9D50>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D162041150>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D16206FB90>, <chimerax.log.tool.Log object at 0x000001D161F97FD0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710> -> <chimerax.atomic.structure.AtomicStructure object at
0x000001D118282050> 'Title'  
  
ValueError: error processing: 'tools' -> [, , , , ] -> -> 'Title': Error while
saving session data for 'tools' -> [, , , , ] -> -> 'Title'  
  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\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 1.10.dev202504240337\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 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1440, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 227, in take_snapshot  
'structure state': StructureData.save_state(self, session, flags),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 2049, in save_state  
data['version'] = f(self._c_pointer, data['ints'], data['floats'],
data['misc'])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
SystemError: D:\a\1\s\Objects\listobject.c:338: bad argument to internal
function  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core\session.py", line 297, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\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.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D1472F9D50>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D162041150>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D16206FB90>, <chimerax.log.tool.Log object at 0x000001D161F97FD0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710> -> <chimerax.atomic.structure.AtomicStructure object at
0x000001D118282050> 'Title'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\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 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\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 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3219, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\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 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core\session.py", line 1053, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core\session.py", line 741, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
ValueError: error processing: 'tools' ->
[<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D1472F9D50>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D162041150>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D16206FB90>, <chimerax.log.tool.Log object at 0x000001D161F97FD0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710> -> <chimerax.atomic.structure.AtomicStructure object at
0x000001D118282050> 'Title': Error while saving session data for 'tools' ->
[<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710>, <chimerax.model_panel.tool.ModelPanel object at
0x000001D1472F9D50>, <chimerax.cmd_line.tool.CommandLine object at
0x000001D162041150>, <chimerax.toolbar.tool.ToolbarTool object at
0x000001D16206FB90>, <chimerax.log.tool.Log object at 0x000001D161F97FD0>] ->
<chimerax.std_commands.coordset_gui.CoordinateSetSlider object at
0x000001D19976A710> -> <chimerax.atomic.structure.AtomicStructure object at
0x000001D118282050> 'Title'  
  
ValueError: error processing: 'tools' -> [, , , , ] -> -> 'Title': Error while
saving session data for 'tools' -> [, , , , ] -> -> 'Title'  
  
File "C:\Program Files\ChimeraX 1.10.dev202504240337\bin\Lib\site-
packages\chimerax\core\session.py", line 301, in discovery  
raise ValueError(  
  
See log for complete Python traceback.  
  

> select

747043 atoms, 564813 bonds, 187362 residues, 1 model selected  




OpenGL version: 3.3.0 NVIDIA 369.09
OpenGL renderer: Quadro 600/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1250
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision T1500
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 17,136,992,256
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7 CPU         870  @ 2.93GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.1
    build: 1.2.2.post1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.3
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.15
    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: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202504240337
    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: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.9
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.57.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.6
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.14
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.7
    pluggy: 1.5.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.13.2
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

Change History (7)

comment:1 by Eric Pettersen, 7 months ago

Component: Unassigned → Sessions
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Problem saving session after adding trajectory coordinates

comment:2 by Eric Pettersen, 7 months ago

Status: accepted → feedback

Hi Sasha,

I'm having difficulty reproducing this. If you change your script to just add additional coordinates _once_, do you still get the error saving the session?

--Eric

comment:3 by alexandra.zahradnikova@…, 7 months ago 

Hi all, I have found out that the error was due to incorrect topology in the input GRO file, in which one residue was by mistake assigned to a different chain. I will let you know more details later if i find out.BestSasha Sent from my Galaxy
-------- Original message --------From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> Date: 08/05/2025  15:14  (GMT+01:00) To: alexandra.zahradnikova@savba.sk Subject: Re: [ChimeraX] #17582: ChimeraX bug report submission #17582: ChimeraX bug report submission--------------------------------------+----------------------------- Reporter:  alexandra.zahradnikova@…  |                Type:  defect   Status:  new                       |            Priority:  normalComponent:  Unassigned                |          Blocked By: Blocking:                            |  Notify when closed:--------------------------------------+------------------------------- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17582>ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>ChimeraX Issue Tracker

comment:4 by Eric Pettersen, 7 months ago

Was this the .gro file you used as input to Gromacs, or to ChimeraX?

comment:5 by Eric Pettersen, 7 months ago

(Or both I guess...)

comment:6 by alexandra.zahradnikova@…, 7 months ago 

It was to both but the problem was in Gromacs because of faulty minimization step. With proper minimization this problem disappeared.
Best
Sasha

-----Original Message-----
From: ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Sent: Friday, May 9, 2025 22:52
To: alexandra.zahradnikova@savba.sk; pett@cgl.ucsf.edu
Subject: Re: [ChimeraX] #17582: Problem saving session after adding trajectory coordinates

#17582: Problem saving session after adding trajectory coordinates
-----------------------------------------------+----------------------
          Reporter:  alexandra.zahradnikova@\u2026  |      Owner:  pett
              Type:  defect                    |     Status:  feedback
          Priority:  normal                    |  Milestone:
         Component:  Sessions                  |    Version:
        Resolution:                            |   Keywords:
        Blocked By:                            |   Blocking:
Notify when closed:                            |   Platform:  all
           Project:  ChimeraX                  |
-----------------------------------------------+----------------------
Comment (by pett):

 Was this the .gro file you used as input to Gromacs, or to ChimeraX?

comment:7 by Eric Pettersen, 7 months ago

Resolution: → nonchimerax
Status: feedback → closed

Glad you worked it out.

--Eric

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