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#19455 closed defect (can't reproduce)

MemoryError saving session including maps

Reported by:	wangyue1@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Sessions	Version:
Keywords:		Cc:	Greg Couch
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: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Registration file 'C:\\\Users\\\Admin\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\registration' has expired  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "F:/wangruolan_project/zhanghuanhuan/paper writing/to
> NC/revision/20251125/cryosparc_P145_J65_007_volume_map_sharp_1-youwei-20230829.mrc"

Opened cryosparc_P145_J65_007_volume_map_sharp_1-youwei-20230829.mrc as #1,
grid size 320,320,320, pixel 0.824, shown at level 0.184, step 2, values
float32  

> open "F:/wangruolan_project/zhanghuanhuan/paper writing/to
> NC/revision/20251125/cryosparc_P145_J65_007_volume_map_half_A_and_cryosparc_P145_J65_007_volume_map_half_B_local_resolution.ccp4"

Opened
cryosparc_P145_J65_007_volume_map_half_A_and_cryosparc_P145_J65_007_volume_map_half_B_local_resolution.ccp4
as #2, grid size 320,320,320, pixel 0.824, shown at level 8.44, step 2, values
float32  

> volume #1 step 1

> volume #2 step 1

> ui tool show "Surface Color"

> color sample #1.1 map #2 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 2.402, mean 3.427, maximum 9.305  

> color sample #1.1 map #2 palette
> #ff0000:#ffffff:#0000ff:#808080:#808080:#808080:#808080:#808080

Map values for surface "surface": minimum 2.402, mean 3.427, maximum 9.305  

> set bgColor white

> lighting soft

> color sample #1.1 map #2 palette
> 2.4,#5500ff:2.6,#5555ff:2.8,#55aaff:3,#ffffff:3.2,#ffaa7f:3.4,#ff557f:3.6,#ff007f:3.8,#ff0000

Map values for surface "surface": minimum 2.402, mean 3.427, maximum 9.305  

> volume #1 level 0.2407

> surface dust #1 size 8.24

[Repeated 1 time(s)]

> volume #1 level 0.2856

> volume #1 level 0.4092

> color sample #1.1 map #2 palette
> 2.2,#5500ff:2.4,#5555ff:2.6,#55aaff:2.8,#ffffff:3,#ffaa7f:3.2,#ff557f:3.4,#ff007f:3.6,#ff0000

Map values for surface "surface": minimum 2.402, mean 2.587, maximum 5.995  

> volume #1 level 0.4429

> volume #1 level 0.4541

> volume #1 level 0.3755

> volume #1 level 0.3642

> volume #1 level 0.38

> volume #1 level 0.3912

> volume #1 level 0.34

> volume #1 level 0.4

> volume #1 level 0.39

> key #5500ff:2.2 #5555ff:2.4 #55aaff:2.6 white:2.8 #ffaa7f:3.0 #ff557f:3.2
> #ff007f:3.4 red:3.6 showTool true

> ui mousemode right "color key"

> key pos 0.893805,0.152615 size 0.0300885,0.580576

> ui mousemode right translate

> save "F:/wangruolan_project/zhanghuanhuan/paper writing/to NC/revision/map
> situation of local/difilikefalin-local.cxs"

> save "F:/wangruolan_project/zhanghuanhuan/paper writing/to NC/revision/map
> situation of local/difilikefalin-local.png" width 1130 height 937
> supersample 4 transparentBackground true

> ui tool show "Side View"

> open "F:/wangruolan_project/zhanghuanhuan/paper writing/to
> NC/figshare_30121027/KOR-difelikefalin-20240723.pdb"

Chain information for KOR-difelikefalin-20240723.pdb #4  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
R | No description available  
  

> show cartoons

> style stick

Changed 9067 atom styles  

> select clear

[Repeated 1 time(s)]

> select /R:401@C20

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

49 atoms, 51 bonds, 1 residue, 1 model selected  

> volume zone #1 nearAtoms sel range 2.5 newMap false

> select ~sel & ##selected

9018 atoms, 9205 bonds, 2 pseudobonds, 1142 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select clear

> volume #1 level 0.3788

> transparency #1.1 50

> transparency #1.1 0

> hide #!4 models

> show #!4 models

> hide #!4 models

> volume #1 level 0.39

> color sample #1.1 map #2 palette
> 2.2,#5500ff:2.4,#5555ff:2.6,#55aaff:2.8,#ffffff:3,#ffaa7f:3.2,#ff557f:3.4,#ff007f:3.6,#ff0000

Map values for surface "surface": minimum 2.402, mean 2.615, maximum 6.037  

> show #!4 models

> select /R:401@C13

1 atom, 1 residue, 1 model selected  

> select up

49 atoms, 51 bonds, 1 residue, 1 model selected  

> volume zone #1 nearAtoms sel range 3 newMap false

> ui tool show "Surface Zone"

> surface zone #1 nearAtoms #4 distance 3.23

> surface zone #1 nearAtoms sel distance 3.23

> surface zone #1 nearAtoms sel distance 2.73

> surface zone #1 nearAtoms sel distance 2.65

> hide #!4 models

> transparency #1.1 50

> show #!4 models

> color sel hot pink

> color sel byhetero

> transparency #1.1 0

> ui tool show "Map Eraser"

> volume erase #1 center 137.25,160.1,152.77 radius 1.8089

Opened cryosparc_P145_J65_007_volume_map_sharp_1-youwei-20230829.mrc copy as
#6, grid size 320,320,320, pixel 0.824, shown at step 1, values float32  

> surface zone #1 nearAtoms sel distance 2.65

> surface zone #6 nearAtoms sel distance 4.94

> color sample #6.1 map #2 palette
> 2.2,#5500ff:2.4,#5555ff:2.6,#55aaff:2.8,#ffffff:3,#ffaa7f:3.2,#ff557f:3.4,#ff007f:3.6,#ff0000

Map values for surface "surface": minimum 2.402, mean 2.615, maximum 6.037  

> surface zone #6 nearAtoms sel distance 2.97

> surface zone #6 nearAtoms sel distance 2.65

> volume erase #6 center 135.53,153.78,154.35 radius 1.7139

> volume erase #6 center 132.11,152.79,147.21 radius 1.7139

> volume erase #6 center 131.91,153.41,143.55 radius 1.7139

> volume erase #6 center 136.79,158.42,152.33 radius 1.7139

> transparency #6.1 50

> transparency #6.1 0

> hide #!6 models

> show #!6 models

> hide #!4 models

> show #5 models

> hide #5 models

> hide #!6 models

> show #!6 models

> show #!4 models

> hide #!4 models

> save "F:/wangruolan_project/zhanghuanhuan/paper writing/to NC/revision/map
> situation of local/difilikefalin-1.png" width 1130 height 937 supersample 4
> transparentBackground true

> surface dust #6 size 8.24

> surface zone #6 nearAtoms sel distance 2.65

> save "F:/wangruolan_project/zhanghuanhuan/paper writing/to NC/revision/map
> situation of local/difilikefalin-1l.cxs" includeMaps true

Traceback (most recent call last):  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 651, in save  
fserialize(stream, data)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "E:\chimeraX1.8\ChimeraX 1.8\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 "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimeraX1.8\ChimeraX 1.8\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 "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 651, in save  
fserialize(stream, data)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  

> save "F:/wangruolan_project/zhanghuanhuan/paper writing/to NC/revision/map
> situation of local/difilikefalin-1.cxs" includeMaps true

Traceback (most recent call last):  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 651, in save  
fserialize(stream, data)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "E:\chimeraX1.8\ChimeraX 1.8\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 "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimeraX1.8\ChimeraX 1.8\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 "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 651, in save  
fserialize(stream, data)  
File "E:\chimeraX1.8\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 560.94
OpenGL renderer: NVIDIA GeForce GTX 1650 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: IPASON
Model:  
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 25,720,573,952
MaxProcessMemory: 137,438,953,344
CPU: 6 AMD Ryzen 5 3500X 6-Core Processor             
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 11 hours ago

Cc:	Greg Couch added
Component:	Unassigned → Sessions
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → MemoryError saving session including maps

Reported by Yue Wang

comment:2 by Tom Goddard, 9 hours ago

Resolution:	→ can't reproduce
Status:	assigned → closed

It doesn't look like you have large maps or atomic models open in ChimeraX so I am not sure why ChimeraX gave an out of memory error when saving a session. You used the "includeMaps true" option which tries to include the density maps in the session but your maps were only about 100 MB each. Your machine reports having 24 GB of memory. We only ever see these out of memory errors on Windows. I'm not sure if other applications that are taking a lot of memory on Windows can cause this. Another possibility is that your old ChimeraX version 1.8 has a memory leak problem. Some years ago on Windows ChimeraX would run out of memory opening PDB files and maybe that is the cause of your problem. In that case updating to the current ChimeraX would help.

You could try saving your session without the "includeMaps true" option.

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